WorldWideScience

Sample records for underlying chromatin structure

  1. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  2. Effects of fast neutrons on chromatin: dependence on chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)

    2002-07-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  3. Effects of fast neutrons on chromatin: dependence on chromatin structure

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.

    2002-01-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  4. UV-induced structural changes in chromatin

    International Nuclear Information System (INIS)

    Lang, H.; Zimmer, C.; Vengerov, Yu.Yu.

    1985-01-01

    UV-induced structural alterations of chromatin were studied by means of CD, electron microscopic, and gel electrophoretic measurements. The results indicate that chromatin undergoes serious structural changes after irradiation even at very low fluences. In the low fluence range the structural transitions from the higher ordered chromatin structure to the unfolded state occur without detectable changes in the content of histone H1 and of the core histones. Histone H1 disappears only at fluences above 10 kJ/m 2 . Furthermore, DNA in chromatin is much more sensitive against UV-irradiation and shows a higher degree of strand scission relative to free DNA. While fragmentation in free DNA occurs at fluences above 15 kJ/m 2 , it occurs even at 5.5 kJ/m 2 in the case of chromatin. The biological meaning of the observed UV-induced structural alterations of chromatin is discussed. (author)

  5. Structured illumination to spatially map chromatin motions.

    Science.gov (United States)

    Bonin, Keith; Smelser, Amanda; Moreno, Naike Salvador; Holzwarth, George; Wang, Kevin; Levy, Preston; Vidi, Pierre-Alexandre

    2018-05-01

    We describe a simple optical method that creates structured illumination of a photoactivatable probe and apply this method to characterize chromatin motions in nuclei of live cells. A laser beam coupled to a diffractive optical element at the back focal plane of an excitation objective generates an array of near diffraction-limited beamlets with FWHM of 340  ±  30  nm, which simultaneously photoactivate a 7  ×  7 matrix pattern of GFP-labeled histones, with spots 1.70  μm apart. From the movements of the photoactivated spots, we map chromatin diffusion coefficients at multiple microdomains of the cell nucleus. The results show correlated motions of nearest chromatin microdomain neighbors, whereas chromatin movements are uncorrelated at the global scale of the nucleus. The method also reveals a DNA damage-dependent decrease in chromatin diffusion. The diffractive optical element instrumentation can be easily and cheaply implemented on commercial inverted fluorescence microscopes to analyze adherent cell culture models. A protocol to measure chromatin motions in nonadherent human hematopoietic stem and progenitor cells is also described. We anticipate that the method will contribute to the identification of the mechanisms regulating chromatin mobility, which influences most genomic processes and may underlie the biogenesis of genomic translocations associated with hematologic malignancies. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  6. Capturing Structural Heterogeneity in Chromatin Fibers.

    Science.gov (United States)

    Ekundayo, Babatunde; Richmond, Timothy J; Schalch, Thomas

    2017-10-13

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory.

    Science.gov (United States)

    Watson, L Ashley; Tsai, Li-Huei

    2017-04-01

    Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron. For instance, neuronal activity induces relocalization of gene loci to 'transcription factories', and specific enhancer-promoter looping contacts allow for precise transcriptional regulation. Moreover, neuronal activity-dependent DNA double-strand break formation in the promoter of immediate early genes appears to overcome topological constraints on transcription. Together, these findings point to a critical role for genome topology in integrating dynamic environmental signals to define precise spatiotemporal gene expression programs supporting cognitive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Interphase Chromosome Conformation and Chromatin-Chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

    Science.gov (United States)

    Zhang, Ye; Wong, Michael; Hada, Megumi; Wu, Honglu

    2015-01-01

    Microgravity has been shown to alter global gene expression patterns and protein levels both in cultured cells and animal models. It has been suggested that the packaging of chromatin fibers in the interphase nucleus is closely related to genome function, and the changes in transcriptional activity are tightly correlated with changes in chromatin folding. This study explores the changes of chromatin conformation and chromatin-chromatin interactions in the simulated microgravity environment, and investigates their correlation to the expression of genes located at different regions of the chromosome. To investigate the folding of chromatin in interphase under various culture conditions, human epithelial cells, fibroblasts, and lymphocytes were fixed in the G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome as separate colors. After images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multi-mega base pair scale. In order to determine the effects of microgravity on chromosome conformation and orientation, measures such as distance between homologous pairs, relative orientation of chromosome arms about a shared midpoint, and orientation of arms within individual chromosomes were all considered as potentially impacted by simulated microgravity conditions. The studies revealed non-random folding of chromatin in interphase, and suggested an association of interphase chromatin folding with radiation-induced chromosome aberration hotspots. Interestingly, the distributions of genes with expression changes over chromosome 3 in cells cultured under microgravity environment are apparently clustered on specific loci and chromosomes. This data provides important insights into how mammalian cells respond to microgravity at molecular level.

  9. [Neutron scatter studies of chromatin structure related to function

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1990-01-01

    This study is concerned with the application of neutron scatter techniques to the different structural states of nucleosomes and chromatin with the long term objective of understanding how the enormous lengths of DNA are folded into chromosomes. Micrococcal nuclease digestion kinetics have defined two subnucleosome particles; the chromatosome with 168 bp DNA, the histone octamer and one H1 and the nucleosome core particle with 146 bp DNA and the histone octamer. As will be discussed, the structure of the 146 bp DNA core particle is known in solution at low resolution from neutron scatter studies and in crystals. Based on this structure, the authors have a working model for the chromatosome and the mode of binding of H1. In order to define the structure of the nucleosome and also the different orders of chromatin structures they need to know the paths of DNA that link nucleosomes and the factors associated with chromosome functions that act on those DNA paths. The major region for this situation is the inherent variabilities in nucleosome DNA sequences, in the histone subtypes and their states of chemical modification and in the precise locations of nucleosomes. Such variabilities obscure the underlying principles that govern the packaging of DNA into the different structural states of nucleosomes and chromatin. The only way to elucidate these principles is to study the structures of nucleosomes and oligonucleosomes that are fully defined. They have largely achieved these objectives

  10. Chromatin Structure in Bands and Interbands of Polytene Chromosomes Imaged by Atomic Force Microscopy

    NARCIS (Netherlands)

    de Grauw, C.J.; de Grauw, C.J.; Avogadro, A.; van den Heuvel, D.J.; van den Heuvel, D.J.; van der Werf, Kees; Otto, Cornelis; Kraan, Yvonne M.; van Hulst, N.F.; Greve, Jan

    1998-01-01

    Polytene chromosomes from Drosophila melanogaster, observed from squash preparations, and chromosomes from Chironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed

  11. Nuclear visions enhanced: chromatin structure, organization and dynamics

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

    The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

  12. Chromosome aberration model combining radiation tracks, chromatin structure, DSB repair and chromatin mobility

    International Nuclear Information System (INIS)

    Friedland, W.; Kundrat, P.

