WorldWideScience

Sample records for candidate structured rnas

  1. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

    Directory of Open Access Journals (Sweden)

    Schwalbach Michael S

    2009-06-01

    Full Text Available Abstract Background Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. Results To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc. shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. Conclusion This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.

  2. Structural analysis of aligned RNAs.

    Science.gov (United States)

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  3. Tackling Structures of Long Noncoding RNAs

    Directory of Open Access Journals (Sweden)

    Irina V. Novikova

    2013-12-01

    Full Text Available RNAs are important catalytic machines and regulators at every level of gene expression. A new class of RNAs has emerged called long non-coding RNAs, providing new insights into evolution, development and disease. Long non-coding RNAs (lncRNAs predominantly found in higher eukaryotes, have been implicated in the regulation of transcription factors, chromatin-remodeling, hormone receptors and many other processes. The structural versatility of RNA allows it to perform various functions, ranging from precise protein recognition to catalysis and metabolite sensing. While major housekeeping RNA molecules have long been the focus of structural studies, lncRNAs remain the least characterized class, both structurally and functionally. Here, we review common methodologies used to tackle RNA structure, emphasizing their potential application to lncRNAs. When considering the complexity of lncRNAs and lack of knowledge of their structure, chemical probing appears to be an indispensable tool, with few restrictions in terms of size, quantity and heterogeneity of the RNA molecule. Probing is not constrained to in vitro analysis and can be adapted to high-throughput sequencing platforms. Significant efforts have been applied to develop new in vivo chemical probing reagents, new library construction protocols for sequencing platforms and improved RNA prediction software based on the experimental evidence.

  4. Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci

    DEFF Research Database (Denmark)

    Mirza, Aashiq H; Kaur, Simranjeet; Brorsson, Caroline A; Pociot, Flemming

    2014-01-01

    -nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) lie outside of the protein coding regions, and map to the non-coding intervals. However, the relationship between phenotype-associated loci and the non-coding regions including the long non-coding RNAs (lncRNAs) is poorly understood. Here......, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs...... within and in close proximity (+/-5 kb flanking regions) of IBD and T1D loci-associated candidate genes, suggesting that these RNA conformation-altering polymorphisms might be associated with diseased-phenotype. Disruption of lncRNA secondary structure due to presence of GWAS SNPs provides valuable...

  5. Structure and Gene-Silencing Mechanisms of Small Noncoding RNAs

    Science.gov (United States)

    Chu, Chia-Ying; Rana, Tariq M.

    Small (19-31-nucleotides) noncoding RNAs were identified in the past 10 years for their distinct function in gene silencing. The best known gene-silencing phenomenon, RNA interference (RNAi), is triggered in a sequence-specific manner by endogenously produced or exogenously introduced small doubled-stranded RNAs. As knowledge of the structure and function of the RNAi machinery has expanded, this phenomenon has become a powerful tool for biochemical research; it has enormous potential for therapeutics. This chapter summarizes significant aspects of three major classes of small noncoding, regulatory RNAs: small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). Here, we focus on the biogenesis of these small RNAs, their structural features and coupled effectors as well as the mechanisms of each small regulatory RNA pathway which reveal fascinating ways by which gene silencing is controlled and fine-tuned at an epigenetic level.

  6. Enumerating secondary structures and structural moieties for circular RNAs

    CERN Document Server

    Cuesta, José A

    2016-01-01

    A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenotype. Here, we count the secondary structures of circular RNAs of length $n$ and calculate the asymptotic distributions of different structural moieties, such as stems or hairpin loops, by means of symbolic combinatorics. Circular RNAs differ in essential ways from their linear counterparts. From the mathematical viewpoint, the enumeration of the corresponding secondary structures demands the use of combinatorial techniques additional to those used for linear RNAs. The asymptotic number of secondary structures for circular RNAs grows as $a^nn^{-5/2}$, with a depending on particular constraints applied to the secondary structure. The abundance of any structural moiety is normally distributed in th...

  7. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

    DEFF Research Database (Denmark)

    Mourier, Tobias; Carret, Celine; Kyes, Sue;

    2008-01-01

    We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome...... sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured...... ncRNAs in P. falciparum and are not represented in any RNA databases. We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related...

  8. Computational prediction of candidate miRNAs and their potential functions in biomineralization in pearl oyster Pinctada martensii.

    Science.gov (United States)

    Zheng, Zhe; Jiao, Yu; Du, Xiaodong; Tian, Qunli; Wang, Qingheng; Huang, Ronglian; Deng, Yuewen

    2016-05-01

    MicroRNAs (miRNAs) are a class of non-coding RNA molecules with presumed post-transcriptional regulatory activity in various biological processes, such as development and biomineralization. Pinctada martensii is one of the main species cultured for marine pearl production in China and Japan. In our previous research, 258 pm-miRNAs had been identified by solexa deep sequencing in P. martensii, while it is far from the number of miRNAs found in other species. In this study, based on the transcriptome database of pearl sac, we identified 30 candidate pm-miRNAs by computational prediction. Among the obtained 30 pm-miRNAs, 13 pm-miRNAs were generated from the complementary strand of protein-coding mRNAs, and 17 pm-miRNAs could not be annotated using blastx and tblastn analysis. Notably, 10 of the 30 pm-miRNAs, such as pm-miR-1b, pm-miR-205b and pm-miR-375b, were homologous with the reported pm-miRNAs, respectively. To validate the existence of the identified pm-miRNAs, eight randomly selected pm-miRNAs were tested by stem loop quantitative RT-PCR analyses using 5.8S as the internal reference gene. Target prediction between the obtained pm-miRNAs and biomineralization-related genes by microTar, miRanda and RNA22 indicated pm-miR-2386 and pm-miR-13b may be the key factors in the regulation network by regulating the formation of organic matrix or the differentiation of mineralogenic cell during shell formation. Thus, this study enriched miRNA databases of pearl oyster and provided a new way to understand biomineralization. PMID:27081363

  9. Structured RNAs that evade or confound exonucleases: function follows form.

    Science.gov (United States)

    Akiyama, Benjamin M; Eiler, Daniel; Kieft, Jeffrey S

    2016-02-01

    Cells contain powerful RNA decay machinery to eliminate unneeded RNA from the cell, and this process is an important and regulated part of controlling gene expression. However, certain structured RNAs have been found that can robustly resist degradation and extend the lifetime of an RNA. In this review, we present three RNA structures that use a specific three-dimensional fold to provide protection from RNA degradation, and discuss how the recently-solved structures of these RNAs explain their function. Specifically, we describe the Xrn1-resistant RNAs from arthropod-borne flaviviruses, exosome-resistant long non-coding RNAs associated with lung cancer metastasis and found in Kaposi's sarcoma-associated herpesvirus, and tRNA-like sequences occurring in certain plant viruses. These three structures reveal three different mechanisms to protect RNAs from decay and suggest RNA structure-based nuclease resistance may be a widespread mechanism of regulation. PMID:26797676

  10. Describing the structural robustness landscape of bacterial small RNAs

    Directory of Open Access Journals (Sweden)

    Rodrigo Guillermo

    2012-04-01

    Full Text Available Abstract Background The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes. Results Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity. Conclusion Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.

  11. Structured RNAs in the ENCODE selected regions of the human genome

    DEFF Research Database (Denmark)

    Washietl, Stefan; Pedersen, Jakob Skou; Korbel, Jan O;

    2007-01-01

    characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding......Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack...... several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison...

  12. Computational prediction of candidate miRNAs and their targets from the completed Linum ussitatissimum genome and EST database

    Directory of Open Access Journals (Sweden)

    Tiffanie Y. Moss

    2012-06-01

    Full Text Available Flax is an important agronomic crop grown for its fiber (linen and oil (linseed oil. In spite of many thousands of years of breeding some fiber varieties have been shown to rapidly respond to environmental stress with heritable changes to its genome. Many miRNAs appear to be induced by abiotic or biotic conditions experienced through the plant life cycle. Computational miRNA analysis of the flax genome provides a foundation for subsequent research on miRNA function in Linum usitatissimum and may also provide novel insight into any regulatory role the RNAi pathway may play in generating adaptive structural variation in response to environmental stress. Here a bioinformatics approach is used to screen for miRNAs previously identified in other plant species, as well as to predict putative miRNAs unique to a particular species which may not have been identified as they are less abundant or dependent upon a specific set of environmental conditions. Twelve miRNA genes were identified in flax on the basis of unique pre-miRNA positions with structural homology to plant pre-miRNAs and complete sequence homology to published plant miRNAs. These miRNAs were found to belong to 7 miRNA families, with an additional 2 matches corresponding to as yet unnamed poplar miRNAs and a parologous miRNA with partial sequence homology to mtr-miR4414b. An additional 649 novel and distinct flax miRNA genes were identified to form from canonical hairpin structures and to have putative targets among the ~30,000 flax Unigenes.

  13. Structured RNAs and synteny regions in the pig genome

    DEFF Research Database (Denmark)

    Anthon, Christian; Tafer, Hakim; Havgaard, Jakob H;

    2014-01-01

    Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). CONCLUSIONS: We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the...

  14. Probing-directed identification of novel structured RNAs.

    Science.gov (United States)

    Vinogradova, Svetlana V; Sutormin, Roman A; Mironov, Andrey A; Soldatov, Ruslan A

    2016-02-01

    Transcripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art ab initio approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them. PMID:26732206

  15. The structure and function of catalytic RNAs

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Before the discovery of ribozymes,RNA had been proposed to function as a catalyst,based on the discovery that RNA folded into high-ordered structures as protein did.This hypothesis was confirmed in the 1980s,after the discovery of Tetrahymena group I intron and RNase P ribozyme.There have been about ten ribozymes identified during the past thirty years,as well as the fact that ribosomes function as ribozymes.Advances have been made in understanding the structures and functions of ribozymes,with numerous crystal structures resolved in the past years.Here we review the structure-function relationship of both small and large ribozymes,especially the structural basis of their catalysis.

  16. The structure and function of catalytic RNAs

    Institute of Scientific and Technical Information of China (English)

    WU QiJia; HUANG Lin; ZHANG Yi

    2009-01-01

    Before the discovery of ribozymes, RNA had been proposed to function as a catalyst, based on the discovery that RNA folded into high-ordered structures as protein did. This hypothesis was confirmed in the 1980s, after the discovery of Tetrahymena group I intron and RNase P ribozyme. There have been about ten ribozymes identified during the past thirty years, as well as the fact that ribosomes function as ribozymes. Advances have been made in understanding the structures and functions of ribozymes, with numerous crystal structures resolved in the past years. Here we review the structure-function re-lationship of both small and large ribozymes, especially the structural basis of their catalysis.

  17. Alu element-containing RNAs maintain nucleolar structure and function.

    Science.gov (United States)

    Caudron-Herger, Maïwen; Pankert, Teresa; Seiler, Jeanette; Németh, Attila; Voit, Renate; Grummt, Ingrid; Rippe, Karsten

    2015-11-12

    Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production. PMID:26464461

  18. CASE via MS: Ranking Structure Candidates by Mass Spectra

    OpenAIRE

    Kerber, Adalbert; Meringer, Markus; Rücker, Christoph

    2006-01-01

    Two important tasks in computer-aided structure elucidation (CASE) are the generation of candidate structures from a given molecular formula, and the ranking of structure candidates according to compatibility with an experimental spectrum. Candidate ranking with respect to electron impact mass spectra is based on virtual fragmentation of a candidate structure and comparison of the fragments’ isotope distributions against the spectrum of the unknown compound, whence a structure–spectrum compat...

  19. Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

    OpenAIRE

    Mourier, Tobias; Carret, Celine; Kyes, Sue; Christodoulou, Zoe; Gardner, Paul P; Jeffares, Daniel C.; Pinches, Robert; Barrell, Bart; Berriman, Matt; Griffiths-Jones, Sam; Ivens, Alasdair; Newbold, Chris; Pain, Arnab

    2008-01-01

    We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including ...

  20. A benchmark of multiple sequence alignment programs upon structural RNAs

    DEFF Research Database (Denmark)

    Gardner, P. P.; Wilm, A.; Washietl, S.

    2005-01-01

    , we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates...... where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current...

  1. RNAstrand: reading direction of structured RNAs in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-05-01

    Full Text Available Abstract Motivation Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. Results While folding energies of an RNA and its reverse complement are similar, the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. Software RNAstrand is freely available as a stand-alone tool from http://www.bioinf.uni-leipzig.de/Software/RNAstrand and is also included in the latest release of RNAz, a part of the Vienna RNA Package.

  2. Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures.

    Science.gov (United States)

    Kieft, Jeffrey S

    2009-02-01

    The intergenic region (IGR) internal ribosome entry site (IRES) RNAs do not require any of the canonical translation initiation factors to recruit the ribosome to the viral RNA, they eliminate the need for initiator tRNA, and they begin translation from the A-site. The function of these IRESs depends on a specific three-dimensional folded RNA structure. Thus, a complete understanding of the mechanisms of action of these IRESs requires that we understand their structure in detail. Recently, the structures of both domains of the IGR IRES RNAs were solved by X-ray crystallography, providing the first glimpse into an entire IRES RNA structure. Here, I present an analysis of these structures, emphasizing how the structures explain many aspects of IGR IRES function, discussing how these structures have similarities to motifs found in other viral RNAs, and illustrating how these structures give rise to new mechanistic hypotheses. PMID:18672012

  3. Circulating microRNAs: Promising candidates serving as novel biomarkers of acute hepatitis

    Directory of Open Access Journals (Sweden)

    Natalia Elfimova

    2012-12-01

    Full Text Available Acute liver failure as life threatening condition comprises a difficult diagnostic situation to evaluate potential outcomes and therapeutic options. Thus, prognostic indicators are urgently needed for evaluation of progression of liver injury, clinical outcome, prognosis, and for therapeutic response. Recently, circulating microRNA, in particular miR-122, was described as a potential biomarker of acute liver injury after intoxication of mice. Circulating miRNA molecules are very stable and RNase-resistant due to protein aggregation and vesicle enclosure. Since miRNA species are known to be associated with chronic liver damage or with liver cancer, circulating miRNA patterns are suggested to serve also as reporters for progression of acute liver failure. miRNA profiling analyses using PCR arrays or next generation sequencing, may achieve identification of miRNA species that are linked to the rapid progression of acute liver injury, to the outcome of liver failure, or to the therapeutic response. Therefore, circulating miRNAs are promising, non-invasive biomarkers of future diagnostic approaches. However, normalisation of circulating miRNA levels is essential and further standardisation of miRNA quantification assays is needed.

  4. Structured RNAs and synteny regions in the pig genome

    DEFF Research Database (Denmark)

    Anthon, Christian; Tafer, Hakim; Havgaard, Jakob Hull; Thomsen, Bo; Hedegaard, Jakob; Seemann, Ernst Stefan; Pundhir, Sachin; Kehr, Stephanie; Bartschat, Sebastian; Nielsen, Mathilde; Nielsen, Rasmus O.; Fredholm, Merete; Stadler, Peter F.; Gorodkin, Jan

    2014-01-01

    BACKGROUND: Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. Howeve...

  5. HD-RNAS: An automated hierarchical database of RNA structures

    Directory of Open Access Journals (Sweden)

    Shubhra Sankar eRay

    2012-04-01

    Full Text Available One of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. Although there is a huge amount of information on RNA structures in PDB, there are redundant files, ambiguous synthetic sequences etc. Moreover, a systematic hierarchical organization, reflecting RNA classification, is missing in PDB. In this investigation, we have classified all the available RNA crystal structures from PDB through a programmatic approach. Hence, it would be now a simple assignment to regularly update the classification as and when new structures are released. The classification can further determine (i a non-redundant set of RNA structures and (ii if available, a set of structures of identical sequence and function, which can highlight structural polymorphism, ligand-induced conformational alterations etc. Presently, we have classified the available structures (2095 PDB entries having RNA chain longer than 9 nucleotides solved by X-ray crystallography or NMR spectroscopy into nine functional classes. The structures of same function and same source are mostly seen to be similar with subtle differences depending on their functional complexation. The web-server is available online at http://www.saha.ac.in/biop/www/HD-RNAS.html and is updated regularly.

  6. Structural and evolutionary analysis of the two chimpanzee alpha-globin mRNAs.

    OpenAIRE

    Liebhaber, S A; Begley, K A

    1983-01-01

    Two distinct alpha-globin mRNAs were detected in chimpanzee reticulocyte mRNA using a primer extension assay. DNA copies of these two mRNAs were cloned in the bacterial plasmid pBR322, and their sequence was determined. The two alpha-globin mRNAs have obvious structural homology to the two human alpha-globin mRNAs, alpha 1 and alpha 2. Comparison of the two chimpanzee alpha-globin mRNAs to each other and to their corresponding human counterparts revealed evidence of a recent gene conversion i...

  7. Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics – assessment and update

    Directory of Open Access Journals (Sweden)

    Tamas Ivica

    2008-07-01

    Full Text Available Abstract Background The H/ACA family of small nucleolar RNAs (snoRNAs plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA. In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program – Fisher – and previously presented several candidate snoRNAs based on our analysis 1. Findings In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs 2 identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. Conclusion Our results confirm the validity of using minimum free energy (MFE secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

  8. Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures

    OpenAIRE

    Kieft, Jeffrey S.

    2008-01-01

    The intergenic region (IGR) internal ribosome entry site (IRES) RNAs do not require any of the canonical translation initiation factors to recruit the ribosome to the viral RNA, they eliminate the need for initiator tRNA, and they begin translation from the A-site. The function of these IRESs depends on a specific three-dimensional folded RNA structure. Thus, a complete understanding of the mechanisms of action of these IRESs requires that we understand their structure in detail. Recently, th...

  9. Structured non-coding RNAs and the RNP Renaissance

    OpenAIRE

    Hogg, J. Robert; Collins, Kathleen

    2008-01-01

    Non-protein-coding (nc) RNAs are diverse in their modes of synthesis, processing, assembly, and function. The inventory of transcripts known or suspected to serve their biological roles as RNA has increased dramatically in recent years. Although studies of ncRNA function are only beginning to match the pace of ncRNA discovery, some principles are emerging. Here we focus on a framework for understanding functions of ncRNAs that have evolved in a protein-rich cellular environment, as distinct f...

  10. Expression Profiling and Structural Characterization of MicroRNAs in Adipose Tissues of Hibernating Ground Squirrels

    Directory of Open Access Journals (Sweden)

    Cheng-Wei Wu

    2014-12-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT and white adipose tissue (WAT during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (P < 0.05, which was 16%–54% of euthermic non-torpid control squirrels, whereas expression of three miRNAs including miR-143, miR-200a and miR-519d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more miRNAs was downregulated in BAT during torpor. We detected reduced expression of 6 miRNAs including miR-103a, miR-107, miR-125b, miR-21, miR-221 and miR-31 (48%–70% of control, while only expression of miR-138 was significantly upregulated (2.91 ± 0.8-fold of the control, P < 0.05. Interestingly, miRNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas miRNAs with altered expression in BAT during torpor were linked to mitochondrial β-oxidation. miRPath target prediction analysis showed that miRNAs downregulated in both WAT and BAT were associated with the regulation of mitogen-activated protein kinase (MAPK signaling, while the miRNAs upregulated in WAT were linked to transforming growth factor β (TGFβ signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-miRNAs for the miRNAs used in this study, suggesting no structure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may

  11. Expression Profiling and Structural Characterization of MicroRNAs in Adipose Tissues of Hibernating Ground Squirrels

    Institute of Scientific and Technical Information of China (English)

    Cheng-Wei Wu; Kyle K. Biggar; Kenneth B. Storey

    2014-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 miRNAs in brown (BAT) and white adipose tissue (WAT) during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six miRNAs including let-7a, let-7b, miR-107, miR-150, miR-222 and miR-31 was significantly downregulated in WAT (P < 0.05), which was 16%–54% of euthermic non-torpid control squirrels, whereas expression of three miRNAs including miR-143, miR-200a and miR-519d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more miRNAs was downregulated in BAT during torpor. We detected reduced expression of 6 miRNAs including miR-103a, miR- 107, miR-125b, miR-21, miR-221 and miR-31 (48%–70% of control), while only expression of miR-138 was significantly upregulated (2.91 ± 0.8-fold of the control, P <0.05). Interestingly, miRNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas miRNAs with altered expression in BAT during torpor were linked to mitochondrial b-oxidation. miRPath target prediction analysis showed that miRNAs downregulated in both WAT and BAT were associated with the regulation of mitogen- activated protein kinase (MAPK) signaling, while the miRNAs upregulated in WAT were linked to transforming growth factor b (TGFb) signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-miRNAs for the miRNAs used in this study, suggesting no structure-influenced changes in pre-miRNA processing efficiency in the squirrel. As well, the expression of miRNA processing enzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of miRNA expression in adipose tissues may be linked to

  12. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights

    Directory of Open Access Journals (Sweden)

    Chen Chun-Long

    2009-11-01

    Full Text Available Abstract Background SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. Results Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. Conclusion This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex

  13. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures.

    Science.gov (United States)

    Li, Rui; Zhu, Hongliang; Luo, Yunbo

    2016-01-01

    Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure-function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq), selective 2'-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq), parallel analysis of RNA structure (PARS), and fragmentation sequencing (FragSeq). The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level. PMID:27196897

  14. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul P; Krogh, Anders

    2007-01-01

    multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost...

  15. Computational prediction of candidate miRNAs and their targets from the completed Linum ussitatissimum genome and EST database

    OpenAIRE

    Tiffanie Y. Moss; Cullis, Christopher A.

    2012-01-01

    Flax is an important agronomic crop grown for its fiber (linen) and oil (linseed oil). In spite of many thousands of years of breeding some fiber varieties have been shown to rapidly respond to environmental stress with heritable changes to its genome. Many miRNAs appear to be induced by abiotic or biotic conditions experienced through the plant life cycle. Computational miRNA analysis of the flax genome provides a foundation for subsequent research on miRNA function in Linum usitatissimum an...

  16. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures

    Directory of Open Access Journals (Sweden)

    Rui Li

    2016-05-01

    Full Text Available Although thousands of long non-coding RNAs (lncRNAs have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure–function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq, selective 2′-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq, parallel analysis of RNA structure (PARS, and fragmentation sequencing (FragSeq. The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level.

  17. Specific structural probing of plasmid-coded ribosomal RNAs from Escherichia coli

    DEFF Research Database (Denmark)

    Aagaard, C; Rosendahl, G; Dam, M; Powers, T; Douthwaite, S

    1991-01-01

    ribosome population, which consequently hinders direct probing of mutant rRNAs. Here, we describe how nonconserved helical regions of plasmid-coded rRNA have been altered in a manner that preserves their secondary structures while creating new sites for primer extension of mutant rRNAs. This facilitates...... specific biochemical probing of mutagenised rRNA regions despite the background of wild-type molecules. Four priming sites have been made to investigate the structural effects of mutations in the GTPase centre, helix 1200-1250, the peptidyl transferase region and the alpha-sarcin loop of 23S rRNA....

  18. Synaptic enrichment of microRNAs in adult mouse forebrain is related to structural features of their precursors

    OpenAIRE

    Smalheiser Neil R

    2008-01-01

    Abstract Within mouse forebrain, a subset of microRNAs are significantly enriched in synaptoneurosomes (a synaptic fraction containing pinched-off dendritic spines) and a subset are significantly depleted relative to total forebrain homogenate. Here I show that, as a group, the pre-miR hairpin precursors of synaptically enriched microRNAs exhibit significantly different structural features than those that are non-enriched or depleted. Precursors of synaptically enriched microRNAs tend to hav...

  19. Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development.

    Science.gov (United States)

    Bao, Weier; Greenwold, Matthew J; Sawyer, Roger H

    2016-10-15

    MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. Previous studies have shown that miRNA regulation contributes to a diverse set of processes including cellular differentiation and morphogenesis which leads to the creation of different cell types in multicellular organisms and is thus key to animal development. Feathers are one of the most distinctive features of extant birds and are important for multiple functions including flight, thermal regulation, and sexual selection. However, the role of miRNAs in feather development has been woefully understudied despite the identification of cell signaling pathways, cell adhesion molecules and structural genes involved in feather development. In this study, we performed a microarray experiment comparing the expression of miRNAs and mRNAs among three embryonic stages of development and two tissues (scutate scale and feather) of the chicken. We combined this expression data with miRNA target prediction tools and a curated list of feather related genes to produce a set of 19 miRNA-mRNA duplexes. These targeted mRNAs have been previously identified as important cell signaling and cell adhesion genes as well as structural genes involved in feather and scale morphogenesis. Interestingly, the miRNA target site of the cell signaling pathway gene, Aldehyde Dehydrogenase 1 Family, Member A3 (ALDH1A3), is unique to birds indicating a novel role in Aves. The identified miRNA target site of the cell adhesion gene, Tenascin C (TNC), is only found in specific chicken TNC splice variants that are differentially expressed in developing scutate scale and feather tissue indicating an important role of miRNA regulation in epidermal differentiation. Additionally, we found that β-keratins, a major structural component of avian and reptilian epidermal appendages, are targeted by multiple miRNA genes. In conclusion, our work provides quantitative expression data on miRNAs and mRNAs

  20. Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity

    Energy Technology Data Exchange (ETDEWEB)

    Gupta,Y.; Nair, D.; Wharton, R.; Aggarwal, A.

    2008-01-01

    Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycBreverse and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a 'spacer.' The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.

  1. Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

    Science.gov (United States)

    Gupta, Yogesh K; Nair, Deepak T; Wharton, Robin P; Aggarwal, Aneel K

    2008-04-01

    Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycB(reverse) and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a "spacer." The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo. PMID:18328718

  2. Structure and evolution of barley powdery mildew effector candidates

    Directory of Open Access Journals (Sweden)

    Pedersen Carsten

    2012-12-01

    Full Text Available Abstract Background Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease. Results Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen’s annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100–150 amino acids, with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300–400 amino acids, with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons. Conclusions We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f

  3. The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAsusing suboptimal RNA structures

    Czech Academy of Sciences Publication Activity Database

    Pánek, Josef; Krásný, Libor; Bobek, Jan; Ježková, E.; Korelusová, Jana; Vohradský, Jiří

    -, - (2010), s. 1-9. ISSN 1362-4962 R&D Projects: GA MŠk 2B06065; GA ČR GA303/09/0475; GA ČR GA310/07/1009 Institutional research plan: CEZ:AV0Z50200510 Keywords : ncRNAs * RNA structures Subject RIV: EE - Microbiology, Virology

  4. Computational RNomics:Structure identification and functional prediction of non-coding RNAs in silico

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The eukaryotic genome contains varying numbers of non-coding RNA(ncRNA) genes."Computational RNomics" takes a multidisciplinary approach,like information science,to resolve the structure and function of ncRNAs.Here,we review the main issues in "Computational RNomics" of data storage and management,ncRNA gene identification and characterization,ncRNA target identification and functional prediction,and we summarize the main methods and current content of "computational RNomics".

  5. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

    DEFF Research Database (Denmark)

    Will, Sebastian; Joshi, Tejal; Hofacker, Ivo L.;

    2012-01-01

    from AUC 0.71 to AUC 0.87, significantly reduces the cost of successive analysis steps. The ready-to-use software tool LocARNA-P produces structure-based multiple RNA alignments with associated columnwise STARs and predicts ncRNA boundaries. We provide additional results, a web server for Loc...... on sequence and structure similarity; we refer to these structure-based alignment reliabilities as STARs. The columnwise STARs of alignments, or STAR profiles, provide a versatile tool for the manual and automatic analysis of ncRNAs. In particular, we improve the boundary prediction of the widely...

  6. From structure prediction to genomic screens for novel non-coding RNAs

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.

    2011-01-01

    the increased amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristic feature....... Whereas early methods focused on energy-directed folding of single sequences, comparative analysis based on structure preserving changes of base pairs has been efficient in improving accuracy, and today this constitutes a key component in genomic screens. Here, we cover the basic principles of RNA folding...

  7. Compatibility of ITER candidate structural materials with static gallium

    International Nuclear Information System (INIS)

    Tests were conducted on the compatibility of gallium with candidate structural materials for the International Thermonuclear Experimental Reactor, e.g., Type 316 SS, Inconel 625, and Nb-5 Mo-1 Zr alloy, as well as Armco iron, Nickel 270, and pure chromium. Type 316 stainless steel is least resistant to corrosion in static gallium and Nb-5 Mo-1 Zr alloy is most resistant. At 400 degrees C, corrosion rates are ∼4.0, 0.5, and 0.03 mm/yr for type 316 SS, Inconel 625, and Nb-5 Mo- 1 Zr alloy, respectively. The pure metals react rapidly with gallium. In contrast to findings in earlier studies, pure iron shows greater corrosion than nickel. The corrosion rates at 400 degrees C are ≥88 and 18 mm/yr, respectively, for Armco iron and Nickel 270. The results indicate that at temperatures up to 400 degrees C, corrosion occurs primarily by dissolution and is accompanied by formation of metal/gallium intermetallic compounds. The solubility data for pure metals and oxygen in gallium are reviewed. The physical, chemical, and radioactive properties of gallium are also presented. The supply and availability of gallium, as well as price predictions through the year 2020, are summarized

  8. The structures of nonprotein-coding RNAs that drive internal ribosome entry site function.

    Science.gov (United States)

    Plank, Terra-Dawn M; Kieft, Jeffrey S

    2012-01-01

    Internal ribosome entry sites (IRESs) are RNA sequences that can recruit the translation machinery independent of the 5' end of the messenger RNA. IRESs are found in both viral and cellular RNAs and are important for regulating gene expression. There is great diversity in the mechanisms used by IRESs to recruit the ribosome and this is reflected in a variety of RNA sequences that function as IRESs. The ability of an RNA sequence to function as an IRES is conferred by structures operating at multiple levels from primary sequence through higher-order three-dimensional structures within dynamic ribonucleoproteins (RNPs). When these diverse structures are compared, some trends are apparent, but overall it is not possible to find universal rules to describe IRES structure and mechanism. Clearly, many different sequences and structures have evolved to perform the function of recruiting, positioning, and activating a ribosome without using the canonical cap-dependent mechanism. However, as our understanding of the specific sequences, structures, and mechanisms behind IRES function improves, more common features may emerge to link these diverse RNAs. PMID:22215521

  9. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    Science.gov (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

  10. Unique Gene-Silencing and Structural Properties of 2;#8242;-Fluoro-Modified siRNAs

    Energy Technology Data Exchange (ETDEWEB)

    Manoharan, Muthiah; Akinc, Akin; Pandey, Rajendra K.; Qin, June; Hadwiger, Philipp; John, Matthias; Mills, Kathy; Charisse, Klaus; Maier, Martin A.; Nechev, Lubomir; Greene, Emily M.; Pallan, Pradeep S.; Rozners, Eriks; Rajeev, Kallanthottathil G.; Egli, Martin (Binghamton); (Alnylam Pharm.); (Vanderbilt)

    2015-10-15

    With little or no negative impact on the activity of small interfering RNAs (siRNAs), regardless of the number of modifications or the positions within the strand, the 2'-deoxy-2'-fluoro (2'-F) modification is unique. Furthermore, the 2'-F-modified siRNA (see crystal structure) was thermodynamically more stable and more nuclease-resistant than the parent siRNA, and produced no immunostimulatory response.

  11. Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs.

    OpenAIRE

    Dekio, S; Yamasaki, R; Jidoi, J; Hori, H.; Osawa, S

    1984-01-01

    Nucleotide sequences of 5S rRNAs from four bacteria, Staphylococcus aureus Smith (diffuse), Staphylococcus epidermidis ATCC 14990, Micrococcus luteus ATCC 9341 and Micrococcus luteus ATCC 4698, were determined. The secondary structural models of S. aureus and S. epidermidis sequences showed characteristics of the gram-positive bacterial 5S rRNA (116-N type [H. Hori and S. Osawa, Proc. Natl. Acad. Sci. U.S.A. 76:381-385, 1979]). Those of M. luteus ATCC 9341 and M. luteus ATCC 4698 together wit...

  12. Identification of Candidate Target Cyp Genes for microRNAs Whose Expression Is Altered by PCN and TCPOBOP, Representative Ligands of PXR and CAR.

    Science.gov (United States)

    Moriya, Nozomu; Kataoka, Hiromi; Nishikawa, Jun-Ichi; Kugawa, Fumihiko

    2016-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are involved in mRNA post-transcriptional regulation. The deregulation of miRNAs affects the expression of drug-metabolizing enzymes, drug transporters, and nuclear receptors, all of which are important in regulating drug metabolism. miRNA expression can be altered by several endogenous or exogenous agents, such as steroid hormones, carcinogens, and therapeutic drugs. However, it is unclear whether hepatic miRNA expression is regulated by nuclear receptors, such as pregnane X receptor (PXR) and constitutive androstane receptor (CAR), which are indispensable for the expression of the CYPs. Here we investigated the effects of the mouse PXR and CAR ligands pregnenolone-16α-carbonitrile (PCN) and 1,4-bis[(3,5-dichloropyridin-2-yl)oxy]benzene (TCPOBOP) on hepatic miRNA expression in mice. We found that the expression of 9 miRNAs was increased (>2-fold) and of 4 miRNAs was decreased (>50%) in response to PCN, while TCPOBOP treatment led to the up-regulation of 8 miRNAs and down-regulation of 6 miRNAs. Using several miRNA target prediction algorithms, we found that the predicted target genes included several lesser known Cyp genes (Cyp1a1, Cyp1b1, Cyp2b10, Cyp2c38, Cyp2u1, Cyp4a12a/b, Cyp4v3, Cyp17a1, Cyp39a1, and Cyp51). We analyzed the expression of these genes in response to PCN and TCPOBOP and found changes in their mRNA levels, some of which were negatively correlated with the expression of their corresponding miRNAs, suggesting that miRNAs may play a role in regulating Cyp enzyme expression. Further studies will be required to fully elucidate the miRNA regulatory mechanisms that contribute to modulating CYP expression. PMID:27237601

  13. Identifying cancer-causing noncoding RNAs

    NARCIS (Netherlands)

    le Sage, Carlos Karel

    2008-01-01

    To circumvent the dependency on prediction models, we developed a microRNA-screen-based assay to establish links between cellular phenotypes and microRNAs (miRNAs). To this end, a miRNA expression library (miR-Lib) was built consisting of 300 annotated miRNAs and around 100 candidate miRNAs. These m

  14. De novo prediction of structured RNAs from genomic sequences

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Þórarinsson, Elfar;

    2010-01-01

    Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology...... currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately......, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions...

  15. Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs.

    Science.gov (United States)

    Ferré-D'Amaré, Adrian R

    2016-01-01

    The preparation of well-ordered crystals of RNAs with complex three-dimensional architecture can be facilitated by engineering a binding site for the spliceosomal protein U1A into a functionally and structurally dispensable stem-loop of the RNA of interest. Once suitable crystals are obtained, the U1A protein, of known structure, can be employed to facilitate preparation of heavy atom or anomalously scattering atom derivatives, or as a source of partial model phases for the molecular replacement method. Here, we describe the methods for making U1A preparations suitable for cocrystallization with RNA. As an example, the cocrystallization of the tetracycline aptamer with U1A is also described. PMID:26227038

  16. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.

    Science.gov (United States)

    Tycowski, Kazimierz T; Shu, Mei-Di; Steitz, Joan A

    2016-05-10

    The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits. PMID:27134163

  17. Structure and kinematics of candidate double-barred galaxies

    CERN Document Server

    Moiseev, A V; Chavushyan, V H

    2003-01-01

    Results of optical and NIR spectral and photometric observations of a sample of candidate double-barred galaxies are presented. Velocity fields and velocity dispersion maps of stars and ionized gas, continuum and emission-line images were constructed from integral-field spectroscopy observations carried out at the 6m telescope (BTA) of SAO RAS, with the MPFS spectrograph and the scanning Fabry-Perot Interferometer. NGC2681 was also observed with long-slit spectrograph of the BTA. Optical and NIR images were obtained at the BTA and at the 2.1m telescope (OAN, M\\'exico). High-resolution images were retrieved from the HST data archive. Morphological and kinematic features of all 13 sample objects are described in detail. Attention is focused on the interpretation of observed non-circular motions of gas and stars in circumnuclear (one kiloparsec- scale) regions. We have shown first of all that these motions are caused by a gravitational potential of large-scale bar. NGC3368 and NGC3786 have nuclear bars only, the...

  18. Molecular, Cellular, and Structural Mechanisms of Cocaine Addiction: A Key Role for MicroRNAs

    OpenAIRE

    Jonkman, Sietse; Kenny, Paul J.

    2012-01-01

    The rewarding properties of cocaine play a key role in establishing and maintaining the drug-taking habit. However, as exposure to cocaine increases, drug use can transition from controlled to compulsive. Importantly, very little is known about the neurobiological mechanisms that control this switch in drug use that defines addiction. MicroRNAs (miRNAs) are small non-protein coding RNA transcripts that can regulate the expression of messenger RNAs that code for proteins. Because of their high...

  19. Pyrochlores and perovskites: candidates for exploring structure functionality relationships

    International Nuclear Information System (INIS)

    Pyrochlores (A2B2O7) and perovskites (ABO3) are two widely studied classes of compounds which exhibit myriad properties like ionic conductivity, magnetism, dielectric behaviour, catalysis, optical properties etc. The stability of these structures is highly dependent upon the radius ratio of the cations occupying A- and B-sites. The intriguing crystal chemistry that originates from varying this radius ratio forms the basis for interesting structural studies. Further, the elemental versatility allows possibility of introducing a variety of guest ions in its lattice which makes it possible to fine tune the structure in order to obtain desirable properties. Some of the recent studies in our group have shown that in rare earth based mixed-pyrochlore oxides like Sm2-xDyxZr2O7, Gd1-xNdxZr2O7(0.0 ≤ x ≤ 2.0) etc., fine tuning of structure could be obtained by varying A-site cation which had a profound bearing on ionic conductivity of the resultant system. Similarly, the ABO3 systems like GdSc1-xInxO3, Gd1-xYxInO3 (0.0 ≤ x ≤ 1.0) etc. showed interesting structural and dielectric behavior due to fine control of BO5, polyhedra in these indates. The careful tuning of A and B-site occupants and the choice of synthesis route lead to stabilization of metastable structures in these classes with tunable electrical behavior. The present talk will thus concentrate upon elucidating the relation between structure and the electrical behavior by taking specific examples in these two classes of compounds. (author)

  20. MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs.

    Directory of Open Access Journals (Sweden)

    Ping Xuan

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are a set of short (19∼24 nt non-coding RNAs that play significant roles as posttranscriptional regulators in animals and plants. The ab initio prediction methods show excellent performance for discovering new pre-miRNAs. While most of these methods can distinguish real pre-miRNAs from pseudo pre-miRNAs, few can predict the positions of miRNAs. Among the existing methods that can also predict the miRNA positions, most of them are designed for mammalian miRNAs, including human and mouse. Minority of methods can predict the positions of plant miRNAs. Accurate prediction of the miRNA positions remains a challenge, especially for plant miRNAs. This motivates us to develop MaturePred, a machine learning method based on support vector machine, to predict the positions of plant miRNAs for the new plant pre-miRNA candidates. METHODOLOGY/PRINCIPAL FINDINGS: A miRNA:miRNA* duplex is regarded as a whole to capture the binding characteristics of miRNAs. We extract the position-specific features, the energy related features, the structure related features, and stability related features from real/pseudo miRNA:miRNA* duplexes. A set of informative features are selected to improve the prediction accuracy. Two-stage sample selection algorithm is proposed to combat the serious imbalance problem between real and pseudo miRNA:miRNA* duplexes. The prediction method, MaturePred, can accurately predict plant miRNAs and achieve higher prediction accuracy compared with the existing methods. Further, we trained a prediction model with animal data to predict animal miRNAs. The model also achieves higher prediction performance. It further confirms the efficiency of our miRNA prediction method. CONCLUSIONS: The superior performance of the proposed prediction model can be attributed to the extracted features of plant miRNAs and miRNA*s, the selected training dataset, and the carefully selected features. The web service of MaturePred, the

  1. Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Jianyu; Korostelev, Andrei; Costantino, David A.; Donohue, John P.; Noller, Harry F.; Kieft, Jeffrey S. (UCSC); (Colorado)

    2011-08-24

    Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA-mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.

  2. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

    Directory of Open Access Journals (Sweden)

    Uzilov Andrew V

    2006-03-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. Results Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. Conclusion The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a

  3. 3'-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs

    International Nuclear Information System (INIS)

    The plus-strand RNA genome of tomato bushy stunt virus (TBSV) contains a 351-nucleotide (nt)-long 3'-untranslated region. We investigated the role of the 3'-proximal 130 nt of this sequence in viral RNA accumulation within the context of a TBSV defective interfering (DI) RNA. Sequence comparisons between different tombusviruses revealed that the 3' portion of the 130-nt sequence is highly conserved and deletion analysis confirmed that this segment is required for accumulation of DI RNAs in protoplasts. Computer-aided sequence analysis and in vitro solution structure probing indicated that the conserved sequence consists of three stem-loop (SL) structures (5'-SL3-SL2-SL1-3'). The existence of SLs 1 and 3 was also supported by comparative secondary structure analysis of sequenced tombusvirus genomes. Formation of the stem regions in all three SLs was found to be very important, and modification of the terminal loop sequences of SL1 and SL2, but not SL3, decreased DI RNA accumulation in vivo. For SL3, alterations to an internal loop resulted in significantly reduced DI RNA levels. Collectively, these data indicate that all three SLs are functionally relevant and contribute substantially to DI RNA accumulation. In addition, secondary structure analysis of other tombusvirus replicons and related virus genera revealed that a TBSV satellite RNA and members of the closely related genus Aureusvirus (family Tombusviridae) share fundamental elements of this general structural arrangement. Thus, this secondary structure model appears to extend beyond tombusvirus genomes. These conserved 3'-terminal RNA elements likely function in vivo by promoting and/or regulating minus-strand synthesis

  4. Evaluations of Structural Failure Probabilities and Candidate Inservice Inspection Programs

    Energy Technology Data Exchange (ETDEWEB)

    Khaleel, Mohammad A.; Simonen, Fredric A.

    2009-05-01

    The work described in this report applies probabilistic structural mechanics models to predict the reliability of nuclear pressure boundary components. These same models are then applied to evaluate the effectiveness of alternative programs for inservice inspection to reduce these failure probabilities. Results of the calculations support the development and implementation of risk-informed inservice inspection of piping and vessels. Studies have specifically addressed the potential benefits of ultrasonic inspections to reduce failure probabilities associated with fatigue crack growth and stress-corrosion cracking. Parametric calculations were performed with the computer code pc-PRAISE to generate an extensive set of plots to cover a wide range of pipe wall thicknesses, cyclic operating stresses, and inspection strategies. The studies have also addressed critical inputs to fracture mechanics calculations such as the parameters that characterize the number and sizes of fabrication flaws in piping welds. Other calculations quantify uncertainties associated with the inputs calculations, the uncertainties in the fracture mechanics models, and the uncertainties in the resulting calculated failure probabilities. A final set of calculations address the effects of flaw sizing errors on the effectiveness of inservice inspection programs.

  5. Evaluations of Structural Failure Probabilities and Candidate Inservice Inspection Programs

    International Nuclear Information System (INIS)

    The work described in this report applies probabilistic structural mechanics models to predict the reliability of nuclear pressure boundary components. These same models are then applied to evaluate the effectiveness of alternative programs for inservice inspection to reduce these failure probabilities. Results of the calculations support the development and implementation of risk-informed inservice inspection of piping and vessels. Studies have specifically addressed the potential benefits of ultrasonic inspections to reduce failure probabilities associated with fatigue crack growth and stress-corrosion cracking. Parametric calculations were performed with the computer code pc-PRAISE to generate an extensive set of plots to cover a wide range of pipe wall thicknesses, cyclic operating stresses, and inspection strategies. The studies have also addressed critical inputs to fracture mechanics calculations such as the parameters that characterize the number and sizes of fabrication flaws in piping welds. Other calculations quantify uncertainties associated with the inputs calculations, the uncertainties in the fracture mechanics models, and the uncertainties in the resulting calculated failure probabilities. A final set of calculations address the effects of flaw sizing errors on the effectiveness of inservice inspection programs.

  6. Changes in microRNAs expression are involved in age-related atrial structural remodeling and atrial fibrillation

    Institute of Scientific and Technical Information of China (English)

    XU Guo-jun; GAN Tian-yi; TANG Bao-peng; CHEN Zu-heng; Mahemuti Ailiman; ZHOU Xian-hui; JIANG Tao

    2013-01-01

    Background Small noncoding microRNAs regulate gene expression in cardiac development and disease and have been implicated in the aging process and in the regulation of extracellular matrix proteins.However,their role in age-related cardiac remodeling and atrial fibrillation (AF) was not well understood.The present study was designed to decipher molecular mechanisms underlying age-related atrial structural remodeling and AF.Methods Three groups of dogs were studied:adult and aged dogs in sinus rhythm and with persistent AF induced by rapid atrial pacing.The expressions of microRNAs were measured by quantitative real-time polymerase chain reaction.Pathohistological and ultrastructural changes were tested by light and electron microscopy.Apoptosis index of myocytes was detected by TUNEL.Results Samples of atrial tissue showed the abnormal pathohistological and ultrastructural changes,the accelerated fibrosis,and apoptosis with aging and/or in AF dogs.Compared to the adult group,the expressions of microRNAs-21 and -29 were significantly increased,whereas the expressions of microRNAs-1 and-133 showed obvious downregulation tendency in the aged group.Compared to the aged group,the expressions of microRNAs-1,-21,and-29 was significantly increased in the old group in AF; contrastingly,the expressions of microRNA-133 showed obvious downregulation tendency.Conclusion These multiple aberrantly expressed microRNAs may be responsible for modulating the transition from adaptation to pathological atrial remodeling with aging and/or in AF.

  7. Molecular, Cellular, and Structural Mechanisms of Cocaine Addiction: A Key Role for MicroRNAs

    Science.gov (United States)

    Jonkman, Sietse; Kenny, Paul J

    2013-01-01

    The rewarding properties of cocaine play a key role in establishing and maintaining the drug-taking habit. However, as exposure to cocaine increases, drug use can transition from controlled to compulsive. Importantly, very little is known about the neurobiological mechanisms that control this switch in drug use that defines addiction. MicroRNAs (miRNAs) are small non-protein coding RNA transcripts that can regulate the expression of messenger RNAs that code for proteins. Because of their highly pleiotropic nature, each miRNA has the potential to regulate hundreds or even thousands of protein-coding RNA transcripts. This property of miRNAs has generated considerable interest in their potential involvement in complex psychiatric disorders such as addiction, as each miRNA could potentially influence the many different molecular and cellular adaptations that arise in response to drug use that are hypothesized to drive the emergence of addiction. Here, we review recent evidence supporting a key role for miRNAs in the ventral striatum in regulating the rewarding and reinforcing properties of cocaine in animals with limited exposure to the drug. Moreover, we discuss evidence suggesting that miRNAs in the dorsal striatum control the escalation of drug intake in rats with extended cocaine access. These findings highlight the central role for miRNAs in drug-induced neuroplasticity in brain reward systems that drive the emergence of compulsive-like drug use in animals, and suggest that a better understanding of how miRNAs control drug intake will provide new insights into the neurobiology of drug addiction. PMID:22968819

  8. A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect

    CERN Document Server

    Shi, Ya-Zhou; Wu, Yuan-Yan; Tan, Zhi-Jie

    2014-01-01

    To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (less than or equal to 45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 {\\AA} and an overall minimum RMSD of 1.9 {\\AA} from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ~ 1.0 degrees Celsius of melting temperatures, as compared wi...

  9. A three-dimensional measurement method based on mesh candidates assisted with structured light

    Science.gov (United States)

    Xu, Gang; Zhang, Wenming; Li, Haibin; Liu, Bin

    2009-07-01

    Rendering three-dimensional information of a scene from optical measurement is very important for a wide variety of applications such as robot navigation, rapid prototyping, medical imaging, industrial inspection, etc. In this paper, a new 3D measurement method based on mesh candidate with structured light illuminating is proposed. The vision sensor consists of two CCD cameras and a DLP projector. The measurement system combines the technology of binocular stereo vision and structured light, so as to simplify the process of acquiring depth information using mesh candidates. The measurement method is based on mesh candidates which represent the potential depth in the three dimensional scene. First the mesh grid was created along the direction of axes in world coordinate system, and the nodes were considered as depth candidates on the surface of object. Then each group of the mesh nodes varying along z axis were mapped to the captured image planes of both cameras. At last, according to the similarity measure of the corresponding pixel pairs, the depth of the object surface can be obtained. The matching process is between the pixels in both camera planes corresponding to the spatial mesh candidates. Aided by the structured light pattern, the accuracy of measurement system improved. Appending the periodic sawtooth pattern on the scene by structured light made measurement easier, while the computational cost did not increased since the projector had no need to be calibrated. The 3DS MAX and Matlab software were used to simulate measurement system and reconstruct the surface of the object. After the positioned cameras have been calibrated using Matlab calibration toolbox, the projector is used to project structured light pattern on the scene. Indicated by experimental results, the mesh-candidate-based method is obviously superior in computation and accuracy. Compared with traditional methods based on image matching, our method has several advantages: (1) the complex

  10. Associating schizophrenia, long non-coding RNAs and neurostructural dynamics

    Directory of Open Access Journals (Sweden)

    Veronica eMerelo

    2015-09-01

    Full Text Available Several lines of evidence indicate that schizophrenia has a strong genetic component. But the exact nature and functional role of this genetic component in the pathophysiology of this mental illness remains a mystery. Long non-coding RNAs (lncRNAs are a recently discovered family of molecules that regulate gene transcription through a variety of means. Consequently, lncRNAs could help us bring together apparent unrelated findings in schizophrenia; namely, genomic deficiencies on one side and neuroimaging, as well as postmortem results on the other. In fact, the most consistent finding in schizophrenia is decreased brain size together with enlarged ventricles. This anomaly appears to originate from shorter and less ramified dendrites and axons. But a decrease in neuronal arborizations cannot explain the complex pathophysiology of this psychotic disorder; however, dynamic changes in neuronal structure present throughout life could. It is well recognized that the structure of developing neurons is extremely plastic. This structural plasticity was thought to stop with brain development. However, breakthrough discoveries have shown that neuronal structure retains some degree of plasticity throughout life. What the neuroscientific field is still trying to understand is how these dynamic changes are regulated and lncRNAs represent promising candidates to fill this knowledge gap. Here, we present evidence that associates specific lncRNAs with schizophrenia. We then discuss the potential role of lncRNAs in neurostructural dynamics. Finally, we explain how dynamic neurostructural modifications present throughout life could, in theory, reconcile apparent unrelated findings in schizophrenia.

  11. Higher-order structure in the 3'-terminal domain VI of the 23 S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus

    DEFF Research Database (Denmark)

    Garrett, R A; Christensen, A; Douthwaite, S

    1984-01-01

    ribonuclease from Naja naja oxiana, and the relatively unstructured and accessible sequences were detected with the single-strand-specific ribonucleases A, T1 and T2. The data enabled the three secondary structural models, proposed for the E. coli 23 S RNAs, to be examined critically and it was concluded that......An experimental approach was used to determine, and compare, the higher-order structure within domain VI of the 23 S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus. This domain, which encompasses approximately 300 nucleotides at the 3' end of the RNAs, consists of two large...... ribosomes of flowering plants. The structure of domain VI within the eubacterial RNAs was probed with chemical reagents in order to establish the degree of stacking and/or accessibility of each adenosine, cytidine and guanosine residue; the double-helical segments were localized with the cobra venom...

  12. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

    OpenAIRE

    Lu, Zhi John; Yip, Kevin Y.; Wang, Guilin; Shou, Chong; Hillier, LaDeana W.; Khurana, Ekta; Agarwal, Ashish; Auerbach, Raymond; Rozowsky, Joel; Cheng, Chao; Kato, Masaomi; Miller, David M.; Slack, Frank; Snyder, Michael; Waterston, Robert H.

    2011-01-01

    We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and data from the modENCODE consortium, we are able to separate known C. elegans ncRNAs from coding sequences and other genomic elements with a high level of accuracy (97% AUC on an independent validation...

  13. Detecting protein candidate fragments using a structural alphabet profile comparison approach.

    Science.gov (United States)

    Shen, Yimin; Picord, Géraldine; Guyon, Frédéric; Tuffery, Pierre

    2013-01-01

    Predicting accurate fragments from sequence has recently become a critical step for protein structure modeling, as protein fragment assembly techniques are presently among the most efficient approaches for de novo prediction. A key step in these approaches is, given the sequence of a protein to model, the identification of relevant fragments - candidate fragments - from a collection of the available 3D structures. These fragments can then be assembled to produce a model of the complete structure of the protein of interest. The search for candidate fragments is classically achieved by considering local sequence similarity using profile comparison, or threading approaches. In the present study, we introduce a new profile comparison approach that, instead of using amino acid profiles, is based on the use of predicted structural alphabet profiles, where structural alphabet profiles contain information related to the 3D local shapes associated with the sequences. We show that structural alphabet profile-profile comparison can be used efficiently to retrieve accurate structural fragments, and we introduce a fully new protocol for the detection of candidate fragments. It identifies fragments specific of each position of the sequence and of size varying between 6 and 27 amino-acids. We find it outperforms present state of the art approaches in terms (i) of the accuracy of the fragments identified, (ii) the rate of true positives identified, while having a high coverage score. We illustrate the relevance of the approach on complete target sets of the two previous Critical Assessment of Techniques for Protein Structure Prediction (CASP) rounds 9 and 10. A web server for the approach is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/SAFrag. PMID:24303019

  14. Surface states and bulk electronic structure in the candidate type-II Weyl semimetal WTe2

    OpenAIRE

    Bruno, F. Y.; Tamai, A.; Wu, Q. S.; Cucchi, I.; Barreteau, C.; A. de la Torre; Walker, S. McKeown; Riccò, S; Wang, Z.; Kim, T K; Hoesch, M.; Shi, M. (Mimi); Plumb, N. C.; Giannini, E; Soluyanov, A. A.

    2016-01-01

    We report angle-resolved photoemission experiments identifying an arc-like surface state connecting the bulk electron and hole pockets of the candidate type-II Weyl semimetal WTe2. This surface state can be isolated clearly on one of two distinct surface terminations observed experimentally, which we associate with the in-equivalent top and bottom surfaces of the non-centrosymmetric crystal structure. We further use the identification of the two different surfaces to clarify the number of bul...

  15. Detailed mechanical/structural test and analysis on the spacer grid candidates for the advanced LWR fuel

    International Nuclear Information System (INIS)

    The spacer grid is one of the structural components of the nuclear fuel assemblies for the pressurized light water reactors. Based on the nuclear fuel assembly mechanical/ thermal-hydraulic design experience and scrutinizing the design features on the foreign advanced nuclear fuel and the foreign patents of the spacer grid, 14 kinds of spacer grid candidates have been conceptually derived and applied for the patents since 1997. Through the screening test on the 5 candidates of the spacer grids 2 leading candidates have been selected for detailed test from the mechanical/structural point of view. In this paper detailed test and analysis results on the leading candidates are discussed

  16. Identification of RNA sequences and structures involved in site-specific cleavage of IGF-II mRNAs.

    OpenAIRE

    van Dijk, E L; Sussenbach, J S; Holthuizen, P E

    1998-01-01

    Insulin-like growth factor-II (IGF-II) mRNAs are subject to site-specific endonucleolytic cleavage in the 3' untranslated region (UTR), rendering an unstable 5' cleavage product containing the coding region and a very stable 3' cleavage product of 1.8 kb consisting of the 3'-UTR sequence and the poly(A) tail. Previously, it was established that two widely separated elements in the 3'-UTR (elements I and II), that can form a duplex structure, are necessary and sufficient for cleavage. To furth...

  17. Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.

    Science.gov (United States)

    Zhu, Jianyu; Korostelev, Andrei; Costantino, David A; Donohue, John P; Noller, Harry F; Kieft, Jeffrey S

    2011-02-01

    Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA • mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines. PMID:21245352

  18. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Anthon, Christian; Bak, Mads; Tommerup, Niels; Skovgaard, Kerstin; Heegaard, Peter M. H.; Gorodkin, Jan; Cirera, Susanna; Fredholm, Merete

    2012-01-01

    still very limited. Results: In this study, the RNA extracted from visually unaffected and necrotic tissue from pigs infected with Actinobacillus pleuropneumoniae was subjected to small RNA deep sequencing. We identified 169 conserved and 11 candidate novel microRNAs in the pig. Of these, 17 were......Background: MicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus...... pleuropneumoniae (APP) causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine is...

  19. Structure and interactions of a malarial vaccine candidate, AMA1, form the parasite plasmodium falciparum

    International Nuclear Information System (INIS)

    Full text: Apical membrane antigen 1 (AMA1), a merozoite surface protein found in all species of Plasmodium and other apicomplexan parasites, is a strong candidate for inclusion in a malarial vaccine. Recombinant AMA1 protected against P. fragile in monkeys and P. chabaudi adami in mice. P. falciparum AMA1 which has a 62-kDa ectodomain consisting of three disulphide-stabilised domains, is a target of antibodies that inhibit merozoite invasion in vitro. Here we describe the solution structure of domain III (14 kDa), determined by NMR on 15N- and 13C/15N-labelled samples. It has a well-defined disulphide-stabilised core interrupted by a disordered loop, and both the N- and C-terminal regions of the molecule are unstructured. The structured region includes all three disulphide bonds. Naturally-occurring mutations across 11 different P falciparum strains that are located far apart in the sequence cluster around the disulphide core in the 3D structure of domain III, suggesting that this region contains the major epitopes recognised by neutralising antibodies. Consistent with this, the disulphide-bond stabilised conformation of the ectodomain was essential for protection, as the antigen was not an effective vaccine after reduction and alkylation. Peptides have been found by phage display that bind to AMA1 and block merozoite invasion of erythrocytes. We have investigated their solution structures and interaction with full-length AMA1 ectodomain in an effort to understand the structure-function relationships of this important vaccine candidate

  20. A nuclear structure study of the proposed gamma-ray laser candidate nucleus 186Re

    International Nuclear Information System (INIS)

    We present results of theoretical nuclear structure model calculations for the gamma-ray laser candidate nucleus 186Re proposed by Collins. Our calculations of this odd-odd transitional nucleus are based on an axially-asymmetric (particle plus triaxial rotor) model for constructing the orbitals of the odd nucleons that couple under the influence of the residual neutron-proton interaction. We include pairing correlations in the determination of these orbitals by using the BCS approximation with newly determined pairing strengths. The matrix elements of the residual neutron-proton interaction are obtained using phenomenological spin-dependent δ function potentials of both surface and volume forms. We examine the sensitivity of the calculated low-excitation level structure of 186Re to the strength of these potentials. Calculated energy levels of 186Re will be presented and compared with experiment. The impact of our results on the proposed use of 186Re as a gamma-ray laser will be discussed. In addition, based upon these and other model calculations to be described, we assess the level of effort necessary in a full-scale theoretical search for a viable candidate nucleus for a gamma-ray laser. 17 refs., 1 fig., 3 tabs

  1. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

    Directory of Open Access Journals (Sweden)

    Podolska Agnieszka

    2012-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus pleuropneumoniae (APP causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine is still very limited. Results In this study, the RNA extracted from visually unaffected and necrotic tissue from pigs infected with Actinobacillus pleuropneumoniae was subjected to small RNA deep sequencing. We identified 169 conserved and 11 candidate novel microRNAs in the pig. Of these, 17 were significantly up-regulated in the necrotic sample and 12 were down-regulated. The expression analysis of a number of candidates revealed microRNAs of potential importance in the innate immune response. MiR-155, a known key player in inflammation, was found expressed in both samples. Moreover, miR-664-5p, miR-451 and miR-15a appear as very promising candidates for microRNAs involved in response to pathogen infection. Conclusions This is the first study revealing significant differences in composition and expression profiles of miRNAs in lungs infected with a bacterial pathogen. Our results extend annotation of microRNA in pig and provide insight into the role of a number of microRNAs in regulation of bacteria induced immune and inflammatory response in porcine lung.