    2015-01-01

    The module that simulates the kinetics and yields of radiation-induced chromosome aberrations within the biophysical code PARTRAC is described. Radiation track structures simulated by Monte Carlo methods are overlapped with multi-scale models of DNA and chromatin to assess the resulting DNA damage. Spatial mobility of individual DNA ends from double-strand breaks is modelled simultaneously with their processing by the non-homologous end-joining enzymes. To score diverse types of chromosome aberrations, the joined ends are classified regarding their original chromosomal location, orientation and the involvement of centromeres. A comparison with experimental data on dicentrics induced by gamma and alpha particles shows that their relative dose dependence is predicted correctly, although the absolute yields are overestimated. The critical model assumptions on chromatin mobility and on the initial damage recognition and chromatin remodelling steps and their future refinements to solve this issue are discussed. (authors)

  13. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V. [Brookhaven National Laboratory, Upton, NY (United States)

    1994-12-31

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

  14. Neutron scattering studies on chromatin higher-order structure

    International Nuclear Information System (INIS)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V.

    1994-01-01

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist

  15. Probing chromatin structure with nuclease sensitivity assays.

    Science.gov (United States)

    Gregory, R I; Khosla, S; Feil, R

    2001-01-01

    To further our understanding of genomic imprinting it will be essential to identify key control elements, and to investigate their regulation by both epigenetic modifications (such as DNA methylation) and trans-acting factors. So far, sequence elements that regulate parental allele-specific gene expression have been identified in a number of imprinted loci, either because of their differential DNA methylation or through functional studies in transgenic mice (1,2). A systematic search for allele-specific chromatin features constitutes an alternative strategy to identify elements that regulate imprinting. The validity of such an in vivo chromatin approach derives from the fact that in several known imprinting control-elements, a specialized organization of chromatin characterized by nuclease hypersensitivity is present on only one of the two parental chromosome (3). For example, the differentially methylated 5 -portion of the human SNRPN gene-a sequence element that controls imprinting in the Prader-Willi and Angelman syndromes' domain on chromosome 15q11- q13-has strong DNase-I hypersensitive sites on the unmethylated paternal chromosome (4). A differentially methylated region that regulates the imprinting of H19 and that of the neighboring insulin-like growth factor-2 gene on mouse chromosome 7 was also found to have parental chromosome-specific hypersensitive sites (5,6). The precise nature of the allelic nuclease hypersensitivity in these and other imprinted loci remains to be determined in more detail, for example, by applying complementary chromatin methodologies (7,8). However, it is commonly observed that a nuclease hypersensitive site corresponds to a small region where nucleosomes are absent or partially disrupted.

  16. Gibberellin-induced change in the structure of chromatin in wheat sprouts: decrease in the accessibility of DNA in preparations of soluble chromatin to the action of EcoRII methylase

    International Nuclear Information System (INIS)

    Noskov, V.A.; Kintsurashvili, L.N.; Smirnova, T.A.; Manamsh'yan, T.A.; Kir'yanov, G.I.; Vanyushin, B.F.

    1986-01-01

    A method has been perfected for producing soluble chromatin from whole wheat sprouts at low ionic strength. The chromatin preparations isolated possess a native structure: they have a nucleosome organization. Under identical conditions the soluble wheat chromatin undergoes more profound degradation by DNase I and staphylococcal nuclease than the chromatin from the rat liver. The DNA contained in the isolated chromatin is capable of accepting CHnumber groups from S-[methyl- 3 H]-adenosylmethionine during incubation with DNA methylase EcoRII; not all the CC A/T GG sequences in DNA are methylated in vivo. Chromatin from gibberellin A 3 -treated wheat sprout DNA accepts 40% fewer CH 3 groups than that from the control sprouts, which is probably due to the greater compactness of the chromatin. In the case of longer incubation, the level of methylation of the chromatin falls, which may be associated with the presence of DNA-demethylating activity

  17. [Automated morphometric evaluation of the chromatin structure of liver cell nuclei after vagotomy].

    Science.gov (United States)

    Butusova, N N; Zhukotskiĭ, A V; Sherbo, I V; Gribkov, E N; Dubovaia, T K

    1989-05-01

    The morphometric analysis of the interphase chromatine structure of the hepatic cells nuclei was carried out on the automated TV installation for the quantitative analysis of images "IBAS-2" (by the OPTON firm, the FRG) according to 50 optical and geometric parameters during various periods (1.2 and 4 weeks) after the vagotomy operation. It is determined that upper-molecular organisation of chromatine undergoes the biggest changes one week after operation, and changes of granular component are more informative than changes of the nongranular component (with the difference 15-20%). It was also revealed that chromatine components differ in tinctorial properties, which are evidently dependent on physicochemical characteristics of the chromatine under various functional conditions of the cell. As a result of the correlation analysis the group of morphometric indices of chromatine structure was revealed, which are highly correlated with level of transcription activity of chromatine during various terms after denervation. The correlation quotient of these parameters is 0.85-0.97. The summing up: vagus denervation of the liver causes changes in the morphofunctional organisation of the chromatine.

  18. Higher-order structure of Saccharomyces cerevisiae chromatin

    International Nuclear Information System (INIS)

    Lowary, P.T.; Widom, J.

    1989-01-01

    We have developed a method for partially purifying chromatin from Saccharomyces cerevisiae (baker's yeast) to a level suitable for studies of its higher-order folding. This has required the use of yeast strains that are free of the ubiquitous yeast killer virus. Results from dynamic light scattering, electron microscopy, and x-ray diffraction show that the yeast chromatin undergoes a cation-dependent folding into 30-nm filaments that resemble those characteristic of higher-cell chromatin; moreover, the packing of nucleosomes within the yeast 30-nm filaments is similar to that of higher cells. These results imply that yeast has a protein or protein domain that serves the role of the histone H 1 found in higher cells; physical and genetic studies of the yeast activity could help elucidate the structure and function of H 1. Images of the yeast 30-nm filaments can be used to test crossed-linker models for 30-nm filament structure

  19. RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization.

    Science.gov (United States)

    Pascali, Chiara; Teichmann, Martin

    2013-01-01

    RNA polymerase III (Pol III) transcription is regulated by modifications of the chromatin. DNA methylation and post-translational modifications of histones, such as acetylation, phosphorylation and methylation have been linked to Pol III transcriptional activity. In addition to being regulated by modifications of DNA and histones, Pol III genes and its transcription factors have been implicated in the organization of nuclear chromatin in several organisms. In yeast, the ability of the Pol III transcription system to contribute to nuclear organization seems to be dependent on direct interactions of Pol III genes and/or its transcription factors TFIIIC and TFIIIB with the structural maintenance of chromatin (SMC) protein-containing complexes cohesin and condensin. In human cells, Pol III genes and transcription factors have also been shown to colocalize with cohesin and the transcription regulator and genome organizer CCCTC-binding factor (CTCF). Furthermore, chromosomal sites have been identified in yeast and humans that are bound by partial Pol III machineries (extra TFIIIC sites - ETC; chromosome organizing clamps - COC). These ETCs/COC as well as Pol III genes possess the ability to act as boundary elements that restrict spreading of heterochromatin.

  20. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

    Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor

  1. Model for the structure of the active nucleolar chromatin

    International Nuclear Information System (INIS)

    Labhart, P.; Ness, P.; Banz, E.; Parish, R.; Koller, T.; Universitaet Zurich, Switzerland)

    1983-01-01

    Transcribed ribosomal genes of Xenopus laevis oocytes and of Dictyostelium discoideum were studied electron microscopically using step gradients at different ionic strengths. Under these conditions the fiber of the active chromatin appears smooth and is indistinguishable from free DNA. The accessibility of the coding region and of a nontranscribed spacer region to restriction enzymes and micrococcal nuclease were investigated. All of the results obtained are consistent with a model in which active nucleolar chromatin is mostly composed of free DNA and the components required for transcription. 50 references, 7 figures

  2. Chromatin Structure of Epstein-Barr Virus Latent Episomes.

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

    EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.

  3. Chromatin Structure in Cell Differentiation, Aging and Cancer

    NARCIS (Netherlands)

    S. Kheradmand Kia (Sima)

    2009-01-01

    textabstractChromatin is the structure that the eukaryotic genome is packaged into, allowing over a metre of DNA to fit into the small volume of the nucleus. It is composed of DNA and proteins, most of which are histones. This DNA-protein complex is the template for a number of essential cell

  4. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

    Directory of Open Access Journals (Sweden)

    Sha Ky

    2010-08-01

    Full Text Available Abstract Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i a source for purified cells (or nuclei of distinct types, and (ii a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models or to amalgamations of diverse cell types (tissue chunks, whole organisms. Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis, our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid genome. Conclusions Validating the DALEC mapping results, we observe a strong association

  5. Relationship between chromatin structure and sensitivity to molecularly targeted auger electron radiation therapy.

    NARCIS (Netherlands)

    Terry, S.Y.A.; Vallis, K.A.

    2012-01-01

    PURPOSE: The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. METHODS AND MATERIALS: Chromatin structure was

  6. Regulation of chromatin structure by poly(ADP-ribosylation

    Directory of Open Access Journals (Sweden)

    Sascha eBeneke

    2012-09-01

    Full Text Available The interaction of DNA with proteins in the context of chromatin has to be tightly regulated to achieve so different tasks as packaging, transcription, replication and repair. The very rapid and transient post-translational modification of proteins by poly(ADP-ribose has been shown to take part in all four. Originally identified as immediate cellular answer to a variety of genotoxic stresses, already early data indicated the ability of this highly charged nucleic acid-like polymer to modulate nucleosome structure, the basic unit of chromatin. At the same time the enzyme responsible for synthesizing poly(ADP-ribose, the zinc-finger protein poly(ADP-ribose polymerase-1 (PARP1, was shown to control transcription initiation as basic factor TFIIC within the RNA-polymerase II machinery. Later research focused more on PARP-mediated regulation of DNA repair and cell death, but in the last few years, transcription as well as chromatin modulation has re-appeared on the scene. This review will discuss the impact of PARP1 on transcription and transcription factors, its implication in chromatin remodeling for DNA repair and probably also replication, and its role in controlling epigenetic events such as DNA methylation and the functionality of the insulator protein CCCTC-binding factor.

  7. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  8. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-01-01

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome

  9. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    Despite of setbacks in the lack of neutrons for the proposed We have made considerable progress in chromatin reconstitution with the VLR histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized an intrinsically bent DNA region flanking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interatctions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  10. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    We have made considerable progress in chromatin reconstitution with very lysine rich histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized in intrinsically bent DNA region flaking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interactions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear Magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  11. RNA is an integral component of chromatin that contributes to its structural organization.

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

    Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

  12. Chromatin Structure and Radiation-Induced Intrachromosome Exchange

    Science.gov (United States)

    Mangala; Zhang, Ye; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    We have recently investigated the location of breaks involved in intrachromosomal type exchange events, using the multicolor banding in situ hybridization (mBAND) technique for human chromosome 3. In human epithelial cells exposed to both low- and high-LET radiations in vitro, intrachromosome exchanges were found to occur preferentially between a break in the 3p21 and one in the 3q11. Exchanges were also observed between a break in 3p21 and one in 3q26, but few exchanges were observed between breaks in 3q11 and 3q26, even though the two regions were on the same arm of the chromosome. To explore the relationships between intrachromosome exchanges and chromatin structure, we used probes that hybridize the three regions of 3p21, 3q11 and 3q26, and measured the distance between two of the three regions in interphase cells. We further analyzed fragile sites on the chromosome that have been identified in various types of cancers. Our results demonstrated that the distribution of breaks involved in radiation-induced intrachromosome aberrations depends upon both the location of fragile sites and the folding of chromatins

  13. Genomic and chromatin signals underlying transcription start-site selection

    DEFF Research Database (Denmark)

    Valen, Eivind; Sandelin, Albin Gustav

    2011-01-01

    A central question in cellular biology is how the cell regulates transcription and discerns when and where to initiate it. Locating transcription start sites (TSSs), the signals that specify them, and ultimately elucidating the mechanisms of regulated initiation has therefore been a recurrent theme....... In recent years substantial progress has been made towards this goal, spurred by the possibility of applying genome-wide, sequencing-based analysis. We now have a large collection of high-resolution datasets identifying locations of TSSs, protein-DNA interactions, and chromatin features over whole genomes...