  2. Structural evaluation of candidate designs for the large space telescope primary mirror

    Science.gov (United States)

    Soosaar, K.; Grin, R.; Furey, M.; Hamilton, J.

    1975-01-01

    Structural performance analyses were conducted on two candidate designs (Itek and Perkin-Elmer designs) for the large space telescope three-meter mirror. The mirror designs and the finite-element models used in the analyses evaluation are described. The results of the structural analyses for several different types of loading are presented in tabular and graphic forms. Several additional analyses are also reported: the evaluation of a mirror design concept proposed by the Boeing Co., a study of the global effects of local cell plate deflections, and an investigation of the fracture mechanics problems likely to occur with Cervit and ULE. Flexibility matrices were obtained for the Itek and Perkin-Elmer mirrors to be used in active figure control studies. Summary, conclusions, and recommendations are included.

  3. Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results

    OpenAIRE

    Yoon, Byung-Jun; Vaidyanathan, P.P.

    2008-01-01

    Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs. Unfortunately, the annotation of ncRNA genes that give rise to functional RNA molecules has begun only recently, and it is far from being complete. Considering the huge amount of genome sequence data, we need efficient computational methods fo...

  4. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  5. Fracture toughness of irradiated candidate materials for ITER first wall/blanket structures: Summary report

    Energy Technology Data Exchange (ETDEWEB)

    Alexander, D.J.; Pawel, J.E.; Grossbeck, M.L.; Rowcliffe, A.F. [Oak Ridge National Lab., TN (United States)] [and others

    1996-04-01

    Disk compact specimens of candidate materials for first wall/blanket structures in ITER have been irradiated to damage levels of about 3 dpa at nominal irradiation temperatures of either 90 250{degrees}C. These specimens have been tested over a temperature range from 20 to 250{degrees}C to determine J-integral values and tearing moduli. The results show that irradiation at these temperatures reduces the fracture toughness of austenic stainless steels, but the toughness remains quite high. The toughness decreases as the temperature increases. Irradiation at 250{degrees}C is more damaging that at 90{degrees}C, causing larger decreases in the fracture toughness. The ferritic-martensitic steels HT-9 and F82H show significantly greater reductions in fracture toughness that the austenitic stainless steels.

  6. Biocomputational prediction of non-coding RNAs in model cyanobacteria

    Directory of Open Access Journals (Sweden)

    Ude Susanne

    2009-03-01

    Full Text Available Abstract Background In bacteria, non-coding RNAs (ncRNA are crucial regulators of gene expression, controlling various stress responses, virulence, and motility. Previous work revealed a relatively high number of ncRNAs in some marine cyanobacteria. However, for efficient genetic and biochemical analysis it would be desirable to identify a set of ncRNA candidate genes in model cyanobacteria that are easy to manipulate and for which extended mutant, transcriptomic and proteomic data sets are available. Results Here we have used comparative genome analysis for the biocomputational prediction of ncRNA genes and other sequence/structure-conserved elements in intergenic regions of the three unicellular model cyanobacteria Synechocystis PCC6803, Synechococcus elongatus PCC6301 and Thermosynechococcus elongatus BP1 plus the toxic Microcystis aeruginosa NIES843. The unfiltered numbers of predicted elements in these strains is 383, 168, 168, and 809, respectively, combined into 443 sequence clusters, whereas the numbers of individual elements with high support are 94, 56, 64, and 406, respectively. Removing also transposon-associated repeats, finally 78, 53, 42 and 168 sequences, respectively, are left belonging to 109 different clusters in the data set. Experimental analysis of selected ncRNA candidates in Synechocystis PCC6803 validated new ncRNAs originating from the fabF-hoxH and apcC-prmA intergenic spacers and three highly expressed ncRNAs belonging to the Yfr2 family of ncRNAs. Yfr2a promoter-luxAB fusions confirmed a very strong activity of this promoter and indicated a stimulation of expression if the cultures were exposed to elevated light intensities. Conclusion Comparison to entries in Rfam and experimental testing of selected ncRNA candidates in Synechocystis PCC6803 indicate a high reliability of the current prediction, despite some contamination by the high number of repetitive sequences in some of these species. In particular, we

  7. Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8.

    Directory of Open Access Journals (Sweden)

    Ibrahim F Farag

    Full Text Available We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8. Our aim was to identify the putative ecological role(s played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples, and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples. While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.

  8. Brain expressed microRNAs implicated in schizophrenia etiology

    DEFF Research Database (Denmark)

    Hansen, Thomas; Olsen, Line; Lindow, Morten;

    2007-01-01

    Protein encoding genes have long been the major targets for research in schizophrenia genetics. However, with the identification of regulatory microRNAs (miRNAs) as important in brain development and function, miRNAs genes have emerged as candidates for schizophrenia-associated genetic factors. I...

  9. Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation.

    Directory of Open Access Journals (Sweden)

    Jiang Shu

    Full Text Available MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in humans. Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612 from 194 species, with 1,102 features derived from the microRNA sequence and structure. Through in-depth bioinformatics analysis, 8 groups of discriminative features have been used to characterize human circulating microRNAs and infer the likelihood that a microRNA will get transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly transportable candidates where 117 of them have identical sequences with their homologs in human and 73 are known to be associated with exosomes. Through a milk feeding experiment, we have validated 9 cow-milk microRNAs in human plasma using microRNA-sequencing analysis, including the top ranked microRNAs such as bta-miR-487b, miR-181b, and miR-421. The implications in health-related processes have been illustrated in the functional analysis. This work demonstrates the data-driven computational analysis is highly promising to study novel molecular characteristics of transportable microRNAs while bypassing the complex mechanistic details.

  10. Characterization of piRNAs across postnatal development in mouse brain

    KAUST Repository

    Ghosheh, Yanal

    2016-04-26

    PIWI-interacting RNAs (piRNAs) are responsible for maintaining the genome stability by silencing retrotransposons in germline tissues– where piRNAs were first discovered and thought to be restricted. Recently, novel functions were reported for piRNAs in germline and somatic cells. Using deep sequencing of small RNAs and CAGE of postnatal development of mouse brain, we identified piRNAs only in adult mouse brain. These piRNAs have similar sequence length as those of MILI-bound piRNAs. In addition, we predicted novel candidate regulators and putative targets of adult brain piRNAs.

  11. Trash or Treasure: extracellular microRNAs and cell-to-cell communication

    OpenAIRE

    Kosaka, Nobuyoshi; Yoshioka, Yusuke; Hagiwara, Keitaro; Tominaga, Naoomi; Katsuda, Takeshi; Ochiya, Takahiro

    2013-01-01

    Circulating RNAs in human body fluids are promising candidates for diagnostic purposes. However, the biological significance of circulating RNAs remains elusive. Recently, small non-coding RNAs, microRNAs (miRNAs), were isolated from multiple human body fluids, and these “circulating miRNAs” have been implicated as novel disease biomarkers. Concurrently, miRNAs were also identified in the extracellular space associated with extracellular vesicles (EVs), which are small membrane vesicles secre...

  12. MicroRNAs in B-cells

    DEFF Research Database (Denmark)

    Marques, Sara Correia; Laursen, Maria Bach; Bødker, Julie Støve; Kjeldsen, Malene Krag; Larsen, Steffen Falgreen; Schmitz, Alexander; Bøgsted, Martin; Johnsen, Hans Erik; Dybkær, Karen

    2015-01-01

    transformation due to their function as oncogenes or tumor suppressors. We know that miRNAs are involved in the development of normal B-cells and that different B-cell subsets express specific miRNA profiles according to their degree of differentiation. B-cell-derived malignancies contain transcription......MicroRNAs (miRNAs) are small non-coding RNAs that play important post-transcriptional regulatory roles in a wide range of biological processes. They are fundamental to the normal development of cells, and evidence suggests that the deregulation of specific miRNAs is involved in malignant...... signatures reminiscent of their cell of origin. Therefore, we believe that normal and malignant B-cells share features of regulatory networks controlling differentiation and the ability to respond to treatment. The involvement of miRNAs in these processes makes them good biomarker candidates. B...

  13. Higher order structure in the 3'-minor domain of small subunit ribosomal RNAs from a gram negative bacterium, a gram positive bacterium and a eukaryote

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1983-01-01

    , T2 and S1. The data enabled the various minimal secondary structural models, proposed for the 3'-regions of the E. coli and S. cerevisiae RNAs, to be critically examined, and to demonstrate that the main common features of these models are correct. The results also reveal the presence and position...... "unstructured" regions. Several unusual structural features were detected. Multiple G X A pairings in two of the putative helices, which are compatible with phylogenetic sequence comparisons, are strongly supported by the occurrence of cobra venom ribonuclease cuts adjacent to, and in one case between, these......An experimental approach was used to determine and compare the highest order structure within the 150 to 200 nucleotides at the 3'-ends of the RNAs from the small ribosomal subunits of Escherichia coli, Bacillus stearothermophilus and Saccharomyces cerevisiae. Chemical reagents were employed to...

  14. Stress corrosion cracking susceptibility of candidate structural materials in supercritical pressurized water

    Energy Technology Data Exchange (ETDEWEB)

    Je, Hwanil, E-mail: hwanil.je@gmail.com; Kimura, Akihiko

    2014-12-15

    The stress corrosion cracking (SCC) susceptibility in supercritical pressurized water (SCPW) was investigated for the candidate structural steels of advanced fusion and fission nuclear system, which are SUS316L austenitic steel, F82H ferritic–martensitic steel and SOC-16 oxide dispersion strengthened (ODS) ferritic steel. In order to evaluate the susceptibility to SCC with those materials, slow strain rate test (SSRT) was carried out at 773 K, under a pressure of 25 MPa of SCPW with deaerated condition. High temperature tensile test in vacuum at 773 K was also performed to compare the deformation and fracture behavior between corrosive environment of SCPW and non-corrosive environment. Although SUS316L showed a change in the fracture mode in the deaerated SCPW from an entire ductile fracture at higher strain rate to a mixed mode of ductile and brittle fracture at lower one, the fracture mode of ODS steel and F82H was not changed in the tested strain rate range. Both the IGSCC and TGSCC were observed in SUS316L. And F82H steel suffered from much severer oxidation than SUS316L and SOC-16.

  15. Structural characterization of the mechanosensitive channel candidate MCA2 from Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Hideki Shigematsu

    Full Text Available Mechanosensing in plants is thought to be governed by sensory complexes containing a Ca²⁺-permeable, mechanosensitive channel. The plasma membrane protein MCA1 and its paralog MCA2 from Arabidopsis thaliana are involved in mechanical stress-induced Ca²⁺ influx and are thus considered as candidates for such channels or their regulators. Both MCA1 and MCA2 were functionally expressed in Sf9 cells using a baculovirus system in order to elucidate their molecular natures. Because of the abundance of protein in these cells, MCA2 was chosen for purification. Purified MCA2 in a detergent-solubilized state formed a tetramer, which was confirmed by chemical cross-linking. Single-particle analysis of cryo-electron microscope images was performed to depict the overall shape of the purified protein. The three-dimensional structure of MCA2 was reconstructed at a resolution of 26 Å from 5,500 particles and appears to comprise a small transmembrane region and large cytoplasmic region.

  16. Stress corrosion cracking susceptibility of candidate structural materials in supercritical pressurized water

    International Nuclear Information System (INIS)

    The stress corrosion cracking (SCC) susceptibility in supercritical pressurized water (SCPW) was investigated for the candidate structural steels of advanced fusion and fission nuclear system, which are SUS316L austenitic steel, F82H ferritic–martensitic steel and SOC-16 oxide dispersion strengthened (ODS) ferritic steel. In order to evaluate the susceptibility to SCC with those materials, slow strain rate test (SSRT) was carried out at 773 K, under a pressure of 25 MPa of SCPW with deaerated condition. High temperature tensile test in vacuum at 773 K was also performed to compare the deformation and fracture behavior between corrosive environment of SCPW and non-corrosive environment. Although SUS316L showed a change in the fracture mode in the deaerated SCPW from an entire ductile fracture at higher strain rate to a mixed mode of ductile and brittle fracture at lower one, the fracture mode of ODS steel and F82H was not changed in the tested strain rate range. Both the IGSCC and TGSCC were observed in SUS316L. And F82H steel suffered from much severer oxidation than SUS316L and SOC-16

  17. Structure-activity relationship analysis of cytotoxic cyanoguanidines: selection of CHS 828 as candidate drug

    Directory of Open Access Journals (Sweden)

    Gullbo Joachim

    2009-06-01

    Full Text Available Abstract Background N-(6-(4-chlorophenoxyhexyl-N'-cyano-N''-4-pyridyl guanidine (CHS 828 is the first candidate drug from a novel group of anti-tumour agents – the pyridyl cyanoguanidines, shown to be potent compounds interfering with cellular metabolism (inhibition of nicotinamide phosphoribosyl transferase and NF-κB signalling. Substituted cyanoguanidines are also found in anti-hypertensive agents such as the potassium channel opener pinacidil (N-cyano-N'-(4-pyridyl-N''-(1,2,2-trimethylpropylguanidine and histamine-II receptor antagonists (e.g. cimetidine, N-cyano-N'-methyl-N''-[2-[[(5-methylimidazol-4-yl]methyl]thio]ethylguanidine. In animal studies, CHS 828 has shown very promising activity, and phase I and II studies resulted in further development of a with a water soluble prodrug. Findings To study the structural requirements for cyanoguanidine cytotoxicity a set of 19 analogues were synthesized. The cytotoxic effects were then studied in ten cell lines selected for different origins and mechanisms of resistance, using the fluorometric microculture cytotoxicity assay (FMCA. The compounds showed varying cytotoxic activity even though the dose-response curves for some analogues were very shallow. Pinacidil and cimetidine were found to be non-toxic in all ten cell lines. Starting with cyanoguanidine as the crucial core it was shown that 4-pyridyl substitution was more efficient than was 3-pyridyl substitution. The 4-pyridyl cyanoguanidine moiety should be linked by an alkyl chain, optimally a hexyl, heptyl or octyl chain, to a bulky end group. The exact composition of this end group did not seem to be of crucial importance; when the end group was a mono-substituted phenyl ring it was shown that the preferred position was 4-substitution, followed by 3- and, finally, 2-substitution as the least active. Whether the substituent was a chloro, nitro or methoxy substituent seemed to be of minor importance. Finally, the activity patterns in the

  18. Identification and characterization of new plant microRNAs using EST analysis

    Institute of Scientific and Technical Information of China (English)

    Bao Hong ZHANG; Xiao Ping PAN; Qing Lian WANG; George P.COBB; Todd A.ANDERSON

    2005-01-01

    Seventy-five previously known plant microRNAs (miRNAs) were classified into 14 families according to their gene sequence identity. A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to GenBank's plant EST databases with BLAST algorithms. After removing the EST sequences with high numbers (more than 2) of mismatched nucleotides, a total of 812 EST contigs were identified. After predicting and scoring the RNA secondary structure of the 812 EST sequences using mFold software, 338 new potential miRNAs were identified in 60 plant species, miRNAs are widespread. Some microRNAs may highly conserve in the plant kingdom, and they may have the same ancestor in very early evolution. There is no nucleotide substitution in most miRNAs among many plant species. Some of the new identified potential miRNAs may be induced and regulated by environmental biotic and abiotic stresses. Some may be preferentially expressed in specific tissues, and are regulated by developmental switching. These findings suggest that EST analysis is a good alternative strategy for identifying new miRNA candidates, their targets, and other genes. A large number of miRNAs exist in different plant species and play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction. Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized.

  19. Genomic Organization of Zebrafish microRNAs

    Directory of Open Access Journals (Sweden)

    Paydar Ima

    2008-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are small (~22 nt non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.

  20. MicroRNAs as molecular markers in lung cancer

    Directory of Open Access Journals (Sweden)

    Javier Silva

    2013-10-01

    Full Text Available Lung cancer is the most common cause of cancer death in the western world for both men and women. Lung cancer appears to be a perfect candidate for a screening program, since it is the number one cancer killer, it has a long preclinical phase, curative treatment for the minority of patients who are diagnosed early and a target population at risk (smokers and it is also a major economic burden. The earliest approaches to identifying cancer markers were based on preliminary clinical or pathological observations, although molecular biology is a strong candidate for occupying a place among the set of methods. In search of markers, several alterations, such as mutations, loss of heterozygosity, microsatellite instability, DNA methylation, mitochondrial DNA mutations, viral DNA, modified expression of mRNA, miRNA and proteins, and structurally altered proteins have all been analysed. MicroRNAs (miRNA are small RNA molecules, about 19-25 nucleotides long and encoded in genomes of plants, animals, fungi and viruses. It has been reported that miRNAs may have multiple functions in lung development and that aberrant expression of miRNAs could induce lung tumorigenesis. We review here the role of miRNAs in lung tumorigenesis and also as a novel type of biomarker.-----------------------------------Cite this article as:Silva J, Garcia V, Lopez-Gonzalez A, Provencio M. MicroRNAs as molecular markers in lung cancer. Int J Cancer Ther Oncol 2013;1(1:010111. DOI: http://dx.doi.org/10.14319/ijcto.0101.11

  1. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

    KAUST Repository

    Khraiwesh, Basel

    2012-02-01

    Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress. © 2011 Elsevier B.V.

  2. Inner Structure of Protostellar Collapse Candidate B335 Derived from Millimeter-Wave Interferometry

    Science.gov (United States)

    Harvey, Daniel W. A.; Wilner, David J.; Myers, Philip C.; Tafalla, Mario; Mardones, Diego

    2003-02-01

    We present a study of the density structure of the protostellar collapse candidate B335 using continuum observations from the IRAM Plateau de Bure Interferometer made at wavelengths of 1.2 and 3.0 mm. We analyze these data, which probe spatial scales from 5000 to 500 AU, directly in the visibility domain by comparison with synthetic observations constructed from models that assume different physical conditions. This approach allows for much more stringent constraints to be derived from the data than from analysis of images. A single radial power law in density provides a good description of the data, with a best-fit power-law density index p=1.65+/-0.05. Through simulations, we quantify the sensitivity of this result to various model uncertainties, including assumptions of temperature distribution, outer boundary, dust opacity spectral index, and an unresolved central component. The largest uncertainty comes from the unknown presence of a centralized point source. The maximal point source, with 1.2 mm flux of F=12+/-7 mJy, reduces the power-law density index to p=1.47+/-0.07. The remaining sources of systematic uncertainty, of which the most important is the radial dependence of the temperature distribution, likely contribute a total uncertainty at the level of δpcrude model of the outflow as a hollow bipolar cone of constant opening angle improves the fit and leaves the resulting density power-law index unchanged. These results conform well to the generic paradigm of isolated, low-mass star formation, which predicts a power-law density index close to p=1.5 for an inner region of gravitational free fall onto the protostar. However, the standard inside-out collapse model does not fit the data as successfully as a simple p=1.5 power law, because of the relative shallowness of the predicted density profile just within the infall radius. Based on observations carried out with the IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG

  3. microRNAs and Endometrial Pathophysiology.

    Science.gov (United States)

    Chill, Henry H; Dior, Uri P; Kogan, Liron; Revel, Ariel

    2015-01-01

    Embryo implantation requires a reciprocal interaction between the blastocyst and endometrium and is associated with complex regulatory mechanisms. Since their discovery, microRNAs became prominent candidates providing missing links for many biological pathways. In recent years, microRNAs were implicated as one of the important players in regulation of various biological and physiological endometrial related processes. This chapter aims to present recent knowledge pertaining to the diverse aspects of microRNAs in the embryo-endometrial relationship. We will focus on the role of microRNAs in decidualization and their part in natural and stimulated cycles. Next, we will present recent studies deliberating the role of microRNAs in recurrent pregnancy loss and in the important phenomenon of recurrent implantation failure. Lastly, demonstrating an important aspect of embryo implantation and invasion, we will outline few microRNA related shared pathways of implantation and carcinogenesis. PMID:26662990

  4. Infectious long non-coding RNAs.

    Science.gov (United States)

    Katsarou, Konstantina; Rao, A L N; Tsagris, Mina; Kalantidis, Kriton

    2015-10-01

    Long non protein coding RNAs (lncRNAs) constitute a large category of the RNA world, able to regulate different biological processes. In this review we are focusing on infectious lncRNAs, their classification, pathogenesis and impact on the infected organisms. Here they are presented in two separate groups: 'dependent lncRNAs' (comprising satellites RNA, Hepatitis D virus and lncRNAs of viral origin) which need a helper virus and 'independent lncRNAs' (viroids) that can self-replicate. Even though these lncRNA do not encode any protein, their structure and/or sequence comprise all the necessary information to drive specific interactions with host factors and regulate several cellular functions. These new data that have emerged during the last few years concerning lncRNAs modify the way we understand molecular biology's 'central dogma' and give new perspectives for applications and potential therapeutic strategies. PMID:25986218

  5. Contriving new spacer grid shapes and choosing the leading candidates of the spacer grid from the mechanical/structural point of view

    International Nuclear Information System (INIS)

    Based on the fuel assembly mechanical/thermal-hydraulic design experience and scrutinizing the design features on the foreign advanced nuclear fuel and the foreign patents of the spacer grid, 13 kinds of spacer grid candidates are derived. Among, the candidates the mechanical/structural performance on the five candidates was evaluated by the screening test and the analysis. As a result of the test and the analysis, two spacer grid shapes are finally selected to be the leading candidates in order to investigate the mechanical/structural performance in detail

  6. miRNAs in brain development

    International Nuclear Information System (INIS)

    MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. In the brain, a large number of miRNAs are expressed and there is a growing body of evidence demonstrating that miRNAs are essential for brain development and neuronal function. Conditional knockout studies of the core components in the miRNA biogenesis pathway, such as Dicer and DGCR8, have demonstrated a crucial role for miRNAs during the development of the central nervous system. Furthermore, mice deleted for specific miRNAs and miRNA-clusters demonstrate diverse functional roles for different miRNAs during the development of different brain structures. miRNAs have been proposed to regulate cellular functions such as differentiation, proliferation and fate-determination of neural progenitors. In this review we summarise the findings from recent studies that highlight the importance of miRNAs in brain development with a focus on the mouse model. We also discuss the technical limitations of current miRNA studies that still limit our understanding of this family of non-coding RNAs and propose the use of novel and refined technologies that are needed in order to fully determine the impact of specific miRNAs in brain development. - Highlights: • miRNAs are essential for brain development and neuronal function. • KO of Dicer is embryonically lethal. • Conditional Dicer KO results in defective proliferation or increased apoptosis. • KO of individual miRNAs or miRNA families is necessary to determine function

  7. Catalytic Metal Free Production of Large Cage Structure Carbon Particles: A Candidate for Hydrogen Storage

    Science.gov (United States)

    Kimura, Yuki; Nuth, Joseph A., III; Ferguson, Frank T.

    2005-01-01

    We will demonstrate that carbon particles consisting of large cages can be produced without catalytic metal. The carbon particles were produced in CO gas as well as by introduction of 5% methane gas into the CO gas. The gas-produced carbon particles were able to absorb approximately 16.2 wt% of hydrogen. This value is 2.5 times higher than the 6.5 wt% goal for the vehicular hydrogen storage proposed by the Department of Energy in the USA. Therefore, we believe that this carbon particle is an excellent candidate for hydrogen storage for fuel cells.

  8. Corrosion tests of candidate fuel cladding and reactor internal structural materials

    International Nuclear Information System (INIS)

    Corrosion screening tests were conducted on candidate materials for nuclear fuel cladding and reactor internals of supercritical water reactor (SCWR) in static and flowing supercritical water (SCW) autoclave at the temperatures of 550, 600 and 650°C, pressure of about 25MPa, deaerated or saturated dissolved hydrogen (STP). Samples are nickel base alloy type Hastelloy C276, austenitic stainless steels type 304NG and AL-6XN, ferritic/martensitic (F/M) steel type P92, and oxide dispersion strengthened steel MA 956. This paper focuses on the formation and breakdown of corrosion oxide scales, and proposes the future trend for the development of SCWR fuel cladding materials. (author)

  9. Corrosion tests of candidate fuel cladding and reactor internal structural materials

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, L.; Zhu, F.; Bao, Y. [Shanghai Jiao Tong Univ., School of Nuclear Science and Engineering, Shanghai (China); Tang, R. [Nuclear Power Inst. of China, National Key Lab. for Nuclear Fuel and Materials, Chengdu, Sichuan (China)

    2010-07-01

    Corrosion screening tests were conducted on candidate materials for nuclear fuel cladding and reactor internals of supercritical water reactor (SCWR) in static and flowing supercritical water (SCW) autoclave at the temperatures of 550, 600 and 650°C, pressure of about 25MPa, deaerated or saturated dissolved hydrogen (STP). Samples are nickel base alloy type Hastelloy C276, austenitic stainless steels type 304NG and AL-6XN, ferritic/martensitic (F/M) steel type P92, and oxide dispersion strengthened steel MA 956. This paper focuses on the formation and breakdown of corrosion oxide scales, and proposes the future trend for the development of SCWR fuel cladding materials. (author)

  10. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

    Science.gov (United States)

    Le Rhun, Anaïs; Beer, Yan Yan; Reimegård, Johan; Chylinski, Krzysztof; Charpentier, Emmanuelle

    2016-02-01

    Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation. PMID:26580233

  11. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes

    Science.gov (United States)

    Le Rhun, Anaïs; Beer, Yan Yan; Reimegård, Johan; Chylinski, Krzysztof; Charpentier, Emmanuelle

    2016-01-01

    ABSTRACT Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation. PMID:26580233

  12. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata

    Directory of Open Access Journals (Sweden)

    Yu Huaping

    2010-07-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. Results In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata which is an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues. Based on sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 63 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates whose precursors were all potentially generated from citrus ESTs. In addition, five miRNA* sequences were also sequenced. These sequences had not been earlier described in other plant species and accumulation of the 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes including one encoding IRX12 copper ion binding/oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata. Conclusion Deep sequencing of short RNAs from C. trifoliata flowers and fruits identified 10 new potential miRNAs and 42 highly conserved miRNA families, indicating that specific miRNAs exist in C. trifoliata. These results show that regulatory miRNAs exist in agronomically important trifoliate orange

  13. Structural origination of charge transfer complex nanostructures: Excellent candidate for field emission

    Science.gov (United States)

    Pal, Shreyasi; Chattopadhyay, Kalyan Kumar

    2016-05-01

    Worldwide strategies for amalgamating rationally controlled one-dimensional organic nanowires are of fundamental importance for their applications in flexible, cheaper and lighter electronics. In this work we have fabricated large-area, ordered CuTCNQ (copper-7,7,8,8-tetracyanoquinodimethane) nano architecture arrays over flexible conducting substrate and discussed the rational growth and integration of nanostructures. Here we adopted the organic solid phase reaction (VLS) technique for the growth of organic hierarchies and investigated how field emission properties changes by tuning the nanostructures morphology i.e., by varying length, diameter, alignment and orientation over flexible substrate. The CuTCNQ nanowires with optimized geometry exhibit excellent high field emission performance with low turn-on and threshold field values. The result strongly indicate that CuTCNQ nanowires on flexible carbon cloth substrate are promising candidates for constructing cold cathode based emission display devices, vacuum nanoelectronics, and etc.

  14. HIVsirDB: a database of HIV inhibiting siRNAs.

    Directory of Open Access Journals (Sweden)

    Atul Tyagi

    Full Text Available BACKGROUND: Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes. DESCRIPTIONS: HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs. CONCLUSION: HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

  15. Recombination structure and genetic relatedness among members of the family Bromoviridae based on their RNAs 1 and 2 sequence analyses.

    Science.gov (United States)

    Boulila, Moncef

    2009-06-01

    In determining putative recombination events and their evolution rates in the RNAs 1 and 2 of currently the known members of the family Bromoviridae, a detailed study comprising 107 accessions retrieved from the international databases, has been carried out by using RECCO and RDP v3.31beta algorithms. These programs allowed the detection of potential recombination sites in all the five virus genera composing the family Bromoviridae with various degrees of consistency. The RNAs 1 and 2 showed inferred phylogenies fully congruent and clearly delineated five clusters representing the five studied virus genera. In this respect, we proposed to classify the Ilarviruses in three distinct subgroups instead of 10 as mentioned in several reports of the International Committee on Taxonomy of Viruses where its suggestions were based on antigenic differences. Moreover, we confirmed that Alfalfa mosaic virus should be considered as a component of the Ilarvirus genus instead of being the unique representative of Alfamovirus genus. In addition, Pelargonium zonate spot and Olive latent 2 viruses fully deserve their affiliation to the family Bromoviridae. PMID:19255837

  16. Global characterization of microRNAs in Trichomonas gallinae

    OpenAIRE

    Xu, Min-Jun; Qiu, Shen-Ben; Nisbet, Alasdair J.; Fu, Jing-Hua; Shao, Chang-Chun; Zhu, Xing-Quan

    2014-01-01

    Background Trichomonas gallinae is a protozoan parasite causing trichomonosis in many species of domestic poultry and birds world-wide. microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in gene regulation. However, no miRNAs have been characterized from T. gallinae. Methods Here, we investigated the global miRNA profile of this parasite by high throughput sequencing technology, bioinformatics platform analysis and quantitative RT-PCR. Results Three miRNA candidates, ...

  17. Brain expressed microRNAs implicated in schizophrenia etiology

    DEFF Research Database (Denmark)

    Hansen, Thomas; Olsen, Line; Lindow, Morten;

    2007-01-01

    Protein encoding genes have long been the major targets for research in schizophrenia genetics. However, with the identification of regulatory microRNAs (miRNAs) as important in brain development and function, miRNAs genes have emerged as candidates for schizophrenia-associated genetic factors....... Indeed, the growing understanding of the regulatory properties and pleiotropic effects that miRNA have on molecular and cellular mechanisms, suggests that alterations in the interactions between miRNAs and their mRNA targets may contribute to phenotypic variation....

  18. Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Paolo Miotto

    Full Text Available Only few small RNAs (sRNAs have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report we show that 258 (19% of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5'/3' UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%, terminator consensus motifs for 22 sRNAs (8.5%, and both motifs for 35 sRNAs (14%. Additionally, 20/23 candidates were visualized by Northern blot analysis and 5' end mapping by primer extension confirmed the RNA-seq data. We also used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. We found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.

  19. Exploiting tRNAs to Boost Virulence

    Directory of Open Access Journals (Sweden)

    Suki Albers

    2016-01-01

    Full Text Available Transfer RNAs (tRNAs are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it difficult to characterize individual species quantitatively. However, due to the central role of the tRNA pool in protein biosynthesis as well as newly emerging roles played by tRNAs, their quantitative assessment yields important information, particularly relevant for virus research. Viruses which depend on the host protein expression machinery have evolved various strategies to optimize tRNA usage—either by adapting to the host codon usage or encoding their own tRNAs. Additionally, several viruses bear tRNA-like elements (TLE in the 5′- and 3′-UTR of their mRNAs. There are different hypotheses concerning the manner in which such structures boost viral protein expression. Furthermore, retroviruses use special tRNAs for packaging and initiating reverse transcription of their genetic material. Since there is a strong specificity of different viruses towards certain tRNAs, different strategies for recruitment are employed. Interestingly, modifications on tRNAs strongly impact their functionality in viruses. Here, we review those intersection points between virus and tRNA research and describe methods for assessing the tRNA pool in terms of concentration, aminoacylation and modification.

  20. Trash or Treasure: extracellular microRNAs and cell-to-cell communication

    Directory of Open Access Journals (Sweden)

    Nobuyoshi eKosaka

    2013-09-01

    Full Text Available Circulating RNAs in human body fluids are promising candidates for diagnostic purposes. However, the biological significance of circulating RNAs remains elusive. Recently, small non-coding RNAs, microRNAs (miRNAs, were isolated from multiple human body fluids, and these circulating miRNAs have been implicated as novel disease biomarkers. Concurrently, miRNAs were also identified in the extracellular space associated with extracellular vesicles (EVs, which are small membrane vesicles secreted from various types of cells. The function of these secreted miRNAs has been revealed in several papers. Circulating miRNAs have been experimentally found to be associated with EVs, however, other types of extracellular miRNAs were also described. This review discusses studies related to extracellular miRNAs, including circulating miRNAs and secreted miRNAs, to highlight the importance of studying not only secreted miRNAs but also circulating miRNAs to determine the contribution of extracellular miRNAs especially in cancer development.

  1. Effects of surface condition on the corrosion of candidate structural materials in a simulated HTGR-GT environment

    International Nuclear Information System (INIS)

    A simulated high-temperature gas-cooled reactor (HTGR) helium environment was used to study the effects of surface finish conditions on the subsequent elevated-temperature corrosion behavior of key candidate structural materials. The environment contained helium with 500 μatm H2/50 μatm CO/50 μatm CH4/2O at 9000C with total test exposure durations of 3000 hours. Specimens with lapped, grit-blasted, pickled, and preoxidized surface conditions were studied. Materials tested included two cast superalloys, IN 100 and IN 713LC; one centrifugally cast high-temperature alloy, HK 40 one oxice-dispersion-strengthened alloy, Inconel MA 754; and three wrought high-temperature alloys, Hastelloy Alloy X, Inconel Alloy 617, and Alloy 800H

  2. Biocomputational prediction of small non-coding RNAs in Streptomyces

    Directory of Open Access Journals (Sweden)

    Basler Marek

    2008-05-01

    Full Text Available Abstract Background The first systematic study of small non-coding RNAs (sRNA, ncRNA in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, have remained unstudied. This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs. Results Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a Streptomyces 6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs. Conclusion Streptomyces is the largest genus of Actinomyces, whose sRNAs have not been studied. The Actinomyces is a group of bacterial species with unique genomes and phenotypes. Therefore, in Actinomyces, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted Streptomyces sRNAs demonstrated by this study serve as the first evidence of the uniqueness of Actinomyces sRNAs.

  3. The Host RNAs in Retroviral Particles.

    Science.gov (United States)

    Telesnitsky, Alice; Wolin, Sandra L

    2016-01-01

    As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive. PMID:27548206

  4. A novel candidate compound with urethane structure for anticancer drug development.

    Science.gov (United States)

    Matsuoka, Atsuko; Isama, Kazuo; Tanimura, Susumu; Kohno, Michiaki; Yamori, Takao

    2007-08-01

    Diethyl-4,4'-methylenebis(N-phenylcarbamate) (MDU) is a urethane compound that we originally synthesized, along with three other compounds, to investigate how polyurethane is hydrolysed. We tested the four compounds for cytotoxicity in two Chinese hamster cell lines (CHL and V79) and a human cancer cell line (HeLa S3). MDU showed the strongest cytotoxicity in all the cell lines with an IC50 of around 0.1 microg/ml. We further investigated MDU for its ability to induce chromosome aberrations (CAs) and micronuclei (MN) in CHL cells. MDU induced around 100% polyploid cells at 0.5 microg/ml after 24- and 48-h treatment in the CA test and a significantly increased frequency of micronuclei, polynuclear cells, and mitotic cells in the MN test, suggesting that it may induce numerical CAs. MDU's ability to cause mitotic arrest in CHL cells was greater than that of taxol and colchicine. Based on a COMPARE analysis using JFCR39, a panel of cancer cell lines, we predicted MDU to be a tubulin inhibitor. We confirmed this possibility in nerve growth factor-stimulated PC12 cells as well as in HT1080 cells, in which MDU exhibited the activity to inhibit tubulin polymerization. MDU is simpler in structure than existing anticancer drugs taxol and vincristine and can be synthesized relatively easily. Here we offer MDU as a potential new type of anticancer drug, stable even at room temperature, and inexpensive. PMID:17691911

  5. Extracellular MicroRNAs in Urologic Malignancies: Chances and Challenges

    Directory of Open Access Journals (Sweden)

    Liang Wang

    2013-07-01

    Full Text Available Small noncoding RNAs that are 19-23 nucleotides long, known as microRNAs (miRNAs, are involved in almost all biological mechanisms during carcinogenesis. Recent studies show that miRNAs released from live cells are detectable in body fluids and may be taken up by other cells to confer cell-cell communication. These released miRNAs (here referred to as extracellular miRNAs are often protected by RNA-binding proteins or embedded inside circulating microvesicles. Due to their relative stability, extracellular miRNAs are believed to be promising candidates as biomarkers for diagnosis and prognosis of disease, or even as therapeutic agents for targeted treatment. In this review, we first describe biogenesis and characteristics of these miRNAs. We then summarize recent publications involving extracellular miRNA profiling studies in three representative urologic cancers, including: prostate cancer, bladder cancer, and renal cell carcinoma. We focus on the diagnostic, prognostic, and therapeutic potential of these miRNAs in biological fluids, such as serum, plasma, and urine. Finally, we discuss advantages and challenges of these miRNAs in clinical applications.

  6. Alternative modelling of brittle structures in a sub-area of the SKB candidate area at Forsmark, eastern Sweden.

    Energy Technology Data Exchange (ETDEWEB)

    Askling, Per; Tiren, Sven A.; Beckholmen, Monica; Straeng, Thomas (Geosigma AB, Uppsala (Sweden))

    2008-11-15

    One way to test the confidence of a presented model is to construct an alternative model. Such work is cognitive process of skill acquisition and also a process of understanding data in the sense of sorting and classifying data. This is of particular interest for the Swedish Radiation Safety Authority (SSM) in their technical review of SKB's on-going site investigation programme for potential repository sites. In this study, an alternative brittle deformation model of a selected part of the SKB candidate area in eastern Sweden was constructed. The input data set was obtained from SKB's database SICADA and is a selected set of data from five cored boreholes drilled from two drill-sites and comprises geophysical borehole logs, geological core-logs, hydrological logs (PFL; Posiva Flow Log) and borehole deviation measurements. Statistical cluster analysis applied on the geophysical borehole data were used to obtain the locations of bedrock with contrasting physical characteristics similar to those of brittle deformation zones. The cluster analysis is an objective procedure, contrasting with SKB's more subjective approach to the single-hole interpretation. Thus some differences are expected which could illustrate the effect of methodology that includes subjective 'expert judgement.' and indicate the possibility of alternative interpretations. The information about brittle structures in the geological boreholes logs was sorted and classification was made according to character of the structures (all fractures, open fractures, partly open fractures, frequency, orientate on/identification of fracture sets, sections of crush rock, and alteration). A separate study was performed to relate rock alteration with structures. The resolution applied in the fracture statistics is one metre, i.e. all studied entities were expressed per metre borehole length. All clusters were structurally characterized by the fractures inside the clusters (orientation and

  7. Alternative modelling of brittle structures in a sub-area of the SKB candidate area at Forsmark, eastern Sweden

    International Nuclear Information System (INIS)

    One way to test the confidence of a presented model is to construct an alternative model. Such work is cognitive process of skill acquisition and also a process of understanding data in the sense of sorting and classifying data. This is of particular interest for the Swedish Radiation Safety Authority (SSM) in their technical review of SKB's on-going site investigation programme for potential repository sites. In this study, an alternative brittle deformation model of a selected part of the SKB candidate area in eastern Sweden was constructed. The input data set was obtained from SKB's database SICADA and is a selected set of data from five cored boreholes drilled from two drill-sites and comprises geophysical borehole logs, geological core-logs, hydrological logs (PFL; Posiva Flow Log) and borehole deviation measurements. Statistical cluster analysis applied on the geophysical borehole data were used to obtain the locations of bedrock with contrasting physical characteristics similar to those of brittle deformation zones. The cluster analysis is an objective procedure, contrasting with SKB's more subjective approach to the single-hole interpretation. Thus some differences are expected which could illustrate the effect of methodology that includes subjective 'expert judgement.' and indicate the possibility of alternative interpretations. The information about brittle structures in the geological boreholes logs was sorted and classification was made according to character of the structures (all fractures, open fractures, partly open fractures, frequency, orientate on/identification of fracture sets, sections of crush rock, and alteration). A separate study was performed to relate rock alteration with structures. The resolution applied in the fracture statistics is one metre, i.e. all studied entities were expressed per metre borehole length. All clusters were structurally characterized by the fractures inside the clusters (orientation and density of fractures) and

  8. Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39.

    Science.gov (United States)

    Tsui, Ho-Ching Tiffany; Mukherjee, Dhriti; Ray, Valerie A; Sham, Lok-To; Feig, Andrew L; Winkler, Malcolm E

    2010-01-01

    We report a search for small RNAs (sRNAs) in the low-GC, gram-positive human pathogen Streptococcus pneumoniae. Based on bioinformatic analyses by Livny et al. (J. Livny, A. Brencic, S. Lory, and M. K. Waldor, Nucleic Acids Res. 34:3484-3493, 2006), we tested 40 candidates by Northern blotting and confirmed the expression of nine new and one previously reported (CcnA) sRNAs in strain D39. CcnA is one of five redundant sRNAs reported by Halfmann et al. (A. Halfmann, M. Kovacs, R. Hakenbeck, and R. Bruckner, Mol. Microbiol. 66:110-126, 2007) that are positively controlled by the CiaR response regulator. We characterized 3 of these 14 sRNAs: Spd-sr17 (144 nucleotides [nt]; decreased in stationary phase), Spd-sr37 (80 nt; strongly expressed in all growth phases), and CcnA (93 nt; induced by competence stimulatory peptide). Spd-sr17 and CcnA likely fold into structures containing single-stranded regions between hairpin structures, whereas Spd-sr37 forms a base-paired structure. Primer extension mapping and ectopic expression in deletion/insertion mutants confirmed the independent expression of the three sRNAs. Microarray analyses indicated that insertion/deletion mutants in spd-sr37 and ccnA exerted strong cis-acting effects on the transcription of adjacent genes, indicating that these sRNA regions are also cotranscribed in operons. Deletion or overexpression of the three sRNAs did not cause changes in growth, certain stress responses, global transcription, or virulence. Constitutive ectopic expression of CcnA reversed some phenotypes of D39 Delta ciaR mutants, but attempts to link CcnA to -E to comC as a target were inconclusive in ciaR(+) strains. These results show that S. pneumoniae, which lacks known RNA chaperones, expresses numerous sRNAs, but three of these sRNAs do not strongly affect common phenotypes or transcription patterns. PMID:19854910

  9. Structural, phylogenetic and docking studies of D-amino acid oxidase activator (DAOA, a candidate schizophrenia gene

    Directory of Open Access Journals (Sweden)

    Sehgal Sheikh

    2013-01-01

    Full Text Available Abstract Background Schizophrenia is a neurodegenerative disorder that occurs worldwide and can be difficult to diagnose. It is the foremost neurological disorder leading to suicide among patients in both developed and underdeveloped countries. D-amino acid oxidase activator (DAOA, also known as G72, is directly implicated in the glutamateric hypothesis of schizophrenia. It activates D-amino acid oxidase, which oxidizes D-serine, leading to modulation of the N-methyl-D-aspartate receptor. Methods MODELLER (9v10 was utilized to generate three dimensional structures of the DAOA candidate gene. The HOPE server was used for mutational analysis. The Molecular Evolutionary Genetics Analysis (MEGA5 tool was utilized to reconstruct the evolutionary history of the candidate gene DAOA. AutoDock was used for protein-ligand docking and Gramm-X and PatchDock for protein-protein docking. Results A suitable template (1ZCA was selected by employing BLASTp on the basis of 33% query coverage, 27% identity and E-value 4.9. The Rampage evaluation tool showed 91.1% favored region, 4.9% allowed region and 4.1% outlier region in DAOA. ERRAT demonstrated that the predicted model had a 50.909% quality factor. Mutational analysis of DAOA revealed significant effects on hydrogen bonding and correct folding of the DAOA protein, which in turn affect protein conformation. Ciona was inferred as the outgroup. Tetrapods were in their appropriate clusters with bifurcations. Human amino acid sequences are conserved, with chimpanzee and gorilla showing more than 80% homology and bootstrap value based on 1000 replications. Molecular docking analysis was employed to elucidate the binding mode of the reported ligand complex for DAOA. The docking experiment demonstrated that DAOA is involved in major amino acid interactions: the residues that interact most strongly with the ligand C28H28N3O5PS2 are polar but uncharged (Gln36, Asn38, Thr 122 and non-polar hydrophobic (Ile119, Ser171

  10. Network of microRNAs-mRNAs Interactions in Pancreatic Cancer

    Directory of Open Access Journals (Sweden)

    Elnaz Naderi

    2014-01-01

    Full Text Available Background. MicroRNAs are small RNA molecules that regulate the expression of certain genes through interaction with mRNA targets and are mainly involved in human cancer. This study was conducted to make the network of miRNAs-mRNAs interactions in pancreatic cancer as the fourth leading cause of cancer death. Methods. 56 miRNAs that were exclusively expressed and 1176 genes that were downregulated or silenced in pancreas cancer were extracted from beforehand investigations. MiRNA–mRNA interactions data analysis and related networks were explored using MAGIA tool and Cytoscape 3 software. Functional annotations of candidate genes in pancreatic cancer were identified by DAVID annotation tool. Results. This network is made of 217 nodes for mRNA, 15 nodes for miRNA, and 241 edges that show 241 regulations between 15 miRNAs and 217 target genes. The miR-24 was the most significantly powerful miRNA that regulated series of important genes. ACVR2B, GFRA1, and MTHFR were significant target genes were that downregulated. Conclusion. Although the collected previous data seems to be a treasure trove, there was no study simultaneous to analysis of miRNAs and mRNAs interaction. Network of miRNA-mRNA interactions will help to corroborate experimental remarks and could be used to refine miRNA target predictions for developing new therapeutic approaches.

  11. The Candidate

    OpenAIRE

    Osborn, John C

    2013-01-01

    ABSTRACT   The Candidate is an attempt to marry elements of journalism and gaming into a format that both entertains and educates the player. The Google-AP Scholarship, a new scholarship award that is given to several journalists a year to work on projects at the threshold of technology and journalism, funded the project. The objective in this prototype version of the game is to put the player in the shoes of a congressional candidate during an off-year election, specificall...

  12. HA03 as an Iranian Candidate Concealed Antigen for Vaccination against Hyalomma anatolicum anatolicum: Comparative Structural and In silico Studies

    Directory of Open Access Journals (Sweden)

    Mohammadi, A.

    2013-12-01

    Full Text Available In the last decades researchers had focused on developing a vaccine against tick based on protective antigen. Recombinant vaccines based on concealed antigen from Boophilus microplus have been developed in Australia and Cuba by the name of TICKGARD and GAVAC (De La Fuente and Kocan, 2006. Further studies on this antigen have shown some extent of protection against other species (De Vos et al., 2001. In Iran most important species is Hyalomma anatolicum and limited information about its control are available. This paper reports structural and polymorphic analysis of HA03 as an Iranian candidate concealed antigen of H. a. anatolicum deposited in Gen-Bank .(Aghaeipour et al. GQ228820. The comparison between this antigen and other mid gut concealed antigen that their characteristics are available in GenBank showed there are high rate of similarity between them. The HA03 amino acid sequence had a homology of around 89%, 64%, 56% with HA98, BM86, BM95 respectively. Potential of MHC class I and II binding region indicated a considerable variation between BM86 antigen and its efficiency against Iranian H. a. anatolicum. In addition, predicted major of hydrophobisity and similarity in N-glycosylation besides large amount of cystein and seven EGF like regions presented in protein structure revealed that value of HA03 as a new protective antigen and the necessity of the development, BM86 homolog of H. a. anatolicum HA03 based recombinant vaccine.

  13. VFV as a New Effective CYP51 Structure-Derived Drug Candidate for Chagas Disease and Visceral Leishmaniasis.

    Science.gov (United States)

    Lepesheva, Galina I; Hargrove, Tatiana Y; Rachakonda, Girish; Wawrzak, Zdzislaw; Pomel, Sébastien; Cojean, Sandrine; Nde, Pius N; Nes, W David; Locuson, Charles W; Calcutt, M Wade; Waterman, Michael R; Daniels, J Scott; Loiseau, Philippe M; Villalta, Fernando

    2015-11-01

    Sterol 14α-demethylases (CYP51) are the enzymes essential for sterol biosynthesis. They serve as clinical targets for antifungal azoles and are considered as targets for treatment of human Trypanosomatidae infections. Recently, we have shown that VNI, a potent and selective inhibitor of trypanosomal CYP51 that we identified and structurally characterized in complex with the enzyme, can cure the acute and chronic forms of Chagas disease. The purpose of this work was to apply the CYP51 structure/function for further development of the VNI scaffold. As anticipated, VFV (R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide, the derivative designed to fill the deepest portion of the CYP51 substrate-binding cavity, reveals a broader antiprotozoan spectrum of action. It has stronger antiparasitic activity in cellular experiments, cures the experimental Chagas disease with 100% efficacy, and suppresses visceral leishmaniasis by 89% (vs 60% for VNI). Oral bioavailability, low off-target activity, favorable pharmacokinetics and tissue distribution characterize VFV as a promising new drug candidate. PMID:25883390

  14. The dyslexia candidate locus on 2p12 is associated with general cognitive ability and white matter structure.

    Directory of Open Access Journals (Sweden)

    Thomas S Scerri

    Full Text Available Independent studies have shown that candidate genes for dyslexia and specific language impairment (SLI impact upon reading/language-specific traits in the general population. To further explore the effect of disorder-associated genes on cognitive functions, we investigated whether they play a role in broader cognitive traits. We tested a panel of dyslexia and SLI genetic risk factors for association with two measures of general cognitive abilities, or IQ, (verbal and non-verbal in the Avon Longitudinal Study of Parents and Children (ALSPAC cohort (N>5,000. Only the MRPL19/C2ORF3 locus showed statistically significant association (minimum P = 0.00009 which was further supported by independent replications following analysis in four other cohorts. In addition, a fifth independent sample showed association between the MRPL19/C2ORF3 locus and white matter structure in the posterior part of the corpus callosum and cingulum, connecting large parts of the cortex in the parietal, occipital and temporal lobes. These findings suggest that this locus, originally identified as being associated with dyslexia, is likely to harbour genetic variants associated with general cognitive abilities by influencing white matter structure in localised neuronal regions.

  15. MicroRNAs function primarily in the pathogenesis of human anencephaly via the mitogen-activated protein kinase signaling pathway.

    Science.gov (United States)

    Zhang, W D; Yu, X; Fu, X; Huang, S; Jin, S J; Ning, Q; Luo, X P

    2014-01-01

    Anencephaly is one of the most serious forms of neural tube defects (NTDs), a group of congenital central nervous system (CNS) malformations. MicroRNAs (miRNAs) are involved in diverse biological processes via the post-transcriptional regulation of target mRNAs. Although miRNAs play important roles in the development of mammalian CNS, their function in human NTDs remains unknown. Using a miRNA microarray, we identified a unique expression profile in fetal anencephalic brain tissues, characterized by 70 upregulated miRNAs (ratio ≥ 2) and 7 downregulated miRNAs (ratio ≤ 0.5) compared with healthy human samples. Ten miRNAs with altered expression were selected from the microarray findings for validation with real-time quantitative reverse transcription-polymerase chain reaction. We found that in anencephalic tissues, miR-22, miR-23a, miR-34a, miR-103, miR-125a, miR-132, miR-134, miR-138, and miR-185 were significantly upregulated, while miR-149 was significantly downregulated. Furthermore, 459 potential target genes within the validated miRNAs were revealed using combined four target prediction algorithms in the human genome, and subsequently analyzed with the Molecule Annotation System 3.0. A total of 119 target genes were ultimately identified, including those involved in 22 singular annotations (i.e., transcription, signal transduction, and cell cycle) and 55 functional pathways [i.e., mitogen-activated protein kinase (MAPK) signaling pathway, and actin cytoskeleton regulation]. Six target genes (HNRPU, JAG1, FMR1, EGR3, RUNX1T1, and NDEL1) were chosen as candidate genes and associated with congenital birth abnormalities of the brain structure. Our results, therefore, suggest that miRNA maladjustment mainly contributes to the etiopathogenesis of anencephaly via the MAPK signaling pathway. PMID:24634123

  16. Primary and secondary structures of Tetrahymena and aphid 5.8S rRNAs: structural features of 5.8S rRNA which interacts with the 28S rRNA containing the hidden break.

    OpenAIRE

    Fujiwara, H.; H. Ishikawa

    1982-01-01

    The Tetrahymena 5.8S rRNA is 154 nucleotides long, the shortest so far reported except for the split 5.8S rRNAs of Diptera (m5.8S plus 2S rRNA). In this molecule several nucleotides are deleted in the helix e (GC-rich stem) region. Upon constructing the secondary structure in accordance with "burp-gun" model, the Tetrahymena 5.8S rRNA forms a wide-open "muzzle" of the terminal regions due to both extra nucleotides and several unpaired bases. The aphid 5.8S rRNA consists of 161 nucleotides and...

  17. Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

    Science.gov (United States)

    Cornilescu, Gabriel; Didychuk, Allison L; Rodgers, Margaret L; Michael, Lauren A; Burke, Jordan E; Montemayor, Eric J; Hoskins, Aaron A; Butcher, Samuel E

    2016-02-27

    NMR and SAXS (small-angle X-ray scattering)/WAXS (wide-angle X-ray scattering) are highly complementary approaches for the analysis of RNA structure in solution. Here we describe an efficient NMR-SAXS/WAXS approach for structural investigation of multi-helical RNAs. We illustrate this approach by determining the overall fold of a 92-nt 3-helix junction from the U4/U6 di-snRNA. The U4/U6 di-snRNA is conserved in eukaryotes and is part of the U4/U6.U5 tri-snRNP, a large ribonucleoprotein complex that comprises a major subunit of the assembled spliceosome. Helical orientations can be determined by X-ray scattering data alone, but the addition of NMR RDC (residual dipolar coupling) restraints improves the structure models. RDCs were measured in two different external alignment media and also by magnetic susceptibility anisotropy. The resulting alignment tensors are collinear, which is a previously noted problem for nucleic acids. Including WAXS data in the calculations produces models with significantly better fits to the scattering data. In solution, the U4/U6 di-snRNA forms a 3-helix junction with a planar Y-shaped structure and has no detectable tertiary interactions. Single-molecule Förster resonance energy transfer data support the observed topology. A comparison with the recently determined cryo-electron microscopy structure of the U4/U6.U5 tri-snRNP illustrates how proteins scaffold the RNA and dramatically alter the geometry of the U4/U6 3-helix junction. PMID:26655855

  18. Organellar non-coding RNAs: emerging regulation mechanisms.

    Science.gov (United States)

    Dietrich, André; Wallet, Clémentine; Iqbal, Rana Khalid; Gualberto, José M; Lotfi, Frédérique

    2015-10-01

    Originally focused on the nuclear and cytosolic compartments, the concept of regulation driven by non-coding RNAs (ncRNAs) is extending to mitochondria and chloroplasts. These organelles have distinct genetic systems that need coordination with cellular demands. In mammals, nuclear-encoded microRNAs were found associated with the mitochondria. Some of these contribute to the regulation of mitochondrial transcription and translation. Others were proposed to be stored in the organelles and to be released for regulation of nuclear transcripts. Further ncRNAs of various sizes derive from the mitochondrial genome and it was speculated that organelles host antisense or RNA interference pathways. Long ncRNAs mapping to the mitochondrial DNA seem to operate in the nucleus. Altogether, the origin and trafficking of ncRNAs categorized as mitochondrial in mammals raise questions far beyond the current knowledge. In protozoa, hundreds of guide RNAs specify editing events needed to generate functional messenger RNAs. Only few ncRNAs have been reported in plant mitochondria, but editing sites were revealed in non-coding regions of the organellar genome, suggesting that the corresponding transcripts have a function. Conversely, numerous ncRNA candidates were identified in chloroplasts, essentially mapping to the plastid genome. A synthetic view of the data with their functional implications is given here. PMID:26143009

  19. Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice

    OpenAIRE

    Sano, Naoto; Ono, Hanako; Murata, Kazumasa; Yamada, Tetsuya; Hirasawa, Tadashi; Kanekatsu, Motoki

    2015-01-01

    Highlight Long-lived mRNAs stored in dry seed are translated after imbibition for germination. We report accumulation of long-lived mRNAs in developing rice embryos and candidates of the mRNAs required for germination.

  20. The presence, role and clinical use of spermatozoal RNAs.

    Science.gov (United States)

    Jodar, Meritxell; Selvaraju, Sellappan; Sendler, Edward; Diamond, Michael P; Krawetz, Stephen A

    2013-01-01

    BACKGROUND Spermatozoa are highly differentiated, transcriptionally inert cells characterized by a compact nucleus with minimal cytoplasm. Nevertheless they contain a suite of unique RNAs that are delivered to oocyte upon fertilization. They are likely integrated as part of many different processes including genome recognition, consolidation-confrontation, early embryonic development and epigenetic transgenerational inherence. Spermatozoal RNAs also provide a window into the developmental history of each sperm thereby providing biomarkers of fertility and pregnancy outcome which are being intensely studied. METHODS Literature searches were performed to review the majority of spermatozoal RNA studies that described potential functions and clinical applications with emphasis on Next-Generation Sequencing. Human, mouse, bovine and stallion were compared as their distribution and composition of spermatozoal RNAs, using these techniques, have been described. RESULTS Comparisons highlighted the complexity of the population of spermatozoal RNAs that comprises rRNA, mRNA and both large and small non-coding RNAs. RNA-seq analysis has revealed that only a fraction of the larger RNAs retain their structure. While rRNAs are the most abundant and are highly fragmented, ensuring a translationally quiescent state, other RNAs including some mRNAs retain their functional potential, thereby increasing the opportunity for regulatory interactions. Abundant small non-coding RNAs retained in spermatozoa include miRNAs and piRNAs. Some, like miR-34c are essential to the early embryo development required for the first cellular division. Others like the piRNAs are likely part of the genomic dance of confrontation and consolidation. Other non-coding spermatozoal RNAs include transposable elements, annotated lnc-RNAs, intronic retained elements, exonic elements, chromatin-associated RNAs, small-nuclear ILF3/NF30 associated RNAs, quiescent RNAs, mse-tRNAs and YRNAs. Some non-coding RNAs are

  1. Testing of the OMERACT 8 draft validation criteria for a soluble biomarker reflecting structural damage in rheumatoid arthritis: a systematic literature search on 5 candidate biomarkers

    DEFF Research Database (Denmark)

    Syversen, Silje W; Landewe, Robert; van der Heijde, Désirée;

    2009-01-01

    the importance of each individual criterion; (2) overall strength of evidence in support of each of the 5 candidate biomarkers as reflecting structural damage endpoints in rheumatoid arthritis (RA) and identification of omissions to the criteria set. RESULTS: The search identified 111 articles. The...

  2. The Host RNAs in Retroviral Particles

    Directory of Open Access Journals (Sweden)

    Alice Telesnitsky

    2016-08-01

    Full Text Available As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA, some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs’ packaging determinants differ from the viral genome’s, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1 reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs—if any—have remained elusive.

  3. Noncoding RNAs in breast cancer.

    Science.gov (United States)

    Lo, Pang-Kuo; Wolfson, Benjamin; Zhou, Xipeng; Duru, Nadire; Gernapudi, Ramkishore; Zhou, Qun

    2016-05-01

    The mammalian transcriptome has recently been revealed to encompass a large number of noncoding RNAs (ncRNAs) that play a variety of important regulatory roles in gene expression and other biological processes. MicroRNAs (miRNAs), the best studied of the short noncoding RNAs (sncRNAs), have been extensively characterized with regard to their biogenesis, function and importance in tumorigenesis. Another class of sncRNAs called piwi-interacting RNAs (piRNAs) has also gained attention recently in cancer research owing to their critical role in stem cell regulation. Long noncoding RNAs (lncRNAs) of >200 nucleotides in length have recently emerged as key regulators of developmental processes, including mammary gland development. lncRNA dysregulation has also been implicated in the development of various cancers, including breast cancer. In this review, we describe and discuss the roles of sncRNAs (including miRNAs and piRNAs) and lncRNAs in the initiation and progression of breast tumorigenesis, with a focus on outlining the molecular mechanisms of oncogenic and tumor-suppressor ncRNAs. Moreover, the current and potential future applications of ncRNAs to clinical breast cancer research are also discussed, with an emphasis on ncRNA-based diagnosis, prognosis and future therapeutics. PMID:26685283

  4. MicroRNAs

    DEFF Research Database (Denmark)

    Devaux, Yvan; Stammet, Pascal; Friberg, Hans; Hassager, Christian; Kuiper, Michael A; Wise, Matt P; Nielsen, Niklas

    2015-01-01

    cardiac arrest would allow subsequent health care delivery to be tailored to individual patients. However, currently available predictive methods and biomarkers lack sufficient accuracy and therefore cannot be generally recommended in clinical practice. MicroRNAs have recently emerged as potential...... biomarkers of cardiovascular diseases. While the biomarker value of microRNAs for myocardial infarction or heart failure has been extensively studied, less attention has been devoted to their prognostic value after cardiac arrest. This review highlights the recent discoveries suggesting that microRNAs may be...

  5. Identification of miRNAs contributing to neuroblastoma chemoresistance

    Directory of Open Access Journals (Sweden)

    Duncan Ayers

    2015-01-01

    Conclusions: Based on the initial miRNA findings, this study elucidates the dys-regulation of four miRNAs in three separate NB chemoresistant cell line models, spanning two cell lines (SH-SY5Y and UKF-NB-3 and two chemotherapeutic agents (doxorubicin and etoposide. These miRNAs may thus be possibly linked to chemoresistance induction in NB. Such miRNAs are good candidates to be novel drug targets for future miRNA based therapies against aggressive tumours that are not responding to conventional chemotherapy.

  6. Identifying microRNAs and transcript targets in Jatropha seeds.

    Science.gov (United States)

    Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F V; Loss-Morais, Guilherme; Körbes, Ana P; Silva, Sérgio D A; Margis-Pinheiro, Márcia M A N; Margis, Rogério

    2014-01-01

    MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs. PMID:24551031

  7. Fitness Landscapes of Functional RNAs

    Directory of Open Access Journals (Sweden)

    Ádám Kun

    2015-08-01

    Full Text Available The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.

  8. Synthetic RNAs Mimicking Structural Domains in the Foot-and-Mouth Disease Virus Genome Elicit a Broad Innate Immune Response in Porcine Cells Triggered by RIG-I and TLR Activation

    OpenAIRE

    Belén Borrego; Miguel Rodríguez-Pulido; Concepción Revilla; Belén Álvarez; Francisco Sobrino; Javier Domínguez; Margarita Sáiz

    2015-01-01

    The innate immune system is the first line of defense against viral infections. Exploiting innate responses for antiviral, therapeutic and vaccine adjuvation strategies is being extensively explored. We have previously described, the ability of small in vitro RNA transcripts, mimicking the sequence and structure of different domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs), to trigger a potent and rapid innate immune response. These synthetic non-in...

  9. Riboswitch RNAs: using RNA to sense cellular metabolism

    OpenAIRE

    Henkin, Tina M.

    2008-01-01

    Riboswitches are RNA elements that undergo a shift in structure in response to binding of a regulatory molecule. These elements are encoded within the transcript they regulate, and act in cis to control expression of the coding sequence(s) within that transcript; their function is therefore distinct from that of small regulatory RNAs (sRNAs) that act in trans to regulate the activity of other RNA transcripts. Riboswitch RNAs control a broad range of genes in bacterial species, including those...

  10. FINDING NON-CODING RNAs THROUGH GENOME-SCALE CLUSTERING

    OpenAIRE

    TSENG, HUEI-HUN; Weinberg, Zasha; Gore, Jeremy; Breaker, Ronald R.; RUZZO, WALTER L.

    2009-01-01

    Non-coding RNAs (ncRNAs) are transcripts that do not code for proteins. Recent findings have shown that RNA-mediated regulatory mechanisms influence a substantial portion of typical microbial genomes. We present an efficient method for finding potential ncRNAs in bacteria by clustering genomic sequences based on homology inferred from both primary sequence and secondary structure. We evaluate our approach using a set of predominantly Firmicutes sequences. Our results showed that, though prima...

  11. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.

    Directory of Open Access Journals (Sweden)

    Sebastian Will

    2007-04-01

    Full Text Available The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative genomics have produced very large sets of putative noncoding RNAs and regulatory RNA signals. For many of them, evidence for stabilizing selection acting on their secondary structures has been derived, and at least approximate models of their structures have been computed. The overwhelming majority of these hypothetical RNAs cannot be assigned to established families or classes. We present here a structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs. The LocARNA (local alignment of RNA tool implements a novel variant of the Sankoff algorithm that is sufficiently fast to deal with several thousand candidate sequences. The method is also robust against false positive predictions, i.e., a contamination of the input data with unstructured or nonconserved sequences. We have successfully tested the LocARNA-based clustering approach on the sequences of the RFAM-seed alignments. Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005 Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2: i77-i78. In addition to recovering, e.g., tRNAs as a structure-based class, the method identifies several RNA families, including microRNA and snoRNA candidates, and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized.

  12. Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

    Directory of Open Access Journals (Sweden)

    Makunin Igor V

    2010-02-01

    Full Text Available Abstract Background The increasing interest in small non-coding RNAs (ncRNAs such as microRNAs (miRNAs, small interfering RNAs (siRNAs and Piwi-interacting RNAs (piRNAs and recent advances in sequencing technology have yielded large numbers of short (18-32 nt RNA sequences from different organisms, some of which are derived from small nucleolar RNAs (snoRNAs and transfer RNAs (tRNAs. We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences. Results We combined publicly available datasets of tens of millions of short RNA sequence tags from Drosophila melanogaster, and mapped them to the Drosophila genome. Approximately 6 million perfectly mapping sequence tags were then assembled into 521,302 tag-contigs (TCs based on tag overlap. Most transposon-derived sequences, exons and annotated miRNAs, tRNAs and snoRNAs are detected by TCs, which show distinct patterns of length and tag-depth for different categories. The typical length and tag-depth of snoRNA-derived TCs was used to predict 7 previously unrecognized box H/ACA and 26 box C/D snoRNA candidates. We also identified one snRNA candidate and 86 loci with a high number of tags that are yet to be annotated, 7 of which have a particular 18mer motif and are located in introns of genes involved in development. A subset of new snoRNA candidates and putative ncRNA candidates was verified by Northern blot. Conclusions In this study, we have introduced a new approach to identify new members of known classes of ncRNAs based on the features of TCs corresponding to known ncRNAs. A large number of the identified TCs are yet to be examined experimentally suggesting that many more novel ncRNAs remain to be discovered.

  13. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition.

    Science.gov (United States)

    Lee, Seungwoo; Hwang, Seungwoo; Yu, Hee Jeong; Oh, Dayoung; Choi, Yu Jung; Kim, Myung-Chul; Kim, Yongbaek; Ryu, Doug-Young

    2016-01-01

    MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition. PMID:26731407

  14. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition.

    Directory of Open Access Journals (Sweden)

    Seungwoo Lee

    Full Text Available MicroRNAs (miRNAs in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition.

  15. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition

    Science.gov (United States)

    Lee, Seungwoo; Hwang, Seungwoo; Yu, Hee Jeong; Oh, Dayoung; Choi, Yu Jung; Kim, Myung-Chul; Kim, Yongbaek; Ryu, Doug-Young

    2016-01-01

    MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition. PMID:26731407

  16. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

    Energy Technology Data Exchange (ETDEWEB)

    Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; Arkin, Adam; Bender, Kelly

    2010-05-17

    Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.

  17. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

    International Nuclear Information System (INIS)

    Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ∼87 intergenic, while ∼140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ∼54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.

  18. Micro-RNAs

    DEFF Research Database (Denmark)

    Taipaleenmäki, H.; Hokland, L. B.; Chen, Li;

    2012-01-01

    Osteoblast differentiation and bone formation (osteogenesis) are regulated by transcriptional and post-transcriptional mechanisms. Recently, a novel class of regulatory factors termed microRNAs has been identified as playing an important role in the regulation of many aspects of osteoblast biology...... including proliferation, differentiation, metabolism and apoptosis. Also, preliminary data from animal disease models suggest that targeting miRNAs in bone can be a novel approach to increase bone mass. This review highlights the current knowledge of microRNA biology and their role in bone formation and...

  19. MicroRNA-encoding long non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Zhu Xiaopeng

    2008-05-01

    Full Text Available Abstract Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs. Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 × 10-16 with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800 in the ml-ncRNAs population. Conclusion Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.

  20. Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

    Directory of Open Access Journals (Sweden)

    Carpousis Agamemnon J

    2011-06-01

    Full Text Available Abstract Background Noncoding RNA (ncRNA has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs. Results Using a combination of in silico and experimental approaches, we identified and characterized novel P. abyssi ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in the late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel P. abyssi ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four P. abyssi CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized. Conclusions This work proposes a revised annotation of CRISPR loci in P. abyssi and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.

  1. The new world of RNAs

    Directory of Open Access Journals (Sweden)

    Danyella Barbosa Dogini

    2014-01-01

    Full Text Available One of the major developments that resulted from the human genome sequencing projects was a better understanding of the role of non-coding RNAs (ncRNAs. NcRNAs are divided into several different categories according to size and function; however, one shared feature is that they are not translated into proteins. In this review, we will discuss relevant aspects of ncRNAs, focusing on two main types: i microRNAs, which negatively regulate gene expression either by translational repression or target mRNA degradation, and ii small interfering RNAs (siRNAs, which are involved in the biological process of RNA interference (RNAi. Our knowledge regarding these two types of ncRNAs has increased dramatically over the past decade, and they have a great potential to become therapeutic alternatives for a variety of human conditions.

  2. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition

    OpenAIRE

    Lee, Seungwoo; Hwang, Seungwoo; Yu, Hee Jeong; Oh, DaYoung; Choi, Yu Jung; KIM, Myung-Chul; Kim, Yongbaek; RYU, DOUG-YOUNG

    2016-01-01

    MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-p...

  3. Profiling of microRNA-mRNA reveals roles of microRNAs in cervical cancer

    Institute of Scientific and Technical Information of China (English)

    MA Ding; ZHANG You-yi; GUO Yan-li; LI Zi-jian; GENG Li

    2012-01-01

    Background Cervical cancer is one of the most common malignant tumors in women.This study was designed to explore the expression profiles of microRNAs (miRNAs) and mRNAs and the gene regulation network in cervical tumorigenesis and to find candidate molecular markers and key tumorigenic genes in cervical cancer.Methods miRNAs and mRNAs expression microarrays were used to detect the expression of miRNAs and mRNAs in normal and cancer cervical tissues.TargetScan 5.0 database (UK) was used to predict the target genes of the miRNAs,analyze their intersection with differentially expressed mRNAs and negatively correlate the intersection with miRNAs.Bioinformatic approaches were used to analyze functions and pathways of the target genes and establish miRNA-gene network.Results Twenty-nine miRNAs and 2036 mRNAs were differentially expressed in normal and cervical tumor tissues.Among them,13 miRNAs and 754 mRNAs were up-regulated in cervical tumor tissues and 16 miRNAs and 1282 RNA were down-regulated.The 327 target genes negatively related to miRNAs in the intersection were involved in functions and signal pathways.Down-regulated miRNAs targeted genes and up-regulated miRNAs targeted genes were involved in 415 and 163 functions,respectively,and in 37 and 17 significant pathways,respectively (P <0.05,false discovery rate (FDR) <0.05).We constructed the miRNAs-gene network and found that hsa-miR-15a,hsa-miR-106b and hsa-miR-20b were key nodes in the network.Conclusions The differentially expressed miRNAs and mRNAs in cervical cancer and related miRNA-gene network have been identified.They play important roles in cervical tumorigenesis and are involved in many important biological functions and signal transduction pathways.These findings lay a foundation for research on the molecular mechanism of miRNAs in the pathogenesis of cervical cancer.

  4. Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency.

    Science.gov (United States)

    Chen, Min; Wang, Chenlu; Bao, Hai; Chen, Hui; Wang, Yanwei

    2016-08-01

    Long non-coding RNAs (lncRNAs) have been identified as important regulatory factors of gene expression in eukaryotic species, such as Homo sapiens, Arabidopsis thaliana, and Oryza sativa. However, the systematic identification of potential lncRNAs in trees is comparatively rare. In particular, the characteristics, expression, and regulatory roles of lncRNAs in trees under nutrient stress remain largely unknown. A genome-wide strategy was used in this investigation to identify and characterize novel and low-nitrogen (N)-responsive lncRNAs in Populus tomentosa; 388 unique lncRNA candidates belonging to 380 gene loci were detected and only seven lncRNAs were found to belong to seven conserved non-coding RNA families indicating the majority of P. tomentosa lncRNAs are species-specific. In total, 126 lncRNAs were significantly altered under low-N stress; 8 were repressed, and 118 were induced. Furthermore, 9 and 5 lncRNAs were detected as precursors of 11 known and 14 novel Populus miRNAs, respectively, whereas 4 lncRNAs were targeted by 29 miRNAs belonging to 5 families, including 22 conserved and 7 non-conserved miRNAs. In addition, 15 antisense lncRNAs were identified to be generated from opposite strands of 14 corresponding protein-coding genes. In total, 111 protein-coding genes with regions complementary to 38 lncRNAs were also predicted with some lncRNAs corresponding to multiple genes and vice versa, and their functions were annotated, which further demonstrated the complex regulatory relationship between lncRNAs and protein-coding genes in plants. Moreover, an interaction network among lncRNAs, miRNAs, and mRNAs was investigated. These findings enrich our understanding of lncRNAs in Populus, expand the methods of miRNA identification. Our results present the first global characterization of lncRNAs and their potential target genes in response to nitrogen stress in trees, which provides more information on low-nutrition adaptation mechanisms in woody plants

  5. Small RNAs and Gene Network in a Durable Disease Resistance Gene--Mediated Defense Responses in Rice.

    Directory of Open Access Journals (Sweden)

    Hanming Hong

    Full Text Available Accumulating data have suggested that small RNAs (sRNAs have important functions in plant responses to pathogen invasion. However, it is largely unknown whether and how sRNAs are involved in the regulation of rice responses to the invasion of Xanthomonas oryzae pv. oryzae (Xoo, which causes bacterial blight, the most devastating bacterial disease of rice worldwide. We performed simultaneous genome-wide analyses of the expression of sRNAs and genes during early defense responses of rice to Xoo mediated by a major disease resistance gene, Xa3/Xa26, which confers durable and race-specific qualitative resistance. A large number of sRNAs and genes showed differential expression in Xa3/Xa26-mediated resistance. These differentially expressed sRNAs include known microRNAs (miRNAs, unreported miRNAs, and small interfering RNAs. The candidate genes, with expression that was negatively correlated with the expression of sRNAs, were identified, indicating that these genes may be regulated by sRNAs in disease resistance in rice. These results provide a new perspective regarding the putative roles of sRNA candidates and their putative target genes in durable disease resistance in rice.

  6. Regulation of Skeletal Muscle by microRNAs.

    Science.gov (United States)

    Diniz, Gabriela Placoná; Wang, Da-Zhi

    2016-01-01

    MicroRNAs (miRNAs) are a class of small noncoding RNAs highly conserved across species. miRNAs regulate gene expression posttranscriptionally by base pairing to complementary sequences mainly in the 3'-untranslated region of their target mRNAs to induce mRNA cleavage and translational repression. Thousands of miRNAs have been identified in human and their function has been linked to the regulation of both physiological and pathological processes. The skeletal muscle is the largest human organ responsible for locomotion, posture, and body metabolism. Several conditions such as aging, immobilization, exercise, and diet are associated with alterations in skeletal muscle structure and function. The genetic and molecular pathways that regulate muscle development, function, and regeneration as well as muscular disease have been well established in past decades. In recent years, numerous studies have underlined the importance of miRNAs in the control of skeletal muscle development and function, through its effects on several biological pathways critical for skeletal muscle homeostasis. Furthermore, it has become clear that alteration of the expression of many miRNAs or genetic mutations of miRNA genes is associated with changes on myogenesis and on progression of several skeletal muscle diseases. The present review provides an overview of the current studies and recent progress in elucidating the complex role exerted by miRNAs on skeletal muscle physiology and pathology. © 2016 American Physiological Society. Compr Physiol 6:1279-1294, 2016. PMID:27347893

  7. Clusters of internally primed transcripts reveal novel long noncoding RNAs.

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available Non-protein-coding RNAs (ncRNAs are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases (Kb, respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic rationale of our approach. In silico analysis showed that many regions had evidence of imprinting and/or antisense transcription. These regions were significantly associated with microRNAs and transcripts from the central nervous system. We selected eight novel regions for experimental validation by northern blot and RT-PCR and found that the majority represent previously unrecognized noncoding transcripts that are at least 10 Kb in size and predominantly localized in the nucleus. Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like Xist and Air.

  8. Noncoding Regulatory RNAs in Hematopoiesis.

    Science.gov (United States)

    Jeong, M; Goodell, M A

    2016-01-01

    Hematopoiesis is a dynamic process in which blood cells are continuously generated from hematopoietic stem cells (HSCs). The regulatory mechanisms controlling HSC fate have been studied extensively over the past several decades. Although many protein-coding genes have been shown to regulate hematopoietic differentiation, additional levels of HSC regulation are not well studied. Advances in deep sequencing have revealed many new classes of regulatory noncoding RNAs (ncRNAs), such as enhancer RNAs and antisense ncRNAs. Functional analysis of some of these ncRNAs has provided insights into the molecular mechanisms that regulate hematopoietic development and disease. In this review, we summarize recent advances in our understanding of functional regulatory ncRNAs associated with hematopoietic self-renewal and differentiation, as well as those dysregulated ncRNAs involved in hematologic malignancies. PMID:27137659

  9. Why YRNAs? About Versatile RNAs and Their Functions

    Directory of Open Access Journals (Sweden)

    Stefan Hüttelmaier

    2013-02-01

    Full Text Available Y RNAs constitute a family of highly conserved small noncoding RNAs (in humans: 83-112 nt; Y1, Y3, Y4 and Y5. They are transcribed from individual genes by RNA-polymerase III and fold into conserved stem-loop-structures. Although discovered 30 years ago, insights into the cellular and physiological role of Y RNAs remains incomplete. In this review, we will discuss knowledge on the structural properties, associated proteins and discuss proposed functions of Y RNAs. We suggest Y RNAs to be an integral part of ribonucleoprotein networks within cells and could therefore have substantial influence on many different cellular processes. Putative functions of Y RNAs include small RNA quality control, DNA replication, regulation of the cellular stress response and proliferation. This suggests Y RNAs as essential regulators of cell fate and indicates future avenues of research, which will provide novel insights into the role of small noncoding RNAs in gene expression.

  10. Identification of microRNAs differentially expressed involved in male flower development.

    Science.gov (United States)

    Wang, Zhengjia; Huang, Jianqin; Sun, Zhichao; Zheng, Bingsong

    2015-03-01

    Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees. PMID:25576251

  11. Complex organisation and structure of the ghrelin antisense strand gene GHRLOS, a candidate non-coding RNA gene

    Directory of Open Access Journals (Sweden)

    Herington Adrian C

    2008-10-01

    Full Text Available Abstract Background The peptide hormone ghrelin has many important physiological and pathophysiological roles, including the stimulation of growth hormone (GH release, appetite regulation, gut motility and proliferation of cancer cells. We previously identified a gene on the opposite strand of the ghrelin gene, ghrelinOS (GHRLOS, which spans the promoter and untranslated regions of the ghrelin gene (GHRL. Here we further characterise GHRLOS. Results We have described GHRLOS mRNA isoforms that extend over 1.4 kb of the promoter region and 106 nucleotides of exon 4 of the ghrelin gene, GHRL. These GHRLOS transcripts initiate 4.8 kb downstream of the terminal exon 4 of GHRL and are present in the 3' untranslated exon of the adjacent gene TATDN2 (TatD DNase domain containing 2. Interestingly, we have also identified a putative non-coding TATDN2-GHRLOS chimaeric transcript, indicating that GHRLOS RNA biogenesis is extremely complex. Moreover, we have discovered that the 3' region of GHRLOS is also antisense, in a tail-to-tail fashion to a novel terminal exon of the neighbouring SEC13 gene, which is important in protein transport. Sequence analyses revealed that GHRLOS is riddled with stop codons, and that there is little nucleotide and amino-acid sequence conservation of the GHRLOS gene between vertebrates. The gene spans 44 kb on 3p25.3, is extensively spliced and harbours multiple variable exons. We have also investigated the expression of GHRLOS and found evidence of differential tissue expression. It is highly expressed in tissues which are emerging as major sites of non-coding RNA expression (the thymus, brain, and testis, as well as in the ovary and uterus. In contrast, very low levels were found in the stomach where sense, GHRL derived RNAs are highly expressed. Conclusion GHRLOS RNA transcripts display several distinctive features of non-coding (ncRNA genes, including 5' capping, polyadenylation, extensive splicing and short open reading

  12. Genome-wide identification and functional analysis of long noncoding RNAs involved in the response to graphene oxide.

    Science.gov (United States)

    Wu, Qiuli; Zhou, Xuefeng; Han, Xiaoxiao; Zhuo, Yizhou; Zhu, Siting; Zhao, Yunli; Wang, Dayong

    2016-09-01

    Long noncoding RNAs (lncRNAs), which are defined as noncoding RNAs having at least 200 nucleotides, can potentially regulate various biological processes. However, the roles of lncRNAs in regulating cellular response to engineered nanomaterials (ENMs) are still unclear. Using Hiseq 2000 sequencing technique, we performed a genome-wide screen to identify lncRNAs involved in the control of toxicity of graphene oxide (GO) using in vivo Caenorhabditis elegans assay system. HiSeq 2000 sequencing, followed by quantitative analysis, identified only 34 dysregulated lncRNAs in GO exposed nematodes. Bioinformatics analysis implies the biological processes and signaling pathways mediated by candidate lncRNAs involved in the control of GO toxicity. A lncRNAs-miRNAs network possibly involved in the control of GO toxicity was further raised. Moreover, we identified the shared lncRNAs based on the molecular regulation basis for chemical surface modifications and/or genetic mutations in reducing GO toxicity. We further provide direct evidence that these shared lncRNAs, linc-37 and linc-14, were involved in the control of chemical surface modifications and genetic mutations in reducing GO toxicity. linc-37 binding to transcriptional factor FOXO/DAF-16 might be important for the control of GO toxicity. Our whole-genome identification and functional analysis of lncRNAs highlights the important roles of lncRNAs based molecular mechanisms for cellular responses to ENMs in organisms. PMID:27348851

  13. Cell-free microRNAs in blood and other body fluids, as cancer biomarkers.

    Science.gov (United States)

    Ortiz-Quintero, Blanca

    2016-06-01

    The discovery of cell-free microRNAs (miRNAs) in serum, plasma and other body fluids has yielded an invaluable potential source of non-invasive biomarkers for cancer and other non-malignant diseases. miRNAs in the blood and other body fluids are highly stable in biological samples and are resistant to environmental conditions, such as freezing, thawing or enzymatic degradation, which makes them convenient as potential biomarkers. In addition, they are more easily sampled than tissue miRNAs. Altered levels of cell-free miRNAs have been found in every type of cancer analysed, and increasing evidence indicates that they may participate in carcinogenesis by acting as cell-to-cell signalling molecules. This review summarizes the biological characteristics and mechanisms of release of cell-free miRNAs that make them promising candidates as non-invasive biomarkers of cancer. PMID:27218664

  14. tRNAs as regulators in gene expression

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Transfer RNAs(tRNAs) hold a central place in protein synthesis by interpreting the genetic information stored in DNA into the amino acid sequence of protein,thus functioning as "adaptor" molecules.In recent years,however,various studies have shown that tRNAs have additional functions beyond participating in protein synthesis.When suffering from certain nutritional stresses,tRNAs change the level of aminoacylation to became uncharged,and these uncharged tRNAs act as effector molecules to regulate global gene expression,so that the stressed organism copes with the adverse environmental stresses.In budding yeast and certain mammalian cells,the retrograde movement of mature tRNAs from cytoplasm to nucleus serves as a mechanism for the surveillance system within the nucleus to continue monitoring the integrity of tRNAs.On the other hand,this retrograde action effectively reduces the global protein synthesis level under conditions of nutritional starvation.Quite recently,various publications have shown that tRNAs are not stable molecules in an absolute sense.Under certain physiological or environmental stresses,they are specifically cleaved into fragments of different lengths in the anticodon loop or anticodon left arm.These cleavages are not a meaningless random degradation phenomenon.Instead,a novel class of signal molecules such as tRNA halves or sitRNAs may be produced,which are closely correlated with the modulation of global gene expression.Investigation of the regulatory functions of tRNAs is a frontier,which seeks to reveal the structural and functional diversity of tRNAs as well as their vital functions during the expression of genetic information.

  15. Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis

    Directory of Open Access Journals (Sweden)

    Sun Jiajie

    2013-01-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their expression patterns have been identified in various species. However, to date no miRNAs have been reported to modulate muscle development in beef cattle. Results Total RNAs from the Chinese Qinchuan bovine longissimus thoracis at fetal and adult stages were used to construct small RNA libraries for Solexa SBS technology sequencing. A total of 15,454,182 clean reads were obtained from the fetal bovine library and 13,558,164 clean reads from the adult bovine library. In total, 521 miRNAs including 104 novel miRNA candidates were identified. Furthermore, the nucleotide bias, base edit and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 25 high-read miRNAs were detected, and the results showed that bta-miRNA-206, miRNA-1, miRNA-133, miRNAn12, and miRNAn17 were highly expressed in muscle-related tissue or organs, suggesting that these miRNAs may play a role in the development of bovine muscle tissues. Conclusions This study confirmed the authenticity of 417 known miRNAs, discovered 104 novel miRNAs in bos taurus, and identified five muscle-specific miRNAs. The identification of novel miRNAs significantly expanded the repertoire of bovine miRNAs and could contribute to further studies on the muscle development of cattle.

  16. Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    Peláez Pablo

    2012-03-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume Phaseolus vulgaris (common bean. Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS technology to identify and characterize the miRNA population of Phaseolus vulgaris. Results Small RNA libraries were generated from roots, flowers, leaves, and seedlings of P. vulgaris. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies. Conclusions This work represents the first massive-scale RNA sequencing study performed in Phaseolus vulgaris to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of P. vulgaris miRNAs in relation to those of other legumes.

  17. Profiling micro rnas and their targets in radish (raphanus sativus l.)

    International Nuclear Information System (INIS)

    MicroRNAs (miRNAs) are tiny, non-protein coding and negative regulatory RNAs approximately 21 nucleotides in length. The comparative genomic methodology due to their conserved nature is a reasonable approach for the novel miRNAs discovery. In this research, total 25 novel miRNAs from 18 families (ras-miR-156, 160, 162, 163, 164, 167, 168, 319, 399, 408, 413, 414, 841, 1310, 2936, 5030 and 5661) are identified in an important vegetable radish (Raphanus sativus L.). The 25 miRNA precursor sequences showed secondary structures with the mature miRNAs in the stem region. Total 42 putative targets are also identified for the novel 25 radish miRNAs. These findings suggest that more thorough understanding of the function of such miRNAs will help to unravel the mysteries role in plant biology. (author)

  18. Circulating microRNAs: Novel biomarkers for esophageal cancer

    Directory of Open Access Journals (Sweden)

    Sheng-Li Zhou, Li-Dong Wang

    2010-05-01

    Full Text Available Esophageal carcinogenesis is a multi-stage process, involving a variety of changes in gene expression and physiological structure change. MicroRNAs (miRNAs are a class of small non-coding endogenous RNA molecules. Recent innovation in miRNAs profiling technology have shed new light on the pathology of esophageal carcinoma (EC, and also heralded great potential for exploring novel biomarkers for both EC diagnosis and treatment. Frequent dysregulation of miRNA in malignancy highlights the study of molecular factors upstream of gene expression following the extensive investigation on elucidating the important role of miRNA in carcinogenesis. We herein present a thorough review of the role of miRNAs in EC, addressing miRNA functions, their putative role as oncogenes or tumor suppressors and their potential target genes. The recent progresses in discovering the quantifiable circulating cancer-associated miRNAs indicate the potential clinical use of miRNAs as novel minimally invasive biomarkers for EC and other cancers. We also discuss the potential role of miRNAs in detection, screening and surveillance of EC as miRNAs can be a potential target in personalized treatment of EC.

  19. Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts

    Science.gov (United States)

    Seenprachawong, Kanokwan; Nuchnoi, Pornlada; Nantasenamat, Chanin; Prachayasittikul, Virapong

    2016-01-01

    MicroRNAs (miRNAs) are small endogenous noncoding RNAs that play an instrumental role in post-transcriptional modulation of gene expression. Genes related to osteogenesis (i.e., RUNX2, COL1A1 and OSX) is important in controlling the differentiation of mesenchymal stem cells (MSCs) to bone tissues. The regulated expression level of miRNAs is critically important for the differentiation of MSCs to preosteoblasts. The understanding of miRNA regulation in osteogenesis could be applied for future applications in bone defects. Therefore, this study aims to shed light on the mechanistic pathway underlying osteogenesis by predicting miRNAs that may modulate this pathway. This study investigates RUNX2, which is a major transcription factor for osteogenesis that drives MSCs into preosteoblasts. Three different prediction tools were employed for identifying miRNAs related to osteogenesis using the 3’UTR of RUNX2 as the target gene. Of the 1,023 miRNAs, 70 miRNAs were found by at least two of the tools. Candidate miRNAs were then selected based on their free energy values, followed by assessing the probability of target accessibility. The results showed that miRNAs 23b, 23a, 30b, 143, 203, 217, and 221 could regulate the RUNX2 gene during the differentiation of MSCs to preosteoblasts.

  20. Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis.

    Directory of Open Access Journals (Sweden)

    Megan Woolfit

    Full Text Available Wolbachia pipientis is an endosymbiotic bacterium that induces a wide range of effects in its insect hosts, including manipulation of reproduction and protection against pathogens. Little is known of the molecular mechanisms underlying the insect-Wolbachia interaction, though it is likely to be mediated via the secretion of proteins or other factors. There is an increasing amount of evidence that bacteria regulate many cellular processes, including secretion of virulence factors, using small non-coding RNAs (sRNAs, but sRNAs have not previously been described from Wolbachia. We have used two independent approaches, one based on comparative genomics and the other using RNA-Seq data generated for gene expression studies, to identify candidate sRNAs in Wolbachia. We experimentally characterized the expression of one of these candidates in four Wolbachia strains, and showed that it is differentially regulated in different host tissues and sexes. Given the roles played by sRNAs in other host-associated bacteria, the conservation of the candidate sRNAs between different Wolbachia strains, and the sex- and tissue-specific differential regulation we have identified, we hypothesise that sRNAs may play a significant role in the biology of Wolbachia, and in particular in its interactions with its host.

  1. Targeting of microRNAs for therapeutics

    DEFF Research Database (Denmark)

    Stenvang, Jan; Lindow, Morten; Kauppinen, Sakari

    miRNAs (microRNAs) comprise a class of small endogenous non-coding RNAs that post-transcriptionally repress gene expression by base-pairing with their target mRNAs. Recent evidence has shown that miRNAs play important roles in a wide variety of human diseases, such as viral infections, cancer and...

  2. microRNAs- powerful repression comes from small RNAs

    Institute of Scientific and Technical Information of China (English)

    MA Cong; LIU YuFei; HE Lin

    2009-01-01

    microRNAs (miRNAs) encode a novel class of small, non-coding RNAs that regulate gene expression post-trancriptionally, miRNAs comprise one of the major non-coding RNA families, whose diverse bio-logical functions and unusual capacity for gene regulation have attracted enormous interests in the RNA world. Over the past 16 years, genetic, biochemical and computational approaches have greatly shaped the growth of the field, leading to the identification of thousands of miRNA genes in nearly all metazoans. The key molecular machinery for miRNA biogenesis and silencing has been identified, yet the precise biochemical and regulatory mechanisms still remain elusive. However, recent findings have shed new light on how miRNAs are generated and how they function to repress gene expression.miRNAs provide a paradigm for endogenous small RNAs that mediate gene silencing at a genome-wide level. The gene silencing mediated by these small RNAs constitutes a major component of gene regu-lation during various developmental and physiological processes. The accumulating knowledge about their biogenesis and gene silencing mechanism will add a now dimension to our understanding about the complex gene regulatory networks.

  3. microRNAs-powerful repression comes from small RNAs

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    microRNAs (miRNAs) encode a novel class of small, non-coding RNAs that regulate gene expression post-trancriptionally. miRNAs comprise one of the major non-coding RNA families, whose diverse bio- logical functions and unusual capacity for gene regulation have attracted enormous interests in the RNA world. Over the past 16 years, genetic, biochemical and computational approaches have greatly shaped the growth of the field, leading to the identification of thousands of miRNA genes in nearly all metazoans. The key molecular machinery for miRNA biogenesis and silencing has been identified, yet the precise biochemical and regulatory mechanisms still remain elusive. However, recent findings have shed new light on how miRNAs are generated and how they function to repress gene expression. miRNAs provide a paradigm for endogenous small RNAs that mediate gene silencing at a genome-wide level. The gene silencing mediated by these small RNAs constitutes a major component of gene regu- lation during various developmental and physiological processes. The accumulating knowledge about their biogenesis and gene silencing mechanism will add a new dimension to our understanding about the complex gene regulatory networks.

  4. Structure-Guided Lead Optimization of Triazolopyrimidine-Ring Substituents Identifies Potent Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors with Clinical Candidate Potential

    Energy Technology Data Exchange (ETDEWEB)

    Coteron, Jose M.; Marco, Maria; Esquivias, Jorge; Deng, Xiaoyi; White, Karen L.; White, John; Koltun, Maria; El Mazouni, Farah; Kokkonda, Sreekanth; Katneni, Kasiram; Bhamidipati, Ravi; Shackleford, David M.; Angulo-Barturen, Inigo; Ferrer, Santiago B.; Jimenez-Diaz, Maria Belen; Gamo, Francisco-Javier; Goldsmith, Elizabeth J.; Charman, William N.; Bathurst, Ian; Floyd, David; Matthews, David; Burrows, Jeremy N.; Rathod, Pradipsinh K.; Charman, Susan A.; Phillips, Margaret A. (UWASH); (MMV, Switzerland); (GSK); (Monash); (UW); (UTSMC)

    2012-02-27

    Drug therapy is the mainstay of antimalarial therapy, yet current drugs are threatened by the development of resistance. In an effort to identify new potential antimalarials, we have undertaken a lead optimization program around our previously identified triazolopyrimidine-based series of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. The X-ray structure of PfDHODH was used to inform the medicinal chemistry program allowing the identification of a potent and selective inhibitor (DSM265) that acts through DHODH inhibition to kill both sensitive and drug resistant strains of the parasite. This compound has similar potency to chloroquine in the humanized SCID mouse P. falciparum model, can be synthesized by a simple route, and rodent pharmacokinetic studies demonstrated it has excellent oral bioavailability, a long half-life and low clearance. These studies have identified the first candidate in the triazolopyrimidine series to meet previously established progression criteria for efficacy and ADME properties, justifying further development of this compound toward clinical candidate status.

  5. Dark matter candidates

    International Nuclear Information System (INIS)

    One of the simplest, yet most profound, questions we can ask about the Universe is, how much stuff is in it, and further what is that stuff composed of? Needless to say, the answer to this question has very important implications for the evolution of the Universe, determining both the ultimate fate and the course of structure formation. Remarkably, at this late date in the history of the Universe we still do not have a definitive answer to this simplest of questions---although we have some very intriguing clues. It is known with certainty that most of the material in the Universe is dark, and we have the strong suspicion that the dominant component of material in the Cosmos is not baryons, but rather is exotic relic elementary particles left over from the earliest, very hot epoch of the Universe. If true, the Dark Matter question is a most fundamental one facing both particle physics and cosmology. The leading particle dark matter candidates are: the axion, the neutralino, and a light neutrino species. All three candidates are accessible to experimental tests, and experiments are now in progress. In addition, there are several dark horse, long shot, candidates, including the superheavy magnetic monopole and soliton stars. 13 refs

  6. Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii

    Science.gov (United States)

    Schroeder, Casey L. C.; Narra, Hema P.; Sahni, Abha; Rojas, Mark; Khanipov, Kamil; Patel, Jignesh; Shah, Riya; Fofanov, Yuriy; Sahni, Sanjeev K.

    2016-01-01

    Emerging evidence implicates a critically important role for bacterial small RNAs (sRNAs) as post-transcriptional regulators of physiology, metabolism, stress/adaptive responses, and virulence, but the roles of sRNAs in pathogenic Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, α-tmRNA, 4.5S RNA, 6S RNA) was further confirmed by Northern blot or RT-PCR analyses. The transcriptional start sites of five novel rickettsial sRNAs and 6S RNA were next determined using 5′ RLM-RACE yielding evidence for their independent biogenesis in R. prowazekii. Finally, computational approaches were employed to determine the secondary structures and potential mRNA targets of novel sRNAs. Together, these results establish the presence and expression of sRNAs in R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis. PMID:27375581

  7. Regulation of Small RNAs and Corresponding Targets in Nod Factor-Induced Phaseolus vulgaris Root Hair Cells

    Science.gov (United States)

    Formey, Damien; Martín-Rodríguez, José Ángel; Leija, Alfonso; Santana, Olivia; Quinto, Carmen; Cárdenas, Luis; Hernández, Georgina

    2016-01-01

    A genome-wide analysis identified the set of small RNAs (sRNAs) from the agronomical important legume Phaseolus vulgaris (common bean), including novel P. vulgaris-specific microRNAs (miRNAs) potentially important for the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. In this work, we aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli nodulation factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to the identity of 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples; however, these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events, thus setting the basis for exploring miRNA-mediated improvement of the common bean–rhizobia symbiosis. PMID:27271618

  8. Regulation of Small RNAs and Corresponding Targets in Nod Factor-Induced Phaseolus vulgaris Root Hair Cells.

    Science.gov (United States)

    Formey, Damien; Martín-Rodríguez, José Ángel; Leija, Alfonso; Santana, Olivia; Quinto, Carmen; Cárdenas, Luis; Hernández, Georgina

    2016-01-01

    A genome-wide analysis identified the set of small RNAs (sRNAs) from the agronomical important legume Phaseolus vulgaris (common bean), including novel P. vulgaris-specific microRNAs (miRNAs) potentially important for the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. In this work, we aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli nodulation factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to the identity of 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples; however, these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events, thus setting the basis for exploring miRNA-mediated improvement of the common bean-rhizobia symbiosis. PMID:27271618

  9. Computational identification and analysis of novel sugarcane microRNAs

    Directory of Open Access Journals (Sweden)

    Thiebaut Flávia

    2012-07-01

    Full Text Available Abstract Background MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. Results A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species and DNA methylation (24-nt-species, respectively. Conclusions A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.

  10. CCD photometry of globular cluster core structure. 2: U-band profiles for 15 candidate collapsed-core clusters

    Science.gov (United States)

    Lugger, Phyllis M.; Cohn, Haldan N.; Grindlay, Jonathan E.

    1995-01-01

    We present U-band CCD surface brightness profiles for 15 of the 21 globular clusters that have been identified as having collapsed cores by Djorgovski & King (1986). Fourteen of the clusters were observed with the Cerro Tololo 4 m telescope; NGC 7078 was observed with the Canada-France-Hawaii 3.6 m telescope (CFHT). We have fitted the profiles with seeing-convolved power laws, both with and without cores, to assess the evidence for central power-law structure and to place upper limits on core radius r(sub c). We find nine of the clusters (NGC 5946, NGC 6284, NGC 6293, NGC 6325, NGC 6342, NGC 6558, NGC 6624, NGC 6681, and NGC 7078) to have unresolved cores, with upper limits r(sub c) less than or = 1.9 arcsecs. Three of the clusters (NGC 6453, NGC 6522, and NGC 7099) have marginally resolved cores, with upper limits in the range 2.7 arcsecs less than or = r(sub c) less than or = 3.4 arcsecs. The remaining three clusters (NGC 6355, NGC 6397, and NGC 6752) have resolved cores. Of the latter three clusters, NGC 6355 and NGC 6752 are consistent with single-mass King model structure. The median cluster distances are 9.2 kpc for those with unresolved cores, 7.2 kpc for those with marginally resolved cores, and 4.1 kpc for those with resolved cores. The 13 clusters that do not resemble single-mass King models have central power-law structure with surface brightness slopes in the range of d ln S/d ln r = -0.6 to -0.8. These slopes are consistent with the models of Grabhorn et al. (1992) for clusters evolving beyond core collapse. The models include a centrally concentrated population of nonluminous remnants with masses in the range 1.2-1.4 solar mass, thus providing evidence for significant neutron star populations in most of our cluster sample. This finding is consistent with the observation of centrally concentrated low-mass X-ray binary and millisecond pulsar populations in several clusters.

  11. Non-Protein Coding RNAs

    CERN Document Server

    Walter, Nils G; Batey, Robert T

    2009-01-01

    This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

  12. Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer's Disease.

    Science.gov (United States)

    Nabers, Andreas; Ollesch, Julian; Schartner, Jonas; Kötting, Carsten; Genius, Just; Hafermann, Henning; Klafki, Hans; Gerwert, Klaus; Wiltfang, Jens

    2016-03-01

    The misfolding of the Amyloid-beta (Aβ) peptide into β-sheet enriched conformations was proposed as an early event in Alzheimer's Disease (AD). Here, the Aβ peptide secondary structure distribution in cerebrospinal fluid (CSF) and blood plasma of 141 patients was measured with an immuno-infrared-sensor. The sensor detected the amide I band, which reflects the overall secondary structure distribution of all Aβ peptides extracted from the body fluid. We observed a significant downshift of the amide I band frequency of Aβ peptides in Dementia Alzheimer type (DAT) patients, which indicated an overall shift to β-sheet. The secondary structure distribution of all Aβ peptides provides a better marker for DAT detection than a single Aβ misfold or the concentration of a specific oligomer. The discrimination between DAT and disease control patients according to the amide I frequency was in excellent agreement with the clinical diagnosis (accuracy 90% for CSF and 84% for blood). The amide I band maximum above or below the decisive marker frequency appears as a novel spectral biomarker candidate of AD. Additionally, a preliminary proof-of-concept study indicated an amide I band shift below the marker band already in patients with mild cognitive impairment due to AD. The presented immuno-IR-sensor method represents a promising, simple, robust, and label-free diagnostic tool for CSF and blood analysis. PMID:26828829

  13. Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

    OpenAIRE

    Kenan-Eichler, Michal; Leshkowitz, Dena; Tal, Lior; Noor, Elad; Melamed-Bessudo, Cathy; Feldman, Moshe; Levy, Avraham A.

    2011-01-01

    Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses involving genetic and epigenetic alterations. Such modifications may be induced by small RNAs, which affect key cellular processes, including gene expression, chromatin structure, cytosine methylation and transposable element (TE) activity. To date, the role of small RNAs in the context of wide hybridization and polyploidization has received little attention. In this work, we performed h...

  14. Overview of MicroRNAs in Cardiac Hypertrophy, Fibrosis, and Apoptosis.

    Science.gov (United States)

    Wang, Juan; Liew, Oi Wah; Richards, Arthur Mark; Chen, Yei-Tsung

    2016-01-01

    MicroRNAs (miRNAs) are non-coding RNAs that play essential roles in modulating the gene expression in almost all biological events. In the past decade, the involvement of miRNAs in various cardiovascular disorders has been explored in numerous in vitro and in vivo studies. In this paper, studies focused upon the discovery of miRNAs, their target genes, and functionality are reviewed. The selected miRNAs discussed herein have regulatory effects on target gene expression as demonstrated by miRNA/3' end untranslated region (3'UTR) interaction assay and/or gain/loss-of-function approaches. The listed miRNA entities are categorized according to the biological relevance of their target genes in relation to three cardiovascular pathologies, namely cardiac hypertrophy, fibrosis, and apoptosis. Furthermore, comparison across 86 studies identified several candidate miRNAs that might be of particular importance in the ontogenesis of cardiovascular diseases as they modulate the expression of clusters of target genes involved in the progression of multiple adverse cardiovascular events. This review illustrates the involvement of miRNAs in diverse biological signaling pathways and provides an overview of current understanding of, and progress of research into, of the roles of miRNAs in cardiovascular health and disease. PMID:27213331

  15. Overview of MicroRNAs in Cardiac Hypertrophy, Fibrosis, and Apoptosis

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2016-05-01

    Full Text Available MicroRNAs (miRNAs are non-coding RNAs that play essential roles in modulating the gene expression in almost all biological events. In the past decade, the involvement of miRNAs in various cardiovascular disorders has been explored in numerous in vitro and in vivo studies. In this paper, studies focused upon the discovery of miRNAs, their target genes, and functionality are reviewed. The selected miRNAs discussed herein have regulatory effects on target gene expression as demonstrated by miRNA/3′ end untranslated region (3′UTR interaction assay and/or gain/loss-of-function approaches. The listed miRNA entities are categorized according to the biological relevance of their target genes in relation to three cardiovascular pathologies, namely cardiac hypertrophy, fibrosis, and apoptosis. Furthermore, comparison across 86 studies identified several candidate miRNAs that might be of particular importance in the ontogenesis of cardiovascular diseases as they modulate the expression of clusters of target genes involved in the progression of multiple adverse cardiovascular events. This review illustrates the involvement of miRNAs in diverse biological signaling pathways and provides an overview of current understanding of, and progress of research into, of the roles of miRNAs in cardiovascular health and disease.

  16. Overview of MicroRNAs in Cardiac Hypertrophy, Fibrosis, and Apoptosis

    Science.gov (United States)

    Wang, Juan; Liew, Oi Wah; Richards, Arthur Mark; Chen, Yei-Tsung

    2016-01-01

    MicroRNAs (miRNAs) are non-coding RNAs that play essential roles in modulating the gene expression in almost all biological events. In the past decade, the involvement of miRNAs in various cardiovascular disorders has been explored in numerous in vitro and in vivo studies. In this paper, studies focused upon the discovery of miRNAs, their target genes, and functionality are reviewed. The selected miRNAs discussed herein have regulatory effects on target gene expression as demonstrated by miRNA/3′ end untranslated region (3′UTR) interaction assay and/or gain/loss-of-function approaches. The listed miRNA entities are categorized according to the biological relevance of their target genes in relation to three cardiovascular pathologies, namely cardiac hypertrophy, fibrosis, and apoptosis. Furthermore, comparison across 86 studies identified several candidate miRNAs that might be of particular importance in the ontogenesis of cardiovascular diseases as they modulate the expression of clusters of target genes involved in the progression of multiple adverse cardiovascular events. This review illustrates the involvement of miRNAs in diverse biological signaling pathways and provides an overview of current understanding of, and progress of research into, of the roles of miRNAs in cardiovascular health and disease. PMID:27213331

  17. Identification and validation of human papillomavirus encoded microRNAs.

    Directory of Open Access Journals (Sweden)

    Kui Qian

    Full Text Available We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

  18. Undetected antisense tRNAs in mitochondrial genomes?

    Directory of Open Access Journals (Sweden)

    Seligmann Hervé

    2010-06-01

    Full Text Available Abstract Background The hypothesis that both mitochondrial (mt complementary DNA strands of tRNA genes code for tRNAs (sense-antisense coding is explored. This could explain why mt tRNA mutations are 6.5 times more frequently pathogenic than in other mt sequences. Antisense tRNA expression is plausible because tRNA punctuation signals mt sense RNA maturation: both sense and antisense tRNAs form secondary structures potentially signalling processing. Sense RNA maturation processes by default 11 antisense tRNAs neighbouring sense genes. If antisense tRNAs are expressed, processed antisense tRNAs should have adapted more for translational activity than unprocessed ones. Four tRNA properties are examined: antisense tRNA 5' and 3' end processing by sense RNA maturation and its accuracy, cloverleaf stability and misacylation potential. Results Processed antisense tRNAs align better with standard tRNA sequences with the same cognate than unprocessed antisense tRNAs, suggesting less misacylations. Misacylation increases with cloverleaf fragility and processing inaccuracy. Cloverleaf fragility, misacylation and processing accuracy of antisense tRNAs decrease with genome-wide usage of their predicted cognate amino acid. Conclusions These properties correlate as if they adaptively coevolved for translational activity by some antisense tRNAs, and to avoid such activity by other antisense tRNAs. Analyses also suggest previously unsuspected particularities of aminoacylation specificity in mt tRNAs: combinations of competition between tRNAs on tRNA synthetases with competition between tRNA synthetases on tRNAs determine specificities of tRNA amino acylations. The latter analyses show that alignment methods used to detect tRNA cognates yield relatively robust results, even when they apparently fail to detect the tRNA's cognate amino acid and indicate high misacylation potential. Reviewers This article was reviewed by Dr Juergen Brosius, Dr Anthony M Poole and

  19. Experimental studies on interactions of molten LiF-NaF salt with some candidate structural materials for components of advanced nuclear reactors

    International Nuclear Information System (INIS)

    Interaction of molten 60 LiF - 40 NaF (% mol) salt with candidate structural materials for components of advanced nuclear reactors has been studied using electron probe microanalysis (EPMA) and inductively coupled plasma atomic emission spectrometry (ICP-OES). The corrosion of structural materials (stainless steel, Ni base alloy, nickel), which was induced by the molten salt melt, has been examined in dependence on the time of exposure at operating temperature of 680 deg C. The above choice of the two analytical techniques made it possible to assess on the whole the extent of corrosion. The corrosion phenomena in structural materials were investigated using EPMA. Corrosion-released elements dissolved in solidified molten salt were determined after salt dissolution by means of ICP-OES. The LiF-NaF melt produced corrosion, which proved as a surficial modification of a structural material and a trace contamination of the melt itself. The X-ray maps by EPMA with its 1-μm lateral resolution revealed compositional changes in structural materials, such as, e. g. regular depletion of Cr in alloy A686 to the depth of 10 - 25 μm. While the lateral resolution of LA-ICP-MS with the applied laser spot diameter of 25 μm was not exactly adequate to mapping of the corroded material section and, consequently, yielded less information in comparison with EPMA, this technique was quite sufficient for the mapping of elemental content changes in solidified salt profile. Finally, nickel was proved to be the most resistant material. It was concluded that: (i) EPMA study, involving semi-quantitative elemental mapping / content profiling and detailed spot quantitative analyses makes it possible to obtain quantitative assessment of the corrosion process; (ii) qualitative profiles are provided by LA-ICP-MS, which needs further development on quantification procedure based on matched calibration samples. (author)

  20. Circulating Serum miRNAs as Diagnostic Markers for Colorectal Cancer

    OpenAIRE

    Zekri, Abdel-Rahman N; Youssef, Amira Salah El-Din; Lotfy, Mai M.; Gabr, Reham; Ahmed, Ola S; Nassar, Auhood; Hussein, Nehal; OMRAN, Dalia; Medhat, Eman; Eid, Salam; Hussein, Marwa Mahmoud; Ismail, Maha Yahia; Alenzi, Faris Q.; Bahnassy, Abeer A

    2016-01-01

    Aim The study was designed to assess the possibility of using circulating miRNAs (serum miRNAs) as diagnostic biomarkers in colorectal cancer (CRC) and to identify their possibility as candidates for targeted therapy. Methods The study involved two sample sets: 1- a training set which included 90 patients with colorectal related disease (30 with CRC, 18 with inflammatory bowel disease (IBD), 18 with colonic polyps (CP) and 24 with different colonic symptoms but without any colonoscopic abnorm...

  1. RECOVERY OF THE CANDIDATE PROTOPLANET HD 100546 b WITH GEMINI/NICI AND DETECTION OF ADDITIONAL (PLANET-INDUCED?) DISK STRUCTURE AT SMALL SEPARATIONS

    International Nuclear Information System (INIS)

    We report the first independent, second epoch (re-)detection of a directly imaged protoplanet candidate. Using L' high-contrast imaging of HD 100546 taken with the Near-Infrared Coronagraph and Imager on Gemini South, we recover ''HD 100546 b'' with a position and brightness consistent with the original Very Large Telescope/NAos-COnica detection from Quanz et al., although data obtained after 2013 will be required to decisively demonstrate common proper motion. HD 100546 b may be spatially resolved, up to ≈12-13 AU in diameter, and is embedded in a finger of thermal IR-bright, polarized emission extending inward to at least 0.''3. Standard hot-start models imply a mass of ≈15 MJ . However, if HD 100546 b is newly formed or made visible by a circumplanetary disk, both of which are plausible, its mass is significantly lower (e.g., 1-7 MJ ). Additionally, we discover a thermal IR-bright disk feature, possibly a spiral density wave, at roughly the same angular separation as HD 100546 b but 90° away. Our interpretation of this feature as a spiral arm is not decisive, but modeling analyses using spiral density wave theory implies a wave launching point exterior to ≈0.''45 embedded within the visible disk structure: plausibly evidence for a second, hitherto unseen, wide-separation planet. With one confirmed protoplanet candidate and evidence for one to two others, HD 100546 is an important evolutionary precursor to intermediate-mass stars with multiple super-Jovian planets at moderate/wide separations like HR 8799

  2. RECOVERY OF THE CANDIDATE PROTOPLANET HD 100546 b WITH GEMINI/NICI AND DETECTION OF ADDITIONAL (PLANET-INDUCED?) DISK STRUCTURE AT SMALL SEPARATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Currie, Thayne; Kudo, Tomoyuki [NAOJ, Subaru Telescope, 650 N' Aohoku Pl., Hilo, HI 96720 (United States); Muto, Takayuki [Division of Liberal Arts, Kogashin University, 1-24-2, Nishi-Shinjuku, Shinijuku-ku, Tokyo 163-8677 (Japan); Honda, Mitsuhiko [Department of Mathematics and Physics, Kanagawa University, 2946 Tsuchiya, Hiratsuka 259-1293 (Japan); Brandt, Timothy D. [Astrophysics Department, Institute for Advanced Study, Princeton, NJ 08540 (United States); Grady, Carol [Eureka Scientific, 2452 Delmer, Suite 100, Oakland, CA96002 (United States); Fukagawa, Misato [Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Burrows, Adam [Department of Astrophysical Sciences, Princeton University, 7 Ivy Lane, Princeton, NJ 08544-1001 (United States); Janson, Markus [Stockholm University, SE-106 91 Stockholm (Sweden); Kuzuhara, Masayuki [Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551 (Japan); McElwain, Michael W. [Exoplanets and Stellar Astrophysics Laboratory, Code 667, Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Follette, Katherine [Department of Astronomy, Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721-0065 (United States); Hashimoto, Jun [H. L. Dodge Department of Physics and Astronomy, University of Oklahoma, 440 W. Brooks St Norman, OK 73019 (United States); Henning, Thomas [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Kandori, Ryo; Kusakabe, Nobuhiko; Morino, Jun-ichi; Nishikawa, Jun [National Astronomical Observatory of Japan, 2-21-1, Osawa, Mitaka, Tokyo 181-8588 (Japan); Kwon, Jungmi; Mede, Kyle, E-mail: currie@naoj.org [Department of Astronomy, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); and others

    2014-12-01

    We report the first independent, second epoch (re-)detection of a directly imaged protoplanet candidate. Using L' high-contrast imaging of HD 100546 taken with the Near-Infrared Coronagraph and Imager on Gemini South, we recover ''HD 100546 b'' with a position and brightness consistent with the original Very Large Telescope/NAos-COnica detection from Quanz et al., although data obtained after 2013 will be required to decisively demonstrate common proper motion. HD 100546 b may be spatially resolved, up to ≈12-13 AU in diameter, and is embedded in a finger of thermal IR-bright, polarized emission extending inward to at least 0.''3. Standard hot-start models imply a mass of ≈15 M{sub J} . However, if HD 100546 b is newly formed or made visible by a circumplanetary disk, both of which are plausible, its mass is significantly lower (e.g., 1-7 M{sub J} ). Additionally, we discover a thermal IR-bright disk feature, possibly a spiral density wave, at roughly the same angular separation as HD 100546 b but 90° away. Our interpretation of this feature as a spiral arm is not decisive, but modeling analyses using spiral density wave theory implies a wave launching point exterior to ≈0.''45 embedded within the visible disk structure: plausibly evidence for a second, hitherto unseen, wide-separation planet. With one confirmed protoplanet candidate and evidence for one to two others, HD 100546 is an important evolutionary precursor to intermediate-mass stars with multiple super-Jovian planets at moderate/wide separations like HR 8799.

  3. Stable intronic sequence RNAs (sisRNAs): a new layer of gene regulation.

    Science.gov (United States)

    Osman, Ismail; Tay, Mandy Li-Ian; Pek, Jun Wei

    2016-09-01

    Upon splicing, introns are rapidly degraded. Hence, RNAs derived from introns are commonly deemed as junk sequences. However, the discoveries of intronic-derived small nucleolar RNAs (snoRNAs), small Cajal body associated RNAs (scaRNAs) and microRNAs (miRNAs) suggested otherwise. These non-coding RNAs are shown to play various roles in gene regulation. In this review, we highlight another class of intron-derived RNAs known as stable intronic sequence RNAs (sisRNAs). sisRNAs have been observed since the 1980 s; however, we are only beginning to understand their biological significance. Recent studies have shown or suggested that sisRNAs regulate their own host's gene expression, function as molecular sinks or sponges, and regulate protein translation. We propose that sisRNAs function as an additional layer of gene regulation in the cells. PMID:27147469

  4. A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

    Science.gov (United States)

    Rossi, Ciro C.; Bossé, Janine T.; Li, Yanwen; Witney, Adam A.; Gould, Kate A.; Langford, Paul R.; Bazzolli, Denise M.S.