  14. Fast neutron irradiation effects on liver chromatin structure

    International Nuclear Information System (INIS)

    Constantinescu, B.; Radu, L.

    1996-01-01

    The growing interest in neutron therapy requires complex studies on the mechanisms of neutron action on biological systems, especially on chromatin. The chromatin was extracted from a normal tissue-livers of Wistar rats - and from a tumoral tissue - Walker tumour maintained on Wistar rats. Irradiation doses from 5 Gy to 100 Gy by fast neutron intense beams produced via d(13.5 MeV) +Be (thick target) reaction at Bucharest U-120 Classical Cyclotron were used. To study the post-irradiation effects, various methods were employed. So, the variation in the 260 nm absorbency in chromatin thermal transition was pursuit. The chromatin-ethidium bromide complexes fluorescence with λ ex =480 nm and λ em =600 nm was analyzed. To determine chromatin DNA strand breaks a fluorimetric method, with cells' suspensions as starting material was used. This method requires a partial treatment with alkali producing three components: T-estimating the total fluorescence of DNA double helix, P-assigning the untwisting rate and B-the blank, where DNA is completely unfolded The percentsge of DNA double strand,-D-, remaining after this treatment, is: %D=100x(P-B)/(T-B). The intrinsic chromatin fluorescence was determined for tyrosine (λ ex =280 nm, λ em =305 nm), specific for badic chromatin prooteins, and for tryptophane (λ ex =290 nm, λ em =345 nm) specific for acid chromatin proteins. Polyacrylamide gel electrophoresis was performed: The double fluorescent labelling of chromatin was realized with acridine orange for DNA and with dansyl chloride for chromatin proteins. Fluorescence intensity determinations were done with λ ex =505 nm, λ em =530 nm for acridine orange and with λ ex =323 nm, λ em =505 nm for dansyl chloride. A Pye Unicam SP 1800 spectrophotometer and a Aminco SPF 500 spectrofluorimeter were employed. (author)

  15. Comparative study of cyanotoxins affecting cytoskeletal and chromatin structures in CHO-K1 cells.

    Science.gov (United States)

    Gácsi, Mariann; Antal, Otilia; Vasas, Gábor; Máthé, Csaba; Borbély, György; Saker, Martin L; Gyori, János; Farkas, Anna; Vehovszky, Agnes; Bánfalvi, Gáspár

    2009-06-01

    In this study we compared the effects of the two frequently occuring and most dangerous cyanobacterial toxins on the cellular organization of microfilaments, microtubules and on the chromatin structure in Chinese hamster ovary (CHO-K1) cells. These compounds are the widely known microcystin-LR (MC-LR) and cylindrospermopsin (CYN) classified as the highest-priority cyanotoxin. Toxic effects were tested in a concentration and time dependent manner. The hepatotoxic MC-LR did not cause significant cytotoxicity on CHO-K1 cells under 20 microM, but caused apoptotic changes at higher concentrations. Apoptotic shrinkage was associated with the shortening and loss of actin filaments and with a concentration dependent depolymerization of microtubules. No necrosis was observed over the concentration range (1-50 microM MC-LR) tested. Cylindrospermopsin did cause apoptosis at low concentrations (1-2 microM) and over short exposure periods (12h). Necrosis was observed at higher concentrations (5-10 microM) and following longer exposure periods (24 or 48h). Cyanotoxins also affected the chromatin structure. The condensation process was inhibited by MC-LR at a later stage and manifested as broken elongated prechromosomes. CYN inhibited chromatin condensation at the early fibrillary stage leading to blurred fluorescent images of apoptotic bodies and preventing the formation of metaphase chromosomes. Cylindrospermopsin exhibited a more pronounced toxic effect causing cytoskeletal and nuclear changes as well as apoptotic and necrotic alterations.

  16. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin.

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

    Full Text Available We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10 containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation.

  17. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

    Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

  18. Adenovirus chromatin structure at different stages of infection

    Energy Technology Data Exchange (ETDEWEB)

    Daniell, E.; Groff, D.E.; Fedor, M.J.

    1981-12-01

    The authors investigated the structure of adenovirus deoxyribonecleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parental DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with (/sup 3/)thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure they identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. The authors found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.

  19. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-05-17

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad hoc parameters. Also, we designed a global and a local alignment algorithms to measure the similarity between the templates and the chromatin struc- tures predicted by different modeling methods. Finally, the results from large-scale comparative tests indicated that our alignment algorithms significantly outperform the algorithms in literature.

  20. Structural chromatin organization as a factor determining the rate of chromatin endonucleolysis in irradiated and intact thymocytes

    International Nuclear Information System (INIS)

    Ryabchenko, N.I.; Ivannik, B.P.

    1987-01-01

    A study was made of chromatin endonucleolysis in hypotonized thymocytes incubating in digestive buffers containing different concentrations of potassium, magnesium, calcium, and mercaptoethanol. Inhibition of endonucleolysis by univalent cation during the first 20 min of incubation was followed by intensive chromatin degradation. A decrease in free potassium content retarded chromatin degradation and enhanced the inhibiting effect of the univalent cations. The regularities of changes in the rate of chromatin endonucleolysis in different digestive buffers were similar with both exposed and intact thymocytes

  1. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration.

    Science.gov (United States)

    Matysiak, Julien; Lesbats, Paul; Mauro, Eric; Lapaillerie, Delphine; Dupuy, Jean-William; Lopez, Angelica P; Benleulmi, Mohamed Salah; Calmels, Christina; Andreola, Marie-Line; Ruff, Marc; Llano, Manuel; Delelis, Olivier; Lavigne, Marc; Parissi, Vincent

    2017-07-28

    Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome.

  2. The effect of higher order chromatin structure on DNA damage and repair

    International Nuclear Information System (INIS)

    Yasui, L.S.; Warters, R.L.; Higashikubo, R.