    2016-01-01

    Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies. PMID:27402897

  5. NcRNA-microchip analysis: A novel approach to identify differential expression of non-coding RNAs

    OpenAIRE

    Hutzinger, Roland; Mrázek, Jan; Vorwerk, Sonja; Hüttenhofer, Alexander

    2010-01-01

    Epstein-Barr virus (EBV) infection of human B cells requires the presence of non-coding RNAs (ncRNAs), which regulate expression of viral and host genes. To identify differentially expressed regulatory ncRNAs involved in EBV infection, a specialized cDNA library, enriched for ncRNAs derived from EBV-infected cells, was subjected to deep-sequencing. From the deep-sequencing analysis, we generated a custom-designed ncRNA-microchip to investigate differential expression of ncRNA candidates. By t...

  6. A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation▿

    OpenAIRE

    Itaya, Asuka; Zhong, Xuehua; Bundschuh, Ralf; Qi, Yijun; Wang, Ying; Takeda, Ryuta; Harris, Ann R.; Molina, Carlos; Nelson, Richard S; Ding, Biao

    2007-01-01

    RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21- to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question...

  7. Loa loa and Onchocerca ochengi miRNAs detected in host circulation.

    Science.gov (United States)

    Tritten, Lucienne; O'Neill, Maeghan; Nutting, Chuck; Wanji, Samuel; Njouendoui, Abdel; Fombad, Fanny; Kengne-Ouaffo, Jonas; Mackenzie, Charles; Geary, Timothy

    2014-11-01

    A combination of deep-sequencing and bioinformatics analysis enabled identification of twenty-two microRNA candidates of potential nematode origin in plasma from Loa loa-infected baboons and a further ten from the plasma of an Onchocerca ochengi-infected cow. The obtained data were compared to results from previous work on miRNA candidates from Dirofilaria immitis and O. volvulus found in host circulating blood, to examine the species specificity of the released miRNA. None of the miRNA candidates was found to be present in all four host-parasite scenarios and most of them were specific to only one of them. Eight candidate miRNAs were found to be identical in the full sequence in at least two different infections, while nine candidate miRNAs were found to be similar but not identical in at least four filarial species. PMID:25461483

  8. MicroRNAs associated with the pathogenesis of multiple sclerosis.

    Science.gov (United States)

    Huang, Qingrong; Xiao, Bo; Ma, Xinting; Qu, Mingjuan; Li, Yanmin; Nagarkatti, Prakash; Nagarkatti, Mitzi; Zhou, Juhua

    2016-06-15

    Multiple sclerosis (MS) is not only an autoimmune disease in which autoreactive immune cells against myelin damage axons and nerves in the central nervous system, but also a neurodegenerative disease, in which progressive loss of structure and function of neurons occurs. The mechanisms of MS pathogenesis have not been fully understood. It has been reported that miRNAs may play a critical role in MS pathogenesis. In this review, we have extensively discussed the alterations in the expression of miRNAs detected in patients with MS. The dysregulated miRNAs have been shown to be associated with the pathogenesis of MS. We suggest that such dysregulated miRNAs may potentially be used as biomarkers in the diagnosis of MS, to discover new therapeutic targets for MS treatment, and to predict prognostic markers in responses to MS treatment. PMID:27235360

  9. Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing

    Institute of Scientific and Technical Information of China (English)

    Sujay Paul; Anirban Kundu; Amita Pal

    2014-01-01

    MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. Several conserved and species-specific miRNAs have been characterized to date, predominantly from the plant species whose genome is well characterized. However, information on the variability of these regulatory RNAs in economically important but genetically less characterized crop species are limited. Vigna mungo is an important grain legume, which is grown primarily for its protein-rich edible seeds. miRNAs from this species have not been identified to date due to lack of genome sequence information. To identify miRNAs from V. mungo, a small RNA library was constructed from young leaves. High-throughput Illumina sequencing technology and bioinformat-ic analysis of the small RNA reads led to the identification of 66 miRNA loci represented by 45 conserved miRNAs belonging to 19 families and eight non-conserved miRNAs belonging to seven families. Besides, 13 novel miRNA candidates in V. mungo were also identified. Expression patterns of selected conserved, non-conserved, and novel miRNA candidates have been demonstrated in leaf, stem, and root tissues by quantitative polymerase chain reaction, and potential target genes were predicted for most of the conserved miRNAs. This information offers genomic resour-ces for better understanding of miRNA mediated post-transcriptional gene regulation.

  10. Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing.

    Science.gov (United States)

    Paul, Sujay; Kundu, Anirban; Pal, Amita

    2014-01-01

    MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. Several conserved and species-specific miRNAs have been characterized to date, predominantly from the plant species whose genome is well characterized. However, information on the variability of these regulatory RNAs in economically important but genetically less characterized crop species are limited. Vigna mungo is an important grain legume, which is grown primarily for its protein-rich edible seeds. miRNAs from this species have not been identified to date due to lack of genome sequence information. To identify miRNAs from V. mungo, a small RNA library was constructed from young leaves. High-throughput Illumina sequencing technology and bioinformatic analysis of the small RNA reads led to the identification of 66 miRNA loci represented by 45 conserved miRNAs belonging to 19 families and eight non-conserved miRNAs belonging to seven families. Besides, 13 novel miRNA candidates in V. mungo were also identified. Expression patterns of selected conserved, non-conserved, and novel miRNA candidates have been demonstrated in leaf, stem, and root tissues by quantitative polymerase chain reaction, and potential target genes were predicted for most of the conserved miRNAs. This information offers genomic resources for better understanding of miRNA mediated post-transcriptional gene regulation. PMID:24138283

  11. Noncoding RNAs in Cancer Immunology.

    Science.gov (United States)

    Li, Qian; Liu, Qiang

    2016-01-01

    Cancer immunology is the study of interaction between cancer cells and immune system by the application of immunology principle and theory. With the recent approval of several new drugs targeting immune checkpoints in cancer, cancer immunology has become a very attractive field of research and is thought to be the new hope to conquer cancer. This chapter introduces the aberrant expression and function of noncoding RNAs, mainly microRNAs and long noncoding RNAs, in tumor-infiltrating immune cells, and their significance in tumor immunity. It also illustrates how noncoding RNAs are shuttled between tumor cells and immune cells in tumor microenvironments via exosomes or other microvesicles to modulate tumor immunity. PMID:27376738

  12. Uridylation and adenylation of RNAs.

    Science.gov (United States)

    Song, JianBo; Song, Jun; Mo, BeiXin; Chen, XueMei

    2015-11-01

    The posttranscriptional addition of nontemplated nucleotides to the 3' ends of RNA molecules can have a significant impact on their stability and biological function. It has been recently discovered that nontemplated addition of uridine or adenosine to the 3' ends of RNAs occurs in different organisms ranging from algae to humans, and on different kinds of RNAs, such as histone mRNAs, mRNA fragments, U6 snRNA, mature small RNAs and their precursors etc. These modifications may lead to different outcomes, such as increasing RNA decay, promoting or inhibiting RNA processing, or changing RNA activity. Growing pieces of evidence have revealed that such modifications can be RNA sequence-specific and subjected to temporal or spatial regulation in development. RNA tailing and its outcomes have been associated with human diseases such as cancer. Here, we review recent developments in RNA uridylation and adenylation and discuss the future prospects in this research area. PMID:26563174

  13. Effects of a range of machined and ground surface finishes on the simulated reactor helium corrosion of several candidate structural materials

    International Nuclear Information System (INIS)

    This report discusses the corrosion behavior of several candidate reactor structural alloys in a simulated advanced high-temperature gas-cooled reactor (HTGR) environment over a range of lathe-machined and centerless-ground surface finishes. The helium environment contained 50 Pa H2/5 Pa CO/5 Pa CH4/2O (500 μatm H2/50 μatm CO/50 μatm CH4/2O) at 9000C for a total exposure of 3000 h. The test alloys included two vacuum-cast superalloys (IN 100 and IN 713LC); a centrifugally cast austenitic alloy (HK 40); three wrought high-temperature alloys (Alloy 800H, Hastelloy X, and Inconel 617); and a nickel-base oxide-dispersion-strengthened alloy (Inconel MA 754). Surface finish variations did not affect the simulated advanced-HTGR corrosion behavior of these materials. Under these conditions, the availability of reactant gaseous impurities controls the kinetics of the observed gas-metal interactions. Variations in the near-surface activities and mobilities of reactive solute elements, such as chromium, which might be expected to be affected by changes in surface finish, do not seem to greatly influence corrosion in this simulated advanced HTGR environment. 18 figures, 4 tables

  14. Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis.

    Directory of Open Access Journals (Sweden)

    Frank Guzman

    Full Text Available BACKGROUND: microRNAs or miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance, and there have been no previous studies concerning its gene expression and regulation. To date, no miRNAs have been reported in Myrtaceae species. RESULTS: Small RNA and RNA-seq libraries were constructed to identify miRNAs and pre-miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library, and the data obtained were analyzed using bioinformatics tools. From 14,489,131 small RNA clean reads, we obtained 1,852,722 mature miRNA sequences representing 45 conserved families that have been identified in other plant species. Further analysis using contigs assembled from RNA-seq allowed the prediction of secondary structures of 25 known and 17 novel pre-miRNAs. The expression of twenty-seven identified miRNAs was also validated using RT-PCR assays. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. CONCLUSIONS: This study is the first large scale identification of miRNAs and their potential targets from a species of the Myrtaceae family without genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights species-specific miRNAs.

  15. Long noncoding RNAs in psychiatric disorders.

    Science.gov (United States)

    Zuo, Lingjun; Tan, Yunlong; Wang, Zhiren; Wang, Ke-Sheng; Zhang, Xiangyang; Chen, Xiangning; Li, Chiang-Shan R; Wang, Tong; Luo, Xingguang

    2016-06-01

    Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Many of these lncRNAs have regulatory functions and have recently emerged as major players in governing fundamental biological processes. Here, we review the definition, distribution, identification, databases, analysis, classification, and functions of lncRNAs. We also discuss the potential roles of lncRNAs in the etiological processes of psychiatric disorders and the implications for clinical diagnosis and treatment. PMID:26974119

  16. Long Noncoding RNAs, Chromatin, and Development

    Directory of Open Access Journals (Sweden)

    Daniel P. Caley

    2010-01-01

    Full Text Available The way in which the genome of a multicellular organism can orchestrate the differentiation of trillions of cells and many organs, all from a single fertilized egg, is the subject of intense study. Different cell types can be defined by the networks of genes they express. This differential expression is regulated at the epigenetic level by chromatin modifications, such as DNA and histone methylation, which interact with structural and enzymatic proteins, resulting in the activation or silencing of any given gene. While detailed mechanisms are emerging on the role of different chromatin modifications and how these functions are effected at the molecular level, it is still unclear how their deposition across the epigenomic landscape is regulated in different cells. A raft of recent evidence is accumulating that implicates long noncoding RNAs (lncRNAs in these processes. Most genomes studied to date undergo widespread transcription, the majority of which is not translated into proteins. In this review, we will describe recent work suggesting that lncRNAs are more than transcriptional "noise", but instead play a functional role by acting as tethers and guides to bind proteins responsible for modifying chromatin and mediating their deposition at specific genomic locations. We suggest that lncRNAs are at the heart of developmental regulation, determining the epigenetic status and transcriptional network in any given cell type, and that they provide a means to integrate external differentiation cues with dynamic nuclear responses through the regulation of a metastable epigenome. Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.

  17. Non-Coding RNAs: Functional Aspects and Diagnostic Utility in Oncology

    Directory of Open Access Journals (Sweden)

    Armin Reitmair

    2013-03-01

    Full Text Available Noncoding RNAs (ncRNAs have been found to have roles in a large variety of biological processes. Recent studies indicate that ncRNAs are far more abundant and important than initially imagined, holding great promise for use in diagnostic, prognostic, and therapeutic applications. Within ncRNAs, microRNAs (miRNAs are the most widely studied and characterized. They have been implicated in initiation and progression of a variety of human malignancies, including major pathologies such as cancers, arthritis, neurodegenerative disorders, and cardiovascular diseases. Their surprising stability in serum and other bodily fluids led to their rapid ascent as a novel class of biomarkers. For example, several properties of stable miRNAs, and perhaps other classes of ncRNAs, make them good candidate biomarkers for early cancer detection and for determining which preneoplastic lesions are likely to progress to cancer. Of particular interest is the identification of biomarker signatures, which may include traditional protein-based biomarkers, to improve risk assessment, detection, and prognosis. Here, we offer a comprehensive review of the ncRNA biomarker literature and discuss state-of-the-art technologies for their detection. Furthermore, we address the challenges present in miRNA detection and quantification, and outline future perspectives for development of next-generation biodetection assays employing multicolor alternating-laser excitation (ALEX fluorescence spectroscopy.

  18. MicroRNAs as a diagnostic tool for heart failure and atrial fibrillation.

    Science.gov (United States)

    Weckbach, Ludwig T; Grabmaier, Ulrich; Clauss, Sebastian; Wakili, Reza

    2016-04-01

    MicroRNAs (miRNAs) are small non-coding RNAs, which are directly involved in the regulation of post-transcriptional gene expression. Their biological function represents a repression of protein expression of the targeted messenger-RNA(s). Expression of several miRNAs is somehow tissue-specific or cell-specific and their expression pattern can reflect an underlying pathophysiological condition. Beyond this biological function their role as potential biomarkers has been emerged in the past years. This was based on the fact that miRNAs can be detected in blood samples (serum or plasma) in a surprisingly stable form, by contrast to mRNAs. This fact made miRNAs interesting candidates for biomarkers providing information with respect to a potentially ongoing pathophysiological condition and could thereby have an impact on specific treatment strategies in patients. In this review we try to provide an overview of the potential role of miRNAs as a diagnostic tool in atrial fibrillation and heart failure patients taken different methodological aspects and distinct type of patients into account. PMID:26852213

  19. Plasma microRNAs expression profile in female workers occupationally exposed to mercury

    Science.gov (United States)

    Ding, Enmin; Zhao, Qiuni; Bai, Ying; Xu, Ming; Pan, Liping; Liu, Qingdong; Wang, Bosheng; Song, Xianping; Wang, Jun; Chen, Lin

    2016-01-01

    Background Circulating microRNAs (miRNAs) have attracted interests as non-invasive biomarkers of physiological and pathological conditions. Several studies have examined the potential effects of mercury exposure on miRNAs expression profiles of general population environmentally exposed to mercury. The objective is to identify mercury-related miRNAs of female workers occupationally exposed to mercury. Methods In this case-control study, we used a microarray assay to detect the miRNA expression profiles in pooled plasma samples between (I) chronic mercury poisoning group; (II) mercury absorbing group and (III) control group in the discovery stage. Each group has ten individuals. In addition, we conducted a validation of eight candidate miRNAs in the same 30 workers by quantitative real-time PCR. Results In the discovery stage, eight miRNAs were conformed following our selection criteria. In the validation stage, RT-PCR confirmed up-regulation of miR-92a and miR-486 in the mercury poisoned group (Pmercury exposure. However, further studies are necessary to prove the causal association between miRNAs changes and mercury exposure, and to determine whether these two miRNAs are clear biomarkers to mercury exposure. PMID:27162656

  20. Expression Profiling of Circulating MicroRNAs in Canine Myxomatous Mitral Valve Disease

    Directory of Open Access Journals (Sweden)

    Qinghong Li

    2015-06-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that have shown promise as noninvasive biomarkers in cardiac disease. This study was undertaken to investigate the miRNA expression profile in dogs with myxomatous mitral valve disease (MMVD. 277 miRNAs were quantified using RT-qPCR from six normal dogs (American College of Veterinary Internal Medicine Stage A, six dogs with MMVD mild to moderate cardiac enlargement (ACVIM Stage B1/B2 and six dogs with MMVD and congestive heart failure (ACVIM Stage C/D. Eleven miRNAs were differentially expressed (False Discovery Rate < 0.05. Dogs in Stage B1/B2 or C/D had four upregulated miRNAs, including three cfa-let-7/cfa-miR-98 family members, while seven others were downregulated, compared to Stage A. Expression of six of the 11 miRNAs also were significantly different between dogs in Stage C/D and those in Stage B1/B2. The expression changes were greater as disease severity increased. These miRNAs may be candidates for novel biomarkers and may provide insights into genetic regulatory pathways in canine MMVD.

  1. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

    Science.gov (United States)

    Li, Sanshu; Hwang, Xue Ying; Stav, Shira; Breaker, Ronald R.

    2016-01-01

    The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or “azaaromatics,” trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics. PMID:26843526

  2. Systematic structure modifications of multitarget prostate cancer drug candidate galeterone to produce novel androgen receptor down-regulating agents as an approach to treatment of advanced prostate cancer.

    Science.gov (United States)

    Purushottamachar, Puranik; Godbole, Abhijit M; Gediya, Lalji K; Martin, Marlena S; Vasaitis, Tadas S; Kwegyir-Afful, Andrew K; Ramalingam, Senthilmurugan; Ates-Alagoz, Zeynep; Njar, Vincent C O

    2013-06-27

    As part of our program to explore the influence of small structural modifications of our drug candidate 3β-(hydroxy)-17-(1H-benzimidazol-1-yl)androsta-5,16-diene (galeterone, 5) on the modulation of the androgen receptor (AR), we have prepared and evaluated a series of novel C-3, C-16, and C-17 analogues. Using structure activity analysis, we established that the benzimidazole moiety at C-17 is essential and optimal and also that hydrophilic and heteroaromatic groups at C-3 enhance both antiproliferative (AP) and AR degrading (ARD) activities. The most potent antiproliferative compounds were 3β-(1H-imidazole-1-carboxylate)-17-(1H-benzimidazol-1-yl)androsta-5,16-diene (47), 3-((EZ)-hydroximino)-17-(1H-benzimidazol-1-yl)androsta-4,16-diene (36), and 3β-(pyridine-4-carboxylate)-17-(1H-benzimidazol-1-yl)androsta-5,16-diene (43), with GI50 values of 0.87, 1.91, and 2.57 μM, respectively. Compared to 5, compound 47 was 4- and 8-fold more potent with respect to AP and ARD activities, respectively. Importantly, we also discovered that our compounds, including 5, 36, 43, and 47, could degrade both full-length and truncated ARs in CWR22rv1 human prostate cancer cells. With these activities, they have potential for development as new drugs for the treatment of all forms of prostate cancer. PMID:23713567

  3. Clinical implications of microRNAs in human glioblastoma

    Directory of Open Access Journals (Sweden)

    Masahiro eMizoguchi

    2013-02-01

    Full Text Available Glioblastoma (GBM is one of the most common and dismal brain tumors in adults. Further elucidation of the molecular pathogenesis of GBM is mandatory to improve the overall survival of patients. A novel small non-coding RNA molecule, microRNA (miRNA, appears to represent one of the most attractive target molecules contributing to the pathogenesis of various types of tumors. Recent global analyses have revealed that several miRNAs are clinically implicated in GBM, with some reports indicating the association of miRNA dysregulation with acquired temozolomide (TMZ resistance. More recent studies have revealed that miRNAs could play a role in cancer stem cell (CSC properties, contributing to treatment resistance. In addition, greater impact might be expected from miRNA-targeted therapies based on tumor-derived exosomes that contain numerous functional miRNAs, which could be transferred between tumor cells and surrounding structures. Tumor-derived miRNAs are now considered to be a novel molecular mechanism promoting the progression of GBM. Establishment of miRNA-targeted therapies based on miRNA dysregulation of CSCs could provide effective therapeutic strategies for TMZ-resistant GBM. Recent progress has revealed that miRNAs are not only putative biological markers for diagnosis, but also one of the most promising targets for GBM treatment. Herein, we summarize the translational aspects of miRNAs in the diagnosis and treatment of GBM.

  4. Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects

    OpenAIRE

    Bronkhorst, Alfred W.; Miesen, Pascal; Ronald P. van Rij

    2013-01-01

    The antiviral RNA interference (RNAi) pathway processes viral double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNA) that guide the recognition and cleavage of complementary viral target RNAs. In RNA virus infections, viral replication intermediates, dsRNA genomes or viral structured RNAs have been implicated as Dicer-2 substrates. In a recent publication, we demonstrated that a double-stranded DNA virus, Invertebrate iridescent virus 6, is a target of the Drosophila RNAi mach...

  5. Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum

    Directory of Open Access Journals (Sweden)

    Leterme Nathalie

    2010-05-01

    Full Text Available Abstract Background Post-transcriptional regulation in eukaryotes can be operated through microRNA (miRNAs mediated gene silencing. MiRNAs are small (18-25 nucleotides non-coding RNAs that play crucial role in regulation of gene expression in eukaryotes. In insects, miRNAs have been shown to be involved in multiple mechanisms such as embryonic development, tissue differentiation, metamorphosis or circadian rhythm. Insect miRNAs have been identified in different species belonging to five orders: Coleoptera, Diptera, Hymenoptera, Lepidoptera and Orthoptera. Results We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 149 miRNAs including 55 conserved and 94 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. Pea aphid microRNA sequences have been posted to miRBase: http://microrna.sanger.ac.uk/sequences/ Conclusions Our study has identified candidates as putative regulators involved in reproductive polyphenism in aphids and opens new avenues for further functional analyses.

  6. Search for MicroRNAs Expressed by Intracellular Bacterial Pathogens in Infected Mammalian Cells

    Science.gov (United States)

    Furuse, Yuki; Finethy, Ryan; Saka, Hector A.; Xet-Mull, Ana M.; Sisk, Dana M.; Smith, Kristen L. Jurcic; Lee, Sunhee; Coers, Jörn; Valdivia, Raphael H.; Tobin, David M.; Cullen, Bryan R.

    2014-01-01

    MicroRNAs are expressed by all multicellular organisms and play a critical role as post-transcriptional regulators of gene expression. Moreover, different microRNA species are known to influence the progression of a range of different diseases, including cancer and microbial infections. A number of different human viruses also encode microRNAs that can attenuate cellular innate immune responses and promote viral replication, and a fungal pathogen that infects plants has recently been shown to express microRNAs in infected cells that repress host cell immune responses and promote fungal pathogenesis. Here, we have used deep sequencing of total expressed small RNAs, as well as small RNAs associated with the cellular RNA-induced silencing complex RISC, to search for microRNAs that are potentially expressed by intracellular bacterial pathogens and translocated into infected animal cells. In the case of Legionella and Chlamydia and the two mycobacterial species M. smegmatis and M. tuberculosis, we failed to detect any bacterial small RNAs that had the characteristics expected for authentic microRNAs, although large numbers of small RNAs of bacterial origin could be recovered. However, a third mycobacterial species, M. marinum, did express an ∼23-nt small RNA that was bound by RISC and derived from an RNA stem-loop with the characteristics expected for a pre-microRNA. While intracellular expression of this candidate bacterial microRNA was too low to effectively repress target mRNA species in infected cultured cells in vitro, artificial overexpression of this potential bacterial pre-microRNA did result in the efficient repression of a target mRNA. This bacterial small RNA therefore represents the first candidate microRNA of bacterial origin. PMID:25184567

  7. Search for microRNAs expressed by intracellular bacterial pathogens in infected mammalian cells.

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    Full Text Available MicroRNAs are expressed by all multicellular organisms and play a critical role as post-transcriptional regulators of gene expression. Moreover, different microRNA species are known to influence the progression of a range of different diseases, including cancer and microbial infections. A number of different human viruses also encode microRNAs that can attenuate cellular innate immune responses and promote viral replication, and a fungal pathogen that infects plants has recently been shown to express microRNAs in infected cells that repress host cell immune responses and promote fungal pathogenesis. Here, we have used deep sequencing of total expressed small RNAs, as well as small RNAs associated with the cellular RNA-induced silencing complex RISC, to search for microRNAs that are potentially expressed by intracellular bacterial pathogens and translocated into infected animal cells. In the case of Legionella and Chlamydia and the two mycobacterial species M. smegmatis and M. tuberculosis, we failed to detect any bacterial small RNAs that had the characteristics expected for authentic microRNAs, although large numbers of small RNAs of bacterial origin could be recovered. However, a third mycobacterial species, M. marinum, did express an ∼ 23-nt small RNA that was bound by RISC and derived from an RNA stem-loop with the characteristics expected for a pre-microRNA. While intracellular expression of this candidate bacterial microRNA was too low to effectively repress target mRNA species in infected cultured cells in vitro, artificial overexpression of this potential bacterial pre-microRNA did result in the efficient repression of a target mRNA. This bacterial small RNA therefore represents the first candidate microRNA of bacterial origin.

  8. The interplay of long non-coding RNAs and MYC in cancer

    Directory of Open Access Journals (Sweden)

    Michael J. Hamilton

    2015-12-01

    Full Text Available Long non-coding RNAs (lncRNAs are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.

  9. Bioinformatic identification of microRNAs and their target genes from Solanum tuberosum expressed sequence tags

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene post-transcriptional expression in plants and animals. Low levels of some miRNAs and time- and tissue-specific expression patterns lead to the difficulty for experimental identification of miRNAs. Here we present a bioinformatic approach for expressed sequence tags (ESTs) prediction of novel miRNAs as well as their targets in Solanum tuberosum. We blasted the databases of S. Tuberosum ESTs to search for potential miRNAs, using previously known miRNA sequences from Arabidopsis, rice and other plant species. By analyzing parameters of plant precursors, including secondary structure, stem length and conservation of miRNAs, and following a variety of filtering criteria, a total of 22 potential miRNAs were detected. Using the newly identified miRNA sequences, we were able to further blast the S. Tuberosum mRNA database and detected 75 potential targets of miRNAs in S. Tuberosum. According to the mRNA annotations provided by the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/), most of the miRNA target genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism.

  10. Dietary RNAs: New Stories Regarding Oral Delivery

    Directory of Open Access Journals (Sweden)

    Jian Yang

    2015-04-01

    Full Text Available microRNAs (miRNAs, a class of small RNAs, are important regulators of various developmental processes in both plants and animals. Several years ago, a report showed the detection of diet-derived plant miRNAs in mammalian tissues and their regulation of mammalian genes, challenging the traditional functions of plant miRNAs. Subsequently, multiple efforts have attempted to replicate these findings, with the results arguing against the uptake of plant dietary miRNAs in healthy consumers. Moreover, several reports suggest the potential for “false positive” detection of plant miRNAs in human tissues. Meanwhile, some research continues to suggest both the presence and function of dietary miRNAs in mammalian tissues. Here we review the recent literature and discuss the strengths and weaknesses of emerging work that suggests the feasibility of dietary delivery of miRNAs. We also discuss future experimental approaches to address this controversial topic.

  11. Phloem small RNAs, nutrient stress responses, and systemic mobility

    Directory of Open Access Journals (Sweden)

    Kehr Julia

    2010-04-01

    the observation that miR395 and miR399 are phloem-mobile in grafting experiments we conclude that translocatable miRNAs might be candidates for information-transmitting molecules, but that grafting experiments alone are not sufficient to convincingly assign a signaling function.

  12. Involvement of microRNAs in physiological and pathological processes in the lung

    OpenAIRE

    Kriegova Eva; Petrek Martin; Tomankova Tereza

    2010-01-01

    Abstract To date, at least 900 different microRNA (miRNA) genes have been discovered in the human genome. These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often invo...

  13. Classification of ncRNAs using position and size information in deep sequencing data

    OpenAIRE

    Erhard, Florian; Zimmer, Ralf

    2010-01-01

    Motivation: Small non-coding RNAs (ncRNAs) play important roles in various cellular functions in all clades of life. With next-generation sequencing techniques, it has become possible to study ncRNAs in a high-throughput manner and by using specialized algorithms ncRNA classes such as miRNAs can be detected in deep sequencing data. Typically, such methods are targeted to a certain class of ncRNA. Many methods rely on RNA secondary structure prediction, which is not always accurate and not all...

  14. SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity

    International Nuclear Information System (INIS)

    Highlights: ► SiRNAs conjugated with aromatic compounds (Ar-siRNAs) at 5′-sense strand were synthesized. ► Ar-siRNAs increased resistance against nuclease degradation. ► Ar-siRNAs were thermodynamically stable compared with the unmodified siRNA. ► High levels of cellular uptake and cytoplasmic localization were found. ► Strong gene-silencing efficacy was exhibited in the Ar-siRNAs. -- Abstract: Short interference RNA (siRNA) is a powerful tool for suppressing gene expression in mammalian cells. In this study, we focused on the development of siRNAs conjugated with aromatic compounds in order to improve the potency of RNAi and thus to overcome several problems with siRNAs, such as cellular delivery and nuclease stability. The siRNAs conjugated with phenyl, hydroxyphenyl, naphthyl, and pyrenyl derivatives showed strong resistance to nuclease degradation, and were thermodynamically stable compared with unmodified siRNA. A high level of membrane permeability in HeLa cells was also observed. Moreover, these siRNAs exhibited enhanced RNAi efficacy, which exceeded that of locked nucleic acid (LNA)-modified siRNAs, against exogenous Renilla luciferase in HeLa cells. In particular, abundant cytoplasmic localization and strong gene-silencing efficacy were found in the siRNAs conjugated with phenyl and hydroxyphenyl derivatives. The novel siRNAs conjugated with aromatic compounds are promising candidates for a new generation of modified siRNAs that can solve many of the problems associated with RNAi technology.

  15. SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity

    Energy Technology Data Exchange (ETDEWEB)

    Kubo, Takanori, E-mail: kubo-t@yasuda-u.ac.jp [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan); Yanagihara, Kazuyoshi [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan); Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Takei, Yoshifumi [Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumi-cho, Showa-ku, Nagoya 466-8550 (Japan); Mihara, Keichiro [Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 (Japan); Sato, Yuichiro; Seyama, Toshio [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan)

    2012-10-05

    Highlights: Black-Right-Pointing-Pointer SiRNAs conjugated with aromatic compounds (Ar-siRNAs) at 5 Prime -sense strand were synthesized. Black-Right-Pointing-Pointer Ar-siRNAs increased resistance against nuclease degradation. Black-Right-Pointing-Pointer Ar-siRNAs were thermodynamically stable compared with the unmodified siRNA. Black-Right-Pointing-Pointer High levels of cellular uptake and cytoplasmic localization were found. Black-Right-Pointing-Pointer Strong gene-silencing efficacy was exhibited in the Ar-siRNAs. -- Abstract: Short interference RNA (siRNA) is a powerful tool for suppressing gene expression in mammalian cells. In this study, we focused on the development of siRNAs conjugated with aromatic compounds in order to improve the potency of RNAi and thus to overcome several problems with siRNAs, such as cellular delivery and nuclease stability. The siRNAs conjugated with phenyl, hydroxyphenyl, naphthyl, and pyrenyl derivatives showed strong resistance to nuclease degradation, and were thermodynamically stable compared with unmodified siRNA. A high level of membrane permeability in HeLa cells was also observed. Moreover, these siRNAs exhibited enhanced RNAi efficacy, which exceeded that of locked nucleic acid (LNA)-modified siRNAs, against exogenous Renilla luciferase in HeLa cells. In particular, abundant cytoplasmic localization and strong gene-silencing efficacy were found in the siRNAs conjugated with phenyl and hydroxyphenyl derivatives. The novel siRNAs conjugated with aromatic compounds are promising candidates for a new generation of modified siRNAs that can solve many of the problems associated with RNAi technology.

  16. A comparative genome-wide study of ncRNAs in trypanosomatids

    Directory of Open Access Journals (Sweden)

    Wachtel Chaim

    2010-11-01

    Full Text Available Abstract Background Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen to search for novel small ncRNAs in the genome of Trypanosoma brucei using techniques of comparative genomics. Results In this study, we identified by comparative genomics, and validated by experimental analysis several novel ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our procedure was capable of finding almost half of the known repertoire through homology over six genomes, and about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts, were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental validation. Eighteen of the 50 (36% were shown to be expressed, and for 11 of them a distinct expression product was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates were shown to be novel H/ACA and C/D snoRNAs; these included three sequences that appear as singletons in the genome, unlike previously identified snoRNA molecules that are found in clusters. The other candidates appear to be novel ncRNA molecules, and their function is, as yet, unknown. Conclusions Using comparative genomic techniques, we predicted 72 sequences as ncRNA candidates in T. brucei. The expression of 50 candidates was tested in laboratory experiments. This resulted in the discovery of 11 novel short ncRNAs in procyclic stage T. brucei

  17. Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile.

    Directory of Open Access Journals (Sweden)

    Olga A Soutourina

    2013-05-01

    Full Text Available Clostridium difficile is an emergent pathogen, and the most common cause of nosocomial diarrhea. In an effort to understand the role of small noncoding RNAs (sRNAs in C. difficile physiology and pathogenesis, we used an in silico approach to identify 511 sRNA candidates in both intergenic and coding regions. In parallel, RNA-seq and differential 5'-end RNA-seq were used for global identification of C. difficile sRNAs and their transcriptional start sites at three different growth conditions (exponential growth phase, stationary phase, and starvation. This global experimental approach identified 251 putative regulatory sRNAs including 94 potential trans riboregulators located in intergenic regions, 91 cis-antisense RNAs, and 66 riboswitches. Expression of 35 sRNAs was confirmed by gene-specific experimental approaches. Some sRNAs, including an antisense RNA that may be involved in control of C. difficile autolytic activity, showed growth phase-dependent expression profiles. Expression of each of 16 predicted c-di-GMP-responsive riboswitches was observed, and experimental evidence for their regulatory role in coordinated control of motility and biofilm formation was obtained. Finally, we detected abundant sRNAs encoded by multiple C. difficile CRISPR loci. These RNAs may be important for C. difficile survival in bacteriophage-rich gut communities. Altogether, this first experimental genome-wide identification of C. difficile sRNAs provides a firm basis for future RNome characterization and identification of molecular mechanisms of sRNA-based regulation of gene expression in this emergent enteropathogen.

  18. Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs

    Directory of Open Access Journals (Sweden)

    Liang Shaohui

    2009-12-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a novel class of gene regulators whose biogenesis involves hairpin structures called precursor miRNAs, or pre-miRNAs. A pre-miRNA is processed to make a miRNA:miRNA* duplex, which is then separated to generate a mature miRNA and a miRNA*. The mature miRNAs play key regulatory roles during embryonic development as well as other cellular processes. They are also implicated in control of viral infection as well as innate immunity. Direct experimental evidence for mosquito miRNAs has been recently reported in anopheline mosquitoes based on small-scale cloning efforts. Results We obtained approximately 130, 000 small RNA sequences from the yellow fever mosquito, Aedes aegypti, by 454 sequencing of samples that were isolated from mixed-age embryos and midguts from sugar-fed and blood-fed females, respectively. We also performed bioinformatics analysis on the Ae. aegypti genome assembly to identify evidence for additional miRNAs. The combination of these approaches uncovered 98 different pre-miRNAs in Ae. aegypti which could produce 86 distinct miRNAs. Thirteen miRNAs, including eight novel miRNAs identified in this study, are currently only found in mosquitoes. We also identified five potential revisions to previously annotated miRNAs at the miRNA termini, two cases of highly abundant miRNA* sequences, 14 miRNA clusters, and 17 cases where more than one pre-miRNA hairpin produces the same or highly similar mature miRNAs. A number of miRNAs showed higher levels in midgut from blood-fed female than that from sugar-fed female, which was confirmed by northern blots on two of these miRNAs. Northern blots also revealed several miRNAs that showed stage-specific expression. Detailed expression analysis of eight of the 13 mosquito-specific miRNAs in four divergent mosquito genera identified cases of clearly conserved expression patterns and obvious differences. Four of the 13 miRNAs are specific to certain lineage

  19. Circular RNAs and systemic lupus erythematosus.

    Science.gov (United States)

    Li, Lian-Ju; Huang, Qing; Pan, Hai-Feng; Ye, Dong-Qing

    2016-08-15

    Circular RNAs (circRNAs) are a large class of noncoding RNAs that form covalently closed RNA circles. The discovery of circRNAs discloses a new layer of gene regulation occurred post-transcriptionally. Identification of endogenous circRNAs benefits from the advance in high-throughput RNA sequencing and remains challenging. Many studies probing into the mechanisms of circRNAs formation occurred cotranscriptionally or posttranscriptionally emerge and conclude that canonical splicing mechanism, sequence properties, and certain regulatory factors are at play in the process. Although our knowledge on functions of circRNAs is rather limited, a few circRNAs are shown to sponge miRNA and regulate gene transcription. The clearest case is one circRNA CDR1as that serves as sponge of miR-7. Researches on circRNAs in human diseases such as cancers highlight the function and physical relevance of circRNAs. Given the implication of miRNAs in the initiation and progression of systemic lupus erythematosus (SLE) and the roles of circRNAs in sponging miRNA and gene regulation, it is appealing to speculate that circRNAs may associate with SLE and may be potential therapeutic targets for treatment of SLE. Future studies should attach more importance to the relationship between circRNAs and SLE. This review will concern identification, biogenesis, and function of circRNAs, introduce reports exploring the association of circRNAs with human diseases, and conjecture the potential roles of circRNAs in SLE. PMID:27450756

  20. An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

    Directory of Open Access Journals (Sweden)

    Barash Danny

    2008-04-01

    Full Text Available Abstract Background RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best examined using the dot plot representation for RNA secondary structure. Results Using RNAsubopt, the suboptimal solutions for a given wild-type sequence are calculated once. Then, specific mutations are selected that are most likely to cause a conformational rearrangement. For an RNA sequence of about 100 nts and 3-point mutations (n = 100, m = 3, for example, the proposed method reduces the running time from several hours or even days to several minutes, thus enabling the practical application of RNAmute to the analysis of multiple-point mutations. Conclusion A highly efficient addition to RNAmute that is as user friendly as the original application but that facilitates the practical analysis of multiple-point mutations is presented. Such an extension can now be exploited prior to site-directed mutagenesis experiments by virologists, for example, who investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary

  1. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration

    OpenAIRE

    Zhang, Jinwei; Ferré-D’Amare, Adrian R.

    2014-01-01

    Compared to globular proteins, RNAs with complex three-dimensional folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a post-crystallization treatment strategy that exploits the importan...

  2. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

    NARCIS (Netherlands)

    Lau, N.C.; Robine, N.; Martin, R.; Chung, W.J.; Niki, Y.; Berezikov, E.; Lai, E.C

    2009-01-01

    Piwi proteins, a subclass of Argonaute-family proteins, carry approximately 24-30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small in

  3. Analysis of epigenetic effects (microRNAs) in former employees of Wismut; Analyse epigenetischer Effekte (mikro RNAs) in ehemaligen Wismutbeschaeftigten

    Energy Technology Data Exchange (ETDEWEB)

    Johnen, Georg; Bruening, Thomas; Weber, D.G.

    2014-05-15

    Aim of the study was the development and establishment of an oligonucleotide microarray for expression analysis of microRNAs (miRNAs) in whole blood of former uranium miners. To identify possible biomarkers of radiation exposure, samples of high- and low-exposed miners were screened with microarrays that carried 703 human miRNA probes. To that end, 60 RNA samples of the project ''Creation of a biological sample and data collection of occupationally radiation-exposed workers (German Uranium Miners Biobank) - a pilot study'' (3607S04532) were analysed and potential biomarkers verified by quantitative real-time PCR (qRT-PCR). During the initial screening, mirRNA-548d-5p, showing a significantly altered expression between low- and high-exposed miners, was identified as a possible biomarker candidate. Verification by qRT-PCR confirmed the difference in expression, however, the result was not statistically significant.

  4. New roles for ‘old’ microRNAs in nervous system function and disease

    Directory of Open Access Journals (Sweden)

    Marion eHartl

    2013-12-01

    Full Text Available Since their discovery, microRNAs became prominent candidates providing missing links on how to explain the developmental and phenotypical variation within one species or among different species. In addition, microRNAs were implicated in diseases such as neurodegeneration and cancer. More recently, the regulation of animal behavior was shown to be influenced by microRNAs. In spite of their numerous functions, only a few microRNAs were discovered by using classic genetic approaches. Due to the very mild or redundant phenotypes of most microRNAs or their genomic location within introns of other genes many regulatory microRNAs were missed. In this review, we focus on three microRNAs first identified in a forward genetic screen in invertebrates for their essential function in animal development, namely bantam, let-7 and miR-279. All three are essential for survival, are not located in introns of other genes, and are highly conserved among species. We highlight their important functions in the nervous system and discuss their emerging roles, especially during nervous system disease and behavior.

  5. Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila.

    Science.gov (United States)

    Nyberg, Kevin G; Machado, Carlos A

    2016-01-01

    Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid-the evolutionary model Drosophila pseudoobscura Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster, like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, we identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses. PMID:27189981

  6. Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3 Encoded MicroRNAs.

    Directory of Open Access Journals (Sweden)

    Owen H Donohoe

    Full Text Available MicroRNAs (miRNAs are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3 is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio and koi (Cyprinus carpio koi worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA-offset RNAs (moRNAs derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.

  7. MicroRNAs in nasopharyngeal carcinoma

    Institute of Scientific and Technical Information of China (English)

    Jeff P Bruce; Fei-Fei Liu

    2014-01-01

    MicroRNAs (miRNAs) provide insight into both the biology and clinical behavior of many human cancers, including nasopharyngeal carcinoma (NPC). The dysregulation of miRNAs in NPC results in a variety of tumor-promoting effects. Furthermore, several miRNAs are prognostic markers for NPC. In addition to celular miRNAs, NPC samples also often contain miRNAs encoded by Epstein-Barr virus, and these miRNAs may impact NPC biology by targeting both celular and viral genes. Given their numerous putative roles in NPC development and progression, a thorough understanding of the impact of miRNA dysregulation in NPC is expected to shed light on useful biomarkers and therapeutic targets for the clinical management of this disease. In this review, we describe the efforts to date to identify and characterize such miRNAs in the context of NPC.

  8. Changes in circulating microRNAs after radiochemotherapy in head and neck cancer patients

    International Nuclear Information System (INIS)

    Circulating microRNAs (miRNAs) are easily accessible and have already proven to be useful as prognostic markers in cancer patients. However, their origin and function in the circulation is still under discussion. In the present study we analyzed changes in the miRNAs in blood plasma of head and neck squamous cell carcinoma (HNSCC) patients in response to radiochemotherapy and compared them to the changes in a cell culture model of primary HNSCC cells undergoing simulated anti-cancer therapy. MiRNA-profiles were analyzed by qRT-PCR arrays in paired blood plasma samples of HNSCC patients before therapy and after two days of treatment. Candidate miRNAs were validated by single qRT-PCR assays. An in vitro radiochemotherapy model using primary HNSCC cell cultures was established to test the possible tumor origin of the circulating miRNAs. Microarray analysis was performed on primary HNSCC cell cultures followed by validation of deregulated miRNAs via qRT-PCR. Unsupervised clustering of the expression profiles using the six most regulated miRNAs (miR-425-5p, miR-21-5p, miR-106b-5p, miR-590-5p, miR-574-3p, miR-885-3p) significantly (p = 0.012) separated plasma samples collected prior to treatment from plasma samples collected after two days of radiochemotherapy. MiRNA profiling of primary HNSCC cell cultures treated in vitro with radiochemotherapy revealed differentially expressed miRNAs that were also observed to be therapy-responsive in blood plasma of the patients (miR-425-5p, miR-21-5p, miR-106b-5p, miR-93-5p) and are therefore likely to stem from the tumor. Of these candidate marker miRNAs we were able to validate by qRT-PCR a deregulation of eight plasma miRNAs as well as miR-425-5p and miR-93-5p in primary HNSCC cultures after radiochemotherapy. Changes in the abundance of circulating miRNAs during radiochemotherapy reflect the therapy response of primary HNSCC cells after an in vitro treatment. Therefore, the responsive miRNAs (miR-425-5p, miR-93-5p) may represent

  9. The defective RNAs of Closteroviridae

    Directory of Open Access Journals (Sweden)

    MunirMawassi

    2013-05-01

    Full Text Available The family Closteroviridae consists of two genera, Closterovirus and Ampelovirus with monopartite genomes transmitted respectively by aphids and mealybugs and the Crinivirus with bipartite genomes transmitted by whiteflies. The Closteroviridae consists of more than thirty virus species, which differ considerably in their phytopathological significance. Some, like Beet yellows virus (BYV and Citrus tristeza virus (CTV were associated for many decades with their respective hosts, sugar beets and citrus. Others, like the grapevine leafroll-associated ampeloviruses 1, and 3 were also associated with their grapevine hosts for long periods; however difficulties in virus isolation hampered their molecular characterization. The majority of the recently identified Closteroviridae were probably associated with their vegetative propagated host plants for long periods and only detected through the considerable advances in dsRNA isolation and sequencing of PCR amplified replicons. Molecular characterization of CTV and several other Closteroviridae revealed that, in addition to genomic and subgenomic RNAs, infected plants contain several different subviral defective RNAs (dRNAs. The roles and biological functions of dRNAs associated with Closteroviridae remain terra incognita.

  10. MicroRNAs in Rice Innate Immunity

    OpenAIRE

    Baldrich, Patricia; San Segundo, Blanca

    2016-01-01

    MicroRNAs (miRNAs) are short regulatory non-coding RNAs that guide gene silencing in most eukaryotes. They regulate gene expression by triggering sequence-specific cleavage or translational repression of target transcripts. Plant miRNAs are known to play important roles in a wide range of developmental processes. Increasing evidence also supports that the modulation of miRNA levels plays an important role in reprogramming plant responses to abiotic stress (drought, cold, salinity and nutrient...

  11. lincRNAs: Genomics, Evolution, and Mechanisms

    OpenAIRE

    Ulitsky, Igor; Bartel, David P.

    2013-01-01

    Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review outlines the emerging understanding of lincRNAs in vertebrate animals, with emphases on how they are being identified and current conclusions and questions regarding their genomics, evolution and mechanisms of action.

  12. Studying microRNAs in lymphoma

    NARCIS (Netherlands)

    Kluiver, Joost; Slezak-Prochazka, Izabella; van den Berg, Anke

    2013-01-01

    MicroRNAs (miRNAs) play important roles in development, differentiation, homeostasis, and also in diseases such as lymphoma. This chapter describes methods to study the role of miRNAs in lymphoma. First, we describe a multiplex RT reaction followed by qPCR that can be used to determine differential

  13. MicroRNAs in the Hypothalamus

    DEFF Research Database (Denmark)

    Meister, Björn; Herzer, Silke; Silahtaroglu, Asli

    2013-01-01

    MicroRNAs (miRNAs) are short (∼22 nucleotides) non-coding ribonucleic acid (RNA) molecules that negatively regulate the expression of protein-coding genes. Posttranscriptional silencing of target genes by miRNA is initiated by binding to the 3'-untranslated regions of target mRNAs, resulting in...

  14. MicroRNAs in cardiac arrhythmia

    DEFF Research Database (Denmark)

    Hedley, Paula L; Carlsen, Anting L; Christiansen, Kasper M; Kanters, Jørgen K.; Behr, Elijah R; Corfield, Valerie A; Christiansen, Michael

    2014-01-01

    LQTS-causing mutations have been identified in 13 genes worldwide. Despite this, the genetic cause of 30-50% of LQTS is presently unknown. MicroRNAs (miRNAs) are small (∼ 22 nucleotides) noncoding RNAs which post-transcriptionally regulate gene expression by binding complementary sequences within...

  15. MicroRNAs in cardiovascular disease

    OpenAIRE

    Elton, Terry S.; Khan, Mahmood; Terentyev, Dmitry

    2011-01-01

    Rapid and accurate diagnosis of heart attacks—and the assessment of damage—are critical for improving coronary care. Mature microRNAs (miRNAs) are abundant, easily measured, and relatively stable in blood plasma. If they prove indicative of disease states, miRNAs measured from peripheral blood may be a particularly attractive source for routine clinical assessments.

  16. Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites

    Directory of Open Access Journals (Sweden)

    Sharma Amit

    2009-02-01

    Full Text Available Abstract Background Ribosome biogenesis is an energy consuming and stringently controlled process that involves hundreds of trans-acting factors. Small nucleolar RNAs (snoRNAs, important components of ribosome biogenesis are non-coding guide RNAs involved in rRNA processing, nucleotide modifications like 2'-O-ribose methylation, pseudouridylation and possibly gene regulation. snoRNAs are ubiquitous and are diverse in their genomic organization, mechanism of transcription and process of maturation. In vertebrates, most snoRNAs are present in introns of protein coding genes and are processed by exonucleolytic cleavage, while in plants they are transcribed as polycistronic transcripts. Results This is a comprehensive analysis of malaria parasite snoRNA genes and proteins that have a role in ribosomal biogenesis. Computational and experimental approaches have been used to identify several box C/D snoRNAs from different species of Plasmodium and confirm their expression. Our analyses reveal that the gene for endoribonuclease Rnt1 is absent from Plasmodium falciparum genome, which indicates the existence of alternative pre-rRNA processing pathways. The structural features of box C/D snoRNAs are highly conserved in Plasmodium genus; however, unlike other organisms most parasite snoRNAs are present in single copy. The genomic localization of parasite snoRNAs shows mixed patterns of those observed in plants, yeast and vertebrates. We have localized parasite snoRNAs in untranslated regions (UTR of mRNAs, and this is an unprecedented and novel genetic feature. Akin to mammalian snoRNAs, those in Plasmodium may also behave as mobile genetic elements. Conclusion This study provides a comprehensive overview on trans-acting genes involved in ribosome biogenesis and also a genetic insight into malaria parasite snoRNA genes.

  17. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

    DEFF Research Database (Denmark)

    Khan, Aly A; Betel, Doron; Miller, Martin L; Sander, Chris; Leslie, Christina S; Marks, Debora S

    2009-01-01

    among the transfected small RNAs and the endogenous pool of miRNAs for the intracellular machinery that processes small RNAs. To test this hypothesis, we analyzed genome-wide transcript responses from 151 published transfection experiments in seven different human cell types. We show that targets of......Transfection of small RNAs (such as small interfering RNAs (siRNAs) and microRNAs (miRNAs)) into cells typically lowers expression of many genes. Unexpectedly, increased expression of genes also occurs. We investigated whether this upregulation results from a saturation effect--that is, competition...... endogenous miRNAs are expressed at significantly higher levels after transfection, consistent with impaired effectiveness of endogenous miRNA repression. This effect exhibited concentration and temporal dependence. Notably, the profile of endogenous miRNAs can be largely inferred by correlating miRNA sites...

  18. Gene function analysis by artificial microRNAs in Physcomitrella patens.

    KAUST Repository

    Khraiwesh, Basel

    2011-01-01

    MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences resulting in cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs) can be generated by exchanging the miRNA/miRNA sequence of endogenous MIR precursor genes, while maintaining the general pattern of matches and mismatches in the foldback. Thus, for functional gene analysis amiRNAs can be designed to target any gene of interest. During the last decade the moss Physcomitrella patens emerged as a model plant for functional gene analysis based on its unique ability to integrate DNA into the nuclear genome by homologous recombination which allows for the generation of targeted gene knockout mutants. In addition to this, we developed a protocol to express amiRNAs in P. patens that has particular advantages over the generation of knockout mutants and might be used to speed up reverse genetics approaches in this model species.

  19. Long non-coding RNAs in cancer drug resistance development.

    Science.gov (United States)

    Majidinia, Maryam; Yousefi, Bahman

    2016-09-01

    The presence or emergence of chemoresistance in tumor cells is a major burden in cancer therapy. While drug resistance is a multifactorial phenomenon arising from altered membrane transport of drugs, altered drug metabolism, altered DNA repair, reduced apoptosis rate and alterations of drug metabolism, it can also be linked to genetic and epigenetic factors. Long non-coding RNAs (lncRNAs) have important regulatory roles in many aspects of genome function including gene transcription, splicing, and epigenetics as well as biological processes involved in cell cycle, cell differentiation, development, and pluripotency. As such, it may not be surprising that some lncRNAs have been recently linked to carcinogenesis and drug resistance/sensitivity. Research is accelerating to decipher the exact molecular mechanism of lncRNA-regulated drug resistance and its therapeutic implications. In this article, we will review the structure, biogenesis, and mode of action of lncRNAs. Then, the involvement of lncRNAs in drug resistance will be discussed in detail. PMID:27427176

  20. Are circulating microRNAs peripheral biomarkers for Alzheimer's disease?

    Science.gov (United States)

    Kumar, Subodh; Reddy, P Hemachandra

    2016-09-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by memory loss, multiple cognitive abnormalities and intellectual impairments. Currently, there are no drugs or agents that can delay and/or prevent the progression of disease in elderly individuals, and there are no peripheral biomarkers that can detect AD early in its pathogenesis. Research has focused on identifying biomarkers for AD so that treatment can be begun as soon as possible in order to restrict or prevent intellectual impairments, memory loss, and other cognitive abnormalities that are associated with the disease. One such potential biomarker is microRNAs that are found in circulatory biofluids, such as blood and blood components, serum and plasma. Blood and blood components are primary sources where miRNAs are released in either cell-free form and then bind to protein components, or are in an encapsulated form with microvesicle particles. Exosomal miRNAs are known to be stable in biofluids and can be detected by high throughput techniques, like microarray and RNA sequencing. In AD brain, enriched miRNAs encapsulated with exosomes crosses the blood brain barrier and secreted in the CSF and blood circulations. This review summarizes recent studies that have identified miRNAs in the blood, serum, plasma, exosomes, cerebral spinal fluids, and extracellular fluids as potential biomarkers of AD. Recent research has revealed only six miRNAs - miR-9, miR-125b, miR-146a, miR-181c, let-7g-5p, and miR-191-5p - that were reported by multiple investigators. Some studies analyzed the diagnostic potential of these six miRNAs through receiver operating curve analysis which indicates the significant area-under-curve values in different biofluid samples. miR-191-5p was found to have the maximum area-under-curve value (0.95) only in plasma and serum samples while smaller area-under-curve values were found for miR-125, miR-181c, miR-191-5p, miR-146a, and miR-9. This article shortlisted the

  1. MicroRNAs and long non-coding RNAs: prospects in diagnostics and therapy of cancer:

    OpenAIRE

    Hauptman, Nina; Glavač, Damjan

    2013-01-01

    Background Non-coding RNAs (ncRNAs) are key regulatory molecules in cellular processes, and are potential biomarkers in many diseases. Currently, microRNAs and long non-coding RNAs are being pursued as diagnostic and prognostic biomarkers, and as therapeutic tools in cancer, since their expression profiling is able to distinguish different cancer types and classify their sub-types. Conclusions There are numerous studies confirming involvement of ncRNAs in cancer initiation, development and pr...

  2. Targeting non-coding RNAs in Plants with the CRISPR-Cas technology is a challenge yet worth accepting

    Directory of Open Access Journals (Sweden)

    Jolly eBasak

    2015-11-01

    Full Text Available Non-coding RNAs (ncRNAs have emerged as versatile master regulator of biological functions in recent years. MicroRNAs (miRNAs are small endogenous ncRNAs of 18-24 nucleotides in length that originates from long self-complementary precursors. Besides their direct involvement in developmental processes, plant miRNAs play key roles in gene regulatory networks and varied biological processes. Alternatively, long ncRNAs (lncRNAs are a large and diverse class of transcribed ncRNAs whose length exceed that of 200 nucleotides. Plant lncRNAs are transcribed by different RNA polymerases, showing diverse structural features. Plant lncRNAs also are important regulators of gene expression in diverse biological processes. There has been a breakthrough in the technology of genome editing, the CRISPR-Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9 technology, in the last decade. CRISPR loci are transcribed into ncRNA and eventually form a functional complex with Cas9 and further guide the complex to cleave complementary invading DNA. The CRISPR-Cas technology has been successfully applied in model plants such as Arabidopsis and tobacco and important crops like wheat, maize and rice. However, all these studies are focused on protein coding genes. Information about targeting non-coding genes is scarce. Hitherto, the CRISPR-Cas technology has been exclusively used in vertebrate systems to engineer miRNA/lncRNAs, but it is still relatively unexplored in plants. While briefing miRNAs, lncRNAs and applications of the CRISPR-Cas technology in human and animals, this review essentially elaborates several strategies to overcome the challenges of applying the CRISPR-Cas technology in editing ncRNAs in plants and the future perspective of this field.

  3. The Tumor Cytosol miRNAs, Fluid miRNAs and Exosome miRNAs in Lung Cancer

    Directory of Open Access Journals (Sweden)

    Xin eQin

    2015-01-01

    Full Text Available The focus of this review is to provide an update on the progress of microRNAs (miRNAs as potential biomarkers for lung cancer. miRNAs are single-stranded, small noncoding RNAs that regulate gene expression and show tissue-specific signatures. Accumulating evidence indicates that miRNA expression patterns represent the in vivo status in physiology and disease. Moreover, miRNAs are stable in serum and other clinically convenient and available tissue sources, so they are being developed as biomarkers for cancer and other diseases. Cancer is currently the primary driver of the field, but miRNA biomarkers are being developed for many other diseases such as cardiovascular and central nervous system diseases. Here we examine the framework and scope of the miRNA landscape as it specifically relates to the translation of miRNA expression patterns/signatures into biomarkers for developing diagnostics for lung cancer. We focus on examining tumor cytosol miRNAs, fluid miRNAs, and exosome miRNAs in lung cancer, the connections among these miRNAs, and the potential of miRNA biomarkers for the development of diagnostics. In lung cancer, miRNAs have been studied in both cell populations and in the circulation. However, a major challenge is to develop biomarkers to monitor cancer development and to identify circulating miRNAs that are linked to cancer stage. Importantly, the fact that miRNAs can be successfully harvested from biological fluids allows for the development of biofluid biopsies, in which miRNAs as circulating biomarkers can be captured and analyzed ex vivo. Our hope is that these minimally invasive entities provide a window to the in vivo milieu of the patients without the need for costly, complex invasive procedures, rapidly moving miRNAs from research to the clinic.

  4. Retrotransposons and non-protein coding RNAs

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2009-01-01

    does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review......Retrotransposons constitute a significant fraction of mammalian genomes. Considering the finding of widespread transcriptional activity across entire genomes, it is not surprising that retrotransposons contribute to the collective RNA pool. However, the transcriptional output from retrotransposons...... the emerging understanding of how retrotransposons themselves are regulated by small RNAs....

  5. MicroRNAs in tumor stem cells

    Institute of Scientific and Technical Information of China (English)

    Xiaochen Hu; Junqiang Yang; Ruijie Yang; Ruina Yang; Xinshuai Wang; Shegan Gao

    2015-01-01

    MicroRNAs (miRNAs) are a class of non-coding RNAs that are believed to have a significant role in tumori-genesis and cancer metastasis. Cancer stem cel s play a major role in tumor recurrence, metastasis, and drug resistance. Research has shown that miRNAs can promote or inhibit the stemness of cancer stem cel s and regulate the dif erentiation and self-renewal of cancer stem cel s. In this article, the phenotype and regulatory mechanisms of miRNAs in cancer stem cel s wil be described, together with an explanation of their potential role in tumor diagnosis and treatment.

  6. LncRNAs in Stem Cells

    OpenAIRE

    Shanshan Hu; Ge Shan

    2016-01-01

    Noncoding RNAs are critical regulatory factors in essentially all forms of life. Stem cells occupy a special position in cell biology and Biomedicine, and emerging results show that multiple ncRNAs play essential roles in stem cells. We discuss some of the known ncRNAs in stem cells such as embryonic stem cells, induced pluripotent stem cells, mesenchymal stem cells, adult stem cells, and cancer stem cells with a focus on long ncRNAs. Roles and functional mechanisms of these lncRNAs are summa...

  7. microRNAs: Implications for air pollution research

    Energy Technology Data Exchange (ETDEWEB)

    Jardim, Melanie J., E-mail: melaniejardim@gmail.com [Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Chapel Hill, NC (United States)

    2011-12-01

    The purpose of this review is to provide an update of the current understanding on the role of microRNAs in mediating genetic responses to air pollutants and to contemplate on how these responses ultimately control susceptibility to ambient air pollution. Morbidity and mortality attributable to air pollution continues to be a growing public health concern worldwide. Despite several studies on the health effects of ambient air pollution, underlying molecular mechanisms of susceptibility and disease remain elusive. In the last several years, special attention has been given to the role of epigenetics in mediating, not only genetic and physiological responses to certain environmental insults, but also in regulating underlying susceptibility to environmental stressors. Epigenetic mechanisms control the expression of gene products, both basally and as a response to a perturbation, without affecting the sequence of DNA itself. These mechanisms include structural regulation of the chromatin structure, such as DNA methylation and histone modifications, and post-transcriptional gene regulation, such as microRNA mediated repression of gene expression. microRNAs are small noncoding RNAs that have been quickly established as key regulators of gene expression. As such, miRNAs have been found to control several cellular processes including apoptosis, proliferation and differentiation. More recently, research has emerged suggesting that changes in the expression of some miRNAs may be critical for mediating biological, and ultimately physiological, responses to air pollutants. Although the study of microRNAs, and epigenetics as a whole, has come quite far in the field of cancer, the understanding of how these mechanisms regulate gene-environment interactions to environmental exposures in everyday life is unclear. This article does not necessarily reflect the views and policies of the US EPA.

  8. Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene

    Directory of Open Access Journals (Sweden)

    Rathjen Tina

    2011-01-01

    Full Text Available Abstract Background Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~ 2.5 Mb did not reveal any other miRNAs and no novel miRNAs were predicted. Conclusions Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in

  9. Translation Inhibition of Capped and Uncapped Viral RNAs Mediated by Ribosome-Inactivating Proteins.

    Science.gov (United States)

    Vivanco, Jorge M; Tumer, Nilgun E

    2003-05-01

    ABSTRACT Ribosome-inactivating proteins (RIPs) are N-glycosidases that remove specific purine residues from the sarcin/ricin (S/R) loop of the large rRNA and arrest protein synthesis at the translocation step. In addition to their enzymatic activity, RIPs have been reputed to be potent antiviral agents against many plant, animal, and human viruses. We recently showed that pokeweed antiviral protein (PAP), an RIP from pokeweed, inhibits translation in cell extracts by binding to the cap structure of eukaryotic mRNA and viral RNAs and depurinating these RNAs at multiple sites downstream of the cap structure. In this study, we examined the activity of three different RIPs against capped and uncapped viral RNAs. PAP, Mirabilis expansa RIP (ME1), and the Saponaria officinalis RIP (saporin) depurinated the capped Tobacco mosaic virus and Brome mosaic virus RNAs, but did not depurinate the uncapped luciferase RNA, indicating that other type I RIPs besides PAP can distinguish between capped and uncapped RNAs. We did not detect depurination of Alfalfa mosaic virus (AMV) RNAs at multiple sites by PAP or ME1. Because AMV RNAs are capped, these results indicate that recognition of the cap structure alone is not sufficient for depurination of the RNA at multiple sites throughout its sequence. Furthermore, PAP did not cause detectable depurination of uncapped RNAs from Tomato bushy stunt virus (TBSV), Satellite panicum mosaic virus (SPMV), and uncapped RNA containing poliovirus internal ribosome entry site (IRES). However, in vitro translation experiments showed that PAP inhibited translation of AMV, TBSV, SPMV RNAs, and poliovirus IRES dependent translation. These results demonstrate that PAP does not depurinate every capped RNA and that PAP can inhibit translation of uncapped viral RNAs in vitro without causing detectable depurination at multiple sites. Thus, the cap structure is not the only determinant for inhibition of translation by PAP. PMID:18942981

  10. Hidden layers of human small RNAs

    Directory of Open Access Journals (Sweden)

    Daub Carsten O

    2008-04-01

    Full Text Available Abstract Background Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs. Results Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19–40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs. Conclusion Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.

  11. Identification and conformational analysis of putative microRNAs in Maruca vitrata (Lepidoptera: Pyralidae

    Directory of Open Access Journals (Sweden)

    C. Shruthi Sureshan

    2015-12-01

    Full Text Available MicroRNAs (miRNAs are a class of small RNAs, evolutionarily conserved endogenous non-coding RNAs that regulate their target mRNA expression by either inactivating or degrading mRNA genes; thus playing an important role in the growth and development of an organism. Maruca vitrata is an insect pest of leguminous plants like pigeon pea, cowpea and mung bean and is pantropical. In this study, we perform BLAST on all known miRNAs against the transcriptome data of M. vitrata and thirteen miRNAs were identified. These miRNAs were characterised and their target genes were identified using TargetScan and were functionally annotated using FlyBase. The importance of the structure of pre-miRNA in the Drosha activity led to study the backbone torsion angles of predicted pre-miRNAs (mvi-miR-9751, mvi-miR-649-3p, mvi-miR-4057 and mvi-miR-1271 to identify various nucleotide triplets that contribute to the variation of torsion angle values at various structural motifs of a pre-miRNA.

  12. Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng

    Institute of Scientific and Technical Information of China (English)

    Meizhen Wang; Bin Wu; Chao Chen; Shanfa Lu

    2015-01-01

    Increasing evidence suggests that long non‐coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economical y significant medicinal plant species. A total of 3,688 mRNA‐like non‐coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40%of the identified mlncRNAs were processed into smal RNAs, implying their regulatory roles via smal RNA‐mediated mechanisms. Eleven miRNA‐generating mlncRNAs also pro-duced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA‐derived smal RNAs might be 21‐, 22‐, or 24‐nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A ful‐length mlncRNA, termed MAR (multiple‐function‐associated mlncRNA), was cloned. It gener-ated the most abundant siRNAs. The MAR siRNAs were predominantly 24‐nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in al tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.

  13. Identification and characterization of microRNAs in the zoonotic fluke Fasciolopsis buski.

    Science.gov (United States)

    Chen, Mu-Xin; Hu, Wei; Li, Juan; He, Jun-Jun; Ai, Lin; Chen, Jia-Xu

    2016-06-01

    Fasciolopsis buski is a food-borne zoonotic parasite which is transmitted by aquatic plants, with pigs and humans as the definitive hosts. The objective of the present study was to characterize the microRNA (miRNA) profiles of this parasite by Solexa deep sequencing and bioinformatic analysis. Approximately 12 million high-quality reads were obtained from adult F. buski. A total of 286 miRNA candidates were found and 24 miRNA candidates were conserved miRNAs in the miRBase database. Three novel miRNAs were identified and confirmed by stem-loop reverse transcriptase polymerase chain reaction (RT-PCR). The miRNAs found in the present study belong to 13 families whose members showed high bias. The guanine (G) was the dominant nucleotide at the beginning and middle of the conserved miRNAs, particularly at the positions of 2nd, 6th, and 13th. To our knowledge, this is the first report of the miRNA profiles of F. buski, which would lay a foundation for further functional studies of miRNAs of F. buski. PMID:27021181

  14. Local Structural Alignment of RNA with Affine Gap Model

    Science.gov (United States)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  15. MicroRNAs in Salivary Exosome as Potential Biomarkers of Aging

    Directory of Open Access Journals (Sweden)

    Tatsuya Machida

    2015-09-01

    Full Text Available The aim of this study was to examine whether salivary exosomal miRNAs could be identified as aging biomarkers. Fifteen young healthy volunteers (median age, 21.0 years and 13 old individuals (median age, 66.0 years were recruited. Unstimulated whole saliva was collected, salivary exosomes were isolated, and total RNA was extracted. In a microarray, 242 miRNAs were commonly detected in these two mixed samples. Based on the cut-off values of 2- or 0.5-fold changes (FC and regulatory power for aging process, six candidate miRNAs (miR-24-3p, miR-371a-5p, miR-3175, miR-3162-5p, miR-671-5p, and miR-4667-5p were selected. After comparing each total RNA obtained by the 15 young and 13 old individuals to validate the FC values using quantitative real-time PCR, miR-24-3p was identified as a novel candidate aging biomarker. This pilot study suggested that salivary exosomal miRNAs could be identified as candidate aging biomarkers. To confirm whether miR-24-3p in salivary exosomes are suitable biomarkers of aging, further validation research is required.

  16. MicroRNAs in nasopharyngeal carcinoma.

    Science.gov (United States)

    Spence, Tara; Bruce, Jeff; Yip, Kenneth W; Liu, Fei-Fei

    2016-04-01

    It is becoming increasingly evident that aberrantly expressed microRNAs (miRNAs) are responsible for a number of disease processes, including cancer initiation and progression. miRNAs have been implicated as key players in numerous neoplasms, including nasopharyngeal carcinoma (NPC). Functionally, deregulation of miRNAs that act either as tumour suppressors or oncogenes results in numerous cancer-associated phenomena, including changes in proliferation, migration, and cell survival. Furthermore, miRNA expression has been associated with chemoresistant or radioresistant phenotypes; highlighting the importance of miRNAs in mediating oncogenic processes. Prognostic and predictive miRNA signatures have been defined for a variety of cancer types, including NPC, whereby these signatures offer a potentially important clinical tool for assessing the disease state, as well as predicting treatment response and clinical outcome. Therefore, further examination and validation of miRNAs that are deregulated in NPC will provide insight into the fundamental drivers of this disease, which will aid in the identification of novel targeted treatments. This review summarizes recent advances in the study of miRNAs in NPC, with specific discussion on the role of miRNAs in NPC pathogenesis and the potential utility of miRNAs as prognostic biomarkers. Our increasing understanding of the role of miRNAs in NPC tumorigenesis and their application as novel biomarkers will undoubtedly prove useful in the stratification of future patients into clinically relevant treatment classifications, thereby improving and personalizing disease management. PMID:27121877

  17. Identification of novel miRNAs and miRNA dependent developmental shifts of gene expression in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Shuhua Zhan

    Full Text Available microRNAs (miRNAs are small, endogenous RNAs of 20 approximately 25 nucleotides, processed from stem-loop regions of longer RNA precursors. Plant miRNAs act as negative regulators of target mRNAs predominately by slicing target transcripts, and a number of miRNAs play important roles in development. We analyzed a number of published datasets from Arabidopsis thaliana to characterize novel miRNAs, novel miRNA targets, and miRNA-regulated developmental changes in gene expression. These data include microarray profiling data and small RNA (sRNA deep sequencing data derived from miRNA biogenesis/transport mutants, microarray profiling data of mRNAs in a developmental series, and computational predictions of conserved genomic stem-loop structures. Our conservative analyses identified five novel mature miRNAs and seven miRNA targets, including one novel target gene. Two complementary miRNAs that target distinct mRNAs were encoded by one gene. We found that genes targeted by known miRNAs, and genes up-regulated or down-regulated in miRNA mutant inflorescences, are highly expressed in the wild type inflorescence. In addition, transcripts upregulated within the mutant inflorescences were abundant in wild type leaves and shoot meristems and low in pollen and seed. Downregulated transcripts were abundant in wild type pollen and seed and low in shoot meristems, roots and leaves. Thus, disrupting miRNA function causes the inflorescence transcriptome to resemble the leaf and meristem and to differ from pollen and seed. Applications of our computational approach to other species and the use of more liberal criteria than reported here will further expand the number of identified miRNAs and miRNA targets. Our findings suggest that miRNAs have a global role in promoting vegetative to reproductive transitions in A. thaliana.

  18. Circulating MicroRNAs as Promising Biomarkers in Forensic Body Fluids Identification.

    Science.gov (United States)

    Dumache, Raluca; Ciocan, Veronica; Muresan, Camelia; Rogobete, Alexandru Florin; Enache, Alexandra

    2015-01-01

    In the last 20 years, DNA molecular analysis has become an important tool in forensic investigations. Currently, it is possible to genotype all types of biological traces or micro-traces containing nucleated cells if they are not entirely destroyed, chemically or bacterial. The DNA profiling is based on the short tandem repeats (STR) and aids in human identification from biological samples, but due to the recent advances in molecular genetics, other biomarkers have been proposed to be used in forensic identifications, such as: messenger RNA(mRNA), microRNA (miRNA), and DNA methylation. MicroRNAs are part of a class of small, non-coding RNAs that contain 19 - 23 nucleotides. MicroRNAs play an important role in the regulation of biochemical mechanisms, cell proliferation and other cellular mechanisms in the human body. The level of microRNAs in blood and other body fluids (urine, saliva, sweat) increases as a consequence of altered pathophysiological mechanisms and tissue insult. Moreover, the stability and specificity of microRNAs make them ideal candidates for circulating biomarkers in forensic bioanalytical procedures. In this review, we want to present a brief overview of biogenesis, functions, and applications of miRNAs in the identification of forensic body fluids. PMID:26554231

  19. Differential expression of long non-coding RNAs in hyperoxia-induced bronchopulmonary dysplasia.

    Science.gov (United States)

    Bao, Tian-Ping; Wu, Rong; Cheng, Huai-Ping; Cui, Xian-Wei; Tian, Zhao-Fang

    2016-07-01

    Bronchopulmonary dysplasia (BPD) is a common complication of premature birth that seriously affects the survival rate and quality of life among preterm neonates. Long non-coding RNAs (lncRNAs) have been implicated in many human diseases. However, the role of lncRNAs in the pathogenesis of BPD remains poorly understood. Here, we exposed neonatal C57BL/6J mice to 95% concentrations of ambient oxygen and established a mouse lung injury model that mimicked human BPD. Next, we compared lncRNA and messenger RNA (mRNA) expression profiles between BPD and normal lung tissues using a high-throughput mouse lncRNA + mRNA array system. Compared with the control group, 882 lncRNAs were upregulated, and 887 lncRNAs were downregulated in BPD lung tissues. We validated some candidate BPD-associated lncRNAs by real-time quantitative reverse-transcription polymerase chain reaction analysis in eight pairs of BPD and normal lung tissues. Gene ontology, pathway and bioinformatics analyses revealed that a downregulated lncRNA, namely AK033210, associated with tenascin C may be involved in the pathogenesis of BPD. To the best of our knowledge, our study is the first to reveal differential lncRNA expression in BPD, which provides a foundation for further understanding of the molecular mechanism of BPD development. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27137150

  20. Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control

    Science.gov (United States)

    Kagami, Haruna; Akutsu, Tatsuya; Maegawa, Shingo; Hosokawa, Hiroshi; Nacher, Jose C.

    2015-10-01

    Deciphering the association between life molecules and human diseases is currently an important task in systems biology. Research over the past decade has unveiled that the human genome is almost entirely transcribed, producing a vast number of non-protein-coding RNAs (ncRNAs) with potential regulatory functions. More recent findings suggest that many diseases may not be exclusively linked to mutations in protein-coding genes. The combination of these arguments poses the question of whether ncRNAs that play a critical role in network control are also enriched with disease-associated ncRNAs. To address this question, we mapped the available annotated information of more than 350 human disorders to the largest collection of human ncRNA-protein interactions, which define a bipartite network of almost 93,000 interactions. Using a novel algorithmic-based controllability framework applied to the constructed bipartite network, we found that ncRNAs engaged in critical network control are also statistically linked to human disorders (P-value of P = 9.8 × 10-109). Taken together, these findings suggest that the addition of those genes that encode optimized subsets of ncRNAs engaged in critical control within the pool of candidate genes could aid disease gene prioritization studies.

  1. CncRNAs: RNAs with both coding and non-coding roles in development.

    Science.gov (United States)

    Sampath, Karuna; Ephrussi, Anne

    2016-04-15

    RNAs are known to regulate diverse biological processes, either as protein-encoding molecules or as non-coding RNAs. However, a third class that comprises RNAs endowed with both protein coding and non-coding functions has recently emerged. Such bi-functional 'coding and non-coding RNAs' (cncRNAs) have been shown to play important roles in distinct developmental processes in plants and animals. Here, we discuss key examples of cncRNAs and review their roles, regulation and mechanisms of action during development. PMID:27095489

  2. MicroRNAs: Potential Biomarkers and Therapeutic Targets for Alveolar Bone Loss in Periodontal Disease

    Science.gov (United States)

    Kagiya, Tadayoshi

    2016-01-01

    Periodontal disease is an inflammatory disease caused by bacterial infection of tooth-supporting structures, which results in the destruction of alveolar bone. Osteoclasts play a central role in bone destruction. Osteoclasts are tartrate-resistant acid phosphatase (TRAP)-positive multinucleated giant cells derived from hematopoietic stem cells. Recently, we and other researchers revealed that microRNAs are involved in osteoclast differentiation. MicroRNAs are novel, single-stranded, non-coding, small (20–22 nucleotides) RNAs that act in a sequence-specific manner to regulate gene expression at the post-transcriptional level through cleavage or translational repression of their target mRNAs. They regulate various biological activities such as cellular differentiation, apoptosis, cancer development, and inflammatory responses. In this review, the roles of microRNAs in osteoclast differentiation and function during alveolar bone destruction in periodontal disease are described. PMID:27529224

  3. MicroRNAs: Potential Biomarkers and Therapeutic Targets for Alveolar Bone Loss in Periodontal Disease

    Directory of Open Access Journals (Sweden)

    Tadayoshi Kagiya

    2016-08-01

    Full Text Available Periodontal disease is an inflammatory disease caused by bacterial infection of tooth-supporting structures, which results in the destruction of alveolar bone. Osteoclasts play a central role in bone destruction. Osteoclasts are tartrate-resistant acid phosphatase (TRAP-positive multinucleated giant cells derived from hematopoietic stem cells. Recently, we and other researchers revealed that microRNAs are involved in osteoclast differentiation. MicroRNAs are novel, single-stranded, non-coding, small (20–22 nucleotides RNAs that act in a sequence-specific manner to regulate gene expression at the post-transcriptional level through cleavage or translational repression of their target mRNAs. They regulate various biological activities such as cellular differentiation, apoptosis, cancer development, and inflammatory responses. In this review, the roles of microRNAs in osteoclast differentiation and function during alveolar bone destruction in periodontal disease are described.

  4. Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE.

    Science.gov (United States)

    Han, Jian; Li, Aying; Liu, Hong; Wen, Xicheng; Zhao, Mizhen; Korir, Nadira Bilkish; Korir, Nicholas Kibet; Wang, Chen; Fang, Jinggui

    2014-02-15

    In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development. PMID:24333854

  5. Functional screens for cancer-modulating microRNAs

    OpenAIRE

    Poell, J.B.

    2012-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that control various cellular processes by inhibiting messenger RNAs (mRNAs) with partially complementary target sites. Many molecular pathways that are commonly perturbed in cancer, are subject to miRNA regulation. Introducing or reconstituting specific miRNAs in cancer cells may disrupt cancer progression, and ameliorate disease outcome. To identify cancer-modulating miRNAs, I created a lentiviral expression library containing the majority of all...

  6. Identification of microRNAs and their corresponding targets involved in the susceptibility interaction of wheat response to Puccinia striiformis f. sp. tritici.

    Science.gov (United States)

    Feng, Hao; Wang, Ting; Feng, Chuanxin; Zhang, Qiong; Zhang, Xinmei; Huang, Lili; Wang, Xiaojie; Kang, Zhensheng

    2016-05-01

    MicroRNAs (miRNAs) play very important roles in plant defense responses. However, little is known about their roles in the susceptibility interaction between wheat and Puccinia striiformis f. sp. tritici (Pst). In this study, two miRNA libraries were constructed from the leaves of the cultivar Xingzi 9104 inoculated with the virulent Pst race CYR32 and sterile water, respectively. A total of 1316 miRNA candidates, including 173 known miRNAs that were generated from 98 pre-miRNAs, were obtained. The remaining 1143 miRNA candidates included 145 conserved and 998 wheat-specific miRNAs that were generated from 87 and 1088 pre-miRNAs, respectively. The 173 known and 145 conserved miRNAs were sub-classified into 63 miRNA families. The target genes of wheat miRNAs were also confirmed using degradome sequencing technology. Most of the annotated target genes were related to signal transduction or energy metabolism. Additionally, we found that miRNAs and their target genes form complicated regulation networks. The expression profiles of miRNAs and their corresponding target genes were further analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and the results indicate that some miRNAs are involved in the compatible wheat-Pst susceptibility interaction. Importantly, tae-miR1432 was highly expressed when wheat was challenged with CYR32, and the corresponding target gene, predicted to be a calcium ion-binding protein, also exhibited upregulated expression but a divergent expression trend. PC-3P-7484, a specific wheat miRNA, was highly expressed in the wheat response to Pst infection, while the expression of the corresponding target gene ubiquillin was dramatically downregulated. These data provide the foundation for evaluating the important regulatory roles of miRNAs in wheat-Pst susceptibility interaction. PMID:26563616

  7. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line.

    Science.gov (United States)

    Lau, Nelson C; Robine, Nicolas; Martin, Raquel; Chung, Wei-Jen; Niki, Yuzo; Berezikov, Eugene; Lai, Eric C

    2009-10-01

    Piwi proteins, a subclass of Argonaute-family proteins, carry approximately 24-30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piRNAs in abundance. In contrast to intact gonads, which contain mixtures of germline and somatic cell types that express different Piwi-class proteins, OSS cells are a homogenous somatic cell population that expresses only PIWI and primary piRNAs. Detailed examination of its TE-derived piRNAs and endo-siRNAs revealed aspects of TE defense that do not rely upon ping-pong amplification. In particular, we provide evidence that a subset of piRNA master clusters, including flamenco, are specifically expressed in OSS and ovarian follicle cells. These data indicate that the restriction of certain TEs in somatic gonadal cells is largely mediated by a primary piRNA pathway. PMID:19541914

  8. The Biogenesis of Nascent Circular RNAs

    Directory of Open Access Journals (Sweden)

    Yang Zhang

    2016-04-01

    Full Text Available Steady-state circular RNAs (circRNAs have been mapped to thousands of genomic loci in mammals. We studied circRNA processing using metabolic tagging of nascent RNAs with 4-thiouridine (4sU. Strikingly, the efficiency of circRNA processing from pre-mRNA is extremely low endogenously. Additional studies revealed that back-splicing outcomes correlate with fast RNA Polymerase II elongation rate and are tightly controlled by cis-elements in vivo. Additionally, prolonged 4sU labeling in cells shows that circRNAs are largely processed post-transcriptionally and that circRNAs are stable. Circular RNAs that are abundant at a steady-state level tend to accumulate. This is particularly true in cells, such as neurons, that have slow division rates. This study uncovers features of circRNA biogenesis by investigating the link between nascent circRNA processing and transcription.

  9. Expression Profile of microRNAs and Their Targeted Pathways in Human Ovaries Detected by Next-Generation Small RNA Sequencing.

    Science.gov (United States)

    Xu, Bo; Zhang, Yuan-Wei; Zheng, Sheng-Xia; Tong, Xian-Hong; Liu, Yu-Sheng

    2016-05-01

    Recently, post-transcriptional gene regulation by microRNAs (miRNAs) has been reported to play a key role during ovary development and differentiation. However, there are no published studies identifying miRNA profiles of human ovarian tissues directly using next-generation sequencing technology. In the human ovary, a total of 762 known and 21 novel human miRNAs were detected, indicating that human ovaries have a complex population of small RNAs. To confirm the miRNA profile in human ovaries, quantitative real-time polymerase chain reaction was used to validate the expression of known miRNAs and novel miRNAs. The potential regulating roles of miRNA in physiological function of ovaries were analyzed by gene ontology and Kyoto encyclopedia of genes and genomes pathway annotation, and several important processes were identified to be targeted by the most abundantly expressed miRNAs, for example, antral ovarian follicle growth, ovarian follicle rupture, and fertilization. Our current findings extend the knowledge of the regulatory role of miRNAs and their targeted processes in human ovaries, suggesting that miRNAs play important roles in development and physiological function of ovaries. In this study, we provide a useful resource for further research of the regulatory role of miRNAs in the ovaries, which may also provide novel candidates for molecular biomarkers or treatment targets in the research of female infertility. PMID:26828676

  10. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

    Directory of Open Access Journals (Sweden)

    Blencowe Benjamin J

    2005-08-01

    Full Text Available Abstract Background Systematic identification and functional characterization of novel types of noncoding (ncRNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs typically do not possess sequence features such as splicing or translation signals, or long open reading frames. Recent "tiling" microarray studies have reported that a surprisingly larger proportion of mammalian genomes is transcribed than was previously anticipated. However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known. Results To systematically search for functional ncRNAs, we designed microarrays to detect 3,478 intergenic and intronic sequences that are conserved between the human, mouse, and rat genomes, and that score highly by other criteria that characterize ncRNAs. We probed these arrays with total RNA isolated from 16 wild-type mouse tissues. Among 55 candidates for highly-expressed novel ncRNAs tested by northern blotting, eight were confirmed as small, highly-and ubiquitously-expressed RNAs in mouse. Of the eight, five were also detected in rat tissues, but none were detected at appreciable levels in human tissues or cultured cells. Conclusion Since the sequence and expression of most known coding transcripts and functional ncRNAs is conserved between human and mouse, the lack of northern-detectable expression in human cells and tissues of the novel mouse and rat ncRNAs that we identified suggests that they are not functional or possibly have rodent-specific functions. Our results confirm that relatively little of the intergenic sequence conserved between human, mouse and rat is transcribed at high levels in mammalian tissues, possibly suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements.

  11. Antiviral activity of salivary microRNAs for ophthalmic herpes zoster

    Directory of Open Access Journals (Sweden)

    Irmak M

    2012-06-01

    Full Text Available Abstract Ophthalmic herpes zoster is a common ocular infection caused by the varicella-zoster virus (VZV. Viral mRNA transcripts play a major role in the replicative cycle of the virus and current antiviral agents have little effect in preventing and treating the complications. Therapeutic use of saliva for certain painful ocular diseases such as ophthalmic herpes zoster is a well-known public practice in our region. We thought that antiviral activity of saliva may stem from salivary microvesicles and we aimed to look for molecules with antiviral activity in these vesicles. As a possible candidate for antiviral activity, salivary microvesicles contain at least 20 microRNAs (miRNAs, small noncoding RNAs, which suppress the translation of target mRNAs. miRNAs not only participate in maintenance of normal cell functions, but are also involved in host–virus interactions and limit the replication of certain virus types. Thus, miRNA gene therapy by targeting mRNAs required for VZV survival may find a niche in the treatment of ophthalmic herpes zoster. But, how could salivary microvesicles reach into the corneal cells to demonstrate their antiviral activity. We suggest that human salivary microvesicles can be effective carriers of miRNA for corneal cells, because they contain a molecular machinery for vesicle trafficking and fusion allowing them to be endocytosed by target cells. After binding to the plasma membrane, microvesicles seem to enter into the corneal cells through the clathrin-mediated endocytosis. In the cytosol, human salivary miRNAs base-pair with specific viral mRNAs and inhibit their translation, thus limiting the replication of the virus.

  12. Tissular and soluble miRNAs for diagnostic and therapy improvement in digestive tract cancers.

    Science.gov (United States)

    Albulescu, Radu; Neagu, Monica; Albulescu, Lucian; Tanase, Cristiana

    2011-01-01

    Digestive cancers (e.g., gastric, colorectal, pancreatic or hepatocarcinoma) are among the most frequently reported cancers in the world, and are characterized by invasivity, metastatic potential and poor outcomes. This group includes some of the most critical cancers (among them, are those ranked second to forth in cancer-related mortality) and, despite all sustained efforts, they maintain a profile of low survival rates and lack successful therapies. Discovery of biomarkers that improve disease characterization may make optimized or personalized therapy possible. Novel biomarkers are expected to provide, hopefully, less-invasive or noninvasive diagnostic tools that make possible earlier detection of disease. Also, they may provide a more reliable selection instrument in the drug discovery process. miRNAs, short noncoding RNAs, have emerged in the last few years as significant regulators of cellular activities, controlling protein expression at the post-transcriptional level, with a significant implication in pathology in general and, of most relevance, in cancers. Deregulation of miRNA expression levels and some genetic alterations were demonstrated in various cancers, including digestive cancers. Investigations in tissue samples have provided a considerable amount of knowledge, identifying altered expressions of miRNAs associated with tumorigenesis and tumor progression. Overexpression of some tumor-inducing or tumor-promoting miRNAs was demonstrated, as well as the downregulation of tumor-suppressor miRNAs. Both individual miRNAs, as well as sets of multiple miRNAs, were set up as candidate biomarkers for diagnostics or monitoring, offering relevant insights into tumorigenic mechanisms. Circulating miRNAs were demonstrated as valuable instruments in tumor diagnosis and the prognosis of digestive cancers (affecting the esophagus, stomach, intestine, colorectum, liver and pancreas), and are being investigated thoroughly in order to generate and validate less

  13. MicroRNAs - Biology and clinical applications

    OpenAIRE

    Kannan Ranganathan; Vaishnavi Sivasankar

    2014-01-01

    MicroRNAs are a highly conserved group of small, non-coding RNA molecules, which are 19-25 nucleotides in size. Previously thought to be evolutionary debris with no evident function, these small RNAs have been found to control gene expression primarily by silencing the gene. MicroRNAs are critical to cell physiology and development. They are also implicated in pathological processes such as autoimmune diseases, viral infections and carcinogenesis.

  14. MicroRNAs in Common Human Diseases

    OpenAIRE

    Li, Yu; Kowdley, Kris V.

    2012-01-01

    MicroRNAs (miRNAs) are a class of short non-coding RNA molecules that have attracted tremendous attention from the biological and biomedical research communities over the past decade. With over 1900 miRNAs discovered in humans to date, many of them have already been implicated in common human disorders. Facilitated by high-throughput genomics and bioinformatics in conjunction with traditional molecular biology techniques and animal models, miRNA research is now positioned to make the transiti...

  15. MicroRNAs in Pulmonary Arterial Hypertension

    OpenAIRE

    Zhou, Guofei; Chen, Tianji; Raj, J. Usha

    2015-01-01

    Pulmonary arterial hypertension (PAH) is a devastating disease without effective treatment. Despite decades of research and the development of novel treatments, PAH remains a fatal disease, suggesting an urgent need for better understanding of the pathogenesis of PAH. Recent studies suggest that microRNAs (miRNAs) are dysregulated in patients with PAH and in experimental pulmonary hypertension. Furthermore, normalization of a few miRNAs is reported to inhibit experimental pulmonary hypertensi...

  16. Gene expression regulators--MicroRNAs

    Institute of Scientific and Technical Information of China (English)

    CHEN Fang; YIN Q. James

    2005-01-01

    A large class of non-coding RNAs found in small molecule RNAs are closely associated with the regulation of gene expression, which are called microRNA (miRNA). MiRNAs are coded in intergenic or intronic regions and can be formed into foldback hairpin RNAs. These transcripts are cleaved by Dicer, generating mature miRNAs that can silence their target genes in different modes of action. Now, research on small molecule RNAs has gotten breakthrough advance in biology. To discover miRNA genes and their target genes has become hot topics in RNA research. This review attempts to look back the history of miRNA discovery, to introduce the methods of screening miRNAs, to localize miRNA loci in genome, to seek miRNA target genes and the biological function, and to discuss the working mechanisms of miRNAs. Finally, we will discuss the potential important roles of miRNAs in modulating the genesis, development, growth, and differentiation of organisms. Thus, it can be predicted that a complete understanding of miRNA functions will bring us some new concepts, approaches and strategies for the study of living beings.

  17. New microRNAs from mouse and human

    OpenAIRE

    Lagos-Quintana, M.; Rauhut, R; Meyer, J.; Borkhardt, A.; Tuschl, T.

    2003-01-01

    MicroRNAs (miRNAs) represent a new class of noncoding RNAs encoded in the genomes of plants, invertebrates, and vertebrates. MicroRNAs regulate translation and stability of target mRNAs based on (partial) sequence complementarity. Although the number of newly identified miRNAs is still increasing, target mRNAs of animal miRNAs remain to be identified. Here we describe 31 novel miRNAs that were identified by cloning from mouse tissues and the human Saos-2 cell line. Fifty-three percent of all ...

  18. Small RNAs meet their targets: When methylation defends miRNAs from uridylation

    OpenAIRE

    Ren, Guodong; Chen, Xuemei; Yu, Bin

    2014-01-01

    Small RNAs are incorporated into Argonaute protein-containing complexes to guide the silencing of target RNAs in both animals and plants. The abundance of endogenous small RNAs is precisely controlled at multiple levels including transcription, processing and Argonaute loading. In addition to these processes, 3′ end modification of small RNAs, the topic of a research area that has rapidly evolved over the last several years, adds another layer of regulation of their abundance, diversity and f...

  19. Nucleocytoplasmic Transport of RNAs and RNA-Protein Complexes.

    Science.gov (United States)

    Sloan, Katherine E; Gleizes, Pierre-Emmanuel; Bohnsack, Markus T

    2016-05-22

    RNAs and ribonucleoprotein complexes (RNPs) play key roles in mediating and regulating gene expression. In eukaryotes, most RNAs are transcribed, processed and assembled with proteins in the nucleus and then either function in the cytoplasm or also undergo a cytoplasmic phase in their biogenesis. This compartmentalization ensures that sequential steps in gene expression and RNP production are performed in the correct order and it allows important quality control mechanisms that prevent the involvement of aberrant RNAs/RNPs in these cellular pathways. The selective exchange of RNAs/RNPs between the nucleus and cytoplasm is enabled by nuclear pore complexes, which function as gateways between these compartments. RNA/RNP transport is facilitated by a range of nuclear transport receptors and adaptors, which are specifically recruited to their cargos and mediate interactions with nucleoporins to allow directional translocation through nuclear pore complexes. While some transport factors are only responsible for the export/import of a certain class of RNA/RNP, others are multifunctional and, in the case of large RNPs, several export factors appear to work together to bring about export. Recent structural studies have revealed aspects of the mechanisms employed by transport receptors to enable specific cargo recognition, and genome-wide approaches have provided the first insights into the diverse composition of pre-mRNPs during export. Furthermore, the regulation of RNA/RNP export is emerging as an important means to modulate gene expression under stress conditions and in disease. PMID:26434509

  20. Visual screening for localized RNAs in yeast revealed novel RNAs at the bud-tip

    International Nuclear Information System (INIS)

    Several RNAs, including rRNAs, snRNAs, snoRNAs, and some mRNAs, are known to be localized at specific sites in a cell. Although methods have been established to visualize RNAs in a living cell, no large-scale visual screening of localized RNAs has been performed. In this study, we constructed a genomic library in which random genomic fragments were inserted downstream of U1A-tag sequences under a GAL1 promoter. In a living yeast cell, transcribed U1A-tagged RNAs were visualized by U1A-GFP that binds the RNA sequence of the U1A-tag. In this screening, many RNAs showed nuclear signals. Since the nuclear signals of some RNAs were not seen when the U1A-tag was connected to the 3' ends of the RNAs, it is suggested that their nuclear signals correspond to nascent transcripts on GAL1 promoter plasmids. Using this screening method, we successfully identified two novel localized mRNAs, CSR2 and DAL81, which showed bud-tip localization

  1. Defective RNAs of Citrus tristeza virus analogous to Crinivirus genomic RNAs

    International Nuclear Information System (INIS)

    The family Closteroviridae includes the genera Closterovirus and Ampelovirus with monopartite genomes and the genus Crinivirus with bipartite genomes. Plants infected with the Closterovirus, Citrus tristeza virus (CTV), often contain one or more populations of defective RNAs (dRNAs). Although most dRNAs are comparatively small (2-5 kb) consisting of the genomic RNA termini with large internal deletions, we recently characterized large dRNAs of ∼12 kb that retained the open reading frames (ORFs) 1a plus 1b. These were self-replicating RNAs and appeared to be analogous to the genomic RNA 1 of the bipartite criniviruses. The present report describes the finding of an additional group of large dRNAs (LdRNAs) that retained all or most of the 10 3' ORFs and appeared to be analogous to genomic RNA 2 of criniviruses. Isolates associated with LdRNAs were found associated with double-recombinant dRNAs (DR-dRNAs) of various sizes (1.7 to 5.1 kb) that comprised the two termini and a noncontiguous internal sequence from ORF2. The genetic and epidemiological implications of the architectural identities of LdRNAs and DR dRNAs and their apparent analogy with the genomic RNA 2 of criniviruses are discussed

  2. Targeting the production of oncogenic microRNAs with multimodal synthetic small molecules.

    Science.gov (United States)

    Vo, Duc Duy; Staedel, Cathy; Zehnacker, Laura; Benhida, Rachid; Darfeuille, Fabien; Duca, Maria

    2014-03-21

    MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers and revealed to be oncogenic and to play a pivotal role in initiation and progression of these pathologies. It is now clear that the inhibition of oncogenic miRNAs, defined as blocking their biosynthesis or their function, could find an application in the therapy of different types of cancer in which these miRNAs are implicated. Here we report the design, synthesis, and biological evaluation of new small-molecule RNA ligands targeting the production of oncogenic microRNAs. In this work we focused our attention on miR-372 and miR-373 that are implicated in the tumorigenesis of different types of cancer such as gastric cancer. These two oncogenic miRNAs are overexpressed in gastric cancer cells starting from their precursors pre-miR-372 and pre-miR-373, two stem-loop structured RNAs that lead to mature miRNAs after cleavage by the enzyme Dicer. The small molecules described herein consist of the conjugation of two RNA binding motives, i.e., the aminoglycoside neomycin and different natural and artificial nucleobases, in order to obtain RNA ligands with increased affinity and selectivity compared to that of parent compounds. After the synthesis of this new series of RNA ligands, we demonstrated that they are able to inhibit the production of the oncogenic miRNA-372 and -373 by binding their pre-miRNAs and inhibiting the processing by Dicer. Moreover, we proved that some of these compounds bear anti-proliferative activity toward gastric cancer cells and that this activity is likely linked to a decrease in the production of targeted miRNAs. To date, only few examples of small molecules targeting oncogenic miRNAs have been reported, and such inhibitors could be extremely useful for the development of new anticancer therapeutic

  3. Genome wide identification of chilling responsive microRNAs in Prunus persica

    Directory of Open Access Journals (Sweden)

    Barakat Abdelali

    2012-09-01

    species. Several conserved and non-conserved miRNAs and miRNA-regulated genes co-localize with Quantitative Trait Loci (QTLs for chilling requirement (CR-QTL and bloom date (BD-QTL. Conclusions In this work, we identified a large set of conserved and non-conserved miRNAs and describe their evolutionary footprint in angiosperm lineages. Several of these miRNAs were induced in winter buds and co-localized with QTLs for chilling requirement and bloom date thus making their gene targets potential candidates for mediating plant responses to cold stress. Several peach homologs of genes participating in the regulation of vernalization in Arabidopsis were identified as differentially expressed miRNAs targets, potentially linking these gene activities to cold responses in peach dormant buds. The non-conserved miRNAs may regulate cellular, physiological or developmental processes specific to peach and/or other tree species.

  4. Involvement of microRNAs in physiological and pathological processes in the lung

    Directory of Open Access Journals (Sweden)

    Kriegova Eva

    2010-11-01

    Full Text Available Abstract To date, at least 900 different microRNA (miRNA genes have been discovered in the human genome. These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often involved in the regulation of diverse physiological processes ranging from developmental timing to apoptosis, miRNAs have a strong potential to regulate fundamental biological processes also in the lung compartment. However, the knowledge of the role of miRNAs in physiological and pathological conditions in the lung is still limited. This review, therefore, summarizes current knowledge of the mechanism, function of miRNAs and their contribution to lung development and homeostasis. Besides the involvement of miRNAs in pulmonary physiological conditions, there is evidence that abnormal miRNA expression may lead to pathological processes and development of various pulmonary diseases. Next, the review describes current state-of-art on the miRNA expression profiles in smoking-related diseases including lung cancerogenesis, in immune system mediated pulmonary diseases and fibrotic processes in the lung. From the current research it is evident that miRNAs may play role in the posttranscriptional regulation of key genes in human pulmonary diseases. Further studies are, therefore, necessary to explore miRNA expression profiles and their association with target mRNAs in human pulmonary diseases.

  5. The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF localization

    Directory of Open Access Journals (Sweden)

    Taft Ryan J

    2011-08-01

    Full Text Available Abstract Background Transcription initiation RNAs (tiRNAs are nuclear localized 18 nucleotide RNAs derived from sequences immediately downstream of RNA polymerase II (RNAPII transcription start sites. Previous reports have shown that tiRNAs are intimately correlated with gene expression, RNA polymerase II binding and behaviors, and epigenetic marks associated with transcription initiation, but not elongation. Results In the present work, we show that tiRNAs are commonly found at genomic CCCTC-binding factor (CTCF binding sites in human and mouse, and that CTCF sites that colocalize with RNAPII are highly enriched for tiRNAs. To directly investigate the relationship between tiRNAs and CTCF we examined tiRNAs originating near the intronic CTCF binding site in the human tumor suppressor gene, p21 (cyclin-dependent kinase inhibitor 1A gene, also known as CDKN1A. Inhibition of CTCF-proximal tiRNAs resulted in increased CTCF localization and increased p21 expression, while overexpression of CTCF-proximal tiRNA mimics decreased CTCF localization and p21 expression. We also found that tiRNA-regulated CTCF binding influences the levels of trimethylated H3K27 at the alternate upstream p21 promoter, and affects the levels of alternate p21 (p21alt transcripts. Extending these studies to another randomly selected locus with conserved CTCF binding we found that depletion of tiRNA alters nucleosome density proximal to sites of tiRNA biogenesis. Conclusions Taken together, these data suggest that tiRNAs modulate local epigenetic structure, which in turn regulates CTCF localization.

  6. Noncoding RNAs as potential biomarkers to predict the outcome in pancreatic cancer

    Directory of Open Access Journals (Sweden)

    Jin K

    2015-02-01

    Full Text Available Kaizhou Jin,1–3,* Guopei Luo,1–3,* Zhiwen Xiao,1–3 Zuqiang Liu,1–3 Chen Liu,1–3 Shunrong Ji,1–3 Jin Xu,1–3 Liang Liu,1–3 Jiang Long,1–3 Quanxing Ni,1–3 Xianjun Yu1–3 1Department of Pancreatic and Hepatobiliary Surgery, Fudan University Shanghai Cancer Center, 2Department of Oncology, Shanghai Medical College, Fudan University, 3Pancreatic Cancer Institute, Fudan University, Shanghai, People’s Republic of China *These authors contributed equally to this work Abstract: Pancreatic ductal adenocarcinoma (PDAC, a common digestive system cancer, is highly malignant and has a poor disease outcome. Currently, all available examination and detection methods cannot accurately predict the clinical outcome. Therefore, it is extremely important to identify novel molecular biomarkers for personalized medication and to significantly improve the overall outcome. The “noncoding RNAs” (ncRNAs are a group of RNAs that do not code for proteins, and they are categorized as structural RNAs and regulatory RNAs. It has been shown that microRNAs and long ncRNAs function as regulatory RNAs to affect the progression of various diseases. Many studies have confirmed a role for ncRNAs in the progression of PDAC during the last few years. Because of the significant role of ncRNAs in PDAC, ncRNA profiling may be used to predict PDAC outcome with high accuracy. This review comprehensively analyzes the value of ncRNAs as potential biomarkers to predict the outcome in PDAC and the possible mechanisms thereof. Keywords: pancreatic ductal adenocarcinoma, microRNA, long noncoding RNA, outcome prediction

  7. Discovery of replicating circular RNAs by RNA-seq and computational algorithms.

    Directory of Open Access Journals (Sweden)

    Zhixiang Zhang

    2014-12-01

    Full Text Available Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR. However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd and Apple hammerhead viroid-like RNA (AHVd-like RNA, respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small

  8. Discovery of replicating circular RNAs by RNA-seq and computational algorithms.

    Science.gov (United States)

    Zhang, Zhixiang; Qi, Shuishui; Tang, Nan; Zhang, Xinxin; Chen, Shanshan; Zhu, Pengfei; Ma, Lin; Cheng, Jinping; Xu, Yun; Lu, Meiguang; Wang, Hongqing; Ding, Shou-Wei; Li, Shifang; Wu, Qingfa

    2014-12-01

    Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR). However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA), respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small RNAs. PMID:25503469

  9. Identification and characterization of microRNAs from Entamoeba histolytica HM1-IMSS.

    Directory of Open Access Journals (Sweden)

    Fermín Mar-Aguilar

    Full Text Available BACKGROUND: Entamoeba histolytica is the causative agent of amebiasis, a disease that is a major source of morbidity and mortality in the developing world. MicroRNAs (miRNAs are a large group of non-coding RNAs that play important roles in regulating gene expression and protein translation in animals. Genome-wide identification of miRNAs is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and post-transcriptional regulation. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced a small RNA library prepared from a culture of trophozoites of Entamoeba histolytica Strain HM1-IMSS using a deep DNA sequencing approach. Deep sequencing yielded 16 million high-quality short sequence reads containing a total of 5 million non-redundant sequence reads. Based on a bioinformatics pipeline, we found that only 0.5% of these non-redundant small RNA reads were a perfect match with the drafted E. histolytica genome. We did not find miRNA homologs in plant or animal miRNAs. We discovered 199 new potential Entamoeba histolytica miRNAs. The expression and sequence of these Ehi-miRNAs were further validated through microarray by µParaflo Microfluidic Biochip Technology. Ten potential miRNAs were additionally confirmed by real time RT-PCR analysis. Prediction of target genes matched 32 known genes and 34 hypothetical genes. CONCLUSIONS/SIGNIFICANCE: These results show that there is a number of regulatory miRNAs in Entamoeba histolytica. The collection of miRNAs in this parasite could be used as a new platform to study genomic structure, gene regulation and networks, development, and host-parasite interactions.

  10. Long noncoding RNAs: Lessons from genomic imprinting.

    Science.gov (United States)

    Kanduri, Chandrasekhar

    2016-01-01

    Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), antisense lncRNAs (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin-specific expression of target genes. Recent evidence suggests that some of the lncRNAs regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncRNAs play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncRNAs fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncRNAs from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncRNAs in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. PMID:26004516

  11. MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression.

    Directory of Open Access Journals (Sweden)

    Steven W Paugh

    2016-02-01

    Full Text Available MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10(-16 for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription.

  12. Identification and functional analysis of miRNAs in developing kernels of a viviparous mutant in maize

    Directory of Open Access Journals (Sweden)

    Haiping Ding

    2013-12-01

    Full Text Available Given the important roles of miRNAs in post-transcriptional gene regulation, identification of differentially expressed miRNAs will facilitate the elucidation of molecular mechanisms underlying kernel development. In this study, we constructed a small RNA library to comprehensively represent the full complement of individual small RNAs and to characterize miRNA expression profiles in pooled ears of maize (Zea mays L. at 10, 15, 20, 22, 25 and 30 days after pollination (DAP. At least 21 miRNAs were differentially expressed. The differential expression of three of these miRNAs, i.e., miR528a, miR167a and miR160b, at each stage was verified by qRT-PCR. The results indicated that these miRNAs might be involved in kernel development. In addition, the predicted functions of target genes indicated that most of the target genes are involved in signal transduction and cell communication pathways, particularly the auxin signaling pathway. The expression of candidate germination-associated miRNAs was analyzed by hybridization to a maize genome microarray, and revealed differential expression of genes involved in plant hormone signaling pathways. This finding suggests that phytohormones play a critical role in the development of maize kernels. We found that in combination with other miRNAs, miR528a regulated a putative laccase, a Ring-H2 zinc finger protein and a MADS box-like protein, whereas miR167a and miR160b regulated multiple target genes, including ARF (auxin response factor, a member of the B3 transcription factor family. All three miRNAs are important for ear germination, development and physiology. The small RNA transcriptomes and mRNA obtained in this study will help us gain a better understanding of the expression and function of small RNAs in the development of maize kernel.

  13. Identification and functional analysis of miRNAs in developing kernels of a viviparous mutant in maize

    Institute of Scientific and Technical Information of China (English)

    Haiping; Ding; Jian; Gao; Mao; Luo; Hua; Peng; Haijian; Lin; Guangsheng; Yuan; Yaou; Shen; Maojun; Zhao; Guangtang; Pan; Zhiming; Zhang

    2013-01-01

    Given the important roles of miRNAs in post-transcriptional gene regulation, identification of differentially expressed miRNAs will facilitate the elucidation of molecular mechanisms underlying kernel development. In this study, we constructed a small RNA library to comprehensively represent the full complement of individual small RNAs and to characterize miRNA expression profiles in pooled ears of maize(Zea mays L.) at 10, 15,20, 22, 25 and 30 days after pollination(DAP). At least 21 miRNAs were differentially expressed. The differential expression of three of these miRNAs, i.e., miR528a, miR167a and miR160b, at each stage was verified by qRT-PCR. The results indicated that these miRNAs might be involved in kernel development. In addition, the predicted functions of target genes indicated that most of the target genes are involved in signal transduction and cell communication pathways, particularly the auxin signaling pathway. The expression of candidate germination-associated miRNAs was analyzed by hybridization to a maize genome microarray, and revealed differential expression of genes involved in plant hormone signaling pathways. This finding suggests that phytohormones play a critical role in the development of maize kernels. We found that in combination with other miRNAs, miR528a regulated a putative laccase, a Ring-H2 zinc finger protein and a MADS box-like protein, whereas miR167a and miR160b regulated multiple target genes,including ARF(auxin response factor), a member of the B3 transcription factor family. All three miRNAs are important for ear germination, development and physiology. The small RNA transcriptomes and mRNA obtained in this study will help us gain a betterunderstanding of the expression and function of small RNAs in the development of maize kernel.

  14. Identification and analysis of pig chimeric mRNAs using RNA sequencing data

    Directory of Open Access Journals (Sweden)

    Ma Lei

    2012-08-01

    Full Text Available Abstract Background Gene fusion is ubiquitous over the course of evolution. It is expected to increase the diversity and complexity of transcriptomes and proteomes through chimeric sequence segments or altered regulation. However, chimeric mRNAs in pigs remain unclear. Here we identified some chimeric mRNAs in pigs and analyzed the expression of them across individuals and breeds using RNA-sequencing data. Results The present study identified 669 putative chimeric mRNAs in pigs, of which 251 chimeric candidates were detected in a set of RNA-sequencing data. The 618 candidates had clear trans-splicing sites, 537 of which obeyed the canonical GU-AG splice rule. Only two putative pig chimera variants whose fusion junction was overlapped with that of a known human chimeric mRNA were found. A set of unique chimeric events were considered middle variances in the expression across individuals and breeds, and revealed non-significant variance between sexes. Furthermore, the genomic region of the 5′ partner gene shares a similar DNA sequence with that of the 3′ partner gene for 458 putative chimeric mRNAs. The 81 of those shared DNA sequences significantly matched the known DNA-binding motifs in the JASPAR CORE database. Four DNA motifs shared in parental genomic regions had significant similarity with known human CTCF binding sites. Conclusions The present study provided detailed information on some pig chimeric mRNAs. We proposed a model that trans-acting factors, such as CTCF, induced the spatial organisation of parental genes to the same transcriptional factory so that parental genes were coordinatively transcribed to give birth to chimeric mRNAs.

  15. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES cells.

    Directory of Open Access Journals (Sweden)

    Peili Gu

    Full Text Available BACKGROUND: MicroRNAS (miRNAS: a class of short non-coding RNAs are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal, or differentiate into cells that execute a limited number of specific actions (pluripotence. METHODOLOGY/PRINCIPAL FINDINGS: In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer(-/- ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues during retinoic acid (RA-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF(-/- cells, which display loss of repression of pluripotence genes upon differentiation. CONCLUSION/SIGNIFICANCE: Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF(-/- mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.

  16. MicroRNAs in mantle cell lymphoma

    DEFF Research Database (Denmark)

    Husby, Simon; Geisler, Christian; Grønbæk, Kirsten

    2013-01-01

    further develop these drugs for use in patients. Thus, there is hope that specific targeting of pathogenic miRNAs may be used in cases of MCL when conventional therapies fail. Here, we review the current knowledge about the role of miRNAs in MCL, and highlight the perspectives for clinical use....

  17. Recovery of the Candidate Protoplanet HD 100546 b with Gemini/NICI and Detection of Additional (Planet-Induced?) Disk Structure at Small Separations

    CERN Document Server

    Currie, Thayne; Kudo, Tomoyuki; Honda, Mitsuhiko; Brandt, Timothy D; Grady, Carol; Fukagawa, Misato; Burrows, Adam; Janson, Markus; Kuzuhara, Masayuki; McElwain, Michael W; Follette, Katherine; Hashimoto, Jun; Henning, Thomas; Kandori, Ryo; Kusakabe, Nobuhiko; Kwon, Jungmi; Mede, Kyle; Morino, Jun-ichi; Nishikawa, Jun; Pyo, Tae-Soo; Serabyn, Gene; Suenaga, Takuya; Takahashi, Yasuhiro; Wisniewski, John; Tamura, Motohide

    2014-01-01

    We report the first independent, second-epoch (re-)detection of a directly-imaged protoplanet candidate. Using $L^\\prime$ high-contrast imaging of HD 100546 taken with the Near-Infrared Coronagraph and Imager (NICI) on Gemini South, we recover `HD 100546 b' with a position and brightness consistent with the original VLT/NaCo detection from Quanz et al, although data obtained after 2013 will be required to decisively demonstrate common proper motion. HD 100546 b may be spatially resolved, up to $\\approx$ 12-13 AU in diameter, and is embedded in a finger of thermal IR bright, polarized emission extending inwards to at least 0.3". Standard hot-start models imply a mass of $\\approx$ 15 $M_{J}$. But if HD 100546 b is newly formed or made visible by a circumplanetary disk, both of which are plausible, its mass is significantly lower (e.g. 1--7 $M_{J}$). Additionally, we discover a thermal IR-bright disk feature, possibly a spiral density wave, at roughly the same angular separation as HD 100546 b but 90 degrees awa...

  18. Reciprocal regulation of miRNAs and piRNAs in embryonic development.

    Science.gov (United States)

    Du, W W; Yang, W; Xuan, J; Gupta, S; Krylov, S N; Ma, X; Yang, Q; Yang, B B

    2016-09-01

    MicroRNAs (miRNAs) and piwi-interacting RNAs (piRNAs) are two classes of small noncoding RNAs, both of which play roles in regulating tissue development. It is unknown whether these distinct classes of noncoding RNAs can regulate one another. Here we show that ectopic expression of miR-17 inhibited mouse fertility and early embryonic development. Specifically, we found that the piRNA amplification loop was repressed by miR-17-5p, leading to increased levels of transposition mutagenesis. This occurred by suppressing the amplification loop of piRNAs with an identical 5' sequence and by targeting Mili/Miwi2, an essential component of the piRNA amplification loop, and the DNA methyltransferase, Dnmt3a. We also found that increased levels of piRNAs could compete with miRNAs for target binding, resulting in increased expression of Dnmt3a and Mili. Increased Dnmt3a levels could in turn block miR-17-5p expression, while increased Mili expression could accelerate piRNA amplification and inhibit transposon generation, favoring embryonic development. We report for the first time the reciprocal regulation between miRNAs and piRNAs in mouse embryonic development. PMID:26990662

  19. The Role of MicroRNAs as Predictors of Response to Tamoxifen Treatment in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Nina G. Egeland

    2015-10-01

    Full Text Available Endocrine therapy is a key treatment strategy to control or eradicate hormone-responsive breast cancer. However, resistance to endocrine therapy leads to breast cancer relapse. The recent extension of adjuvant tamoxifen treatment up to 10 years actualizes the need for identifying biological markers that may be used to monitor predictors of treatment response. MicroRNAs are promising biomarkers that may fill the gap between preclinical knowledge and clinical observations regarding endocrine resistance. MicroRNAs regulate gene expression by posttranscriptional repression or degradation of mRNA, most often leading to gene silencing. MicroRNAs have been identified directly in the primary tumor, but also in the circulation of breast cancer patients. The few available studies investigating microRNA in patients suggest that seven microRNAs (miR-10a, miR-26, miR-30c, miR-126a, miR-210, miR-342 and miR-519a play a role in tamoxifen resistance. Ingenuity Pathway Analysis (IPA reveals that these seven microRNAs interact more readily with estrogen receptor (ER-independent pathways than ER-related signaling pathways. Some of these pathways are targetable (e.g., PIK3CA, suggesting that microRNAs as biomarkers of endocrine resistance may have clinical value. Validation of the role of these candidate microRNAs in large prospective studies is warranted.

  20. Recovery act. Characterizing structural controls of EGS-candidate and conventional geothermal reservoirs in the Great Basin. Developing successful exploration strategies in extended terranes

    Energy Technology Data Exchange (ETDEWEB)

    Faulds, James [Univ. of Nevada, Reno, NV (United States)

    2015-06-25

    We conducted a comprehensive analysis of the structural controls of geothermal systems within the Great Basin and adjacent regions. Our main objectives were to: 1) Produce a catalogue of favorable structural environments and models for geothermal systems. 2) Improve site-specific targeting of geothermal resources through detailed studies of representative sites, which included innovative techniques of slip tendency analysis of faults and 3D modeling. 3) Compare and contrast the structural controls and models in different tectonic settings. 4) Synthesize data and develop methodologies for enhancement of exploration strategies for conventional and EGS systems, reduction in the risk of drilling non-productive wells, and selecting the best EGS sites.

  1. A glance at subgenomic flavivirus RNAs and microRNAs in flavivirus infections.

    Science.gov (United States)

    Bavia, Lorena; Mosimann, Ana Luiza Pamplona; Aoki, Mateus Nóbrega; Duarte Dos Santos, Claudia Nunes

    2016-01-01

    The family Flaviviridae comprises a wide variety of viruses that are distributed worldwide, some of which are associated with high rates of morbidity and mortality. There are neither vaccines nor antivirals for most flavivirus infections, reinforcing the importance of research on different aspects of the viral life cycle. During infection, cytoplasmic accumulation of RNA fragments mainly originating from the 3' UTRs, which have been designated subgenomic flavivirus RNAs (sfRNAs), has been detected. It has been shown that eukaryotic exoribonucleases are involved in viral sfRNA production. Additionally, viral and human small RNAs (sRNAs) have also been found in flavivirus-infected cells, especially microRNAs (miRNAs). miRNAs were first described in eukaryotic cells and in a mature and functional state present as single-stranded 18-24 nt RNA fragments. Their main function is the repression of translation through base pairing with cellular mRNAs, besides other functions, such as mRNA degradation. Canonical miRNA biogenesis involves Drosha and Dicer, however miRNA can also be generated by alternative pathways. In the case of flaviviruses, alternative pathways have been suggested. Both sfRNAs and miRNAs are involved in viral infection and host cell response modulation, representing interesting targets of antiviral strategies. In this review, we focus on the generation and function of viral sfRNAs, sRNAs and miRNAs in West Nile, dengue, Japanese encephalitis, Murray Valley encephalitis and yellow fever infections, as well as their roles in viral replication, translation and cell immune response evasion. We also give an overview regarding other flaviviruses and the generation of cellular miRNAs during infection. PMID:27233361

  2. Slicing tRNAs to boost functional ncRNA diversity

    OpenAIRE

    Gebetsberger, Jennifer; Polacek, Norbert

    2013-01-01

    Post-transcriptional cleavage of RNA molecules to generate smaller fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes. Substrates for such RNA fragmentations are coding as well as non-protein-coding RNAs. In particular, fragments derived from both precursor and mature tRNAs represent one of the rapidly growing classes of post-transcriptional RNA pieces. Importantly, these tRNA fragments possess distinct expression patterns, abundance,...