    1985-01-01

    Alterations in chromatin structure are thought to play an important role in various radiobiological end points, i.e., DNA damage, DNA damage repair and cell survival. The authors use here the isoleucine deprivation technique to decondense higher order chromatin structure and asses X-ray induced DNA damage, DNA damage repair and cell survival on cells with decondensed chromatin as compared to controls. This chromatin decondensation manifests itself as a 30 fold decrease in nuclear area occupied by heterochromatin, an increased rate of Micrococcal nuclease digestion, 15% increased ethidium bromide intercalation and an altered binding capacity of Hl histone. These chromatin/nuclear changes do not affect X-ray induced DNA damage as measured by the alkaline elution technique or cell survival but slows DNA damage repair by 2 fold. Therefore, even though the chromatin appears more accessible to DNA damage and repair processes, these particular nuclear changes do not affect the DNA damaging effects of X-rays and in addition, repair is not enhanced by the ''relaxed'' state of chromatin. It is proposed that the altered metabolic state of isoleucine deprived cells provides a less efficient system for the repair of X-ray induced DNA damage

  3. Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.

    Science.gov (United States)

    Visone, Valeria; Vettone, Antonella; Serpe, Mario; Valenti, Anna; Perugino, Giuseppe; Rossi, Mosè; Ciaramella, Maria

    2014-09-25

    In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  4. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  5. The global relationship between chromatin physical topology, fractal structure, and gene expression

    DEFF Research Database (Denmark)

    Almassalha, Luay M; Tiwari, A; Ruhoff, P T

    2017-01-01

    in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D...... show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating...

  6. Chromatin degradation under the effect of differentiation inductors and γ-radiation on thymus lymphocytes in vitro

    International Nuclear Information System (INIS)

    Soldatenkov, V.A.; Sorokina, N.I.; Filippovich, I.V.

    1985-01-01

    Chemical inductors of differentiation were shown to cause chromatin degradation in thymus lymphocytes. This process was prevented by the protein synthesis inhibitors. The fragments formed after the effect of chemical differentiation inductors on thymocytes were fully identical to chromatin internucleosome degradation products formed in the exposed cells. Chromatin degradation under the effect of chemical differentiation inductors was most pronounced in a more radiosensitive thymocyte fraction

  7. Nuclear and chromatin structures and their influence on the radiosensitivity of DNA

    International Nuclear Information System (INIS)

    Oleinick, N.L.; Chiu, S.-M.

    1994-01-01

    Among the factors contributing to the distribution of DNA damage within irradiated mammalian cell nuclei are the interactions of DNA with nuclear proteins and the formation of multi-molecular chromatin structures. Studies on the manipulation of chromatin structures of isolated nuclei are summarised. The majority of chromatin within the nucleus of living cells is tightly compacted into nucleosomal superhelices and other higher order structures which have a limited ability to be damaged by radiation. The treatment of isolated nuclei with hypotonic buffers causes a decondensation of these structures and markedly sensitises the DNA to radiation, while retaining the majority of the chromosomal proteins. On the other hand, treatment of nuclei with hypertonic buffers strips the DNA of specific classes of nuclear proteins, destroying chromatin structure, and this procedure also enhances the sensitivity of the DNA to radiation. The various expanded chromatin structures are models for the structure of the minor fraction of DNA which is decondensed in preparation for transcription or replication. The combined results indicate that the majority of nuclear DNA is protected by histones and other nuclear proteins from radiation damage, partially as a result of the limited accessibility of the condensed structures to hydroxyl radical and partially as a result of the scavenging of radicals by the proteins. (Author)

  8. Chromatin structure in the unicellular algae Olisthodiscus luteus, Crypthecodinium cohnii and Peridiniun balticum.

    Science.gov (United States)

    Rizzo, P J; Burghardt, R C

    1980-01-01

    Isolated nuclei of the unicellular alga Olisthodiscus luteus, the uninucleate dinoflagellate Crypthecodinium cohnii and the binucleate dinoflagellate Peridinium balticum were lysed and deposited on grids by the microcentrifugation technique. The ultrastructure of the released chromatin fibers was compared to that of mouse liver nuclei. Chromatin from nuclei of Olisthodiscus luteus and the "eukaryotic" nuclei of Peridinium balticum, appeared as linear arrays of regularly repeating subunits which were identical in size and morphology to mouse nucleosomes. In contrast, the chromatin fibers from Crypthecodinium cohnii nuclei appeared as smoothe threads with a diameter of about 6.5 nm. Nuclear preparations containing mixtures of "dinokaryotic" and "eukaryotic" nuclei of Peridinium balticum also contained smooth fibers which most likely originated from the dinokaryotic nuclei. These and other results demonstrating the presence of nucleosomes in lower eukaryotes suggest that the subunit structure of chromatin arose very early in the evolution of the eukaryotic cell.

  9. Local changes of higher-order chromatin structure during DSB-repair

    International Nuclear Information System (INIS)

    Falk, M; Lukasova, E; Gabrielova, B; Ondrej, V; Kozubek, S

    2008-01-01

    We show that double-strand breaks (DSBs) induced in DNA of human cells by γ-radiation arise mainly in active, gene-rich, decondensed chromatin. We demonstrate that DSBs show limited movement in living cells, occasionally resulting in their permanent clustering, which poses a risk of incorrect DNA rejoining. In addition, some DSBs remain unrepaired for several days after irradiation, forming lesions repairable only with difficulty which are hazardous for genome stability. These 'late' DSBs colocalize with heterochromatin markers (dimethylated histone H3 at lysine 9, HP1 and CENP-A proteins), despite the low density of the surrounding chromatin. This indicates that there is epigenetic silencing of loci close to unrepaired DSBs and/or stabilization of damaged decondensed chromatin loops during repair and post-repair reconstitution of chromatin structure

  10. Chromatin structure and epigenetics of tumour cells: A review

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Krejčí, Jana; Hájek, R.; Harničarová, Andrea; Kozubek, Stanislav

    2009-01-01

    Roč. 9, č. 1 (2009), s. 51-61 ISSN 1871-529X R&D Projects: GA AV ČR(CZ) 1QS500040508; GA ČR(CZ) GA204/06/0978 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  11. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

  12. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization

    International Nuclear Information System (INIS)

    Lebedev, D. V.; Filatov, M. V.; Kuklin, A. I.; Islamov, A. Kh.; Stellbrink, J.; Pantina, R. A.; Denisov, Yu. Yu.; Toperverg, B. P.; Isaev-Ivanov, V. V.