  3. Identification and Analysis of Differentially-Expressed microRNAs in Japanese Encephalitis Virus-Infected PK-15 Cells with Deep Sequencing

    Directory of Open Access Journals (Sweden)

    Yuhan Cai

    2015-01-01

    Full Text Available Japanese encephalitis virus (JEV, a mosquito-borne Flavivirus, causes acute viral encephalitis with high morbidity and mortality in humans and animals. MicroRNAs (miRNAs are small noncoding RNAs that are important modulators of the intricate host-pathogen interaction networks. However, our knowledge of the changes that occur in miRNAs in host cells after JEV infection is still limited. To understand the molecular pathogenesis of JEV at the level of posttranscriptional regulation, we used Illumina deep sequencing to sequence two small RNA libraries prepared from PK-15 cells before and after JEV infection. We identified 522 and 427 miRNAs in the infected and uninfected cells, respectively. Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated. The sequencing results for selected miRNAs were confirmed with RT-qPCR. GO analysis of the host target genes revealed that these dysregulated miRNAs are involved in complex cellular pathways, including the metabolic pathway, inflammatory response and immune response. To our knowledge, this is the first report of the comparative expression of miRNAs in PK-15 cells after JEV infection. Our findings will underpin further studies of miRNAs’ roles in JEV replication and identify potential candidates for antiviral therapies against JEV.

  4. Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer

    OpenAIRE

    Lin, H-M.; Castillo, L.; Mahon, K L; Chiam, K; Lee, B Y; Nguyen, Q.; Boyer, M. J.; Stockler, M R; Pavlakis, N; Marx, G.; Mallesara, G; Gurney, H; Clark, S J; Swarbrick, A; Daly, R. J.

    2014-01-01

    Background: Docetaxel is the first-line chemotherapy for castration-resistant prostate cancer (CRPC). However, response rates are ∼50% and determined quite late in the treatment schedule, thus non-responders are subjected to unnecessary toxicity. The potential of circulating microRNAs as early biomarkers of docetaxel response in CRPC patients was investigated in this study. Methods: Global microRNA profiling was performed on docetaxel-resistant and sensitive cell lines to identify candidate c...

  5. Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs.

    Science.gov (United States)

    Valli, Adrian A; Santos, Bruno A C M; Hnatova, Silvia; Bassett, Andrew R; Molnar, Attila; Chung, Betty Y; Baulcombe, David C

    2016-04-01

    We describe here a forward genetic screen to investigate the biogenesis, mode of action, and biological function of miRNA-mediated RNA silencing in the model algal species,Chlamydomonas reinhardtii Among the mutants from this screen, there were three atDicer-like 3that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell into several classes including transposon- and repeat-derived siRNAs as in higher plants. The DCL3-dependent miRNAs differ from those of higher plants, however, in that many of them are derived from mRNAs or from the introns of pre-mRNAs. Transcriptome analysis of the wild-type anddcl3mutant strains revealed a further difference from higher plants in that the sRNAs are rarely negative switches of mRNA accumulation. The few transcripts that were more abundant indcl3mutant strains than in wild-type cells were not due to sRNA-targeted RNA degradation but to direct DCL3 cleavage of miRNA and siRNA precursor structures embedded in the untranslated (and translated) regions of the mRNAs. Our analysis reveals that the miRNA-mediated RNA silencing inC. reinhardtiidiffers from that of higher plants and informs about the evolution and function of this pathway in eukaryotes. PMID:26968199

  6. Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs.

    Science.gov (United States)

    Rachamadugu, Rakesh; Lee, Jeong Yoon; Wooming, Ann; Kong, Byung-Whi

    2009-12-01

    MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a pivotal role in the regulation of gene expression at the post transcriptional level. Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus belonging to the herpesviridae family. It causes an acute respiratory disorder in chicken resulting in high mortality rates. ILTV encoding miRNAs have been identified in cell cultures infected by ILTV. Seven candidates ILTV encoding miRNAs were identified by the 454 FLX genome sequencing method. Five ILTV miRNAs identified in this study were identical to those previously reported by Waidner et al. (Virology 388:128, 2009). Two unique ILTV miRNAs, iltv-miR-I1-3p and iltv-miR-I7-3p, were identified in this study. The iltv-miR-I1-3p is the passenger strand of I1-5p, which was previously known. The iltv-miR-I7-3p showed a perfect match with the complementary passenger strand in contrast to other miRNA species showing imperfect complementarity with the passenger strand. The I7-3p was mapped in the replication origin (oriL) of the palindrome stem loop sequence of the ILTV genome. Expression of all ILTV miRNAs were confirmed by the end point PCR using small RNA libraries generated from either ILTV infected or uninfected control chicken embryo kidney (CEK) cells. PMID:19728068

  7. Potential role of differentially expressed lncRNAs in the pathogenesis of oral squamous cell carcinoma.

    Science.gov (United States)

    Zhang, Shanchuan; Tian, Lili; Ma, Penghua; Sun, Qiang; Zhang, Kai; GuanchaoWang; Liu, Hongchen; Xu, Baohua

    2015-10-01

    Long non-coding RNAs (lncRNAs) have recently attracted more attention about the role in a broad range of biological processes and complex cancers. We aimed to identify differentially expressed lncRNAs that play an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Microarray data GSE25099 consisting of 57 samples from patients with OSCC and 22 normal samples were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs were identified between OSCC samples and control using samr package in R and noncoder software. Co-expression network was constructed for lncRNAs and candidate target DEGs, followed by functional and pathway enrichment analysis using the Database for Annotation, Visualization and Integrated Discovery online tool. OSCC-related genes were screened by Genetic-Association-DB-Database analysis, and then protein-protein interaction (PPI) network construction of OSCC-related and co-expressed genes. Bioinformatic analysis revealed that there were 998 DEGs and 160 differentially expressed lncRNAs between OSCC and normal control. We found LOC100130547, FTH1P3, PDIA3F and GTF2IRD2P1 targeted most of DEGs. Predicted targets-related functional annotation showed significant changes in inflammation-related functions and Toll-like receptor signaling pathway. By further conducting PPI network with lncRNA co-expressed DEGs, we found that OSCC-associated genes including MMP1 (matrix metallopeptidase), MMP3, MMP9, PLAU (plasminogen activator, urokinase) and IL8 (interleukin 8) were targeted by FTH1P3, PDIA3F and GTF2IRD2P1. Our results indicate that lncRNAs FTH1P3, PDIA3F and GTF2IRD2P1 may responsible for progression and metastasis of OSCC via targeting MMP1, MMP3, MMP9, PLAU and IL8 which are key regulators of tumorigenesis. PMID:26276270

  8. Isolation and Identification of miRNAs in Jatropha curcas

    OpenAIRE

    Chun Ming Wang, Peng Liu, Fei Sun, Lei Li, Peng Liu, Jian Ye, Gen Hua Yue

    2012-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that play crucial regulatory roles by targeting mRNAs for silencing. To identify miRNAs in Jatropha curcas L, a bioenergy crop, cDNA clones from two small RNA libraries of leaves and seeds were sequenced and analyzed using bioinformatic tools. Fifty-two putative miRNAs were found from the two libraries, among them six were identical to known miRNAs and 46 were novel. Differential expression patterns of 15 miRNAs in root, stem, leave, fruit and seed ...

  9. Retrotransposon-associated long non-coding RNAs in mice and men.

    Science.gov (United States)

    Ganesh, Sravya; Svoboda, Petr

    2016-06-01

    Over a half of mammalian genomes is occupied by repetitive elements whose ability to provide functional sequences, move into new locations, and recombine underlies the so-called genome plasticity. At the same time, mobile elements exemplify selfish DNA, which is expanding in the genome at the expense of the host. The selfish generosity of mobile genetic elements is in the center of research interest as it offers insights into mechanisms underlying evolution and emergence of new genes. In terms of numbers, with over 20,000 in count, protein-coding genes make an outstanding >2 % minority. This number is exceeded by an ever-growing list of genes producing long non-coding RNAs (lncRNAs), which do not encode for proteins. LncRNAs are a dynamically evolving population of genes. While it is not yet clear what fraction of lncRNAs represents functionally important ones, their features imply that many lncRNAs emerge at random as new non-functional elements whose functionality is acquired through natural selection. Here, we explore the intersection of worlds of mobile genetic elements (particularly retrotransposons) and lncRNAs. In addition to summarizing essential features of mobile elements and lncRNAs, we focus on how retrotransposons contribute to lncRNA evolution, structure, and function in mammals. PMID:27044413

  10. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

    Directory of Open Access Journals (Sweden)

    Perreault Jean-Pierre

    2010-02-01

    -represented, although these regions are not necessarily forming sufficiently long double-stranded structures to satisfy Dicer-like criteria for substrate specificity. Importantly, this large library of siRNAs gave several hints as to the components of the involved silencing machinery.

  11. Enhanced mucosal immune responses induced by a combined candidate mucosal vaccine based on Hepatitis A virus and Hepatitis E virus structural proteins linked to tuftsin.

    Directory of Open Access Journals (Sweden)

    Yan Gao

    Full Text Available Hepatitis A virus (HAV and Hepatitis E virus (HEV are the most common causes of infectious hepatitis. These viruses are spread largely by the fecal-oral route and lead to clinically important disease in developing countries. To evaluate the potential of targeting hepatitis A and E infection simultaneously, a combined mucosal candidate vaccine was developed with the partial open reading frame 2 (ORF2 sequence (aa 368-607 of HEV (HE-ORF2 and partial virus protein 1 (VP1 sequence (aa 1-198 of HAV (HA-VP1, which included the viral neutralization epitopes. Tuftsin is an immunostimulatory peptide which can enhance the immunogenicity of a protein by targeting it to macrophages and dendritic cells. Here, we developed a novel combined protein vaccine by conjugating tuftsin to HE-ORF2 and HA-VP1 and used synthetic CpG oligodeoxynucleotides (ODNs as the adjuvant. Subsequent experiments in BALB/c mice demonstrated that tuftsin enhanced the serum-specific IgG and IgA antibodies against HEV and HAV at the intestinal, vaginal and pulmonary interface when delivered intranasally. Moreover, mice from the intranasally immunized tuftsin group (HE-ORF2-tuftsin + HA-VP1-tuftsin + CpG showed higher levels of IFN-γ-secreting splenocytes (Th1 response and ratio of CD4+/CD8+ T cells than those of the no-tuftsin group (HE-ORF2 + HA-VP1 + CpG. Thus, the tuftsin group generated stronger humoral and cellular immune responses compared with the no-tuftsin group. Moreover, enhanced responses to the combined protein vaccine were obtained by intranasal immunization compared with intramuscular injection. By integrating HE-ORF2, HA-VP1 and tuftsin in a vaccine, this study validated an important concept for further development of a combined mucosal vaccine against hepatitis A and E infection.

  12. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

    Directory of Open Access Journals (Sweden)

    Santana Clara

    2009-10-01

    Full Text Available Abstract Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. Results A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. Conclusion The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.

  13. In situ synthesis of 3D CoS nanoflake/Ni(OH)2 nanosheet nanocomposite structure as a candidate supercapacitor electrode.

    Science.gov (United States)

    Li, Songzhan; Wen, Jian; Chen, Tian; Xiong, Liangbin; Wang, Jianbo; Fang, Guojia

    2016-04-01

    A three-dimensional (3D) CoS/Ni(OH)2 nanocomposite structure based on CoS nanoflakes and two-dimensional (2D) Ni(OH)2 nanosheets were in situ synthesized on Ni foam by a whole hydrothermal reaction and electrodeposition process. The 3D CoS/Ni(OH)2 nanocomposite structures demonstrate the combined advantages of a sustained cycle stability of CoS and high specific capacitance from Ni(OH)2. The obtained CoS/Ni(OH)2 nanocomposite structures on Ni foam can directly serve as a binder-free electrode for a supercapacitor. For the 3D CoS/Ni(OH)2 nanocomposite electrode, the high specific capacitance is 1837 F g(-1) at a scan rate of 1 mV s(-1), which is obviously higher than both the bare CoS electrode and Ni(OH)2 electrode. The galvanostatic charge and discharge measurements illustrate that the 3D CoS/Ni(OH)2 nanocomposite electrode possesses excellent cycle stability, and it keeps a 95.8% retention of the initial capacity after 5000 cycles. Electrochemical impedance spectroscopy measurements also confirm that the 3D CoS/Ni(OH)2 nanocomposite electrode has better electrochemical characteristics. These remarkable performances can be attributed to the unique 3D nanoporous structure of CoS/Ni(OH)2 which leads to a large accessible surface area and a high stability during long-term operation. In addition, 2D Ni(OH)2 nanosheets in 3D nanocomposite structures can afford rapid mass transport and a strong synergistic effect of CoS and Ni(OH)2 as individual compositions contribute to the high performance of the nanocomposite structure electrode. These results may promote the design and implementation of nanocomposite structures in advanced supercapacitors. PMID:26905933

  14. Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis

    OpenAIRE

    Armisen, Javier; Gilchrist, Michael J; Wilczynska, Anna; Standart, Nancy; Miska, Eric A.

    2009-01-01

    Small regulatory RNAs have recently emerged as key regulators of eukaryotic gene expression. Here we used high-throughput sequencing to determine small RNA populations in the germline and soma of the African clawed frog Xenopus tropicalis. We identified a number of miRNAs that were expressed in the female germline. miRNA expression profiling revealed that miR-202-5p is an oocyte-enriched miRNA. We identified two novel miRNAs that were expressed in the soma. In addition, we sequenced large num...

  15. Particle Dark Matter Candidates

    CERN Document Server

    Scopel, Stefano

    2007-01-01

    I give a short overview on some of the favorite particle Cold Dark Matter candidates today, focusing on those having detectable interactions: the axion, the KK-photon in Universal Extra Dimensions, the heavy photon in Little Higgs and the neutralino in Supersymmetry. The neutralino is still the most popular, and today is available in different flavours: SUGRA, nuSUGRA, sub-GUT, Mirage mediation, NMSSM, effective MSSM, scenarios with CP violation. Some of these scenarios are already at the level of present sensitivities for direct DM searches.

  16. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis.

    Directory of Open Access Journals (Sweden)

    Andrew G Hoss

    2014-02-01

    biomarkers for human diseases and given their relationship to disease expression, these miRNAs are biomarker candidates in HD.

  17. Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.

    Science.gov (United States)

    Xu, Xing; Ji, Yongmei; Stormo, Gary D

    2009-04-01

    An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. We present a new computational program named RSSVM (RNA Sampler+Support Vector Machine), which employs Support Vector Machines (SVMs) for efficient identification of functional RNA motifs from random RNA secondary structures. RSSVM uses a set of distinctive features to represent the common RNA secondary structure and structural alignment predicted by RNA Sampler, a tool for accurate common RNA secondary structure prediction, and is trained with functional RNAs from a variety of bacterial RNA motif/gene families covering a wide range of sequence identities. When tested on a large number of known and random RNA motifs, RSSVM shows a significantly higher sensitivity than other leading RNA identification programs while maintaining the same false positive rate. RSSVM performs particularly well on sets with low sequence identities. The combination of RNA Sampler and RSSVM provides a new, fast, and efficient pipeline for large-scale discovery of regulatory RNA motifs. We applied RSSVM to multiple Shewanella genomes and identified putative regulatory RNA motifs in the 5' untranslated regions (UTRs) in S. oneidensis, an important bacterial organism with extraordinary respiratory and metal reducing abilities and great potential for bioremediation and alternative energy generation. From 1002 sets of 5'-UTRs of orthologous operons, we identified 166 putative regulatory RNA motifs, including 17 of the 19 known RNA motifs from Rfam, an additional 21 RNA motifs that are supported by literature evidence, 72 RNA motifs overlapping predicted transcription terminators or attenuators, and other candidate regulatory RNA motifs

  18. MicroRNAs in Rice Innate Immunity.

    Science.gov (United States)

    Baldrich, Patricia; San Segundo, Blanca

    2016-12-01

    MicroRNAs (miRNAs) are short regulatory non-coding RNAs that guide gene silencing in most eukaryotes. They regulate gene expression by triggering sequence-specific cleavage or translational repression of target transcripts. Plant miRNAs are known to play important roles in a wide range of developmental processes. Increasing evidence also supports that the modulation of miRNA levels plays an important role in reprogramming plant responses to abiotic stress (drought, cold, salinity and nutrient deficiency) and biotic stress (antibacterial resistance). Most of these studies were carried out in the model plant Arabidopsis thaliana. During the last years, the adoption of high-throughput sequencing technologies has significantly contributed to uncover multiple miRNAs while allowing miRNA profiling in plants. However, although a plethora of rice miRNAs have been shown to be regulated by pathogen infection, the biological function remains largely unknown for most of them. In this review, we summarize our current understanding on the contribution of miRNAs to rice immunity and discuss their potential applications in rice biotechnology. A better understanding of the miRNA species controlling rice immunity may lead to practical biotechnological applications leading to the development of appropriate strategies for rice protection. PMID:26897721

  19. Structural and optical properties of ZnO nanostructures grown by aerosol spray pyrolysis: Candidates for room temperature methane and hydrogen gas sensing

    Energy Technology Data Exchange (ETDEWEB)

    Motaung, D.E., E-mail: dmotaung@csir.co.za [DST/CSIR Nanotechnology Innovation Centre, National Centre for Nano-Structured Materials, Council for Scientific and Industrial Research, P. O. Box 395, Pretoria 0001 (South Africa); Mhlongo, G.H., E-mail: gmhlongo@csir.co.za [DST/CSIR Nanotechnology Innovation Centre, National Centre for Nano-Structured Materials, Council for Scientific and Industrial Research, P. O. Box 395, Pretoria 0001 (South Africa); Kortidis, I. [Transparent Conductive Materials Lab, Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, 100N. Plastira str., Vassilika Vouton, 70013 Heraklion, Crete (Greece); Nkosi, S.S., E-mail: skosi@csir.co.za [CSIR-National Laser Centre, 626 Meiring Naude Rd, Brummeria, Pretoria 0001 (South Africa); School of Physics, University of Witwatersrand, Private Bag X3, Johannesburg 2030 (South Africa); Malgas, G.F.; Mwakikunga, B.W.; Ray, S.Sinha [DST/CSIR Nanotechnology Innovation Centre, National Centre for Nano-Structured Materials, Council for Scientific and Industrial Research, P. O. Box 395, Pretoria 0001 (South Africa); Kiriakidis, G., E-mail: kiriakid@iesl.forth.gr [Transparent Conductive Materials Lab, Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, 100N. Plastira str., Vassilika Vouton, 70013 Heraklion, Crete (Greece); University of Crete, Department of Physics, 710 03 Heraklion, Crete (Greece)

    2013-08-15

    We report on the synthesis of ZnO films by aerosol spray pyrolysis method at different deposition times. The surface morphology, crystal structure and the cross-sectional analysis of the prepared ZnO films were characterized by X-ray diffraction (XRD), focused ion beam scanning electron microscopy (FIB-SEM), atomic force microscopy (AFM) and high resolution transmission electron microscopy (HR-TEM). XRD analysis revealed that the ZnO films are polycrystalline in nature. Structural analysis exploiting cross-sectional TEM profile showed that the films composed of nano-particles and columnar structures growing perpendicular to the substrate. AFM revealed that the columnar structures have a higher surface roughness as compared to the nanoparticles. The effect of ZnO crystallite size and crystallinity on the gas sensing performance of hydrogen and methane gases was also evaluated. Sensing film based on ZnO nanoparticles has numerous advantages in terms of its reliability and high sensitivity. These sensing materials revealed an improved response to methane and hydrogen gases at room temperature due to their high surface area, indicating their possible application as a gas sensor.

  20. Structural and optical properties of ZnO nanostructures grown by aerosol spray pyrolysis: Candidates for room temperature methane and hydrogen gas sensing

    Science.gov (United States)

    Motaung, D. E.; Mhlongo, G. H.; Kortidis, I.; Nkosi, S. S.; Malgas, G. F.; Mwakikunga, B. W.; Ray, S. Sinha; Kiriakidis, G.

    2013-08-01

    We report on the synthesis of ZnO films by aerosol spray pyrolysis method at different deposition times. The surface morphology, crystal structure and the cross-sectional analysis of the prepared ZnO films were characterized by X-ray diffraction (XRD), focused ion beam scanning electron microscopy (FIB-SEM), atomic force microscopy (AFM) and high resolution transmission electron microscopy (HR-TEM). XRD analysis revealed that the ZnO films are polycrystalline in nature. Structural analysis exploiting cross-sectional TEM profile showed that the films composed of nano-particles and columnar structures growing perpendicular to the substrate. AFM revealed that the columnar structures have a higher surface roughness as compared to the nanoparticles. The effect of ZnO crystallite size and crystallinity on the gas sensing performance of hydrogen and methane gases was also evaluated. Sensing film based on ZnO nanoparticles has numerous advantages in terms of its reliability and high sensitivity. These sensing materials revealed an improved response to methane and hydrogen gases at room temperature due to their high surface area, indicating their possible application as a gas sensor.

  1. Structural and optical properties of ZnO nanostructures grown by aerosol spray pyrolysis: Candidates for room temperature methane and hydrogen gas sensing

    International Nuclear Information System (INIS)

    We report on the synthesis of ZnO films by aerosol spray pyrolysis method at different deposition times. The surface morphology, crystal structure and the cross-sectional analysis of the prepared ZnO films were characterized by X-ray diffraction (XRD), focused ion beam scanning electron microscopy (FIB-SEM), atomic force microscopy (AFM) and high resolution transmission electron microscopy (HR-TEM). XRD analysis revealed that the ZnO films are polycrystalline in nature. Structural analysis exploiting cross-sectional TEM profile showed that the films composed of nano-particles and columnar structures growing perpendicular to the substrate. AFM revealed that the columnar structures have a higher surface roughness as compared to the nanoparticles. The effect of ZnO crystallite size and crystallinity on the gas sensing performance of hydrogen and methane gases was also evaluated. Sensing film based on ZnO nanoparticles has numerous advantages in terms of its reliability and high sensitivity. These sensing materials revealed an improved response to methane and hydrogen gases at room temperature due to their high surface area, indicating their possible application as a gas sensor.

  2. Next-generation sequencing of 100 candidate genes in young victims of suspected sudden cardiac death with structural abnormalities of the heart

    DEFF Research Database (Denmark)

    Hertz, C L; Christiansen, S L; Ferrero-Miliani, Laura;

    2016-01-01

    non-diagnostic structural abnormalities of the heart. METHODS AND RESULTS: We screened 72 suspected SCD cases (<50 years) using the HaloPlex Target Enrichment System (Agilent) and NGS (Illumina MiSeq) for 100 genes previously associated with inherited cardiomyopathies and channelopathies. Fifty...

  3. Classification of ncRNAs using position and size information in deep sequencing data

    Science.gov (United States)

    Erhard, Florian; Zimmer, Ralf

    2010-01-01

    Motivation: Small non-coding RNAs (ncRNAs) play important roles in various cellular functions in all clades of life. With next-generation sequencing techniques, it has become possible to study ncRNAs in a high-throughput manner and by using specialized algorithms ncRNA classes such as miRNAs can be detected in deep sequencing data. Typically, such methods are targeted to a certain class of ncRNA. Many methods rely on RNA secondary structure prediction, which is not always accurate and not all ncRNA classes are characterized by a common secondary structure. Unbiased classification methods for ncRNAs could be important to improve accuracy and to detect new ncRNA classes in sequencing data. Results: Here, we present a scoring system called ALPS (alignment of pattern matrices score) that only uses primary information from a deep sequencing experiment, i.e. the relative positions and lengths of reads, to classify ncRNAs. ALPS makes no further assumptions, e.g. about common structural properties in the ncRNA class and is nevertheless able to identify ncRNA classes with high accuracy. Since ALPS is not designed to recognize a certain class of ncRNA, it can be used to detect novel ncRNA classes, as long as these unknown ncRNAs have a characteristic pattern of deep sequencing read lengths and positions. We evaluate our scoring system on publicly available deep sequencing data and show that it is able to classify known ncRNAs with high sensitivity and specificity. Availability: Calculated pattern matrices of the datasets hESC and EB are available at the project web site http://www.bio.ifi.lmu.de/ALPS. An implementation of the described method is available upon request from the authors. Contact: florian.erhard@bio.ifi.lmu.de PMID:20823303

  4. Possible involvement of miRNAs in tropism of Parvovirus B19.

    Science.gov (United States)

    Anbarlou, Azadeh; AkhavanRahnama, Mahshid; Atashi, Amir; Soleimani, Masoud; Arefian, Ehsan; Gallinella, Giorgio

    2016-03-01

    Human Parvovirus B19 (PVB19) is one of the most important pathogens that targets erythroid lineage. Many factors were mentioned for restriction to erythroid progenitor cells (EPCs). Previous studies showed that in non-permissive cells VP1 and VP2 (structural proteins) mRNAs were detected but could not translate to proteins. A bioinformatics study showed that this inhibition might be due to specific microRNAs (miRNAs) present in non-permissive cells but not in permissive EPCs. To confirm the hypothesis, we evaluated the effect of miRNAs on VP expression. CD34(+) HSCs were separated from cord blood. Then, CD34(+) cells were treated with differentiation medium to obtain CD36(+) EPCs. To evaluate the effect of miRNAs on VP expression in MCF7 and HEK-293 cell lines (non-permissive cells) and CD36(+) EPCs, dual luciferase assay was performed in presence of shRNAs against Dicer and Drosha to disrupt miRNA biogenesis. QRT-PCR was performed to check down-regulation of Dicer and Drosha after transfection. All measurements were done in triplicate. Data means were compared using one-way ANOVAs. MicroRNA prediction was done by the online microRNA prediction tools. No significant difference was shown in luciferase activity of CD36(+) EPCs after co-transfection with shRNAs, while it was significant in non-permissive cells. Our study revealed that miRNAs may be involved in inhibition of VP expression in non-permissive cells, although further studies are required to demonstrate which miRNAs exactly are involved in regulation of PVB19 replication. PMID:26878856

  5. NMR studies of two spliced leader RNAs using isotope labeling

    Energy Technology Data Exchange (ETDEWEB)

    Lapham, J.; Crothers, D.M. [Yale Univ., New Haven, CT (United States)

    1994-12-01

    Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

  6. Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs.

    Directory of Open Access Journals (Sweden)

    Mingyu Yang

    Full Text Available The giant panda (Ailuropoda melanoleuca is one of the world's most beloved endangered mammals. Although the draft genome of this species had been assembled, little was known about the composition of its microRNAs (miRNAs or their functional profiles. Recent studies demonstrated that changes in the expression of miRNAs are associated with immunity. In this study, miRNAs were extracted from the blood of four healthy giant pandas and sequenced by Illumina next generation sequencing technology. As determined by miRNA screening, a total of 276 conserved miRNAs and 51 novel putative miRNAs candidates were detected. After differential expression analysis, we noticed that the expressions of 7 miRNAs were significantly up-regulated in young giant pandas compared with that of adults. Moreover, 2 miRNAs were up-regulated in female giant pandas and 1 in the male individuals. Target gene prediction suggested that the miRNAs of giant panda might be relevant to the expressions of 4,602 downstream genes. Subseuqently, the predicted target genes were conducted to KEGG (Kyoto Encyclopedia of Genes and Genomes pathway analysis and we found that these genes were mainly involved in host immunity, including the Ras signaling pathway, the PI3K-Akt signaling pathway, and the MAPK signaling pathway. In conclusion, our results provide the first miRNA profiles of giant panda blood, and the predicted functional analyses may open an avenue for further study of giant panda immunity.

  7. Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus

    Science.gov (United States)

    Joshi, Raj Kumar; Megha, Swati; Basu, Urmila; Rahman, Muhammad H.; Kav, Nat N. V.

    2016-01-01

    Sclerotinia stem rot caused by Sclerotinia sclerotiorum affects canola production worldwide. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression in plants, in response to both abiotic and biotic stress. So far, identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to biotic stresses are yet to be characterized in Brassica napus. The present study reports the identification of novel lncRNAs responsive to S. sclerotiorum infection in B. napus at two time points after infection (24 hpi and 48 hpi) using a stranded RNA-Sequencing technique and a detection pipeline for lncRNAs. Of the total 3,181 lncRNA candidates, 2,821 lncRNAs were intergenic, 111 were natural antisense transcripts, 76 possessed exonic overlap with the reference coding transcripts while the remaining 173 represented novel lnc- isoforms. Forty one lncRNAs were identified as the precursors for microRNAs (miRNAs) including miR156, miR169 and miR394, with significant roles in mediating plant responses to fungal phytopathogens. A total of 931 differentially expressed lncRNAs were identified in response to S. sclerotiorum infection and the expression of 12 such lncRNAs was further validated using qRT-PCR. B. napus antisense lncRNA, TCONS_00000966, having 90% overlap with a plant defensin gene, showed significant induction at both infection stages, suggesting its involvement in the transcriptional regulation of defense responsive genes under S. sclerotiorum infection. Additionally, nine lncRNAs showed overlap with cis-regulatory regions of differentially expressed genes of B. napus. Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter. Our findings highlight the potential

  8. Fermi arc electronic structure and Chern numbers in the type-II Weyl semimetal candidate MoxW1 -xTe2

    Science.gov (United States)

    Belopolski, Ilya; Xu, Su-Yang; Ishida, Yukiaki; Pan, Xingchen; Yu, Peng; Sanchez, Daniel S.; Zheng, Hao; Neupane, Madhab; Alidoust, Nasser; Chang, Guoqing; Chang, Tay-Rong; Wu, Yun; Bian, Guang; Huang, Shin-Ming; Lee, Chi-Cheng; Mou, Daixiang; Huang, Lunan; Song, You; Wang, Baigeng; Wang, Guanghou; Yeh, Yao-Wen; Yao, Nan; Rault, Julien E.; Le Fèvre, Patrick; Bertran, François; Jeng, Horng-Tay; Kondo, Takeshi; Kaminski, Adam; Lin, Hsin; Liu, Zheng; Song, Fengqi; Shin, Shik; Hasan, M. Zahid

    2016-08-01

    It has recently been proposed that electronic band structures in crystals can give rise to a previously overlooked type of Weyl fermion, which violates Lorentz invariance and, consequently, is forbidden in particle physics. It was further predicted that MoxW1 -xTe2 may realize such a type-II Weyl fermion. Here, we first show theoretically that it is crucial to access the band structure above the Fermi level ɛF to show a Weyl semimetal in MoxW1 -xTe2 . Then, we study MoxW1 -xTe2 by pump-probe ARPES and we directly access the band structure >0.2 eV above ɛF in experiment. By comparing our results with ab initio calculations, we conclude that we directly observe the surface state containing the topological Fermi arc. We propose that a future study of MoxW1 -xTe2 by pump-probe ARPES may directly pinpoint the Fermi arc. Our work sets the stage for the experimental discovery of the first type-II Weyl semimetal in MoxW1 -xTe2 .

  9. Comparative Analysis of MicroRNAs between Sporophyte and Gametophyte of Porphyra yezoensis

    Directory of Open Access Journals (Sweden)

    Linwen He

    2012-01-01

    Full Text Available Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. yezoensis development, we constructed and sequenced libraries of small RNA from P. yezoensis sporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show that P. yezoensis has a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations of P. yezoensis.

  10. Unifying view of stem-loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses.

    Science.gov (United States)

    Seligmann, Hervé; Raoult, Didier

    2016-06-01

    Putatively, stem-loop RNA hairpins explain networks of selfish elements and RNA world remnants. Their genomic density increases with intracellular lifestyle, especially when comparing giant viruses and their virophages. RNA protogenomes presumably templated for mRNAs and self-replicating stem-loops, ancestors of modern genes and parasitic sequences, including tRNAs and rRNAs. Primary and secondary structure analyses suggest common ancestry for t/rRNAs and parasitic RNAs, parsimoniously link diverse RNA metabolites (replication origins, tRNAs, ribozymes, riboswitches, miRNAs and rRNAs) to parasitic RNAs (ribosomal viroids, Rickettsia repeated palindromic elements (RPE), stem-loop hairpins in giant viruses, their virophages, and transposable retrovirus-derived elements). Results indicate ongoing genesis of small RNA metabolites, and common ancestry or similar genesis for rRNA and retroviral sequences. Assuming functional integration of modular duplicated RNA hairpins evolutionarily unifies diverse molecules, postulating stem-loop hairpin RNAs as origins of genetic innovation, ancestors of rRNAs, retro- and Mimivirus sequences, and cells. PMID:26716728

  11. MicroRNAs in skeletal muscle and their regulation with exercise, ageing and disease

    Directory of Open Access Journals (Sweden)

    Evelyn eZacharewicz

    2013-09-01

    Full Text Available Skeletal muscle makes up approximately 40% of the total body mass, providing structural support and enabling the body to maintain posture, to control motor movements and to store energy. It therefore plays a vital role in whole body metabolism. Skeletal muscle displays remarkable plasticity and is able to alter its size, structure and function in response to various stimuli; an essential quality for healthy living across the lifespan. Exercise is an important stimulator of extracellular and intracellular stress signals that promote positive adaptations in skeletal muscle. These adaptations are controlled by changes in gene transcription and protein translation, with many of these molecules identified as potential therapeutic targets to pharmacologically improve muscle quality in patient groups too ill to exercise. MicroRNAs (miRNAs are recently identified regulators of numerous gene networks and pathways and mainly exert their effect by binding to their target messenger RNAs (mRNAs, resulting in mRNA degradation or preventing protein translation. The role of exercise as a regulatory stimulus of skeletal muscle miRNAs is now starting to be investigated. This review highlights our current understanding of the regulation of skeletal muscle miRNAs with exercise and disease as well as how they may control skeletal muscle health.

  12. deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data.

    Science.gov (United States)

    Zheng, Ling-Ling; Li, Jun-Hao; Wu, Jie; Sun, Wen-Ju; Liu, Shun; Wang, Ze-Lin; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

    2016-01-01

    Small non-coding RNAs (e.g. miRNAs) and long non-coding RNAs (e.g. lincRNAs and circRNAs) are emerging as key regulators of various cellular processes. However, only a very small fraction of these enigmatic RNAs have been well functionally characterized. In this study, we describe deepBase v2.0 (http://biocenter.sysu.edu.cn/deepBase/), an updated platform, to decode evolution, expression patterns and functions of diverse ncRNAs across 19 species. deepBase v2.0 has been updated to provide the most comprehensive collection of ncRNA-derived small RNAs generated from 588 sRNA-Seq datasets. Moreover, we developed a pipeline named lncSeeker to identify 176 680 high-confidence lncRNAs from 14 species. Temporal and spatial expression patterns of various ncRNAs were profiled. We identified approximately 24 280 primate-specific, 5193 rodent-specific lncRNAs, and 55 highly conserved lncRNA orthologs between human and zebrafish. We annotated 14 867 human circRNAs, 1260 of which are orthologous to mouse circRNAs. By combining expression profiles and functional genomic annotations, we developed lncFunction web-server to predict the function of lncRNAs based on protein-lncRNA co-expression networks. This study is expected to provide considerable resources to facilitate future experimental studies and to uncover ncRNA functions. PMID:26590255

  13. Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach.

    Directory of Open Access Journals (Sweden)

    Jian Huang

    Full Text Available BACKGROUND: Human schistosomiasis is one of the most prevalent and serious parasitic diseases worldwide. Schistosoma japonicum is one of important pathogens of this disease. MicroRNAs (miRNAs are a large group of non-coding RNAs that play important roles in regulating gene expression and protein translation in animals. Genome-wide identification of miRNAs in a given organism is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and posttranscriptional regulation. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced two small RNA libraries prepared from different stages of the life cycle of S. japonicum, immature schistosomula and mature pairing adults, through a deep DNA sequencing approach, which yielded approximately 12 million high-quality short sequence reads containing a total of approximately 2 million non-redundant tags. Based on a bioinformatics pipeline, we identified 176 new S. japonicum miRNAs, of which some exhibited a differential pattern of expression between the two stages. Although 21 S. japonicum miRNAs are orthologs of known miRNAs within the metazoans, some nucleotides at many positions of Schistosoma miRNAs, such as miR-8, let-7, miR-10, miR-31, miR-92, miR-124, and miR-125, are indeed significantly distinct from other bilaterian orthologs. In addition, both miR-71 and some miR-2 family members in tandem are found to be clustered in a reversal direction model on two genomic loci, and two pairs of novel S. japonicum miRNAs were derived from sense and antisense DNA strands at the same genomic loci. CONCLUSIONS/SIGNIFICANCE: The collection of S. japonicum miRNAs could be used as a new platform to study the genomic structure, gene regulation and networks, evolutionary processes, development, and host-parasite interactions. Some S. japonicum miRNAs and their clusters could represent the ancestral forms of the conserved orthologues and a model for the genesis of novel miRNAs.

  14. Unoccupied electronic structure and signatures of topological Fermi arcs in the Weyl semimetal candidate Mo$_x$W$_{1-x}$Te$_2$

    OpenAIRE

    Belopolski, Ilya; Xu, Su-Yang; Ishida, Yukiaki; Pan, Xingchen; Yu, Peng; Sanchez, Daniel S.; Neupane, Madhab; Alidoust, Nasser; Chang, Guoqing; Chang, Tay-Rong; WU, YUN; Bian, Guang; Zheng, Hao; Huang, Shin-Ming; Lee, Chi-Cheng

    2015-01-01

    Weyl semimetals have sparked intense research interest, but experimental work has been limited to the TaAs family of compounds. Recently, a number of theoretical works have predicted that compounds in the Mo$_x$W$_{1-x}$Te$_2$ series are Weyl semimetals. Such proposals are particularly exciting because Mo$_x$W$_{1-x}$Te$_2$ has a quasi two-dimensional crystal structure well-suited to many transport experiments, while WTe$_2$ and MoTe$_2$ have already been the subject of numerous proposals for...

  15. Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress.

    Science.gov (United States)

    Akpinar, Bala Ani; Kantar, Melda; Budak, Hikmet

    2015-09-01

    MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties. PMID:26174050

  16. MicroRNAs in pulmonary arterial hypertension.

    Science.gov (United States)

    Zhou, Guofei; Chen, Tianji; Raj, J Usha

    2015-02-01

    Pulmonary arterial hypertension (PAH) is a devastating disease without effective treatment. Despite decades of research and the development of novel treatments, PAH remains a fatal disease, suggesting an urgent need for better understanding of the pathogenesis of PAH. Recent studies suggest that microRNAs (miRNAs) are dysregulated in patients with PAH and in experimental pulmonary hypertension. Furthermore, normalization of a few miRNAs is reported to inhibit experimental pulmonary hypertension. We have reviewed the current knowledge about miRNA biogenesis, miRNA expression pattern, and their roles in regulation of pulmonary artery smooth muscle cells, endothelial cells, and fibroblasts. We have also identified emerging trends in our understanding of the role of miRNAs in the pathogenesis of PAH and propose future studies that might lead to novel therapeutic strategies for the treatment of PAH. PMID:25192340

  17. Non-Coding RNAs in Muscle Dystrophies

    Directory of Open Access Journals (Sweden)

    Alessandra Ferlini

    2013-09-01

    Full Text Available ncRNAs are the most recently identified class of regulatory RNAs with vital functions in gene expression regulation and cell development. Among the variety of roles they play, their involvement in human diseases has opened new avenues of research towards the discovery and development of novel therapeutic approaches. Important data come from the field of hereditary muscle dystrophies, like Duchenne muscle dystrophy and Myotonic dystrophies, rare diseases affecting 1 in 7000–15,000 newborns and is characterized by severe to mild muscle weakness associated with cardiac involvement. Novel therapeutic approaches are now ongoing for these diseases, also based on splicing modulation. In this review we provide an overview about ncRNAs and their behavior in muscular dystrophy and explore their links with diagnosis, prognosis and treatments, highlighting the role of regulatory RNAs in these pathologies.

  18. Prediction of possible other alternate candidate high-T non-cuprate superconductors in perovskite-structure across-the-periodic-table electron-supercarrier metalloids

    International Nuclear Information System (INIS)

    The criteria for high-T/sub c/ superconductivity include perovskite-type crystal structure, proximity to metal-insulator transition, proximity to half-filled (d)-band, maximal frustration (to preclude strong ferromagnetic (FM) or antiferromagnetic (AFM) or spiral-spin-density-wave (SSDW) state interference with superconductivity), maximal...very large on-site intra-atomic Coulomb repulsion, and perhaps low-dimensionality (sheets, chains,...?) can and do exist elsewhere in the periodic table. Identified are a huge number of perovskite-type crystal structures with potential: very large on-site intra-atomic Coulumb repulsion Hubbard U which can exhibit as well the Anderson necessary and sufficient required: proximity to metal-insulator transition, proximity to half-filled (d)-band, via Siegel theory of transition metalloid bonding charging paradox resolution, and maximal frustration. The question of the necessity for low-dimensionality may not arise, with the Stanford-group claim of nearly isotropic high-T/sub c/ cuprate superconductor synthesis: this remains a most controversial point, as does the type of supercarriers and type of Cooper-pairing, if at all

  19. Circadian changes in long noncoding RNAs in the pineal gland

    DEFF Research Database (Denmark)

    Coon, Steven L; Munson, Peter J; Cherukuri, Praveen F;

    2012-01-01

    Long noncoding RNAs (lncRNAs) play a broad range of biological roles, including regulation of expression of genes and chromosomes. Here, we present evidence that lncRNAs are involved in vertebrate circadian biology. Differential night/day expression of 112 lncRNAs (0.3 to >50 kb) occurs in the ra...

  20. Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs Functional Analysis

    Directory of Open Access Journals (Sweden)

    Andrea Masotti

    2011-12-01

    Full Text Available The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs is non-coding. Long non-coding RNAs (lncRNAs have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling. LncRNAs may have different roles: gene activators (signaling, repressors (decoy, cis and trans gene expression regulators (guides and chromatin modificators (scaffolds without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.

  1. Utility of MicroRNAs and siRNAs in Cervical Carcinogenesis

    OpenAIRE

    Sacnite del Mar Díaz-González; Jessica Deas; Odelia Benítez-Boijseauneau; Claudia Gómez-Cerón; Victor Hugo Bermúdez-Morales; Mauricio Rodríguez-Dorantes; Carlos Pérez-Plasencia; Oscar Peralta-Zaragoza

    2015-01-01

    MicroRNAs and siRNAs belong to a family of small noncoding RNAs which bind through partial sequence complementarity to 3′-UTR regions of mRNA from target genes, resulting in the regulation of gene expression. MicroRNAs have become an attractive target for genetic and pharmacological modulation due to the critical function of their target proteins in several signaling pathways, and their expression profiles have been found to be altered in various cancers. A promising technology platform for s...

  2. Interplay of noncoding RNAs, mRNAs, and proteins during the growth of eukaryotic cells

    Science.gov (United States)

    Zhdanov, V. P.

    2010-10-01

    Numerous biological functions of noncoding RNAs (ncRNAs) in eukaryotic cells are based primarily on their ability to pair with target mRNAs and then either to prevent translation or to result in rapid degradation of the mRNA-ncRNA complex. Using a general model describing this scenario, we show that ncRNAs may help to maintain constant mRNA and protein concentrations during the growth of cells. The possibility of observation of this effect on the global scale is briefly discussed.

  3. Interplay of noncoding RNAs, mRNAs, and proteins during the growth of eukaryotic cells

    International Nuclear Information System (INIS)

    Numerous biological functions of noncoding RNAs (ncRNAs) in eukaryotic cells are based primarily on their ability to pair with target mRNAs and then either to prevent translation or to result in rapid degradation of the mRNA-ncRNA complex. Using a general model describing this scenario, we show that ncRNAs may help to maintain constant mRNA and protein concentrations during the growth of cells. The possibility of observation of this effect on the global scale is briefly discussed.

  4. MicroRNAs in Ewing Sarcoma

    OpenAIRE

    PaulJedlicka; LayneDylla

    2013-01-01

    MicroRNAs have emerged recently as important regulators of gene expression in the cell. Frequently dysregulated in cancer, microRNAs have shed new light on molecular mechanisms of oncogenesis, and have generated substantial interest as biomarkers, and novel therapeutic agents and targets. Recently, a number of studies have examined microRNA biology in Ewing Sarcoma. Findings indicate that alterations in microRNA expression in Ewing Sarcoma are widespread, involve both EWS/Ets oncogenic fusion...

  5. microRNAs regulate TAL1 expression in T-cell acute lymphoblastic leukemia.

    Science.gov (United States)

    Correia, Nádia C; Melão, Alice; Póvoa, Vanda; Sarmento, Leonor; Gómez de Cedrón, Marta; Malumbres, Marcos; Enguita, Francisco J; Barata, João T

    2016-02-16

    The transcription factor TAL1 is a proto-oncogene whose aberrant expression in committed T-cell precursors is associated with the development of T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms leading to aberrant activation of TAL1 in T-ALL patients who lack chromosomal rearrangements involving the TAL1 locus remain largely unknown. We hypothesized that TAL1 levels decrease during normal T-cell development at least in part due to miRNA-dependent silencing, in which case TAL1 over-expression in some T-ALL cases could be the consequence of deregulated miRNA expression. By performing computational prediction of miRNAs that bind to the human TAL1 mRNA we compiled a list of miRNAs that are candidates to regulate TAL1. Using a luciferase reporter system and mutagenesis assays we confirmed the miRNA-TAL1 mRNA interactions and selected candidate miRNAs: miR-101, miR-520d-5p, miR-140-5p, miR-448 and miR-485-5p. Over-expression of these microRNAs in different T-ALL cell lines consistently resulted in the down-regulation of TAL1 protein. In accordance, inhibition of miR-101 and miR-520d-5p promoted TAL1 protein expression. Importantly, we found that miR-101, miR-140-5p, miR-448 and miR-485-5p were down-regulated in T-ALL patient specimens and T-ALL cell lines. Our results show for the first time the existence of epigenetic regulation of TAL1 by specific miRNAs which may contribute, at least in part, to the ectopic expression of TAL1 in some T-ALL cases. PMID:26882564

  6. MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression.

    Science.gov (United States)

    Paugh, Steven W; Coss, David R; Bao, Ju; Laudermilk, Lucas T; Grace, Christy R; Ferreira, Antonio M; Waddell, M Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael; LoCascio, Philip F; Panetta, John C; Wilkinson, Mark R; Pui, Ching-Hon; Naeve, Clayton W; Uberbacher, Edward C; Bonten, Erik J; Evans, William E

    2016-02-01

    MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, ptriplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription. PMID:26844769

  7. Pseudouridines in spliceosomal snRNAs

    Institute of Scientific and Technical Information of China (English)

    Andrew T. Yu; Junhui Ge; Yi-Tao Yu

    2011-01-01

    Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing.All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription.Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing.Many of these modified nucleotides are conserved across species lines.Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms:an RNA-dependent mechanism and an RNA-independent mechanism.The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied.Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important.Besides the currently known pseudouridines (constitutive modifications),recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions,thus strongly suggesting that pseudouridylation is also a regulatory modification.

  8. MicroRNAs in rheumatoid arthritis.

    Science.gov (United States)

    Salehi, Eisa; Eftekhari, Rahil; Oraei, Mona; Gharib, Alvand; Bidad, Katayoon

    2015-04-01

    The role of genetic and epigenetic factors in the development of rheumatic diseases has been an interesting field of research over the past decades all around the world. Research on the role of microRNAs (miRNAs) in rheumatoid arthritis (RA) has been active and ongoing, and investigations have attempted to use miRNAs as biomarkers in disease diagnosis, prognosis, and treatment. This review focuses on experimental researches in the field of miRNAs and RA to present the data available up to this date and includes researches searched by keywords "microRNA" and "rheumatoid arthritis" in PubMed from 2008 to January 2015. All references were also searched for related papers. miRNAs are shown to act as proinflammatory or anti-inflammatory agents in diverse cell types, and their role seems to be regulatory in most instances. Researchers have evaluated miRNAs in patients compared to controls or have investigated their role by overexpressing or silencing them. Multiple targets have been identified in vivo, in vitro, or in silico, and the researches still continue to show their efficacy in clinical settings. PMID:25736037

  9. Cloning and expression of new microRNAs from zebrafish

    OpenAIRE

    Kloosterman, Wigard P.; Steiner, Florian A.; Berezikov, Eugene; de Bruijn, Ewart; Van de Belt, Jose; Verheul, Mark; Cuppen, Edwin; Ronald H A Plasterk

    2006-01-01

    MicroRNAs (miRNAs) play an important role in development and regulate the expression of many animal genes by post-transcriptional gene silencing. Here we describe the cloning and expression of new miRNAs from zebrafish. By high-throughput sequencing of small-RNA cDNA libraries from 5-day-old zebrafish larvae and adult zebrafish brain we found 139 known miRNAs and 66 new miRNAs. For 65 known miRNAs and for 11 new miRNAs we also cloned the miRNA star sequence. We analyzed the temporal and spati...

  10. Identification of 20 microRNAs from Oryza sativa

    OpenAIRE

    Wang, Jia-Fu; Zhou, Hui; Chen, Yue-Qin; Luo, Qing-Jun; Qu, Liang-Hu

    2004-01-01

    MicroRNAs (miRNAs) are present in both plant and animal kingdoms and represents a growing family of non-coding RNAs. These tiny RNAs act as small guides and direct negative regulations usually in the process of development through sequence complementarity to target mRNAs. Although a large number of miRNAs have been identified from various animals, so far plant miRNA studies have focused mainly on Arabidopsis. Here we describe the identification of 20 miRNAs from a rice cDNA library. All the m...

  11. Solution structure of a Plasmodium falciparum AMA-1/MSP 1 chimeric protein vaccine candidate (PfCP-2.9 for malaria

    Directory of Open Access Journals (Sweden)

    Jin Changwen

    2010-03-01

    Full Text Available Abstract Background The Plasmodium falciparum chimeric protein PfCP-2.9 is a promising asexual-stage malaria vaccine evaluated in clinical trials. This chimeric protein consists of two cysteine-rich domains: domain III of the apical membrane antigen 1 (AMA-1 [III] and the C-terminal region of the merozoite surface protein 1 (MSP1-19. It has been reported that the fusion of these two antigens enhanced their immunogenicity and antibody-mediated inhibition of parasite growth in vitro. Methods The 15N-labeled and 13C/15N-labeled PfCP-2.9 was produced in Pichia pastoris for nuclear magnetic resonance (NMR structure analysis. The chemical shift assignments of PfCP-2.9 were compared with those previously reported for the individual domains (i.e., PfAMA-1(III or PfMSP 1-19. The two-dimensional spectra and transverse relaxation rates (R2 of the PfMSP1-19 alone were compared with that of the PfCP-2.9. Results Confident backbone assignments were obtained for 122 out of 241 residues of PfCP-2.9. The assigned residues in PfCP-2.9 were very similar to those previously reported for the individual domains. The conformation of the PfMSP1-19 in different constructs is essentially the same. Comparison of transverse relaxation rates (R2 strongly suggests no weak interaction between the domains. Conclusions These data indicate that the fusion of AMA-1(III and MSP1-19 as chimeric protein did not change their structures, supporting the use of the chimeric protein as a potential malaria vaccine.

  12. Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice.

    Science.gov (United States)

    Sano, Naoto; Ono, Hanako; Murata, Kazumasa; Yamada, Tetsuya; Hirasawa, Tadashi; Kanekatsu, Motoki

    2015-07-01

    Mature dry seeds contain translatable mRNAs called long-lived mRNAs. Early studies have shown that protein synthesis during the initial phase of seed germination occurs from long-lived mRNAs, without de novo transcription. However, the gene expression systems that generate long-lived mRNAs in seeds are not well understood. To examine the accumulation of long-lived mRNAs in developing rice embryos, germination tests using the transcriptional inhibitor actinomycin D (Act D) were performed with the Japonica rice cultivar Nipponbare. Although over 70% of embryos at 10 days after flowering (DAF) germinated in the absence of the inhibitor, germination was remarkably impaired in embryos treated with Act D. In contrast, more than 70% of embryos at 20, 25, 30 and 40 DAF germinated in the presence of Act D. The same results were obtained when another cultivar, Koshihikari, was used, indicating that the long-lived mRNAs required for germination predominantly accumulate in embryos between 10 and 20 DAF during seed development. RNA-Seq identified 529 long-lived mRNA candidates, encoding proteins such as ABA, calcium ion and phospholipid signalling-related proteins, and HSP DNA J, increased from 10 to 20 DAF and were highly abundant in 40 DAF embryos of Nipponbare and Koshihikari. We also revealed that these long-lived mRNA candidates are clearly up-regulated in 10 DAF germinating embryos after imbibition, suggesting that the accumulation of these mRNAs in embryos is indispensable for the induction of germination. The findings presented here may facilitate in overcoming irregular seed germination or producing more vigorous seedlings. PMID:25941326

  13. Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Jianqin Li

    Full Text Available Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8 and 5 are negatively correlated (r<-0.8. The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.

  14. Association of MicroRNAs with Antibody Response to Mycoplasma bovis in Beef Cattle.

    Science.gov (United States)

    Casas, Eduardo; Cai, Guohong; Kuehn, Larry A; Register, Karen B; McDaneld, Tara G; Neill, John D

    2016-01-01

    The objective of this study was to identify microRNAs associated with a serum antibody response to Mycoplasma bovis in beef cattle. Serum from sixteen beef calves was collected at three points: in summer after calves were born, in fall at weaning, and in the following spring. All sera collected in the summer were ELISA-negative for anti-M. bovis. By the fall, eight animals were seropositive for IgG (positive group), while eight remained negative (negative group). By spring, all animals in both groups were seropositive. MicroRNAs were extracted from sera and sequenced on the Illumina HiSeq next-generation sequencer. A total of 1,374,697 sequences mapped to microRNAs in the bovine genome. Of these, 82% of the sequences corresponded to 27 microRNAs, each represented by a minimum of 10,000 sequences. There was a statistically significant interaction between ELISA response and season for bta-miR-24-3p (P = 0.0268). All sera collected at the initial summer had a similar number of copies of this microRNA (P = 0.773). In the fall, the positive group had an increased number of copies when compared to the negative group (P = 0.021), and this grew more significant by the following spring (P = 0.0001). There were 21 microRNAs associated (P< 0.05) with season. These microRNAs could be evaluated further as candidates to potentially improve productivity in cattle. The microRNAs bta-let-7b, bta-miR- 24-3p, bta-miR- 92a, and bta-miR-423-5p, were significatly associated with ELISA status (P< 0.05). These microRNAs have been recognized as playing a role in the host defense against bacteria in humans, mice, and dairy cattle. Further studies are needed to establish if these microRNAs could be used as diagnostic marker or indicator of exposure, or whether intervention strategies could be developed as an alternative to antibiotics for controlling disease due to M. bovis. PMID:27537842

  15. Genome-Wide CRISPR-Cas9 Screen Identifies MicroRNAs That Regulate Myeloid Leukemia Cell Growth

    Science.gov (United States)

    Wallace, Jared; Hu, Ruozhen; Mosbruger, Timothy L.; Dahlem, Timothy J.; Stephens, W. Zac; Rao, Dinesh S.; Round, June L.; O’Connell, Ryan M.

    2016-01-01

    Mammalian microRNA expression is dysregulated in human cancer. However, the functional relevance of many microRNAs in the context of tumor biology remains unclear. Using CRISPR-Cas9 technology, we performed a global loss-of-function screen to simultaneously test the functions of individual microRNAs and protein-coding genes during the growth of a myeloid leukemia cell line. This approach identified evolutionarily conserved human microRNAs that suppress or promote cell growth, revealing that microRNAs are extensively integrated into the molecular networks that control tumor cell physiology. miR-155 was identified as a top microRNA candidate promoting cellular fitness, which we confirmed with two distinct miR-155-targeting CRISPR-Cas9 lentiviral constructs. Further, we performed anti-correlation functional profiling to predict relevant microRNA-tumor suppressor gene or microRNA-oncogene interactions in these cells. This analysis identified miR-150 targeting of p53, a connection that was experimentally validated. Taken together, our study describes a powerful genetic approach by which the function of individual microRNAs can be assessed on a global level, and its use will rapidly advance our understanding of how microRNAs contribute to human disease. PMID:27081855

  16. Evidence for large complex networks of plant short silencing RNAs.

    Directory of Open Access Journals (Sweden)

    Daniel MacLean

    Full Text Available BACKGROUND: In plants and animals there are many classes of short RNAs that carry out a wide range of functions within the cell; short silencing RNAs (ssRNAs of 21-25 nucleotides in length are produced from double-stranded RNA precursors by the protein Dicer and guide nucleases and other proteins to their RNA targets through base pairing interactions. The consequence of this process is degradation of the targeted RNA, suppression of its translation or initiation of secondary ssRNA production. The secondary ssRNAs in turn could then initiate further layers of ssRNA production to form extensive cascades and networks of interacting RNA [1]. Previous empirical analysis in plants established the existence of small secondary ssRNA cascade [2], in which a single instance of this event occurred but it was not known whether there are other more extensive networks of secondary sRNA production. METHODOLOGY/PRINCIPAL FINDINGS: We generated a network by predicting targets of ssRNA populations obtained from high-throughput sequencing experiments. The topology of the network shows it to have power law connectivity distribution, to be dissortative, highly clustered and composed of multiple components. We also identify protein families, PPR and ULP1, that act as hubs within the network. Comparison of the repetition of genomic sub-sequences of ssRNA length between Arabidopsis and E.coli suggest that the network structure is made possible by the underlying repetitiveness in the genome sequence. CONCLUSIONS/SIGNIFICANCE: Together our results provide good evidence for the existence of a large, robust ssRNA interaction network with distinct regulatory function. Such a network could have a massive effect on the regulation of gene expression via mediation of transcript levels.

  17. New neurons in aging brains: molecular control by small non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Marijn eSchouten

    2012-02-01

    Full Text Available Adult neurogenesis is a process that continues in the adult and also aging brain. It generates functional neurons from neural stem cells present in specific brain regions. This phenomenon is largely confined to two main regions: the subventricular zone of the lateral ventricle, and the subgranular zone of the dentate gyrus, in the hippocampus. With age, the hippocampus and particularly the dentate gyrus are affected. For instance, adult neurogenesis is decreased with aging, in both the number of proliferating cells as well as their neuronal differentiation, while in parallel an age-associated decline in cognitive performance is often seen. Surprisingly, the synaptogenic potential of adult-born neurons appears unaffected by aging. Therefore, although proliferation, differentiation, survival and synaptogenesis of adult-born new neurons in the dentate gyrus are closely related to each other, they appear differentially regulated with aging. In this review we discuss the crucial role of a novel class of recently discovered regulators of gene expression, i.e. the small non-coding RNAs, in the development of adult neurogenesis from neural stem cells to functionally integrated neurons. In particular, a subgroup of the small non-coding RNAs, the microRNAs, fine-tune many events during adult neurogenesis progression. Moreover, multiple small non-coding RNAs are differentially expressed in the aged hippocampus. This makes small non-coding RNAs appealing candidates to orchestrate, and possibly correct or prevent, the functional alterations in adult neurogenesis and cognition associated with aging. Finally, we briefly summarize observations that link changes in circulating levels of steroid hormones with alterations in adult neurogenesis and subsequent vulnerability to psychopathology in advanced age, and discuss a possible role of microRNAs in stress-associated alterations in adult neurogenesis during aging.

  18. Identification of reference genes for relative quantification of circulating microRNAs in bovine serum.

    Directory of Open Access Journals (Sweden)

    In-Seon Bae

    Full Text Available Circulating microRNAs in body fluids have been implicated as promising biomarkers for physiopathology disorders. Currently, the expression levels of circulating microRNAs are estimated by reverse transcription quantitative real-time polymerase chain reaction. Use of appropriate reference microRNAs for normalization is critical for accurate microRNA expression analysis. However, no study has systematically investigated reference genes for evaluating circulating microRNA expression in cattle. In this study, we describe the identification and characterization of appropriate reference microRNAs for use in the normalization of circulating microRNA levels in bovine serum. We evaluated the expression stability of ten candidate reference genes in bovine serum by using reverse transcription quantitative real-time polymerase chain reaction. Data were analyzed using geNorm, NormFinder, and BestKeeper statistical algorithms. The results consistently showed that a combination of miR-93 and miR-127 provided the most stably expressed reference. The suitability of these microRNAs was validated, and even when compared among different genders or breeds, the combination of miR-93 and miR-127 was ranked as the most stable microRNA reference. Therefore, we conclude that this combination is the optimal endogenous reference for reverse transcription quantitative real-time polymerase chain reaction-based detection of microRNAs in bovine serum. The data presented in this study are crucial to successful biomarker discovery and validation for the diagnosis of physiopathological conditions in cattle.

  19. Differentially expressed wound healing-related microRNAs in the human diabetic cornea.

    Directory of Open Access Journals (Sweden)

    Vincent A Funari

    Full Text Available MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC in vitro. Total RNA was extracted from age-matched human autopsy normal (n=6 and diabetic (n=6 central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR and by in situ hybridization (ISH in independent samples. HCEC were transfected with human pre-miR™miRNA precursors (h-miR or their inhibitors (antagomirs using Lipofectamine 2000. Confluent transfected cultures were scratch-wounded with P200 pipette tip. Wound closure was monitored by digital photography. Expression of signaling proteins was detected by immunostaining and Western blot. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing.

  20. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

    DEFF Research Database (Denmark)

    Orum, H; Nielsen, Henrik; Engberg, J

    1991-01-01

    We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T....... thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other...... organisms. Furthermore, secondary structures closely similar to phylogenetically proven models can be inferred from the T. thermophila data. Analysis of the snRNA sequences identifies three potential snRNA-snRNA base-pairing interactions, all of which are consistent with available phylogenetic data. Two of...

  1. SARS coronavirus nsp1 protein induces template-dependent endonucleolytic cleavage of mRNAs: viral mRNAs are resistant to nsp1-induced RNA cleavage.

    Directory of Open Access Journals (Sweden)

    Cheng Huang

    2011-12-01

    Full Text Available SARS coronavirus (SCoV nonstructural protein (nsp 1, a potent inhibitor of host gene expression, possesses a unique mode of action: it binds to 40S ribosomes to inactivate their translation functions and induces host mRNA degradation. Our previous study demonstrated that nsp1 induces RNA modification near the 5'-end of a reporter mRNA having a short 5' untranslated region and RNA cleavage in the encephalomyocarditis virus internal ribosome entry site (IRES region of a dicistronic RNA template, but not in those IRES elements from hepatitis C or cricket paralysis viruses. By using primarily cell-free, in vitro translation systems, the present study revealed that the nsp1 induced endonucleolytic RNA cleavage mainly near the 5' untranslated region of capped mRNA templates. Experiments using dicistronic mRNAs carrying different IRESes showed that nsp1 induced endonucleolytic RNA cleavage within the ribosome loading region of type I and type II picornavirus IRES elements, but not that of classical swine fever virus IRES, which is characterized as a hepatitis C virus-like IRES. The nsp1-induced RNA cleavage of template mRNAs exhibited no apparent preference for a specific nucleotide sequence at the RNA cleavage sites. Remarkably, SCoV mRNAs, which have a 5' cap structure and 3' poly A tail like those of typical host mRNAs, were not susceptible to nsp1-mediated RNA cleavage and importantly, the presence of the 5'-end leader sequence protected the SCoV mRNAs from nsp1-induced endonucleolytic RNA cleavage. The escape of viral mRNAs from nsp1-induced RNA cleavage may be an important strategy by which the virus circumvents the action of nsp1 leading to the efficient accumulation of viral mRNAs and viral proteins during infection.

  2. Non-coding RNAs: Classification, Biology and Functioning.

    Science.gov (United States)

    Hombach, Sonja; Kretz, Markus

    2016-01-01

    One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action. PMID:27573892

  3. Micropreparative isolation and NMR structure elucidation of metabolites of the drug candidate 1-isopropyl-4-(4-isopropylphenyl)-6-(prop-2-yn-1-yloxy) quinazolin-2(1H)-one from rat bile and urine.

    Science.gov (United States)

    Blanz, Joachim; Délémonté, Thierry; Pearson, David; Luneau, Alexandre; Ritzau, Michael; Gertsch, Werner; Ramstein, Philippe; Dayer, Jérôme; Desrayaud, Sandrine; Braun, Elisabeth; Aichholz, Reiner

    2015-05-01

    LC-MS based drug metabolism studies are effective in the optimization stage of drug discovery for rapid partial structure identification of metabolites. However, these studies usually do not provide unambiguous structural characterization of all metabolites, due to the limitations of MS-based structure identification. LC-MS-SPE-NMR is a technique that allows complete structure identification, but is difficult to apply to complex in vivo samples (such as bile collected during in vivo drug metabolism studies) due to the presence, at high concentrations, of interfering endogenous components, and potentially also dosage excipient components (e.g. polyethylene glycols). Here, we describe the isolation and structure characterization of seven metabolites of the drug development candidate 1-isopropyl-4-(4-isopropylphenyl)-6-(prop-2-yn-1-yloxy) quinazolin-2(1H)-one from a routine metabolism study in a bile-duct cannulated rat by LC-MS-SPE. The metabolites were isolated from bile and urine by repeated automatic trapping of the chromatographic peak of each metabolite on separate Oasis HLB SPE columns. The micropreparative HPLC/MS was performed on an XBridge BEH130 C18 HPLC column using aqueous formic acid/acetonitrile/methanol as mobile phase for the gradient elution. Mass spectrometric detection was performed on a LTQ XL linear ion trap mass spectrometer using electrospray ionization. Desorption of each metabolite was performed after the separation sequence. NMR spectra ((1)H, (13)C, 2D ROESY, HSQC and HMBC were measured on a Bruker AVANCE III spectrometer (600 MHz proton frequency) equipped with a 1.7 mm (1)H{(13)C,(15)N} Bruker Biospin's TCI MicroCryoProbe™. PMID:25797717

  4. Identification of novel miRNAs from drought tolerant rice variety Nagina 22.

    Science.gov (United States)

    Mutum, Roseeta Devi; Kumar, Santosh; Balyan, Sonia; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, Saurabh

    2016-01-01

    MicroRNAs regulate a spectrum of developmental and biochemical processes in plants and animals. Thus, knowledge of the entire miRNome is essential to understand the complete regulatory schema of any organism. The current study attempts to unravel yet undiscovered miRNA genes in rice. Analysis of small RNA libraries from various tissues of drought-tolerant 'aus' rice variety Nagina 22 (N22) identified 71 novel miRNAs. These were validated based on precursor hairpin structure, small RNA mapping pattern, 'star' sequence, conservation and identification of targets based on degradome data. While some novel miRNAs were conserved in other monocots and dicots, most appear to be lineage-specific. They were segregated into two different classes based on the closeness to the classical miRNA definition. Interestingly, evidence of a miRNA-like cleavage was found even for miRNAs that lie beyond the classical definition. Several novel miRNAs displayed tissue-enriched and/or drought responsive expression. Generation and analysis of the degradome data from N22 along with publicly available degradome identified several high confidence targets implicated in regulation of fundamental processes such as flowering and stress response. Thus, discovery of these novel miRNAs considerably expands the dimension of the miRNA-mediated regulation in rice. PMID:27499088

  5. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Carte, Jason; Wang, Ruiying; Li, Hong; Terns, Rebecca M.; Terns, Michael P. (FSU); (Georgia)

    2010-11-09

    An RNA-based gene silencing pathway that protects bacteria and archaea from viruses and other genome invaders is hypothesized to arise from guide RNAs encoded by CRISPR loci and proteins encoded by the cas genes. CRISPR loci contain multiple short invader-derived sequences separated by short repeats. The presence of virus-specific sequences within CRISPR loci of prokaryotic genomes confers resistance against corresponding viruses. The CRISPR loci are transcribed as long RNAs that must be processed to smaller guide RNAs. Here we identified Pyrococcus furiosus Cas6 as a novel endoribonuclease that cleaves CRISPR RNAs within the repeat sequences to release individual invader targeting RNAs. Cas6 interacts with a specific sequence motif in the 5{prime} region of the CRISPR repeat element and cleaves at a defined site within the 3{prime} region of the repeat. The 1.8 angstrom crystal structure of the enzyme reveals two ferredoxin-like folds that are also found in other RNA-binding proteins. The predicted active site of the enzyme is similar to that of tRNA splicing endonucleases, and concordantly, Cas6 activity is metal-independent. cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea.

  6. siRNAmod: A database of experimentally validated chemically modified siRNAs.

    Science.gov (United States)

    Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

    2016-01-01

    Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod. PMID:26818131

  7. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

    Science.gov (United States)

    Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

    2016-01-01

    The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers. PMID:27336480

  8. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs.

    Science.gov (United States)

    Montelli, Stefano; Peruffo, Antonella; Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

    2016-01-01

    The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers. PMID:27336480

  9. New drug candidates in tuberculosis treatment

    Directory of Open Access Journals (Sweden)

    Begüm Evranos Aksöz

    2014-12-01

    makes them quit the treatment. From these problems emerges the need for development of effective new drugs, with smaller duration of therapy, less side effects and without the problem of resistance. After a long period such as 40 years, a new drug molecule bedaquiline was approved in December 2012 by FDA while the drug was in phase II research. Bedaquiline will be used in multidrug resistant tuberculosis therapy. When the chemical structures of bedaquilline and other candidate drugs were examined, the structures such as diarylquinoline, oxazolidinone, nitroimidazole, ethylenediamine drew attention. These common structures will be directive in designing new molecules. In this review, bedaquiline and other candidate drug molecules such as sutezolide, linezolide, PA-824, delamanide, rifapentine, gatifloxacin, moxifloxacin, BTZ-043, TBA-354, CPZEN-45, DC-159a, Q201, SQ-609, SQ-641 were mentioned.

  10. Progress and Prospects of Long Noncoding RNAs (lncRNAs in Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Chen Li

    2015-05-01

    Full Text Available Hepatocellular carcinoma (HCC is one of the most frequently occurring cancers with poor prognosis, and novel diagnostic or prognostic biomarkers and therapeutic targets for HCC are urgently required. With the advance of high-resolution microarrays and massively parallel sequencing technology, lncRNAs are suggested to play critical roles in the tumorigenesis and development of human HCC. To date, dysregulation of many HCC-related lncRNAs such as HULC, HOTAIR, MALAT1, and H19 have been identified. From transcriptional “noise” to indispensable elements, lncRNAs may re-write the central dogma. Also, lncRNAs found in body fluids have demonstrated their utility as fluid-based noninvasive markers for clinical use and as therapeutic targets for HCC. Even though several lncRNAs have been characterized, the underlying mechanisms of their contribution to HCC remain unknown, and many important questions about lncRNAs need resolving. A better understanding of the molecular mechanism in HCC-related lncRNAs will provide a rationale for novel effective lncRNA-based targeted therapies. In this review, we highlight the emerging roles of lncRNAs in HCC, and discuss their potential clinical applications as biomarkers for the diagnosis, prognosis, monitoring and treatment of HCC.

  11. Progress and Prospects of Long Noncoding RNAs (lncRNAs) in Hepatocellular Carcinoma.

    Science.gov (United States)

    Li, Chen; Chen, Jing; Zhang, Kai; Feng, Bing; Wang, Rui; Chen, Longbang

    2015-01-01

    Hepatocellular carcinoma (HCC) is one of the most frequently occurring cancers with poor prognosis, and novel diagnostic or prognostic biomarkers and therapeutic targets for HCC are urgently required. With the advance of high-resolution microarrays and massively parallel sequencing technology, lncRNAs are suggested to play critical roles in the tumorigenesis and development of human HCC. To date, dysregulation of many HCC-related lncRNAs such as HULC, HOTAIR, MALAT1, and H19 have been identified. From transcriptional "noise" to indispensable elements, lncRNAs may re-write the central dogma. Also, lncRNAs found in body fluids have demonstrated their utility as fluid-based noninvasive markers for clinical use and as therapeutic targets for HCC. Even though several lncRNAs have been characterized, the underlying mechanisms of their contribution to HCC remain unknown, and many important questions about lncRNAs need resolving. A better understanding of the molecular mechanism in HCC-related lncRNAs will provide a rationale for novel effective lncRNA-based targeted therapies. In this review, we highlight the emerging roles of lncRNAs in HCC, and discuss their potential clinical applications as biomarkers for the diagnosis, prognosis, monitoring and treatment of HCC. PMID:25968300

  12. Structural Alignment of RNA with Complex Pseudoknot Structure

    Science.gov (United States)

    Wong, Thomas K. F.; Lam, T. W.; Sung, Wing-Kin; Yiu, S. M.

    The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this paper, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

  13. The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics—Identifying biomarker signatures by multivariate data analysis

    Science.gov (United States)

    Melanie, Spornraft; Benedikt, Kirchner; Pfaffl, Michael W.; Irmgard, Riedmaier

    2015-01-01

    Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, ‘black sheep‘ among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative and reliable detection method. Transcriptomics is a promising new approach in the discovery of veterinary medicine biomarkers and also a missing puzzle piece, as up to date, metabolomics and proteomics are paramount. Due to increased stability and easy sampling, circulating extracellular small RNAs (smexRNAs) in bovine plasma were small RNA-sequenced and their potential to serve as biomarker candidates was evaluated using multivariate data analysis tools. After running the data evaluation pipeline, the proportion of miRNAs (microRNAs) and piRNAs (PIWI-interacting small non-coding RNAs) on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol) is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse. PMID:27077039

  14. The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics-Identifying biomarker signatures by multivariate data analysis.

    Science.gov (United States)

    Melanie, Spornraft; Benedikt, Kirchner; Pfaffl, Michael W; Irmgard, Riedmaier

    2015-09-01

    Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, 'black sheep' among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative and reliable detection method. Transcriptomics is a promising new approach in the discovery of veterinary medicine biomarkers and also a missing puzzle piece, as up to date, metabolomics and proteomics are paramount. Due to increased stability and easy sampling, circulating extracellular small RNAs (smexRNAs) in bovine plasma were small RNA-sequenced and their potential to serve as biomarker candidates was evaluated using multivariate data analysis tools. After running the data evaluation pipeline, the proportion of miRNAs (microRNAs) and piRNAs (PIWI-interacting small non-coding RNAs) on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol) is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse. PMID:27077039

  15. Identification of miRNAs Responsive to Botrytis cinerea in Herbaceous Peony (Paeonia lactiflora Pall. by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Daqiu Zhao

    2015-09-01

    Full Text Available Herbaceous peony (Paeonia lactiflora Pall., one of the world’s most important ornamental plants, is highly susceptible to Botrytis cinerea, and improving resistance to this pathogenic fungus is a problem yet to be solved. MicroRNAs (miRNAs play an essential role in resistance to B. cinerea, but until now, no studies have been reported concerning miRNAs induction in P. lactiflora. Here, we constructed and sequenced two small RNA (sRNA libraries from two B. cinerea-infected P. lactiflora cultivars (“Zifengyu” and “Dafugui” with significantly different levels of resistance to B. cinerea, using the Illumina HiSeq 2000 platform. From the raw reads generated, 4,592,881 and 5,809,796 sRNAs were obtained, and 280 and 306 miRNAs were identified from “Zifengyu” and “Dafugui”, respectively. A total of 237 conserved and 7 novel sequences of miRNAs were differentially expressed between the two cultivars, and we predicted and annotated their potential target genes. Subsequently, 7 differentially expressed candidate miRNAs were screened according to their target genes annotated in KEGG pathways, and the expression patterns of miRNAs and corresponding target genes were elucidated. We found that miR5254, miR165a-3p, miR3897-3p and miR6450a might be involved in the P. lactiflora response to B. cinerea infection. These results provide insight into the molecular mechanisms responsible for resistance to B. cinerea in P. lactiflora.

  16. Identification of Zinc Deficiency-Responsive MicroRNAs in Brassica juncea Roots by Small RNA Sequencing

    Institute of Scientific and Technical Information of China (English)

    SHI Dong-qing; ZHANG Yuan; MA Jin-hu; LI Yu-long; and XU Jin

    2013-01-01

    The importance of zinc (Zn) as a micronutrient essential for plant growth and development is becoming increasingly apparent. Much of the world’s soil is Zn-deficient, and soil-based Zn deficiency is often accompanied by Zn deficiency in human populations. MicroRNAs (miRNAs) play important roles in the regulation of plant gene expression at the level of translation. Many miRNAs involved in the modulation of heavy metal toxicity responses in plants have been identiifed;however, the role of miRNAs in the plant Zn deifciency response is almost completely unknown. Using high-throughput Solexa sequencing, we identiifed several miRNAs that respond to Zn deifciency in Brassica juncea roots. At least 21 conserved candidate miRNA families, and 101 individual members within those families, were identiifed in both the control and the Zn-deifcient B. juncea roots. Among this, 15 miRNAs from 9 miRNA families were differentially expressed in the control and Zn-deifcient plants. Of the 15 differentially expressed miRNAs, 13 were up-regulated in the Zn-deifcient B. juncea roots, and only two, miR399b and miR845a, were down-regulated. Bioinformatics analysis indicated that these miRNAs were involved in modulating phytohormone response, plant growth and development, and abiotic stress responses in B. juncea roots. These data help to lay the foundation for further understanding of miRNA function in the regulation of the plant Zn deifciency response and its impact on plant growth and development.

  17. Identification of miRNAs Responsive to Botrytis cinerea in Herbaceous Peony (Paeonia lactiflora Pall.) by High-Throughput Sequencing.

    Science.gov (United States)

    Zhao, Daqiu; Gong, Saijie; Hao, Zhaojun; Tao, Jun

    2015-01-01

    Herbaceous peony (Paeonia lactiflora Pall.), one of the world's most important ornamental plants, is highly susceptible to Botrytis cinerea, and improving resistance to this pathogenic fungus is a problem yet to be solved. MicroRNAs (miRNAs) play an essential role in resistance to B. cinerea, but until now, no studies have been reported concerning miRNAs induction in P. lactiflora. Here, we constructed and sequenced two small RNA (sRNA) libraries from two B. cinerea-infected P. lactiflora cultivars ("Zifengyu" and "Dafugui") with significantly different levels of resistance to B. cinerea, using the Illumina HiSeq 2000 platform. From the raw reads generated, 4,592,881 and 5,809,796 sRNAs were obtained, and 280 and 306 miRNAs were identified from "Zifengyu" and "Dafugui", respectively. A total of 237 conserved and 7 novel sequences of miRNAs were differentially expressed between the two cultivars, and we predicted and annotated their potential target genes. Subsequently, 7 differentially expressed candidate miRNAs were screened according to their target genes annotated in KEGG pathways, and the expression patterns of miRNAs and corresponding target genes were elucidated. We found that miR5254, miR165a-3p, miR3897-3p and miR6450a might be involved in the P. lactiflora response to B. cinerea infection. These results provide insight into the molecular mechanisms responsible for resistance to B. cinerea in P. lactiflora. PMID:26393656

  18. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection.

    Directory of Open Access Journals (Sweden)

    Evgeny A Glazov

    Full Text Available MicroRNA (miRNA and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.

  19. Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs).

    Science.gov (United States)

    Sharma, Namisha; Sahu, Pranav Pankaj; Puranik, Swati; Prasad, Manoj

    2013-09-01

    Regulation of several biological functions in plants has now been known to involve diverse RNA silencing pathways. These vital pathways involve various components such as dsRNA, Dicer, RNA-dependent RNA polymerase and Argonaute proteins, which lead to the production of several small RNAs (sRNAs) varying in their sizes. These sRNAs have significant role in the regulation of gene expression at transcriptional and translational levels. Among them, small interfering RNAs (siRNAs; majorly 21, 22 and 24 nt) have been shown to play an important role in plants' resistance against many viruses by inhibiting the viral gene expression. Furthermore, it has also been highlighted that siRNA-mediated methylation of viral DNA confers resistance to various plant DNA viruses. In this review, we have outlined the recent advances made using the siRNA-mediated antiviral strategy, along with methylation-based epigenetic defensive mechanisms as a protective measure against diverse plant viruses. PMID:23086491

  20. Profiling of circulating microRNAs for prostate cancer biomarker discovery

    DEFF Research Database (Denmark)

    Haldrup, Christa; Kosaka, Nobuyoshi; Ochiya, Takahiro;

    2014-01-01

    and T-stage of the primary PC. Better tools to assess PC aggressiveness could aid in treatment decisions. Recently, circulating miRNAs have been suggested as potential new biomarkers for PC with diagnostic and prognostic potential. Here, to identify new serum miRNA biomarker candidates for PC, we...... well-documented candidate miRNA markers for PC. Moreover, we identified several new potential serum miRNA markers for PC and developed three novel and highly specific (100 %) miRNA candidate marker panels able to identify 84 % of all PC patients (miR-562/miR-210/miR-501-3p/miR-375/miR-551b), 80 % of...

  1. Data of in vitro synthesized dsRNAs on growth and development of Helicoverpa armigera.

    Science.gov (United States)

    Chikate, Yojana R; Dawkar, Vishal V; Barbole, Ranjit S; Tilak, Priyadarshini V; Gupta, Vidya S; Giri, Ashok P

    2016-06-01

    The data presented in this article is related to the research article "RNAi of selected candidate genes interrupts growth and development of Helicoverpa armigera" (Chikate et al., 2016) [1]. RNA interference (RNAi) is emerging as a potent insect pest control strategy over current methods and their resistance by pest. In this study we tested 15 different in vitro synthesized dsRNAs for gene silencing in Helicoverpa armigera. These dsRNAs were specific against H. armigera enzymes/proteins such as proteases like trypsins (HaTry2, 3, 4 and 6), chymotrypsin (HaChy4) and cysteine proteases such as cathepsin (HaCATHL); glutathione S-transferases (HaGST1a, 6 and 8); esterases (HaAce4, HaJHE); catalase (HaCAT); super-oxide-dismutase (HaCu/ZnSOD); fatty acid binding protein (HaFabp) and chitin deacetylase (HaCda5b). These dsRNAs were fed to second instar larvae at an optimized dose (60 µg/day) for 3 days separately. Effects of dsRNA feeding were observed in terms of larval mass gain, percentage mortality and phenotypic abnormalities in later developmental stages of H. armigera. These findings might provide potential new candidates for designing sequence-specific dsRNA as pesticide in crop protection. PMID:27222861

  2. MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea.

    Directory of Open Access Journals (Sweden)

    Yan-Liang Lin

    Full Text Available Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium were sequenced using the next-generation sequencing (NGS technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs, we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.

  3. The regulatory epicenter of miRNAs

    Indian Academy of Sciences (India)

    Ashwani Jha; Mrigaya Mehra; Ravi Shankar

    2011-09-01

    miRNAs are small non-coding RNAs with average length of ∼21 bp. miRNA formation seems to be dependent upon multiple factors besides Drosha and Dicer, in a tissue/stage-specific manner, with interplay of several specific binding factors. In the present study, we have investigated transcription factor binding sites in and around the genomic sequences of precursor miRNAs and RNA-binding protein (RBP) sites in miRNA precursor sequences, analysed and tested in comprehensive manner. Here, we report that miRNA precursor regions are positionally enriched for binding of transcription factors as well as RBPs around the 3′ end of mature miRNA region in 5′ arm. The pattern and distribution of such regulatory sites appears to be a characteristic of precursor miRNA sequences when compared with non-miRNA sequences as negative dataset and tested statistically. When compared with 1 kb upstreamregions, a sudden sharp peak for binding sites arises in the enriched zone near the mature miRNA region. An expression-data-based correlation analysis was performed between such miRNAs and their corresponding transcription factors and RBPs for this region. Some specific groups of binding factors and associated miRNAs were identified. We also identified some of the overrepresented transcription factors and associated miRNAs with high expression correlation values which could be useful in cancer-related studies. The highly correlated groups were found to host experimentally validated composite regulatory modules, in which Lmo2-GATA1 appeared as the predominant one. For many of RBP–miRNAs associations, co-expression similarity was also evident among the associated miRNA common to given RBPs, supporting the Regulon model, suggesting a common role and common control of these miRNAs by the associated RBPs. Based on our findings, we propose that the observed characteristic distribution of regulatory sites in precursor miRNA sequence regions could be critical inmiRNA transcription, processing

  4. MicroRNAs in Cardiometabolic Diseases

    Directory of Open Access Journals (Sweden)

    Anna Meiliana

    2013-08-01

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are ~22-nucleotide noncoding RNAs with critical functions in multiple physiological and pathological processes. An explosion of reports on the discovery and characterization of different miRNA species and their involvement in almost every aspect of cardiac biology and diseases has established an exciting new dimension in gene regulation networks for cardiac development and pathogenesis. CONTENT: Alterations in the metabolic control of lipid and glucose homeostasis predispose an individual to develop cardiometabolic diseases, such as type 2 diabetes mellitus and atherosclerosis. Work over the last years has suggested that miRNAs play an important role in regulating these physiological processes. Besides a cell-specific transcription factor profile, cell-specific miRNA-regulated gene expression is integral to cell fate and activation decisions. Thus, the cell types involved in atherosclerosis, vascular disease, and its myocardial sequelae may be differentially regulated by distinct miRNAs, thereby controlling highly complex processes, for example, smooth muscle cell phenotype and inflammatory responses of endothelial cells or macrophages. The recent advancements in using miRNAs as circulating biomarkers or therapeutic modalities, will hopefully be able to provide a strong basis for future research to further expand our insights into miRNA function in cardiovascular biology. SUMMARY: MiRNAs are small, noncoding RNAs that function as post-transcriptional regulators of gene expression. They are potent modulators of diverse biological processes and pathologies. Recent findings demonstrated the importance of miRNAs in the vasculature and the orchestration of lipid metabolism and glucose homeostasis. MiRNA networks represent an additional layer of regulation for gene expression that absorbs perturbations and ensures the robustness of biological systems. A detailed understanding of the molecular and cellular mechanisms of mi

  5. Resveratrol, MicroRNAs, Inflammation, and Cancer

    Directory of Open Access Journals (Sweden)

    Esmerina Tili

    2011-01-01

    Full Text Available MicroRNAs are short noncoding RNAs that regulate the expression of many target genes posttranscriptionally and are thus implicated in a wide array of cellular and developmental processes. The expression of miR-155 or miR-21 is upregulated during the course of the inflammatory response, but these microRNAs are also considered oncogenes due to their upregulation of expression in several types of tumors. Furthermore, it is now well established that inflammation is associated with the induction or the aggravation of nearly 25% of cancers. Therefore, the above microRNAs are thought to link inflammation and cancer. Recently, resveratrol (trans-3,4′,5-trihydroxystilbene, a natural polyphenol with antioxidant, anti-inflammatory, and anticancer properties, currently at the stage of preclinical studies for human cancer prevention, has been shown to induce the expression of miR-663, a tumor-suppressor and anti-inflammatory microRNA, while downregulating miR-155 and miR-21. In this paper we will discuss how the use of resveratrol in therapeutics may benefit from the preanalyses on the status of expression of miR-155 or miR-21 as well as of TGFβ1. In addition, we will discuss how resveratrol activity might possibly be enhanced by simultaneously manipulating the levels of its key target microRNAs, such as miR-663.

  6. Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets.

    Science.gov (United States)

    Prakash, Pravin; Ghosliya, Dolly; Gupta, Vikrant

    2015-01-10

    MicroRNAs are small endogenous non-coding RNAs of ~19-24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants. PMID:25445288

  7. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

    Directory of Open Access Journals (Sweden)

    Chong Kang

    2009-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

  8. Electoral Systems and Candidate Selection

    NARCIS (Netherlands)

    Hazan, Reuven Y.; Voerman, Gerrit

    2006-01-01

    Electoral systems at the national level and candidate selection methods at the party level are connected, maybe not causally but they do influence each other. More precisely, the electoral system constrains and conditions the parties' menu of choices concerning candidate selection. Moreover, in ligh

  9. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.

    Directory of Open Access Journals (Sweden)

    Beatriz Navarro

    Full Text Available BACKGROUND: Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21-24 nt small RNAs (vd-sRNAs with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms. METHODOLOGY/PRINCIPAL FINDINGS: To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd and Grapevine yellow speckle viroid 1 (GYSVd1 were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots of the genomic (+ and (- viroid RNAs, with a prevalence of those from the (- strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots. CONCLUSIONS/SIGNIFICANCE: These findings show that different Dicer-like enzymes (DCLs target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.

  10. MicroRNAs in cancers and neurodegenerative disorders

    OpenAIRE

    Saito, Yoshimasa; Saito, Hidetsugu

    2012-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs which function as endogenous silencers of various target genes. miRNAs are expressed in a tissue-specific manner and playing important roles in cell proliferation, apoptosis, and differentiation during mammalian development. Links between miRNAs and the initiation and progression of human diseases including cancer are becoming increasingly apparent. Recent studies have revealed that some miRNAs such as miR-9, miR-29 family, and miR-34 family are di...

  11. Long noncoding RNAs and Alzheimer’s disease

    Science.gov (United States)

    Luo, Qiong; Chen, Yinghui

    2016-01-01

    Long noncoding RNAs (lncRNAs) are typically defined as transcripts longer than 200 nucleotides. lncRNAs can regulate gene expression at epigenetic, transcriptional, and posttranscriptional levels. Recent studies have shown that lncRNAs are involved in many neurological diseases such as epilepsy, neurodegenerative conditions, and genetic disorders. Alzheimer’s disease is a neurodegenerative disease, which accounts for >80% of dementia in elderly subjects. In this review, we will highlight recent studies investigating the role of lncRNAs in Alzheimer’s disease and focus on some specific lncRNAs that may underlie Alzheimer’s disease pathophysiology and therefore could be potential therapeutic targets. PMID:27418812

  12. A New Strategy for Identification of Highly Conserved microRNAs in Non-Model Insect, Spodoptera litura

    Directory of Open Access Journals (Sweden)

    Guohua Zhong

    2012-01-01

    Full Text Available The indigenous small non-coding RNAs, known as microRNAs (miRNAs, are important regulators of gene expression and many of them are evolutionarily conserved. Whether stem-loop RT-PCR, as a sensitive method, could be utilized to clone conserved miRNAs from non-model insects lacks information. Here, three miRNAs, sli-miR-14, sli-miR-2a and sli-bantam, were cloned from Spodoptera litura by stem-loop RT-PCR. Two groups of primers were designed, and one of them performed especially well and proved stable. The sequences of two highly conserved miRNAs, sli-miR-14 and sli-miR-2a were identical to those in Drosophila melanogaster. To validate the reliability of this strategy, pre-miR-14 and pre-miR-2a in S. litura as representatives were given as well; this shared high homology with those in D. melanogaster and Bombyx mori, and both mature sequences of sli-miR-14 and sli-miR-2a in their precursors shared 100% identity to the results shown by stem-loop RT-PCR. Moreover, expression patterns of these miRNAs were investigated by real-time quantitative PCR. Sli-miR-14 and sli-miR-2a could be detected successfully and their expression patterns showed similar characteristics with those in model insects, further suggesting stem-loop RT-PCR technology can be used for identification of highly conserved miRNAs in non-model insects. These results provide a simplified and efficient strategy for studying the structure and function of highly conserved miRNAs, especially some critical miRNAs in non-model insects.

  13. Discovery of MicroRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs.

    Directory of Open Access Journals (Sweden)

    Xinhua Hou

    Full Text Available MicroRNAs (miRNAs are short, single-stranded non-coding RNAs that repress their target genes by binding their 3' UTRs. These RNAs play critical roles in myogenesis. To gain knowledge about miRNAs involved in the regulation of myogenesis, porcine longissimus muscles were collected from 18 developmental stages (33-, 40-, 45-, 50-, 55-, 60-, 65-, 70-, 75-, 80-, 85-, 90-, 95-, 100- and 105-day post-gestation fetuses, 0 and 10-day postnatal piglets and adult pigs to identify miRNAs using Solexa sequencing technology. We detected 197 known miRNAs and 78 novel miRNAs according to comparison with known miRNAs in the miRBase (release 17.0 database. Moreover, variations in sequence length and single nucleotide polymorphisms were also observed in 110 known miRNAs. Expression analysis of the 11 most abundant miRNAs were conducted using quantitative PCR (qPCR in eleven tissues (longissimus muscles, leg muscles, heart, liver, spleen, lung, kidney, stomach, small intestine and colon, and the results revealed that ssc-miR-378, ssc-miR-1 and ssc-miR-206 were abundantly expressed in skeletal muscles. During skeletal muscle development, the expression level of ssc-miR-378 was low at 33 days post-coitus (dpc, increased at 65 and 90 dpc, peaked at postnatal day 0, and finally declined and maintained a comparatively stable level. This expression profile suggested that ssc-miR-378 was a new candidate miRNA for myogenesis and participated in skeletal muscle development in pigs. Target prediction and KEGG pathway analysis suggested that bone morphogenetic protein 2 (BMP2 and mitogen-activated protein kinase 1 (MAPK1, both of which were relevant to proliferation and differentiation, might be the potential targets of miR-378. Luciferase activities of report vectors containing the 3'UTR of porcine BMP2 or MAPK1 were downregulated by miR-378, which suggested that miR-378 probably regulated myogenesis though the regulation of these two genes.

  14. Plant microRNAs and Stressors: A Commentary on Stressresponsive miRNAs in Glycine max (L. Merrill

    Directory of Open Access Journals (Sweden)

    Shunmugiah V Ramesh

    2015-05-01

    Full Text Available Small non-coding RNAs (sncRNAs are potent regulators of indispensable biological functions such as gene expression, maintenance of chromatin status, defence against invading nucleic acids like viruses, transposons etc in plants and animals. sncRNA repertoire of plants comprises small interfering RNAs (siRNAs and microRNAs (miRNAs as ultimate regulators of gene expression pathways. First small ncRNA (lin-4 with a role in post-transcriptional gene silencing (PTGS was discovered way back in 1993 in C. elegans [1]. Nonetheless, it was not until 1998 the basic phenomenon of sequence dependent RNA based gene silencing or RNA interference (RNAi itself was uncovered. Later on, the significance of sRNAs especially, miRNAs and their role in multitude of host developmental and growth activities including response to biotic and abiotic stresses were reported. miRNAs down regulate expression of cognate mRNAs that exhibit sequence complementary thereby functions as negative regulators of such genes. Hence under the influence of stress, miRNAs that are upregulated lead to repression of cognate mRNAs whereas miRNAs whose levels are suppressed result in abundant target mRNAs which may assist the plants tide over adverse stress conditions.

  15. Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum

    Directory of Open Access Journals (Sweden)

    Wang Heng

    2010-01-01

    Full Text Available Abstract Background Small endogenous non-coding RNAs (sncRNAs such as small interfering RNA (siRNA, microRNA and other small RNA transcripts are derived from distinct loci in the genome and play critical roles in RNA-mediated gene silencing mechanisms in plants and metazoa. They are approximately 22 nucleotides long; regulate mRNA stability through perfect or imperfect match to the targets. The biological activities of sncRNAs have been related to many biological events, from resistance to microbe infections to cellular differentiation. The development of the zoonotic parasite Schistosoma japonicum parasite includes multiple steps of morphological alterations and biological differentiations, which provide a unique model for studies on the functions of small RNAs. Characterization of the genome-wide transcription of the sncRNAs will be a major step in understanding of the parasite biology. The objective of this study is to investigate the transcriptional profile and potential function of the small non-coding RNAs in the development of S. japanicum. Results The endogenous siRNAs were found mainly derived from transposable elements (TE or transposons and the natural antisense transcripts (NAT. In contrast to other organisms, the TE-derived siRNAs in S. japonicum were more predominant than other sncRNAs including microRNAs (miRNAs. Further, there were distinct length and 3'end variations in the sncRNAs, which were associated with the developmental differentiation of the parasite. Among the identified miRNA transcripts, there were 38 unique to S. japonicum and 16 that belonged to 13 miRNA families are common to other metazoan lineages. These miRNAs were either ubiquitously expressed, or they exhibited specific expression patterns related to the developmental stages or sex. Genes that encoded miRNAs are mainly located in clusters within the genome of S. japonicum. However, genes within one cluster could be differentially transcribed, which suggested

  16. Small RNAs controlling outer membrane porins

    DEFF Research Database (Denmark)

    Valentin-Hansen, Poul; Johansen, Jesper; Rasmussen, Anders A

    2007-01-01

    Gene regulation by small non-coding RNAs has been recognized as an important post-transcriptional regulatory mechanism for several years. In Gram-negative bacteria such as Escherichia coli and Salmonella, these RNAs control stress response and translation of outer membrane proteins and therefore...... are key regulators of environmental stress. Recent work has revealed an intimate interplay between small RNA regulation of outer membrane proteins and the stress-induced sigmaE-signalling system, which has an essential role in the maintenance of the integrity of the outer membrane....

  17. Targeting microRNAs in heart failure.

    Science.gov (United States)

    Duygu, Burcu; de Windt, Leon J; da Costa Martins, Paula A

    2016-02-01

    MicroRNAs play pivotal roles in cardiac disease, and their therapeutic modulation raises exciting and unique opportunities, as well as challenges in the path toward clinical development and implementation. In this review, we provide a detailed overview of recent studies highlighting the important role of microRNAs in heart failure (HF) and the potential use of microRNA-based technology for diagnosis, prevention, and treatment of HF. We will focus on the strategies presently used for microRNA-based therapy by discussing their use and drawbacks, as well as the challenges and future directions for their development in the context of human HF. PMID:26119078

  18. Isolation of circulating microRNAs from microvesicles found in human plasma.

    Science.gov (United States)

    Quackenbush, John F; Cassidy, Pamela B; Pfeffer, Lawrence M; Boucher, Kenneth M; Hawkes, Jason E; Pfeffer, Susan R; Kopelovich, Levy; Leachman, Sancy A

    2014-01-01

    Intact miRNAs can be isolated from the circulation in significant quantities despite the presence of extremely high levels of RNase activity. The remarkable stability of circulating miRNAs makes them excellent candidates for biomarkers in diagnostic applications as well as therapeutic targets in a variety of disease states including melanoma. Circulating RNA molecules are resistant to degradation by RNases because they are encapsulated in membrane-bound microvesicles. We describe a convenient method for the use of ExoQuick, a proprietary resin developed by Systems Biosciences (Mountain View, CA), whereby microvesicles can be purified under gentle conditions using readily available laboratory equipment. This protocol allows for isolation all microvesicles, regardless of their origin, and provides a convenient method for identifying potential cancer-specific biomarkers from biological fluids including serum and plasma. PMID:24259003

  19. Analysis of epigenetic effects (microRNAs) in former employees of Wismut

    International Nuclear Information System (INIS)

    Aim of the study was the development and establishment of an oligonucleotide microarray for expression analysis of microRNAs (miRNAs) in whole blood of former uranium miners. To identify possible biomarkers of radiation exposure, samples of high- and low-exposed miners were screened with microarrays that carried 703 human miRNA probes. To that end, 60 RNA samples of the project ''Creation of a biological sample and data collection of occupationally radiation-exposed workers (German Uranium Miners Biobank) - a pilot study'' (3607S04532) were analysed and potential biomarkers verified by quantitative real-time PCR (qRT-PCR). During the initial screening, mirRNA-548d-5p, showing a significantly altered expression between low- and high-exposed miners, was identified as a possible biomarker candidate. Verification by qRT-PCR confirmed the difference in expression, however, the result was not statistically significant.

  20. Optimized methods for extracting circulating small RNAs from long-term stored equine samples.

    Science.gov (United States)

    Unger, Lucia; Fouché, Nathalie; Leeb, Tosso; Gerber, Vincent; Pacholewska, Alicja

    2016-01-01

    Circulating miRNAs in body fluids, particularly serum, are promising candidates for future routine biomarker profiling in various pathologic conditions in human and veterinary medicine. However, reliable standardized methods for miRNA extraction from equine serum and fresh or archived whole blood are sorely lacking. We systematically compared various miRNA extraction methods from serum and whole blood after short and long-term storage without addition of RNA stabilizing additives prior to freezing. Time of storage at room temperature prior to freezing did not affect miRNA quality in serum. Furthermore, we showed that miRNA of NGS-sufficient quality can be recovered from blood samples after >10 years of storage at -80 °C. This allows retrospective analyses of miRNAs from archived samples. PMID:27356979

  1. Identification and Characterization of Erysiphe necator-Responsive MicroRNAs in Chinese Wild Vitis pseudoreticulata by High-Throughput Sequencing

    Science.gov (United States)

    Han, Lijuan; Weng, Kai; Ma, Hui; Xiang, Gaoqing; Li, Zhiqian; Wang, Yuejin; Liu, Guotian; Xu, Yan

    2016-01-01

    Grapevine powdery mildew is one of the most damaging fungal diseases. Therefore, a precise understanding of the grapevine disease resistance system becomes a subject of significant importance. Plant microRNAs(miRNAs) have been implicated to play regulatory roles in plant biotic stress responses. In this study, high-throughput sequencing and miRDeep-P were employed to identify miRNAs in Chinese wild Vitis pseudoreticulata leaves following inoculation with Erysiphe necator. Altogether, 126 previously identified microRNAs and 124 novel candidates of miRNA genes were detected. Among them, 43 conserved miRNAs belong to 20 families and 23 non-conserved but previously-known miRNAs belong to 15 families. Following E. necator inoculation, 119 miRNAs were down-regulated and 131 were up-regulated. Furthermore, the expression changes occurring in 32 miRNAs were significant. The expression patterns of some miRNAs were validated by semi-quantitative RT-PCR and qRT-PCR. A total of 485 target genes were predicted and categorized by Gene Ontology (GO). In addition, 14 vvi-miRNAs were screened with 36 targets which may be involved in powdery mildew resistance in grape. Highly accumulated vvi-NewmiR2118 was detected from accession “Baihe-35-1,” whose targets were mostly NBS-LRR resistance genes. It was down-regulated rapidly and strongly in “Baihe-35-1” leaves after inoculated with E. necator, indicating its involvement in grape powdery mildew resistance. Finally, the study verified interaction between vvi-NewmiR2118 and RPP13 by histochemical staining and GUS fluorescence quantitative assay. PMID:27303408

  2. Detection of piRNAs in whitespotted bamboo shark liver.

    Science.gov (United States)

    Yang, Lingrong; Ge, Yinghua; Cheng, Dandan; Nie, Zuoming; Lv, Zhengbing

    2016-09-15

    Piwi-interacting RNAs (piRNAs) are 26 to 31-nt small non-coding RNAs that have been reported mostly in germ-line cells and cancer cells. However, the presence of piRNAs in the whitespotted bamboo shark liver has not yet been reported. In a previous study of microRNAs in shark liver, some piRNAs were detected from small RNAs sequenced by Solexa technology. A total of 4857 piRNAs were predicted and found in shark liver. We further selected 17 piRNAs with high and significantly differential expression between normal and regenerative liver tissues for subsequent verification by Northern blotting. Ten piRNAs were further identified, and six of these were matched to known piRNAs in piRNABank. The actual expression of six known and four novel piRNAs was validated by qRT-PCR. In addition, a total of 401 target genes of the 10 piRNAs were predicted by miRanda. Through GO and pathway function analyses, only five piRNAs could be annotated with eighteen GO annotations. The results indicated that the identified piRNAs are involved in many important biological responses, including immune inflammation, cell-specific differentiation and development, and angiogenesis. This manuscript provides the first identification of piRNAs in the liver of whitespotted bamboo shark using Solexa technology as well as further elucidation of the regulatory role of piRNAs in whitespotted bamboo shark liver. These findings may provide a useful resource and may facilitate the development of therapeutic strategies against liver damage. PMID:27267405

  3. MicroRNAs in Human Placental Development and Pregnancy Complications

    Directory of Open Access Journals (Sweden)

    Chun Peng

    2013-03-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs, which function as critical posttranscriptional regulators of gene expression by promoting mRNA degradation and translational inhibition. Placenta expresses many ubiquitous as well as specific miRNAs. These miRNAs regulate trophoblast cell differentiation, proliferation, apoptosis, invasion/migration, and angiogenesis, suggesting that miRNAs play important roles during placental development. Aberrant miRNAs expression has been linked to pregnancy complications, such as preeclampsia. Recent research of placental miRNAs focuses on identifying placental miRNA species, examining differential expression of miRNAs between placentas from normal and compromised pregnancies, and uncovering the function of miRNAs in the placenta. More studies are required to further understand the functional significance of miRNAs in placental development and to explore the possibility of using miRNAs as biomarkers and therapeutic targets for pregnancy-related disorders. In this paper, we reviewed the current knowledge about the expression and function of miRNAs in placental development, and propose future directions for miRNA studies.

  4. Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

    Directory of Open Access Journals (Sweden)

    Vincentz Michel

    2010-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp. is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. Results In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots. Conclusions Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two

  5. Clinical Candidate VT-1161's Antiparasitic Effect In Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme CYP51 from Trypanosoma cruzi.

    Science.gov (United States)

    Hoekstra, William J; Hargrove, Tatiana Y; Wawrzak, Zdzislaw; da Gama Jaen Batista, Denise; da Silva, Cristiane F; Nefertiti, Aline S G; Rachakonda, Girish; Schotzinger, Robert J; Villalta, Fernando; Soeiro, Maria de Nazaré C; Lepesheva, Galina I

    2016-02-01

    A novel antifungal drug candidate, the 1-tetrazole-based agent VT-1161 [(R)-2-(2,4-difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-{5-[4-(2,2,2-trifluoroethoxy)phenyl]pyridin-2-yl}propan-2-ol], which is currently in two phase 2b antifungal clinical trials, was found to be a tight-binding ligand (apparent dissociation constant [Kd], 24 nM) and a potent inhibitor of cytochrome P450 sterol 14α-demethylase (CYP51) from the protozoan pathogen Trypanosoma cruzi. Moreover, VT-1161 revealed a high level of antiparasitic activity against amastigotes of the Tulahuen strain of T. cruzi in cellular experiments (50% effective concentration, 2.5 nM) and was active in vivo, causing >99.8% suppression of peak parasitemia in a mouse model of infection with the naturally drug-resistant Y strain of the parasite. The data strongly support the potential utility of VT-1161 in the treatment of Chagas disease. The structural characterization of T. cruzi CYP51 in complex with VT-1161 provides insights into the molecular basis for the compound's inhibitory potency and paves the way for the further rational development of this novel, tetrazole-based inhibitory chemotype both for antiprotozoan chemotherapy and for antifungal chemotherapy. PMID:26643331

  6. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.

    Directory of Open Access Journals (Sweden)

    Nisha Joy

    Full Text Available Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L., an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs. We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.

  7. Abberent expression of oncogenic and tumor-suppressive microRNAs and their target genes in human adenocarcinoma alveolar basal epithelial cells

    Directory of Open Access Journals (Sweden)

    Elham Tafsiri

    2016-01-01

    Conclusion: The significant differential expression level of these miRNAs made them as candidate biomarkers in NSCLC tumor tissues of patients. Perhaps Bcl-2 down-regulation and Akt-3 up-regulation can be linked with survival signals in A549 cell line. We can conclude that Bcl-2 and Akt-3 might be therapeutic targets to inhibit cell proliferation in NSCLC.

  8. The potential of circulating extracellular small RNAs (smexRNA in veterinary diagnostics—Identifying biomarker signatures by multivariate data analysis

    Directory of Open Access Journals (Sweden)

    Spornraft Melanie

    2015-09-01

    After running the data evaluation pipeline, the proportion of miRNAs (microRNAs and piRNAs (PIWI-interacting small non-coding RNAs on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse.

  9. Identification and profiling of conserved and novel microRNAs in Laodelphax striatellus in response to rice black-streaked dwarf virus (RBSDV infection

    Directory of Open Access Journals (Sweden)

    Jun-Min Li

    2015-03-01

    Full Text Available MicroRNAs (miRNAs are small non-coding endogenous RNA molecules that play important roles in various biological processes. This study examined microRNA profiles of Laodelphax striatellus using the small RNA libraries derived from virus free (VF and rice black-streaked dwarf virus (RBSDV infected (RB insects. A total of 59 mature miRNAs (46 miRNA families were identified as conserved insect miRNAs in both VF and RB libraries. Among these conserved miRNAs, 24 were derived from the two arms of 12 miRNA precursors. Nine conserved L. striatellus miRNAs were up-regulated and 12 were down-regulated in response to RBSDV infection. In addition, a total of 20 potential novel miRNA candidates were predicted in the VF and RB libraries. The miRNA transcriptome profiles and the identification of L. striatellus miRNAs differentially expressed in response to RBSDV infection will contribute to future studies to elucidate the complex miRNA-mediated regulatory network activated by pathogen challenge in insect vectors.

  10. Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus

    Directory of Open Access Journals (Sweden)

    Hakenbeck Regine

    2010-11-01

    Full Text Available Abstract Background Post-transcriptional regulation by small RNAs (sRNAs in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system. Results Genes for csRNAs were predicted in streptococcal genomes and data base entries other than S. pneumoniae by searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions, S. mitis, S. oralis, and S. sanguinis were subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene from S. thermophilus plasmid pST0 introduced into S. pneumoniae was also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision. Conclusions The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of

  11. The mitochondrial genome encodes abundant small noncoding RNAs

    Institute of Scientific and Technical Information of China (English)

    Seungil Ro; Hsiu-Yen Ma; Chanjae Park; Nicole Ortogero; Rui Song; Grant W Hennig; Huili Zheng

    2013-01-01

    Small noncoding RNAs identified thus far are all encoded by the nuclear genome.Here,we report that the murine and human mitochondriai genomes encode thousands of small noncoding RNAs,which are predominantly derived from the sense transcripts of the mitochondrial genes (host genes),and we termed these small RNAs mitochondrial genome-encoded small RNAs (mitosRNAs).DICER inactivation affected,but did not completely abolish mitosRNA production.MitosRNAs appear to be products of currently unidentified mitochondrial ribonucleases.Overexpression of mitosRNAs enhanced expression levels of their host genes in vitro,and dysregulated mitosRNA expression was generally associated with aberrant mitochondrial gene expression in vivo.Our data demonstrate that in addition to 37 known mitochondrial genes,the mammalian mitochondrial genome also encodes abundant mitosRNAs,which may play an important regulatory role in the control of mitochondrial gene expression in the cell.

  12. Long Non-coding RNAs in the Cytoplasm

    Institute of Scientific and Technical Information of China (English)

    Farooq Rashid; Abdullah Shah; Ge Shan

    2016-01-01

    An enormous amount of long non-coding RNAs (lncRNAs) transcribed from eukaryotic genome are important regulators in different aspects of cellular events. Cytoplasm is the residence and the site of action for many lncRNAs. The cytoplasmic lncRNAs play indispensable roles with multiple molecular mechanisms in animal and human cells. In this review, we mainly talk about functions and the underlying mechanisms of lncRNAs in the cytoplasm. We highlight relatively well-studied examples of cytoplasmic lncRNAs for their roles in modulating mRNA stability, regulating mRNA translation, serving as competing endogenous RNAs, functioning as precursors of microRNAs, and mediating protein modifications. We also elaborate the perspectives of cytoplasmic lncRNA studies.

  13. Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

    Directory of Open Access Journals (Sweden)

    Patenge Nadja

    2012-10-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49, employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases. Results We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5′ rapid amplification of cDNA ends-PCR (RACE-PCR analysis. Conclusions In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of sRNAs

  14. Cross-packaging of genetically distinct mouse and primate retroviral RNAs

    Directory of Open Access Journals (Sweden)

    Jaballah Soumeya

    2009-07-01

    Full Text Available Abstract Background The mouse mammary tumor virus (MMTV is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV that has intracellular assembly process similar to that of MMTV. Results Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (ψ, we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of ψ by the heterologous virus proteins. Conclusion The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for

  15. MicroRNAs horizon in retinoblastoma.

    Directory of Open Access Journals (Sweden)

    Mojgan Mirakholi

    2013-12-01

    Full Text Available In the retinoblastoma research, it is of great interest to identify molecular markers associated with the genetics of tumorigenesis. microRNAs (miRNAs are small non-coding RNA molecules that play a regulatory role in many crucial cellular pathways such as differentiation, cell cycle progression, and apoptosis. A body of evidences showed dysregulation of miRNAs in tumor biology and many diseases. They potentially play a significant role in tumorigenesis processes and have been the subject of research in many types of cancers including retinal tumorigenesis. miRNA expression profiling was found to be associated with tumor development, progression and treatment. These associations demonstrate the putative applications of miRNAs in monitoring of different aspect of tumors consisting diagnostic, prognostic and therapeutic. Herein, we review the current literature concerning to the study of miRNA target recognition, function to tumorigenesis and treatment in retinoblastoma. Identification the specific miRNA biomarkers associated with retinoblastoma cancer may help to establish new therapeutic approaches for salvage affected eyes in patients.

  16. MicroRNAs in pancreatic ductal adenocarcinoma

    Institute of Scientific and Technical Information of China (English)

    Jong Y Park; James Helm; Domenico Coppola; Donghwa Kim; Mokenge Malafa; Seung Joon Kim

    2011-01-01

    Ductal adenocarcinoma of the pancreas is a lethal cancer for which the only chance of long-term survival belongs to the patient with localized disease in whom a potentially curative resection can be done.Therefore,biomarkers for early detection and new therapeutic strategies are urgently needed.miRNAs are a recently discovered class of small endogenous non-coding RNAs of about 22 nucleotides that have gained attention for their role in downregulation of mRNA expression at the posttranscriptional level.miRNAs regulate proteins involved in critical cellular processes such as differentiation,proliferation,and apoptosis.Evidence suggests that deregulated miRNA expression is involved in carcinogenesis at many sites,including the pancreas.Aberrant expression of miRNAs may upregulate the expression of oncogenes or downregulate the expression of tumor suppressor genes,as well as play a role in other mechanisms of carcinogenesis.The purpose of this review is to summarize our knowledge of deregulated miRNA expression in pancreatic cancer and discuss the implication for potential translation of this knowledge into clinical practice.

  17. microRNAs in CNS disorders

    DEFF Research Database (Denmark)

    Kocerha, Jannet; Kauppinen, Sakari; Wahlestedt, Claes

    2009-01-01

    In recent years, there has been a shift in the conventional paradigms for transcriptional and translational regulation as extensive sequencing efforts have yielded new insights into the landscape of the human genome and transcriptome. Hundreds of non-coding regulatory RNA molecules called microRNAs...

  18. Hidden layers of human small RNAs

    DEFF Research Database (Denmark)

    Kawaji, Hideya; Nakamura, Mari; Takahashi, Yukari; Sandelin, Albin; Katayama, Shintaro; Fukuda, Shiro; Daub, Carsten O; Kai, Chikatoshi; Kawai, Jun; Yasuda, Jun; Carninci, Piero; Hayashizaki, Yoshihide

    2008-01-01

    BACKGROUND: Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile sm...

  19. Systematic Structure Modifications of Multi-target Prostate Cancer Drug Candidate Galeterone to Produce Novel Androgen Receptor Down-regulating Agents as an Approach to Treatment of Advanced Prostate Cancer

    Science.gov (United States)

    Purushottamachar, Puranik; Godbole, Abhijit M.; Gediya, Lalji K.; Martin, Marlena S.; Vasaitis, Tadas S.; Kwegyir-Afful, Andrew K.; Ramalingam, Senthilmurugan; Ates-Alagoz, Zeynep; Njar, Vincent C. O.

    2013-01-01

    As part of our program to explore the influence of small structural modifications of our drug candidate, 3β-(hydroxy)-17-(1H-benzimidazol-1-yl)-androsta-5,16-diene (galeterone, 5) on the modulation of the androgen receptor (AR), we have prepared and evaluated a series of novel C-3, C-16 and C-17 analogs. Using structure activity analysis, we established that the benzimidazole moiety at C-17 is essential and optimal and also that hydrophilic and heteroaromatic groups at C-3 enhance both anti-proliferative (AP) and AR degrading (ARD) activities. The most potent anti-proliferative compounds were 3β-(1H-imidazole-1-carboxylate)- 17-(1H-benzimidazol-1-yl)-androsta-5,16-diene (47), 3-((EZ)-hydroximino)-17-(1Hbenzimidazol- 1-yl)-androsta-4,16-diene (36), 3β-(pyridine-4-carboxylate)-17-(1H-benzimidazol- 1-yl)-androsta-5,16-diene (43), with GI50 values of 0.87, 1.91 and 2.57 μM, respectively. Compared to 5, compound 47 was 4- and 8-fold more potent with respect to AP and ARD activities, respectively. Importantly, we also discovered that our compounds, including 5, 36, 43 and 47 could degrade both full-length and truncated AR in CWR22rv1 human prostate cancer cells. With these activities, their potential for development as new drugs for the treatment of all forms of prostate cancer. PMID:23713567

  20. The role of microRNAs in bladder cancer

    OpenAIRE

    ENOKIDA, HIDEKI; YOSHINO, HIROFUMI; Matsushita, Ryosuke; Nakagawa, Masayuki

    2016-01-01

    Bladder cancer (BC) is the fifth most common cancer worldwide and is associated with significant morbidity and mortality. The prognosis of muscle invasive BC is poor, and recurrence is common after radical surgery or chemotherapy. Therefore, new diagnostic methods and treatment modalities are critical. MicroRNAs (miRNAs), a class of small noncoding RNAs, regulate the expression of protein-coding genes by repressing translation or cleaving RNA transcripts in a sequence-specific manner. miRNAs ...

  1. Molecular call and response: the physiology of bacterial small RNAs

    OpenAIRE

    Richards, Gregory R.; Vanderpool, Carin K.

    2011-01-01

    The vital role of bacterial small RNAs (sRNAs) in cellular regulation is now well-established. Although many diverse mechanisms by which sRNAs effect changes in gene expression have been thoroughly described, comparatively less is known about their biological roles and effects on cell physiology. Nevertheless, for some sRNAs, insight has been gained into the intricate regulatory interplay that is required to sense external environmental and internal metabolic cues and turn them into physiolog...

  2. Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs

    OpenAIRE

    Tikhanovich, I.; Liang, B.; Seoighe, C.; et al.

    2011-01-01

    Small noncoding RNAs regulate a variety of cellular processes, including genomic imprinting, chromatin remodeling, replication, transcription, and translation. Here, we report small replication-regulating RNAs (srRNAs) that specifically inhibit DNA replication of the human BK polyomavirus (BKV) in vitro and in vivo. srRNAs from FM3A murine mammary tumor cells were enriched by DNA replication assay-guided fractionation and hybridization to the BKV noncoding control region (NCCR) and synthesize...