    2008-01-01

    The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10 -1 to 10 -4 A -1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm

  13. Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.

    Science.gov (United States)

    Chen, Yunru; Zeng, Shiyang; Hu, Ruikun; Wang, Xiangxiu; Huang, Weilai; Liu, Jiangfang; Wang, Luying; Liu, Guifen; Cao, Ying; Zhang, Yong

    2017-01-01

    Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.

  14. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP

    DEFF Research Database (Denmark)

    Muratcioglu, Serena; Presman, Diego M; Pooley, John R

    2015-01-01

    The glucocorticoid receptor (GR) is a steroid-hormone-activated transcription factor that modulates gene expression. Transcriptional regulation by the GR requires dynamic receptor binding to specific target sites located across the genome. This binding remodels the chromatin structure to allow...... interaction with other transcription factors. Thus, chromatin remodeling is an essential component of GR-mediated transcriptional regulation, and understanding the interactions between these molecules at the structural level provides insights into the mechanisms of how GR and chromatin remodeling cooperate...

  15. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

    Directory of Open Access Journals (Sweden)

    Ana Paula Santos

    2017-01-01

    Full Text Available The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

  16. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    Directory of Open Access Journals (Sweden)

    Monica Soldi

    2013-03-01

    Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

  17. At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence

    Directory of Open Access Journals (Sweden)

    Ryosuke eOhsawa

    2013-07-01

    Full Text Available It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.

  18. Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

    Science.gov (United States)

    Fournier, David; Redl, Stefan; Best, Gerrit; Borsos, Máté; Tiwari, Vijay K.; Tachibana-Konwalski, Kikuë; Ketting, René F.; Parekh, Sapun H.; Cremer, Christoph; Birk, Udo J.

    2015-01-01

    During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated. PMID:26561583

  19. DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes.

    Science.gov (United States)

    Guha, Mithu; Saare, Mario; Maslovskaja, Julia; Kisand, Kai; Liiv, Ingrid; Haljasorg, Uku; Tasa, Tõnis; Metspalu, Andres; Milani, Lili; Peterson, Pärt

    2017-04-21

    The autoimmune regulator (AIRE) protein is the key factor in thymic negative selection of autoreactive T cells by promoting the ectopic expression of tissue-specific genes in the thymic medullary epithelium. Mutations in AIRE cause a monogenic autoimmune disease called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. AIRE has been shown to promote DNA breaks via its interaction with topoisomerase 2 (TOP2). In this study, we investigated topoisomerase-induced DNA breaks and chromatin structural alterations in conjunction with AIRE-dependent gene expression. Using RNA sequencing, we found that inhibition of TOP2 religation activity by etoposide in AIRE-expressing cells had a synergistic effect on genes with low expression levels. AIRE-mediated transcription was not only enhanced by TOP2 inhibition but also by the TOP1 inhibitor camptothecin. The transcriptional activation was associated with structural rearrangements in chromatin, notably the accumulation of γH2AX and the exchange of histone H1 with HMGB1 at AIRE target gene promoters. In addition, we found the transcriptional up-regulation to co-occur with the chromatin structural changes within the genomic cluster of carcinoembryonic antigen-like cellular adhesion molecule genes. Overall, our results suggest that the presence of AIRE can trigger molecular events leading to an altered chromatin landscape and the enhanced transcription of low-expressed genes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Circulating chromatin-anti-chromatin antibody complexes bind with high affinity to dermo-epidermal structures in murine and human lupus nephritis

    DEFF Research Database (Denmark)

    Fismen, S; Hedberg, A; Fenton, K A

    2009-01-01

    Murine and human lupus nephritis are characterized by glomerular deposits of electron-dense structures (EDS). Dominant components of EDS are chromatin fragments and IgG antibodies. Whether glomerular EDS predispose for similar deposits in skin is unknown. We analysed (i) whether dermo-epidermal i......Murine and human lupus nephritis are characterized by glomerular deposits of electron-dense structures (EDS). Dominant components of EDS are chromatin fragments and IgG antibodies. Whether glomerular EDS predispose for similar deposits in skin is unknown. We analysed (i) whether dermo......-epidermal immune complex deposits have similar molecular composition as glomerular deposits, (ii) whether chromatin fragments bind dermo-epidermal structures, and (iii) whether deposits in nephritic glomeruli predispose for accumulation of similar deposits in skin. Paired skin and kidney biopsies from nephritic...... (NZBxNZW)F1 and MRL-lpr/lpr mice and from five patients with lupus nephritis were analysed by immunofluorescence, immune electron microscopy (IEM) and co-localization TUNEL IEM. Affinity of chromatin fragments for membrane structures was determined by surface plasmon resonance. Results demonstrated (i...

  1. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

    2007-01-01

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  2. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea.

    Science.gov (United States)

    Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li

    2008-03-01

    Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

  3. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

    NARCIS (Netherlands)

    M. Rosa-Garrido (Manuel); Chapski, D.J. (Douglas J.); Schmitt, A.D. (Anthony D.); Kimball, T.H. (Todd H.); Karbassi, E. (Elaheh); Monte, E. (Emma); Balderas, E. (Enrique); Pellegrini, M. (Matteo); Shih, T.-T. (Tsai-Ting); Soehalim, E. (Elizabeth); D.A. Liem (David); Ping, P. (Peipei); N.J. Galjart (Niels); Ren, S. (Shuxun); Wang, Y. (Yibin); Ren, B. (Bing); Vondriska, T.M. (Thomas M.)

    2017-01-01

    textabstractBACKGROUND: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined.METHODS: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation

  4. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

    Science.gov (United States)

    Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

    2017-10-24

    Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

  5. Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

    2013-01-01

    In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

  6. Decrease of H1 histone and changes in chromatin structure and transcription in pea seedlings after γ-irradiation

    International Nuclear Information System (INIS)

    Bagi, G.; Hidvegi, E.J.