  3. Non-coding RNAs as regulators of embryogenesis

    OpenAIRE

    Pauli, Andrea; Rinn, John L; Schier, Alexander F.

    2011-01-01

    Non-coding RNAs (ncRNAs) are emerging as key regulators of embryogenesis. They control embryonic gene expression by several means, ranging from microRNA-induced degradation of mRNAs to long ncRNA-mediated modification of chromatin. Many aspects of embryogenesis seem to be controlled by ncRNAs, including the maternal–zygotic transition, the maintenance of pluripotency, the patterning of the body axes, the specification and differentiation of cell types and the morphogenesis of organs. Drawing ...

  4. MicroRNAs in multiple myeloma and related bone disease

    OpenAIRE

    Rossi, Marco; Tagliaferri, Pierosandro; Tassone, Pierfrancesco

    2015-01-01

    MicroRNAs (miRNAs) are short non coding RNAs aberrantly expressed in solid and hematopoietic malignancies where they play a pivotal function as post-transcriptional regulators of gene expression. Recent reports have unveiled a central role of miRNAs in multiple myeloma onset and progression and preclinical findings are progressively disclosing their potential therapeutic value as drugs or targets. In this review, we provide the basic insights of miRNA biology and function, showing how these m...

  5. Retrovirus infected cells contain viral microRNAs

    OpenAIRE

    Klase Zachary A; Sampey Gavin C; Kashanchi Fatah

    2013-01-01

    Abstract The encoding of microRNAs in retroviral genomes has remained a controversial hypothesis despite significant supporting evidence in recent years. A recent publication demonstrating the production of functional miRNAs from the retrovirus bovine leukemia virus adds further credence to the fact that retroviruses do indeed encode their own miRNAs. Here we comment on the importance of this paper to the field, as well as examine the other known examples of miRNAs encoded by RNA viruses.

  6. The miRacle in Pancreatic Cancer by miRNAs: Tiny Angels or Devils in Disease Progression.

    Science.gov (United States)

    Hawa, Zuhair; Haque, Inamul; Ghosh, Arnab; Banerjee, Snigdha; Harris, LaCoiya; Banerjee, Sushanta K

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with increasing incidence and high mortality. Surgical resection is the only potentially curative treatment of patients with PDAC. Because of the late presentation of the disease, about 20 percent of patients are candidates for this treatment. The average survival of resected patients is between 12 and 20 months, with a high probability of relapse. Standard chemo and radiation therapies do not offer significant improvement of the survival of these patients. Furthermore, novel treatment options aimed at targeting oncogenes or growth factors in pancreatic cancer have proved unsuccessful. Thereby, identifying new biomarkers that can detect early stages of this disease is of critical importance. Among these biomarkers, microRNAs (miRNAs) have supplied a profitable recourse and become an attractive focus of research in PDAC. MiRNAs regulate many genes involved in the development of PDAC through mRNA degradation or translation inhibition. The possibility of intervention in the molecular mechanisms of miRNAs regulation could begin a new generation of PDAC therapies. This review summarizes the reports describing miRNAs involvement in cellular processes involving pancreatic carcinogenesis and their utility in diagnosis, survival and therapeutic potential in pancreatic cancer. PMID:27240340

  7. High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne

    Science.gov (United States)

    Pan, Lang; Wang, Zhaoyun; Cai, Jia; Gao, Haitao; Zhao, Hongwei; Dong, Liyao

    2016-01-01

    Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies. PMID:27353151

  8. High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne.

    Science.gov (United States)

    Pan, Lang; Wang, Zhaoyun; Cai, Jia; Gao, Haitao; Zhao, Hongwei; Dong, Liyao

    2016-01-01

    Non-target site resistance (NTSR) to herbicides is an increasing concern for weed control. The majority of previous studies have focused on metabolic resistance mechanisms of NTSR, but no research exists on gene regulation mechanisms behind herbicide resistance, such as microRNA (miRNA). Here, we identified 3 American sloughgrass (Beckmannia syzigachne Steud.) populations containing fenoxaprop-P-ethyl-resistant plants. We then constructed small RNA libraries and subjected them to deep sequencing and bioinformatics analyses. Forty known and 36 potentially novel, predicted miRNAs were successfully identified. Of these, we identified 3 conserved, predicted candidate NTSR-determinant miRNAs and their potential corresponding target genes, as well as 4 novel potential miRNAs with high count. Target gene prediction and annotation indicated that these 7 differentially expressed miRNAs potentially play a role in regulating specific stress-responsive genes, very likely related to herbicide resistance. Expression profiles were determined with quantitative real-time PCR. The present study is a novel, large-scale characterization of weed miRNAs. The results should further our understanding of miRNA expression profiles associated with herbicide resistance, allowing for the development of more effective weed management strategies. PMID:27353151

  9. Identification of reference genes for quantitative RT-PCR analysis of microRNAs and mRNAs in castor bean (Ricinus communis L.) under drought stress.

    Science.gov (United States)

    Cassol, Daniela; Cruz, Fernanda P; Espindola, Kauê; Mangeon, Amanda; Müller, Caroline; Loureiro, Marcelo Ehlers; Corrêa, Régis L; Sachetto-Martins, Gilberto

    2016-09-01

    Quantitative real-time PCR (RT-qPCR) is one of the most powerful and sensitive techniques to the study of gene expression. Several factors influence RT-qPCR performance though, including the stability of the reference genes used for data normalization. While the selection of appropriate reference genes is crucial for accurate and reliable gene expression analysis, no suitable reference genes have been previously identified in castor bean under drought stress. In this study, the expression stability of eleven mRNAs, thirteen microRNAs (miRNAs) and one small nuclear RNA were analyzed in roots and leaves across different levels of water deficit. Three different algorithms were employed to analyze the RT-qPCR data, and the resulting outputs were merged using a non-weighted unsupervised rank aggregation method. Our analysis indicated that the Elongation factor 1-beta (EF1B), Protein phosphatase 2A (PP2A) and ADP-ribosylation factor (ADP) ranked as the best candidates across diverse samples submitted to different levels of drought conditions. EF1B and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and EF1B and SKP1/ASK-interacting protein 16 (SKIP16) were found as the most suitable reference genes for expression analysis in roots and leaves, respectively. In addition, miRNAs miR168, miR160 and miR397 were selected as optimal reference genes across all tissues and treatments. miR168 and miR156 were recommended as reference for roots, while miR168 and miR160 were recommended for leaves. Together, our results constitute the first attempt to identify and validate the most suitable reference genes for accurate normalization of gene expression in castor bean under drought stress. PMID:27156134

  10. Diverse self-association properties within a family of phage packaging RNAs.

    Science.gov (United States)

    Hao, Yumeng; Kieft, Jeffrey S

    2014-11-01

    The packaging RNA (pRNA) found in phi29 bacteriophage is an essential component of a molecular motor that packages the phage's DNA genome. The pRNA forms higher-order multimers by intermolecular "kissing" interactions between identical molecules. The phi29 pRNA is a proven building block for nanotechnology and a model to explore the rare phenomenon of naturally occurring RNA self-association. Although the self-association properties of the phi29 pRNA have been extensively studied and this pRNA is used in nanotechnology, the characteristics of phylogenetically related pRNAs with divergent sequences are comparatively underexplored. These diverse pRNAs may lend new insight into both the rules governing RNA self-association and for RNA engineering. Therefore, we used a combination of biochemical and biophysical methods to resolve ambiguities in the proposed secondary structures of pRNAs from M2, GA1, SF5, and B103 phage, and to discover that different naturally occurring pRNAs form multimers of different stoichiometry and thermostability. Indeed, the M2 pRNA formed multimers that were particularly thermostable and may be more useful than phi29 pRNA for many applications. To determine if diverse pRNA behaviors are conferred by different kissing loop sequences, we designed and tested chimeric RNAs based on our revised secondary structural models. We found that although the kissing loops are essential for self-association, the critical determinant of multimer stability and stoichiometry is likely the diverse three-way junctions found in these RNAs. Using known features of RNA three-way junctions and solved structures of phi29 pRNA's junction, we propose a model for how different junctions affect self-association. PMID:25246655

  11. MicroRNAs and drug addiction

    Directory of Open Access Journals (Sweden)

    Paul J Kenny

    2013-05-01

    Full Text Available Drug addiction is considered a disorder of neuroplasticity in brain reward and cognition systems resulting from aberrant activation of gene expression programs in response to prolonged drug consumption. Noncoding RNAs are key regulators of almost all aspects of cellular physiology. MicroRNAs (miRNAs are small (~21–23 nucleotides noncoding RNA transcripts that regulate gene expression at the post-transcriptional level. Recently, microRNAs were shown to play key roles in the drug-induced remodeling of brain reward systems that likely drives the emergence of addiction. Here, we review evidence suggesting that one particular miRNA, miR-212, plays a particularly prominent role in vulnerability to cocaine addiction. We review evidence showing that miR-212 expression is increased in the dorsal striatum of rats that show compulsive-like cocaine-taking behaviors. Increases in miR-212 expression appear to protect against cocaine addiction, as virus-mediated striatal miR-212 over-expression decreases cocaine consumption in rats. Conversely, disruption of striatal miR-212 signaling using an antisense oligonucleotide increases cocaine intake. We also review data that identify two mechanisms by which miR-212 may regulate cocaine intake. First, miR-212 has been shown to amplify striatal CREB signaling through a mechanism involving activation of Raf1 kinase. Second, miR-212 was also shown to regulate cocaine intake by repressing striatal expression of methyl CpG binding protein 2 (MeCP2, consequently decreasing protein levels of brain-derived neurotrophic factor (BDNF. The concerted actions of miR-212 on striatal CREB and MeCP2/BDNF activity greatly attenuate the motivational effects of cocaine. These findings highlight the unique role for miRNAs in simultaneously controlling multiple signaling cascades implicated in addiction.

  12. The biogenesis and function of small RNAs in C. elegans

    NARCIS (Netherlands)

    Tops, B.B.J.

    2007-01-01

    RNAi is the process by which double-stranded RNA (dsRNA) induces sequence-specific mRNA degradation. DsRNA is diced into small interfering RNAs (siRNAs) of ~21-23 nt by a complex containing the RNaseIII enzyme DICER. The mature siRNAs are subsequently bound by Argonaute proteins and incorporated int

  13. Identification of Bacterial Small RNAs by RNA Sequencing

    DEFF Research Database (Denmark)

    Gómez Lozano, María; Marvig, Rasmus Lykke; Molin, Søren;

    2014-01-01

    Small regulatory RNAs (sRNAs) in bacteria are known to modulate gene expression and control a variety of processes including metabolic reactions, stress responses, and pathogenesis in response to environmental signals. A method to identify bacterial sRNAs on a genome-wide scale based on RNA seque...

  14. Circulating microRNAs as biomarkers of adult Crohn's disease

    DEFF Research Database (Denmark)

    Jensen, Michael D; Andersen, Rikke F; Christensen, Henry;

    2015-01-01

    OBJECTIVE: Previous studies have found a differential expression of microRNAs (miRNAs) in the blood of patients with Crohn's disease (CD) compared with healthy controls. The aim of this study was to identify circulating miRNAs expressed in CD and assess their performance as biomarkers in patients...

  15. Non-Coding RNAs in Arabidopsis

    DEFF Research Database (Denmark)

    van Wonterghem, Miranda

    This work evolves around elucidating the mechanisms of micro RNAs (miRNAs) in Arabidopsis thaliana. I identified a new class of nuclear non-coding RNAs derived from protein coding genes. The genes are miRNA targets with extensive gene body methylation. The RNA species are nuclear localized and de...

  16. Noncoding RNAs in cancer and cancer stem cells

    Institute of Scientific and Technical Information of China (English)

    Tianzhi Huang; Angel Alvarez; Bo Hu; Shi-Yuan Cheng

    2013-01-01

    In recent years, it has become increasingly apparent that noncoding RNAs (ncRNA) are of crucial importance for human cancer. The functional relevance of ncRNAs is particularly evident for microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). miRNAs are endogenously expressed small RNA sequences that act as post-transcriptional regulators of gene expression and have been extensively studied for their roles in cancers, whereas lncRNAs are emerging as important players in the cancer paradigm in recent years. These noncoding genes are often aberrantly expressed in a variety of human cancers. However, the biological functions of most ncRNAs remain largely unknown. Recently, evidence has begun to accumulate describing how ncRNAs are dysregulated in cancer and cancer stem cells, a subset of cancer cells harboring self-renewal and differentiation capacities. These studies provide insight into the functional roles that ncRNAs play in tumor initiation, progression, and resistance to therapies, and they suggest ncRNAs as attractive therapeutic targets and potential y useful diagnostic tools.

  17. Getting to PTI of bacterial RNAs: Triggering plant innate immunity by extracellular RNAs from bacteria.

    Science.gov (United States)

    Park, Yong-Soon; Lee, Boyoung; Ryu, Choong-Min

    2016-07-01

    Defense against diverse biotic and abiotic stresses requires the plant to distinguish between self and non-self signaling molecules. Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are pivotal for triggering innate immunity in plants. Unlike in animals and humans, the precise roles of nucleic acids in plant innate immunity are unclear. We therefore investigated the effects of infiltration of total Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) RNAs into Arabidopsis plants. The pathogen population was 10-fold lower in bacterial RNAs pre-treated Arabidopsis plants than in the control. Bacterial RNAs purity was confirmed by physical (sonication) and chemical (RNase A and proteinase K digestion) methods. The perception of bacterial RNAs, especially rRNAs, positively regulated mitogen-activated protein kinase (MAPK) and induced a reactive oxygen species burst, callose deposition, salicylic acid (SA) and jasmonic acid (JA) signaling, and defense-related genes. Therefore, bacterial RNAs function as a new MAMP that activates plant innate immunity, providing a new paradigm for plant-microbe interactions. PMID:27301792

  18. Utility of microRNAs and siRNAs in cervical carcinogenesis.

    Science.gov (United States)

    Díaz-González, Sacnite del Mar; Deas, Jessica; Benítez-Boijseauneau, Odelia; Gómez-Cerón, Claudia; Bermúdez-Morales, Victor Hugo; Rodríguez-Dorantes, Mauricio; Pérez-Plasencia, Carlos; Peralta-Zaragoza, Oscar

    2015-01-01

    MicroRNAs and siRNAs belong to a family of small noncoding RNAs which bind through partial sequence complementarity to 3'-UTR regions of mRNA from target genes, resulting in the regulation of gene expression. MicroRNAs have become an attractive target for genetic and pharmacological modulation due to the critical function of their target proteins in several signaling pathways, and their expression profiles have been found to be altered in various cancers. A promising technology platform for selective silencing of cell and/or viral gene expression using siRNAs is currently in development. Cervical cancer is the most common cancer in women in the developing world and sexually transmitted infection with HPV is the cause of this malignancy. Therefore, a cascade of abnormal events is induced during cervical carcinogenesis, including the induction of genomic instability, reprogramming of cellular metabolic pathways, deregulation of cell proliferation, inhibition of apoptotic mechanisms, disruption of cell cycle control mechanisms, and alteration of gene expression. Thus, in the present review article, we highlight new research on microRNA expression profiles which may be utilized as biomarkers for cervical cancer. Furthermore, we discuss selective silencing of HPV E6 and E7 with siRNAs which represents a potential gene therapy strategy against cervical cancer. PMID:25874209

  19. Utility of MicroRNAs and siRNAs in Cervical Carcinogenesis

    Directory of Open Access Journals (Sweden)

    Sacnite del Mar Díaz-González

    2015-01-01

    Full Text Available MicroRNAs and siRNAs belong to a family of small noncoding RNAs which bind through partial sequence complementarity to 3′-UTR regions of mRNA from target genes, resulting in the regulation of gene expression. MicroRNAs have become an attractive target for genetic and pharmacological modulation due to the critical function of their target proteins in several signaling pathways, and their expression profiles have been found to be altered in various cancers. A promising technology platform for selective silencing of cell and/or viral gene expression using siRNAs is currently in development. Cervical cancer is the most common cancer in women in the developing world and sexually transmitted infection with HPV is the cause of this malignancy. Therefore, a cascade of abnormal events is induced during cervical carcinogenesis, including the induction of genomic instability, reprogramming of cellular metabolic pathways, deregulation of cell proliferation, inhibition of apoptotic mechanisms, disruption of cell cycle control mechanisms, and alteration of gene expression. Thus, in the present review article, we highlight new research on microRNA expression profiles which may be utilized as biomarkers for cervical cancer. Furthermore, we discuss selective silencing of HPV E6 and E7 with siRNAs which represents a potential gene therapy strategy against cervical cancer.

  20. RNA secondary structure prediction from multi-aligned sequences

    OpenAIRE

    Hamada, Michiaki

    2013-01-01

    It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the...

  1. Nuclear safety in EU candidate countries

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-10-01

    Nuclear safety in the candidate countries to the European Union is a major issue that needs to be addressed in the framework of the enlargement process. Therefore WENRA members considered it was their duty to offer their technical assistance to their Governments and the European Union Institutions. They decided to express their collective opinion on nuclear safety in those candidate countries having at least one nuclear power plant: Bulgaria, the Czech Republic, Hungary, Lithuania, Romania, Slovakia and Slovenia. The report is structured as follows: A foreword including background information, structure of the report and the methodology used, General conclusions of WENRA members reflecting their collective opinion, For each candidate country, an executive summary, a chapter on the status of the regulatory regime and regulatory body, and a chapter on the nuclear power plant safety status. Two annexes are added to address the generic safety characteristics and safety issues for RBMK and VVER plants. The report does not cover radiation protection and decommissioning issues, while safety aspects of spent fuel and radioactive waste management are only covered as regards on-site provisions. In order to produce this report, WENRA used different means: For the chapters on the regulatory regimes and regulatory bodies, experts from WENRA did the work. For the chapters on nuclear power plant safety status, experts from WENRA and from French and German technical support organisations did the work. Taking into account the contents of these chapters, WENRA has formulated its general conclusions in this report.

  2. Nuclear safety in EU candidate countries

    International Nuclear Information System (INIS)

    Nuclear safety in the candidate countries to the European Union is a major issue that needs to be addressed in the framework of the enlargement process. Therefore WENRA members considered it was their duty to offer their technical assistance to their Governments and the European Union Institutions. They decided to express their collective opinion on nuclear safety in those candidate countries having at least one nuclear power plant: Bulgaria, the Czech Republic, Hungary, Lithuania, Romania, Slovakia and Slovenia. The report is structured as follows: A foreword including background information, structure of the report and the methodology used, General conclusions of WENRA members reflecting their collective opinion, For each candidate country, an executive summary, a chapter on the status of the regulatory regime and regulatory body, and a chapter on the nuclear power plant safety status. Two annexes are added to address the generic safety characteristics and safety issues for RBMK and VVER plants. The report does not cover radiation protection and decommissioning issues, while safety aspects of spent fuel and radioactive waste management are only covered as regards on-site provisions. In order to produce this report, WENRA used different means: For the chapters on the regulatory regimes and regulatory bodies, experts from WENRA did the work. For the chapters on nuclear power plant safety status, experts from WENRA and from French and German technical support organisations did the work. Taking into account the contents of these chapters, WENRA has formulated its general conclusions in this report

  3. Virus-associated small satellite RNAs and viroids display similarities in their replication strategies.

    Science.gov (United States)

    Rao, A L N; Kalantidis, Kriton

    2015-05-01

    Since the discovery of non-coding, small, highly structured, satellite RNAs (satRNAs) and viroids as subviral pathogens of plants , have been of great interest to molecular biologists as possible living fossils of pre-cellular evolution in an RNA world. Despite extensive studies performed in the last four decades, there is still mystery surrounding the origin and evolutionary relationship between these subviral pathogens. Recent technical advances revealed some commonly shared replication features between these two subviral pathogens. In this review, we discuss our current perception of replication and evolutionary origin of these petite RNA pathogens. PMID:25731957

  4. Genome-wide comparative analysis of microRNAs in three non-human primates

    Directory of Open Access Journals (Sweden)

    Brameier Markus

    2010-03-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are negative regulators of gene expression in multicellular eukaryotes. With the recently completed sequencing of three primate genomes, the study of miRNA evolution within the primate lineage has only begun and may be expected to provide the genetic and molecular explanations for many phenotypic differences between human and non-human primates. Findings We scanned all three genomes of non-human primates, including chimpanzee (Pan troglodytes, orangutan (Pongo pygmaeus, and rhesus monkey (Macaca mulatta, for homologs of human miRNA genes. Besides sequence homology analysis, our comparative method relies on various postprocessing filters to verify other features of miRNAs, including, in particular, their precursor structure or their occurrence (prediction in other primate genomes. Our study allows direct comparisons between the different species in terms of their miRNA repertoire, their evolutionary distance to human, the effects of filters, as well as the identification of common and species-specific miRNAs in the primate lineage. More than 500 novel putative miRNA genes have been discovered in orangutan that show at least 85 percent identity in precursor sequence. Only about 40 percent are found to be 100 percent identical with their human ortholog. Conclusion Homologs of human precursor miRNAs with perfect or near-perfect sequence identity may be considered to be likely functional in other primates. The computational identification of homologs with less similar sequence, instead, requires further evidence to be provided.

  5. More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature.

    Science.gov (United States)

    Ladunga, Istvan

    2007-01-01

    Highly accurate knockdown functional analyses based on RNA interference (RNAi) require the possible most complete hydrolysis of the targeted mRNA while avoiding the degradation of untargeted genes (off-target effects). This in turn requires significant improvements to target selection for two reasons. First, the average silencing activity of randomly selected siRNAs is as low as 62%. Second, applying more than five different siRNAs may lead to saturation of the RNA-induced silencing complex (RISC) and to the degradation of untargeted genes. Therefore, selecting a small number of highly active siRNAs is critical for maximizing knockdown and minimizing off-target effects. To satisfy these needs, a publicly available and transparent machine learning tool is presented that ranks all possible siRNAs for each targeted gene. Support vector machines (SVMs) with polynomial kernels and constrained optimization models select and utilize the most predictive effective combinations from 572 sequence, thermodynamic, accessibility and self-hairpin features over 2200 published siRNAs. This tool reaches an accuracy of 92.3% in cross-validation experiments. We fully present the underlying biophysical signature that involves free energy, accessibility and dinucleotide characteristics. We show that while complete silencing is possible at certain structured target sites, accessibility information improves the prediction of the 90% active siRNA target sites. Fast siRNA activity predictions can be performed on our web server at http://optirna.unl.edu/. PMID:17169992

  6. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs

    Science.gov (United States)

    In eukaryotes, RNA silencing pathways utilize 20–30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focuse...

  7. Bias in High-Throughput Analysis of miRNAs and Implications for Biomarker Studies.

    Science.gov (United States)

    Backes, Christina; Sedaghat-Hamedani, Farbod; Frese, Karen; Hart, Martin; Ludwig, Nicole; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2016-02-16

    A certain degree of bias in high-throughput molecular technologies including microarrays and next-generation sequencing (NGS) is known. To quantify the actual impact of the biomarker discovery platform on miRNA profiles, we first performed a meta-analysis: raw data of 1 539 microarrays and 705 NGS blood-borne miRNomes were statistically evaluated, suggesting a substantial influence of the technology on biomarker profiles. We observed highly significant dependency of the miRNA nucleotide composition on the expression level. Higher expression in NGS was discovered for uracil-rich miRNAs (p = 7 × 10(-37)), while high expression in microarrays was found predominantly for guanine-rich miRNAs (p = 3 × 10(-33)). To verify the findings, 10 identical replicates of one individual were measured using NGS and microarrays (2 525 miRNAs from miRBase version 21). Overall, we calculated a correlation coefficient of 0.414 for both technologies. Detailed analysis however revealed that the correlation was observed only for miRNAs in the early miRBase versions (microarray and NGS. Specifically, we observed 67 miRNAs with a median read count above 10 in NGS, while they were not detected in any of the 10 replicated array experiments. In contrast, 234 miRNAs were discovered in all 10 replicated array measurements but were not found in any of the NGS experiments of the same individual. While the first group had average guanine content of 22%, the latter group consisted of 41% of this nucleotide. Selected concordant and discordant miRNAs were tested in quantitative real-time-polymerase chain reaction (RT-qPCR) experiments again of the same individual, providing further evidence for the substantial bias depending on the base composition. As a consequence, biomarkers that have been discovered by specific high-throughout technologies have to be carefully considered. Especially for validation of the platform, the selection of reasonable candidates is essential. PMID:26760198

  8. Role of microRNAs in Alcohol-Induced Multi-Organ Injury

    Directory of Open Access Journals (Sweden)

    Sathish Kumar Natarajan

    2015-11-01

    Full Text Available Alcohol consumption and its abuse is a major health problem resulting in significant healthcare cost in the United States. Chronic alcoholism results in damage to most of the vital organs in the human body. Among the alcohol-induced injuries, alcoholic liver disease is one of the most prevalent in the United States. Remarkably, ethanol alters expression of a wide variety of microRNAs that can regulate alcohol-induced complications or dysfunctions. In this review, we will discuss the role of microRNAs in alcoholic pancreatitis, alcohol-induced liver damage, intestinal epithelial barrier dysfunction, and brain damage including altered hippocampus structure and function, and neuronal loss, alcoholic cardiomyopathy, and muscle damage. Further, we have reviewed the role of altered microRNAs in the circulation, teratogenic effects of alcohol, and during maternal or paternal alcohol consumption.

  9. Detection of RNA structures in porcine EST data and related mammals

    Directory of Open Access Journals (Sweden)

    Seemann Stefan E

    2007-09-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and mRNA like ncRNAs in eukaryotes. To investigate this further, we examined the large data set in the Sino-Danish PigEST resource http://pigest.ku.dk which also contains expression information distributed on 97 non-normalized cDNA libraries. Results We constructed a pipeline, EST2ncRNA, to search for known and novel ncRNAs. The pipeline utilises sequence similarity to ncRNA databases (blast, structure similarity to Rfam (RaveNnA as well as multiple alignments to predict conserved novel putative RNA structures (RNAz. EST2ncRNA was fed with 48,000 contigs and 73,000 singletons available from the PigEST resource. Using the pipeline we identified known RNA structures in 137 contigs and single reads (conreads, and predicted high confidence RNA structures in non-protein coding regions of additional 1,262 conreads. Of these, structures in 270 conreads overlap with existing predictions in human. To sum up, the PigEST resource comprises trans-acting elements (ncRNAs in 715 contigs and 340 singletons as well as cis-acting elements (inside UTRs in 311 contigs and 51 singletons, of which 18 conreads contain both predictions of trans- and cis-acting elements. The predicted RNAz candidates were compared with the PigEST expression information and we identify 114 contigs with an RNAz prediction and expression in at least ten of the non-normalised cDNA libraries. We conclude that the contigs with RNAz and known predictions are in general expressed at a much lower level than protein coding transcripts. In addition, we also observe that our ncRNA candidates constitute about one to two percent of the genes expressed in the cDNA libraries. Intriguingly, the cDNA libraries from developmental (brain tissues contain the highest amount of ncRNA candidates, about two percent. These

  10. An annotated history of container candidate material selection

    International Nuclear Information System (INIS)

    This paper documents events in the Nevada Nuclear Waste Storage Investigations (NNWSI) Project that have influenced the selection of metals and alloys proposed for fabrication of waste package containers for permanent disposal of high-level nuclear waste in a repository at Yucca Mountain, Nevada. The time period from 1981 to 1988 is covered in this annotated history. The history traces the candidate materials that have been considered at different stages of site characterization planning activities. At present, six candidate materials are considered and described in the 1988 Consultation Draft of the NNWSI Site Characterization Plan (SCP). The six materials are grouped into two alloy families, copper-base materials and iron to nickel-base materials with an austenitic structure. The three austenitic candidates resulted from a 1983 survey of a longer list of candidate materials; the other three candidates resulted from a special request from DOE in 1984 to evaluate copper and copper-base alloys. 24 refs., 2 tabs

  11. Long Non-coding RNAs in Response to Genotoxic Stress

    Institute of Scientific and Technical Information of China (English)

    Xiaoman Li; Dong Pan; Baoquan Zhao; Burong Hu

    2016-01-01

    Long non-coding RNAs(lncRNAs) are increasingly involved in diverse biological processes.Upon DNA damage,the DNA damage response(DDR) elicits a complex signaling cascade,which includes the induction of lncRNAs.LncRNA-mediated DDR is involved in non-canonical and canonical manners.DNA-damage induced lncRNAs contribute to the regulation of cell cycle,apoptosis,and DNA repair,thereby playing a key role in maintaining genome stability.This review summarizes the emerging role of lncRNAs in DNA damage and repair.

  12. MicroRNAs in Experimental Models of Movement Disorders

    OpenAIRE

    Soon-Tae Lee; Manho Kim

    2011-01-01

    MicroRNAs (miRNAs) are small RNAs comprised of 20–25 nucleotides that regulates gene expression by inducing translational repression or degradation of target mRNA. The importance of miRNAs as a mediator of disease pathogenesis and therapeutic targets is rapidly emerging in neuroscience, as well as oncology, immunology, and cardiovascular diseases. In Parkinson’s disease and related disorders, multiple studies have identified the implications of specific miRNAs and the polymorphisms of miRNA t...

  13. Identifying MicroRNAs and Transcript Targets in Jatropha Seeds

    OpenAIRE

    Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F. V.; Loss-Morais, Guilherme; Körbes, Ana P.; Silva, Sérgio D. A.; Margis-Pinheiro, Márcia M. A. N.; Margis, Rogério

    2014-01-01

    MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identifica...

  14. MicroRNAs and their role in viral infection

    Institute of Scientific and Technical Information of China (English)

    MU Junjie; YAO Xue; CHEN Qimin; GENG Yunqi; QIAO Wentao

    2007-01-01

    Recently,a class of about 22 nucleotides (nt)small RNA has been discovered in many eukaryotes,termed microRNAs (miRNAs),which have a variety of functions.Many recent findings have demonstrated that viruses can also encode their own miRNAs.Meanwhile,other findings reveal a relationship between host miRNA and viral infection.These findings suggest a tight relationship between host and viral infection via miRNA pathway.This article introduces the miRNAs encoded by viruses and reviews the advances of the interaction of the mammalian host miRNAs and viral infection.

  15. Non-Coding RNAs in Primary Liver Cancer.

    Science.gov (United States)

    Ghidini, Michele; Braconi, Chiara

    2015-01-01

    Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with poor prognosis and limited therapeutic options. Over the past few years, many studies have evaluated the role of non-coding RNAs (ncRNAs) in hepatocarcinogenesis and tumor progression. ncRNAs were shown to have diagnostic, prognostic, and therapeutic potential in HCC. In this manuscript, we review the latest major discoveries concerning microRNAs and long ncRNAs in HCC pathogenesis, and discuss the potentials and the limitations for their use in clinical practice. PMID:26131450

  16. Identification and Function of MicroRNAs Encoded by Herpesviruses

    Institute of Scientific and Technical Information of China (English)

    Zhi-qing Bai; Xiu-fen Lei; Lin-ding Wang; Shou-jiang Gao

    2008-01-01

    MicroRNAs (miRNAs) play important roles in eukaryotes,plants and some viruses.It is increasingly clear that miRNAs-encoded by viruses can affect the viral life cycle and host physiology.Viral miRNAs could repress the innate and adaptive host immunity,modulate cellular signaling pathways,and regulate the expression of cellular and viral genes.These functions facilitate viral acute and persistent infections,and have profound effects on the host cell survival and disease progression.Here,we discuss the miRNAs encoded by herpesviruses,and their regulatory roles involved in virus-host interactions.

  17. Recombination between satellite RNAs of turnip crinkle virus.

    OpenAIRE

    Cascone, P J; Carpenter, C. D.; Li, X.H.; Simon, A. E.

    1990-01-01

    Turnip crinkle virus (TCV) is associated with satellite (sat) RNAs (sat-RNA D, sat-RNA F), defective interfering (DI) RNAs (DI RNA G, DI1 RNA), and one RNA with properties of both sat-RNAs and DI RNAs (sat-RNA C). When plants were inoculated with TCV, sat-RNA D and in vitro sat-RNA C transcripts containing non-viable mutations in the 5' domain, recombinant sat-RNAs were recovered. These recombinants were composed of sat-RNA D at the 5' end and sat-RNA C sequences at the 3' end. Analysis of 20...

  18. Genome organization and characteristics of soybean microRNAs

    Directory of Open Access Journals (Sweden)

    Turner Marie

    2012-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is not well understood. We examined a library of small RNAs from Bradyrhizobium japonicum-inoculated soybean roots and identified novel miRNAs. In order to enhance our understanding of miRNA evolution, diversification and function, we classified all known soybean miRNAs based on their phylogenetic conservation (conserved, legume- and soybean-specific miRNAs and examined their genome organization, family characteristics and target diversity. We predicted targets of these miRNAs and experimentally validated several of them. We also examined organ-specific expression of selected miRNAs and their targets. Results We identified 120 previously unknown miRNA genes from soybean including 5 novel miRNA families. In the soybean genome, genes encoding miRNAs are primarily intergenic and a small percentage were intragenic or less than 1000 bp from a protein-coding gene, suggesting potential co-regulation between the miRNA and its parent gene. Difference in number and orientation of tandemly duplicated miRNA genes between orthologous genomic loci indicated continuous evolution and diversification. Conserved miRNA families are often larger in size and produce less diverse mature miRNAs than legume- and soybean-specific families. In addition, the majority of conserved and legume-specific miRNA families produce 21 nt long mature miRNAs with distinct nucleotide distribution and regulate a more conserved set of target mRNAs compared to soybean-specific families. A set of nodule-specific target mRNAs and their cognate regulatory miRNAs had inverse expression between root and nodule tissues suggesting that spatial restriction of target gene transcripts by miRNAs might govern nodule-specific gene expression in soybean. Conclusions Genome

  19. MicroRNAs and the genetic network in aging

    OpenAIRE

    Inukai, Sachi; Slack, Frank

    2013-01-01

    MicroRNAs (miRNAs) comprise a class of small RNAs important for the post-transcriptional regulation of numerous biological processes. Their combinatorial mode of function, in which an individual miRNA can target many genes and multiple miRNAs share targets, makes them especially suited for regulating processes and pathways at the “network” level. In particular, miRNAs have recently been implicated in aging which is a complex process known to involve multiple pathways. Findings from genome-wid...

  20. Transposon defense by endo-siRNAs, piRNAs and somatic pilRNAs in Drosophila: contributions of Loqs-PD and R2D2.

    Directory of Open Access Journals (Sweden)

    Milijana Mirkovic-Hösle

    Full Text Available Transposable elements are a serious threat for genome integrity and their control via small RNA mediated silencing pathways is an ancient strategy. The fruit fly Drosophila melanogaster has two silencing activities that target transposons: endogenous siRNAs (esiRNAs or endo-siRNAs and Piwi-interacting small RNAs (piRNAs. The biogenesis of endo-siRNAs involves the Dicer-2 co-factors Loqs-PD, which acts predominantly during processing of dsRNA by Dcr-2, and R2D2, which primarily helps to direct siRNAs into the RNA interference effector Ago2. Nonetheless, loss of either protein is not sufficient to produce a phenotype comparable with a dcr-2 mutation. We provide further deep sequencing evidence supporting the notion that R2D2 and Loqs-PD have partially overlapping function. Certain transposons display a preference for either dsRBD-protein during production or loading; this appeared to correlate neither with overall abundance, classification of the transposon or a specific site of genomic origin. The endo-siRNA biogenesis pathway in germline operates according to the same principles as the existing model for the soma, and its impairment does not significantly affect piRNAs. Expanding the analysis, we confirmed the occurrence of somatic piRNA-like RNAs (pilRNAs that show a ping-pong signature. We detected expression of the Piwi-family protein mRNAs only barely above background, indicating that the somatic pilRNAs may arise from a small sub-population of somatic cells that express a functional piRNA pathway.

  1. Dynamics of microRNAs in bull spermatozoa

    Directory of Open Access Journals (Sweden)

    Govindaraju Aruna

    2012-09-01

    Full Text Available Abstract Background MicroRNAs are small non-coding RNAs that regulate gene expression and thus play important roles in mammalian development. However, the comprehensive lists of microRNAs, as well as, molecular mechanisms by which microRNAs regulate gene expression during gamete and embryo development are poorly defined. The objectives of this study were to determine microRNAs in bull sperm and predict their functions. Methods To accomplish our objectives we isolated miRNAs from sperm of high and low fertility bulls, conducted microRNA microarray experiments and validated expression of a panel of microRNAs using real time RT-PCR. Bioinformatic approaches were carried out to identify regulated targets. Results We demonstrated that an abundance of microRNAs were present in bovine spermatozoa, however, only seven were differentially expressed; hsa-aga-3155, -8197, -6727, -11796, -14189, -6125, -13659. The abundance of miRNAs in the spermatozoa and the differential expression in sperm from high vs. low fertility bulls suggests that the miRNAs possibly play important functions in the regulating mechanisms of bovine spermatozoa. Conclusion Identification of specific microRNAs expressed in spermatozoa of bulls with different fertility phenotypes will help better understand mammalian gametogenesis and early development.

  2. MicroRNAs Implicated in the Immunopathogenesis of Lupus Nephritis

    Directory of Open Access Journals (Sweden)

    Cristen B. Chafin

    2013-01-01

    Full Text Available Systemic lupus erythematosus (SLE is an autoimmune disease characterized by the deposition of immune complexes due to widespread loss of immune tolerance to nuclear self-antigens. Deposition in the renal glomeruli results in the development of lupus nephritis (LN, the leading cause of morbidity and mortality in SLE. In addition to the well-recognized genetic susceptibility to SLE, disease pathogenesis is influenced by epigenetic regulators such as microRNAs (miRNAs. miRNAs are small, noncoding RNAs that bind to the 3′ untranslated region of target mRNAs resulting in posttranscriptional gene modulation. miRNAs play an important and dynamic role in the activation of innate immune cells and are critical in regulating the adaptive immune response. Immune stimulation and the resulting cytokine milieu alter miRNA expression while miRNAs themselves modify cellular responses to stimulation. Here we examine dysregulated miRNAs implicated in LN pathogenesis from human SLE patients and murine lupus models. The effects of LN-associated miRNAs in the kidney, peripheral blood mononuclear cells, macrophages, mesangial cells, dendritic cells, and splenocytes are discussed. As the role of miRNAs in immunopathogenesis becomes delineated, it is likely that specific miRNAs may serve as targets for therapeutic intervention in the treatment of LN and other pathologies.

  3. Progress, challenges and new concepts in microRNAs

    Institute of Scientific and Technical Information of China (English)

    ZHANG YouYi

    2011-01-01

    MicroRNAs are a group of small noncoding RNAs.They have rapidly gained attention in the field as novel regulators of cellular morphology and function.Currently hundreds of microRNAs have been described in human genome.MicroRNAs play important roles in posttranscriptional regulation of gene expression by inhibiting protein translation and/or promoting mRNA degradation.MicroRNAs were initially thought to be subtle regulators of gene expression,but increasing evidence demonstrates that the regulatory functions of microRNAs are crucial for the cell.MicroRNAs have been found to be involved in the development,tissue homeostasis as well as diseases.

  4. The evolving world of small RNAs from RNA viruses.

    Science.gov (United States)

    Li, Mei-Ling; Weng, Kuo-Feng; Shih, Shin-Ru; Brewer, Gary

    2016-09-01

    RNA virus infection in plants and invertebrates can produce virus-derived small RNAs. These RNAs share features with host endogenous small interfering RNAs (siRNAs). They can potentially mediate RNA interference (RNAi) and related RNA silencing pathways, resulting in specific antiviral defense. Although most RNA silencing components such as Dicer, Ago2, and RISC are conserved among eukaryotic hosts, whether RNA virus infection in mammals can generate functional small RNAs that act in antiviral defense remains under discussion. Here, we review recent studies on the molecular and biochemical features of viral siRNAs and other virus-derived small RNAs from infected plants, arthropods, nematodes, and vertebrates and discuss the genetic pathways for their biogenesis and their roles in antiviral activity. WIREs RNA 2016, 7:575-588. doi: 10.1002/wrna.1351 For further resources related to this article, please visit the WIREs website. PMID:27046163

  5. The therapeutic potential of MicroRNAs in cancer

    DEFF Research Database (Denmark)

    Thorsen, Susanne; Obad, S.; Jensen, N.F.;

    2012-01-01

    MicroRNAs (miRNAs) have been uncovered as important posttranscriptional regulators of nearly every biological process in the cell. Furthermore, mounting evidence implies that miRNAs play key roles in the pathogenesis of cancer and that many miRNAs can function either as oncogenes or tumor...... suppressors. Thus, miRNAs have rapidly emerged as promising targets for the development of novel anticancer therapeutics. The development of miRNA-based cancer therapeutics relies on restoring the activity of tumor suppressor miRNAs using double-stranded miRNA mimics or inhibition of oncogenic miRNAs using...... single-stranded antisense oligonucleotides, termed antimiRs. In the present review, we focus on recent advancements in the discovery and development of miRNA-based cancer therapeutics using these 2 approaches. In addition, we summarize selected studies, in which modulation of miRNA activity in...

  6. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery.

    Science.gov (United States)

    Eidem, Tess M; Kugel, Jennifer F; Goodrich, James A

    2016-06-19

    Transcription by RNA polymerase II (Pol II) is required to produce mRNAs and some noncoding RNAs (ncRNAs) within mammalian cells. This coordinated process is precisely regulated by multiple factors, including many recently discovered ncRNAs. In this perspective, we will discuss newly identified ncRNAs that facilitate DNA looping, regulate transcription factor binding, mediate promoter-proximal pausing of Pol II, and/or interact with Pol II to modulate transcription. Moreover, we will discuss new roles for ncRNAs, as well as a novel Pol II RNA-dependent RNA polymerase activity that regulates an ncRNA inhibitor of transcription. As the multifaceted nature of ncRNAs continues to be revealed, we believe that many more ncRNA species and functions will be discovered. PMID:26920110

  7. Discoveries and functions of virus-encoded MicroRNAs

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, ChinaVirus-encoded microRNAs (miRNAs) are a new kind of miRNAs that regulate the expression of target gene in host cells or viruses through inducing cleavage of mRNA, repressing translation, etc., and change the processes of host cells or replicate viruses to escape or resist immune surveillance of host and protect viruses themselves. It has become a hot topic to discover viral genes encoding miRNAs and their target genes, and to identify their functions. This review provides background information on the history of virally encoded miRNAs including their genomic distribution, functions and mechanisms.In addition, we discuss the similarities and differences between virus- and host-encoded miRNAs, the future directions of researches in viral miRNAs and their applications in diseases control and therapy.

  8. Non-coding RNAs in cancer brain metastasis.

    Science.gov (United States)

    Wu, Kerui; Sharma, Sambad; Venkat, Suresh; Liu, Keqin; Zhou, Xiaobo; Watabe, Kounosuke

    2016-01-01

    More than 90% of cancer death is attributed to metastatic disease, and the brain is one of the major metastatic sites of melanoma, colon, renal, lung and breast cancers. Despite the recent advancement of targeted therapy for cancer, the incidence of brain metastasis is increasing. One reason is that most therapeutic drugs can't penetrate blood-brain-barrier and tumor cells find the brain as sanctuary site. In this review, we describe the pathophysiology of brain metastases to introduce the latest understandings of metastatic brain malignancies. This review also particularly focuses on non-coding RNAs and their roles in cancer brain metastasis. Furthermore, we discuss the roles of the extracellular vesicles as they are known to transport information between cells to initiate cancer cell-microenvironment communication. The potential clinical translation of non-coding RNAs as a tool for diagnosis and for treatment is also discussed in this review. At the end, the computational aspects of non-coding RNA detection, the sequence and structure calculation and epigenetic regulation of non-coding RNA in brain metastasis are discussed. PMID:26709907

  9. Telomeric RNAs are essential to maintain telomeres.

    Science.gov (United States)

    Montero, Juan José; López de Silanes, Isabel; Graña, Osvaldo; Blasco, Maria A

    2016-01-01

    Telomeres are transcribed generating long non-coding RNAs known as TERRA. Deciphering the role of TERRA has been one of the unsolved issues of telomere biology in the past decade. This has been, in part, due to lack of knowledge on the TERRA loci, thus preventing functional genetic studies. Here, we describe that long non-coding RNAs with TERRA features are transcribed from the human 20q and Xp subtelomeres. Deletion of the 20q locus by using the CRISPR-Cas9 technology causes a dramatic decrease in TERRA levels, while deletion of the Xp locus does not result in decreased TERRA levels. Strikingly, 20q-TERRA ablation leads to dramatic loss of telomere sequences and the induction of a massive DNA damage response. These findings identify chromosome 20q as a main TERRA locus in human cells and represent the first demonstration in any organism of the essential role of TERRA in the maintenance of telomeres. PMID:27531349

  10. MicroRNAs, epigenetics and disease

    DEFF Research Database (Denmark)

    Silahtaroglu, Asli; Stenvang, Jan

    2010-01-01

    Epigenetics is defined as the heritable chances that affect gene expression without changing the DNA sequence. Epigenetic regulation of gene expression can be through different mechanisms such as DNA methylation, histone modifications and nucleosome positioning. MicroRNAs are short RNA molecules...... which do not code for a protein but have a role in post-transcriptional silencing of multiple target genes by binding to their 3' UTRs (untranslated regions). Both epigenetic mechanisms, such as DNA methylation and histone modifications, and the microRNAs are crucial for normal differentiation......, development and maintenance of tissue-specific gene expression. These mechanisms also explain how cells with the same DNA content can differentiate into cells with different functions. Changes in epigenetic processes can lead to changes in gene function, cancer formation and progression, as well as other...

  11. MicroRNAs and Endothelial (Dys) Function.

    Science.gov (United States)

    Santulli, Gaetano

    2016-08-01

    Accumulating evidence indicates that microRNAs (miRs)-non-coding RNAs that can regulate gene expression via translational repression and/or post-transcriptional degradation-are becoming one of the most fascinating areas of physiology, given their fundamental roles in countless pathophysiological processes. The relative roles of different miRs in vascular biology as direct or indirect post-transcriptional regulators of fundamental genes implied in vascular remodeling designate miRs as potential biomarkers and/or promising drug targets. The mechanistic importance of miRs in modulating endothelial cell (EC) function in physiology and in disease is addressed here. Drawbacks of currently available therapeutic options are also discussed, pointing at the challenges and clinical opportunities provided by miR-based treatments. J. Cell. Physiol. 231: 1638-1644, 2016. © 2015 Wiley Periodicals, Inc. PMID:26627535

  12. Identification and evolutionary implication of four novel box H/ACA snoRNAs from Giardia lamblia

    Institute of Scientific and Technical Information of China (English)

    LUO Jun; ZHOU Hui; CHEN Chongjian; LI Yan; CHEN Yueqin; QU Lianghu

    2006-01-01

    From a specialized cDNA library, four novel box H/ACA snoRNAs, named GLsR22,GLsR23, GLsR24 and GLsR25, were identified from the primitive eukaryote, Giardia lamblia. Bioinformatics analyses indicated that all of them can be potentially folded into double hairpins, the typical secondary structures of box H/ACA snoRNAs. GLsR24 and GLsR25 are predicted to guide the site-specific pseudouridylation at U1753 and U2396 on 23S rRNA,respectively, while GLsR22 and GLsR23 belong to the family of "orphan" snoRNAs. All of the four novel snoRNAs are encoded by single copy genes and located in small intergenic regions. Interestingly,compared with the counterparts previously reported in Archaea and other unicellular protozoan, the box H/ACA snoRNAs identified from G. lamblia have unique structural features, implying that snoRNAs evolved from prokaryotes to eukaryotes in different ways.

  13. tRFs: miRNAs in disguise.

    Science.gov (United States)

    Venkatesh, Thejaswini; Suresh, Padmanaban S; Tsutsumi, Rie

    2016-04-01

    tRFs and tiRNAs are two new classes of regulatory non-coding small RNAs that are derived from the cleavage of pre-existing tRNAs. tRFs are 18-22 nt long and are classified into the tRF-5, tRF-3, and tRF-1 series. Here, we discuss in detail the regulatory roles of tRFs in translation, viral infections, and carcinogenesis. Moreover, we have reviewed the association of tRFs with Argonaute proteins, including their potential to function as miRNAs. Interestingly, few miRNAs are generated from pre-existing tRNAs. Hence, tRNAs generate similar-sized tRFs and miRNAs, leading to misannotations due to cross mapping of tRFs and tRNA-derived miRNAs during deep sequencing data analysis. Therefore, it is important to catalogue the overlapping sequences between tRNA-derived miRNAs and tRFs. We have catalogued the miRNAs that overlap with tRFs sequences in humans using miRBase. We identified 20 tRNA-derived miRNAs that share sequences with tRFs. Of the 20 miRNAs, 5 miRNAs (miR-3182, miR-4521, miR-1260a, miR-1260b, and miR-7977) showed significant prediction scores. Furthermore, we have identified a lysine degradation pathway as a common regulatory pathway for miR-1260a, miR-1260b, and miR-3182 by using DIANA-mirPath. PMID:26743126

  14. Bacterial small RNAs in the Genus Rickettsia

    OpenAIRE

    Schroeder, Casey L. C.; Narra, Hema P.; Rojas, Mark; Sahni, Abha; Patel, Jignesh; Khanipov, Kamil; Wood, Thomas G.; Fofanov, Yuriy; Sahni, Sanjeev K.

    2015-01-01

    Background Rickettsia species are obligate intracellular Gram-negative pathogenic bacteria and the etiologic agents of diseases such as Rocky Mountain spotted fever (RMSF), Mediterranean spotted fever, epidemic typhus, and murine typhus. Genome sequencing revealed that R. prowazekii has ~25 % non-coding DNA, the majority of which is thought to be either “junk DNA” or pseudogenes resulting from genomic reduction. These characteristics also define other Rickettsia genomes. Bacterial small RNAs,...

  15. Viroids: "living fossils" of primordial RNAs?

    Science.gov (United States)

    Diener, Theodor O

    2016-01-01

    The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities-after discovery of the "subvisual" microorganisms in 1675 and that of the "submicroscopic" viruses in 1892-has been officially endorsed by the International Committee on Virus Taxonomy as a new order called subviral agents.In 1989, I proposed that, based on their respective molecular properties, viroids are more plausible "living fossils" of the hypothetical RNA World (widely assumed to have existed prior to the evolution of DNA or proteins) than are intron-derived RNAs, which were, at that time, suggested as putative survivors. There were few citations of my proposal-and virtually none of viroids-beyond plant virology unil 1994, when Cheles-Flores critically examined the hypothesis and pointed out a serious difficulty, as well as a process by which this difficulty could be overcome. In 2013, when investigations by Koonin and Dolja revealed that of extant RNAs, viroids "strikingly" display some of the molecular properties posited for the earliest evolving, selfish RNAs (primordial RNAs), but, because extant organisms, aside from higher plants, appear not to harbor viroids, they cannot be regarded as primordial fossils, but appear to have evolved post LUCA (the Last Universal Common Ancestor). Here, I review whether some evidence nevertheless is compatible with the original postulate of the 1989 hypothesis. My analysis reveals no unequivocal evidence for an ancient origin of viroids, but suggests, alternatively, that viroids may have evolved de novo more recently, probably by novel processes similar to those suggested by each reviewer.These results are important, because they help illuminate a little understood period of abiogenesis--after the abiotic synthesis of life's chemical building blocks, which is, in principle, understood, and before the evolution of DNA and proteins in the late RNA World. PMID:27016066

  16. Insights on the functional impact of microRNAs present in autism-associated copy number variants.

    Directory of Open Access Journals (Sweden)

    Varadarajan Vaishnavi

    Full Text Available Autism spectrum disorder is a complex neurodevelopmental disorder that appears during the first three years of infancy and lasts throughout a person's life. Recently a large category of genomic structural variants, denoted as copy number variants (CNVs, were established to be a major contributor of the pathophysiology of autism. To date almost all studies have focussed only on the genes present in the CNV loci, but the impact of non-coding regulatory microRNAs (miRNAs present in these regions remain largely unexplored. Hence we attempted to elucidate the biological and functional significance of miRNAs present in autism-associated CNV loci and their target genes by using a series of computational tools. We demonstrate that nearly 11% of the CNV loci harbor miRNAs and a few of these miRNAs were previously reported to be associated with autism. A systematic analysis of the CNV-miRNAs based on their interactions with the target genes enabled the identification of top 10 miRNAs namely hsa-miR-590-3p, hsa-miR-944, hsa-miR-570, hsa-miR-34a, hsa-miR-124, hsa-miR-548f, hsa-miR-429, hsa-miR-200b, hsa-miR-195 and hsa-miR-497 as hub molecules. Further, the CNV-miRNAs formed a regulatory loop with transcription factors and their downstream target genes, and annotation of these target genes indicated their functional involvement in neurodevelopment and synapse. Moreover, miRNAs present in deleted and duplicated CNV loci may explain the difference in dosage of the crucial genes controlled by them. These CNV-miRNAs can also impair the global processing and biogenesis of all miRNAs by targeting key molecules in the miRNA pathway. To our knowledge, this is the first report to highlight the significance of CNV-microRNAs and their target genes to contribute towards the genetic heterogeneity and phenotypic variability of autism.

  17. Vaccine candidates for dengue virus type 1 (DEN1 generated by replacement of the structural genes of rDEN4 and rDEN4Δ30 with those of DEN1

    Directory of Open Access Journals (Sweden)

    Blaney Joseph E

    2007-02-01

    Full Text Available Abstract Background Antigenic chimeric viruses have previously been generated in which the structural genes of recombinant dengue virus type 4 (rDEN4 have been replaced with those derived from DEN2 or DEN3. Two vaccine candidates were identified, rDEN2/4Δ30(ME and rDEN3/4Δ30(ME, which contain the membrane (M precursor and envelope (E genes of DEN2 and DEN3, respectively, and a 30 nucleotide deletion (Δ30 in the 3' untranslated region of the DEN4 backbone. Based on the promising preclinical phenotypes of these viruses and the safety and immunogenicity of rDEN2/4Δ30(ME in humans, we now describe the generation of a panel of four antigenic chimeric DEN4 viruses using either the capsid (C, M, and E (CME or ME structural genes of DEN1 Puerto Rico/94 strain. Results Four antigenic chimeric viruses were generated and found to replicate efficiently in Vero cells: rDEN1/4(CME, rDEN1/4Δ30(CME, rDEN1/4(ME, and rDEN1/4Δ30(ME. With the exception of rDEN1/4(ME, each chimeric virus was significantly attenuated in a SCID-HuH-7 mouse xenograft model with a 25-fold or greater reduction in replication compared to wild type DEN1. In rhesus monkeys, only chimeric viruses with the Δ30 mutation appeared to be attenuated as measured by duration and magnitude of viremia. rDEN1/4Δ30(CME appeared over-attenuated since it failed to induce detectable neutralizing antibody and did not confer protection from wild type DEN1 challenge. In contrast, rDEN1/4Δ30(ME induced 66% seroconversion and protection from DEN1 challenge. Presence of the Δ30 mutation conferred a significant restriction in mosquito infectivity upon rDEN1/4Δ30(ME which was shown to be non-infectious for Aedes aegypti fed an infectious bloodmeal. Conclusion The attenuation phenotype in SCID-HuH-7 mice, rhesus monkeys, and mosquitoes and the protective immunity observed in rhesus monkeys suggest that rDEN1/4Δ30(ME should be considered for evaluation in a clinical trial.

  18. Two oppositely localised frizzled RNAs as axis determinants in a cnidarian embryo.

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Momose

    2007-04-01

    Full Text Available In phylogenetically diverse animals, including the basally diverging cnidarians, "determinants" localised within the egg are responsible for directing development of the embryonic body plan. Many such determinants are known to regulate the Wnt signalling pathway, leading to regionalised stabilisation of the transcriptional coregulator beta-catenin; however, the only strong molecular candidate for a Wnt-activating determinant identified to date is the ligand Wnt11 in Xenopus. We have identified embryonic "oral-aboral" axis determinants in the cnidarian Clytia hemisphaerica in the form of RNAs encoding two Frizzled family Wnt receptors, localised at opposite poles of the egg. Morpholino-mediated inhibition of translation showed that CheFz1, localised at the animal pole, activates the canonical Wnt pathway, promotes oral fates including gastrulation, and may also mediate global polarity in the ectoderm. CheFz3, whose RNA is localised at the egg vegetal cortex, was found to oppose CheFz1 function and to define an aboral territory. Active downregulation mechanisms maintained the reciprocal localisation domains of the two RNAs during early development. Importantly, ectopic expression of either CheFz1 or CheFz3 was able to redirect axis development. These findings identify Frizzled RNAs as axis determinants in Clytia, and have implications for the evolution of embryonic patterning mechanisms, notably that diverse Wnt pathway regulators have been adopted to initiate asymmetric Wnt pathway activation.

  19. Role of microRNAs and DNA methyltransferases in transmitting induced genomic instability between cell generations

    Directory of Open Access Journals (Sweden)

    Katriina eHuumonen

    2014-09-01

    Full Text Available There is limited understanding of how radiation or chemicals induce genomic instability, and how the instability is epigenetically transmitted to the progeny of exposed cells or organisms. Here we measured the expression of microRNAs (miRNAs and DNA methyltransferases (DNMTs in murine embryonal fibroblasts exposed to ionizing radiation or 2,3,7,8 -tetrachlorodibenzo-p-dioxin (TCDD, which were previously shown to induce genomic instability in this cell line. Cadmium was used as a reference agent that does not induce genomic instability in our experimental model. Measurements at 8 and 15 days after exposure did not identify any such persistent changes that could be considered as signals transmitting genomic instability to the progeny of exposed cells. However, measurements at 2 days after exposure revealed findings that may reflect initial stages of genomic instability. Changes that were common to TCDD and two doses of radiation (but not to cadmium included 5 candidate signature miRNAs and general up-regulation of miRNA expression. Expression of DNMT3a, DNMT3b and DNMT2 were suppressed by cadmium but not by TCDD or radiation, consistently with the hypothesis that sufficient expression of DNMTs is necessary in the initial phase of induced genomic instability.

  20. miRNAs and Other Epigenetic Changes as Biomarkers in Triple Negative Breast Cancer

    Directory of Open Access Journals (Sweden)

    Andrea Mathe

    2015-11-01

    Full Text Available Triple negative breast cancer (TNBC is characterised by the lack of receptors for estrogen (ER, progesterone (PR, and human epidermal growth factor 2 (HER2. Since it cannot be treated by current endocrine therapies which target these receptors and due to its aggressive nature, it has one of the worst prognoses of all breast cancer subtypes. The only treatments remain chemo- and/or radio-therapy and surgery and because of this, novel biomarkers or treatment targets are urgently required to improve disease outcomes. MicroRNAs represent an attractive candidate for targeted therapies against TNBC, due to their natural ability to act as antisense interactors and regulators of entire gene sets involved in malignancy and their superiority over mRNA profiling to accurately classify disease. Here we review the current knowledge regarding miRNAs as biomarkers in TNBC and their potential use as therapeutic targets in this disease. Further, we review other epigenetic changes and interactions of these changes with microRNAs in this breast cancer subtype, which may lead to the discovery of new treatment targets for TNBC.