    1983-01-01

    Seeds and seedlings of pea have been irradiated between zero to 300 Gy doses of 60 Co gamma-irradiation and examinations were carried out on the chromatin of shoots of 1-week-old etiolated seedlings. There was only a slight change in the gross composition of chromatin after irradiation (in the mass ratios of DNA:RNA:histone:non-histone proteins). Separation of histones, however, showed that after 300 Gy irradiation the quantity of H1 histones decreased by 33% after seed irradiation and 43% after seedling irradiation. The ratio of H1 subfractions also changed. Enzymes DNAase II and micrococcal nuclease digested the chromatin of the irradiated sample 30% faster than the unirradiated one. Transcription kinetics of chromatin showed a gradual decrease of Ksub(m) value on increasing doses of irradiation. There was, however, no difference in the rate of transcription of DNAs, isolated from the chromatin of the control and irradiated samples. Protease and RNAase activity of whole shoots showed enhancement after irradiation. These data suggest that irradiation of either seeds or seedlings results in loosening of the seedling chromatin structure, while there is no change in basic nucleosomal structure. The specific degradation or dissociation of histone H1, localized in the internucleosomal region may be responsible for these changes in the higher order structure of chromatin. This may explain the easier accessibility of chromatin to DNAase II after irradiation and the more tightly bound RNA polymerase, exhibited in decreasing Ksub(m) values. (Auth.)

  7. Disconnect between alcohol-induced alterations in chromatin structure and gene transcription in a mouse embryonic stem cell model of exposure.

    Science.gov (United States)

    Veazey, Kylee J; Wang, Haiqing; Bedi, Yudhishtar S; Skiles, William M; Chang, Richard Cheng-An; Golding, Michael C

    2017-05-01

    Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact that alcohol and other drugs of abuse exert consistently notes a disconnection between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the 'histone code' induced by prenatal exposures to alcohol implicitly subvert gene expression, or whether the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program. To address this question, we examined the impact of ethanol exposure in mouse embryonic stem cells cultured under 2i conditions, where the transcriptional program is rigidly enforced through the use of small molecule inhibitors. We find that ethanol-induced changes in post-translational histone modifications are dose-dependent, unique to the chromatin modification under investigation, and that the extent and direction of the change differ between the period of exposure and the recovery phase. Similar to in vivo models, we find post-translational modifications affecting histone 3 lysine 9 are the most profoundly impacted, with the signature of exposure persisting long after alcohol has been removed. These changes in chromatin structure associate with dose-dependent alterations in the levels of transcripts encoding Dnmt1, Uhrf1, Tet1, Tet2, Tet3, and Polycomb complex members Eed and Ezh2. However, in this model, ethanol-induced changes to the chromatin template do not consistently associate with changes in gene transcription, impede the process of differentiation, or affect the acquisition of monoallelic patterns of expression for the imprinted gene Igf2R. These findings question the inferred universal relevance of epigenetic changes induced by drugs of abuse and suggest that changes

  8. Diazinon alters sperm chromatin structure in mice by phosphorylating nuclear protamines

    International Nuclear Information System (INIS)

    Pina-Guzman, B.; Solis-Heredia, M.J.; Quintanilla-Vega, B.

    2005-01-01

    Organophosphorus (OP) pesticides, widely used in agriculture and pest control, are associated with male reproductive effects, including sperm chromatin alterations, but the mechanisms underlying these effects are unknown. The main toxic action of OP is related to phosphorylation of proteins. Chemical alterations in sperm nuclear proteins (protamines), which pack DNA during the last steps of spermatogenesis, contribute to male reproductive toxicity. Therefore, in the present study, we tested the ability of diazinon (DZN), an OP compound, to alter sperm chromatin by phosphorylating nuclear protamines. Mice were injected with a single dose of DZN (8.12 mg/kg, i.p.), and killed 8 and 15 days after treatment. Quality of sperm from epididymis and vas deferens was evaluated through standard methods and chromatin condensation by flow cytometry (DNA Fragmented Index parameters: DFI and DFI%) and fluorescence microscopy using chromomycin-A 3 (CMA 3 ). Increases in DFI (15%), DFI% (4.5-fold), and CMA 3 (2-fold) were observed only at 8 days post-treatment, indicating an alteration in sperm chromatin condensation and DNA damage during late spermatid differentiation. In addition, an increase of phosphorous content (approximately 50%) in protamines, especially in the phosphoserine content (approximately 73%), was found at 8 days post-treatment. Sperm viability, motility, and morphology showed significant alterations at this time. These data strongly suggest that spermatozoa exposed during the late steps of maturation were the targets of DZN exposure. The correlation observed between the phosphorous content in nuclear protamines with DFI%, DFI, and CMA 3 provides evidence that phosphorylation of nuclear protamines is involved in the OP effects on sperm chromatin

  9. Chromatin structure influence the sensitivity of DNA to ionizing radiation induced DNA damage

    International Nuclear Information System (INIS)

    Gupta, Sanjay

    2016-01-01

    Chromatin acts as a natural hindrance in DNA-damage recognition, repair and recovery. Histone and their variants undergo differential post-translational modification(s) and regulate chromatin structure to facilitate DNA damage response (DDR). During the presentation we will discuss the importance of chromatin organization and histone modification(s) during IR-induced DNA damage response in human liver cells. Our data shows G1-phase specific decrease of H3 serine10 phosphorylation in response to DNA damage is coupled with chromatin compaction in repair phase of DDR. The loss of H3Ser10P during DNA damage shows an inverse correlation with gain of γH2AX from a same mono-nucleosome in a dose-dependent manner. The loss of H3Ser10P is a universal phenomenon as it is independent of origin of cell lines and nature of genotoxic agents in G1 phase cells. The reversible reduction of H3Ser10P is mediated by opposing activities of phosphatase, MKP1 and kinase, MSK1 of the MAP kinase pathway. The present study suggests distinct reversible histone marks are associated with G1-phase of cell cycle and plays a critical role in chromatin organization which may facilitate differential sensitivity against radiation. Thus, the study raises the possibility of combinatorial modulation of H3Ser10P and histone acetylation with specific inhibitors to target the radio-resistant cancer cells in G1-phase and thus may serve as promising targets for cancer therapy. (author)

  10. Structural domains and conformational changes in nuclear chromatin: a quantitative thermodynamic approach by differential scanning calorimetry.

    Science.gov (United States)

    Balbi, C; Abelmoschi, M L; Gogioso, L; Parodi, S; Barboro, P; Cavazza, B; Patrone, E

    1989-04-18

    A good deal of information on the thermodynamic properties of chromatin was derived in the last few years from optical melting experiments. The structural domains of the polynucleosomal chain, the linker, and the core particle denature as independent units. The differential scanning calorimetry profile of isolated chromatin is made up of three endotherms, at approximately 74, 90, and 107 degrees C, having an almost Gaussian shape. Previous work on this matter, however, was mainly concerned with the dependence of the transition enthalpy on external parameters, such as the ionic strength, or with the melting of nuclei from different sources. In this paper we report the structural assignment of the transitions of rat liver nuclei, observed at 58, 66, 75, 92, and 107 degrees C. They are representative of the quiescent state of the cell. The strategy adopted in this work builds on the method developed for the investigation of complex biological macromolecules. The heat absorption profile of the nucleus was related to the denaturation of isolated nuclear components; electron microscopy and electrophoretic techniques were used for their morphological and molecular characterization. The digestion of chromatin by endogenous nuclease mimics perfectly the decondensation of the higher order structure and represented the source of several misinterpretations. This point was carefully examined in order to define unambiguously the thermal profile of native nuclei. The low-temperature transitions, centered around 58 and 66 degrees C, arise from the melting of scaffolding structures and of the proteins associated with heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure

    International Nuclear Information System (INIS)

    Revaud, D.

    2009-06-01

    Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)

  12. FANCJ couples replication past natural fork barriers with maintenance of chromatin structure.

    Science.gov (United States)

    Schwab, Rebekka A; Nieminuszczy, Jadwiga; Shin-ya, Kazuo; Niedzwiedz, Wojciech

    2013-04-01

    Defective DNA repair causes Fanconi anemia (FA), a rare childhood cancer-predisposing syndrome. At least 15 genes are known to be mutated in FA; however, their role in DNA repair remains unclear. Here, we show that the FANCJ helicase promotes DNA replication in trans by counteracting fork stalling on replication barriers, such as G4 quadruplex structures. Accordingly, stabilization of G4 quadruplexes in ΔFANCJ cells restricts fork movements, uncouples leading- and lagging-strand synthesis and generates small single-stranded DNA gaps behind the fork. Unexpectedly, we also discovered that FANCJ suppresses heterochromatin spreading by coupling fork movement through replication barriers with maintenance of chromatin structure. We propose that FANCJ plays an essential role in counteracting chromatin compaction associated with unscheduled replication fork stalling and restart, and suppresses tumorigenesis, at least partially, in this replication-specific manner.

  13. Chromatin structure and ionizing-radiation-induced chromosome aberrations

    International Nuclear Information System (INIS)

    Muehlmann-Diaz, M.C.

    1993-01-01

    The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 10 5 copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G 0 , the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes

  14. Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure.

    Directory of Open Access Journals (Sweden)

    Ana-Maria Florescu

    2016-06-01

    Full Text Available Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations, we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 105 basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes.

  15. Polymer physics predicts the effects of structural variants on chromatin architecture.

    Science.gov (United States)

    Bianco, Simona; Lupiáñez, Darío G; Chiariello, Andrea M; Annunziatella, Carlo; Kraft, Katerina; Schöpflin, Robert; Wittler, Lars; Andrey, Guillaume; Vingron, Martin; Pombo, Ana; Mundlos, Stefan; Nicodemi, Mario

    2018-05-01

    Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolves the folding complexity of the EPHA4 locus and identifies SV-induced ectopic contacts and alterations of 3D genome organization in homozygous or heterozygous states. We show that SVs can reconfigure topologically associating domains, thereby producing extensive rewiring of regulatory interactions and causing disease by gene misexpression. PRISMR can be used to predict interactions in silico, thereby providing a tool for analyzing the disease-causing potential of SVs.

  16. Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Chang Pyo Hong

    2012-09-01

    Full Text Available Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.

  17. [Changes in the chromatin structure of hepatocyte nuclei of rats trained to hypoxia].

    Science.gov (United States)

    Domkina, L K; Bresler, V M; Simanovskiĭ, L N

    1976-03-01

    Structure of chromatin in the nuclei of the isolated surviving hepatocytes and in the isolated nuclei of hepatocytes were studied by fluorochroming with acridine orange and by microfluorimetry of fluorescenc connected with the stain chromatin at 530 and 590 nm in intact rats and in the animals trained to hypoxia in a pressure chamber for 60 days. The nuclei of hepatocytes of intact rats were distributed by fluorescence at 530 nm into three classes with the intensity ratio of 1:2:4; as to the nuclei of hepatocytes of the rats trained to hypoxia - they formed a single class corresponding to the second class of control. In intact rats the ratio of the fluorescence intensity at 590 nm to such at 530 nm (alpha coefficient) formed normal distribution; in trained rats - a bimodal distribution with a shift of the maximum in the direction of reduction and increase of alpha in comparison with control. It is supposed that in hypoxia there is a repression of one and depression of other genes in the chromatine of the nuclei of the liver.

  18. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  19. Early aberrations in chromatin dynamics in embryos produced under In vitro conditions

    DEFF Research Database (Denmark)

    Deshmukh, Rahul Shahaji; Østrup, Olga; Strejcek, Frantisek

    2012-01-01

    standard to that of embryos produced by IVF, parthenogenetic activation (PA), or SCNT. In contrast to IV embryos, chromatin spatial and temporal dynamics in PA, IVF, and SCNT embryos were altered; starting with aberrant chromatin-nuclear envelope interactions at the two-cell stage, delayed chromatin...... decondensation and nucleolar development at the four-cell stage, and ultimately culminating in failure of proper first lineage segregation at the blastocyst stage, demonstrated by poorly defined inner cell mass. Interestingly, in vitro produced (IVP) embryos also lacked a heterochromatin halo around nucleolar...

  20. Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers.

    Science.gov (United States)

    Madalena, Christiane Rodriguez Gutierrez; Díez, José Luís; Gorab, Eduardo

    2012-01-01

    Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs) located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA), allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

  1. Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers.

    Directory of Open Access Journals (Sweden)

    Christiane Rodriguez Gutierrez Madalena

    Full Text Available Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA, allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

  2. Chromatin structure influences the sensitivity of DNA to gamma-radiation

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Kozubek, Stanislav

    2008-01-01

    Roč. 1783, č. 12 (2008), s. 2398-2414 ISSN 0167-4889 R&D Projects: GA ČR(CZ) GP204/06/P349; GA AV ČR(CZ) IAA500040802; GA AV ČR(CZ) 1QS500040508 Grant - others:GA MŠk(CZ) LC535 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : sensitivity to DNA double- strand breaks induction * DSB repair * higher-order chromatin structure Subject RIV: BO - Biophysics Impact factor: 4.893, year: 2008

  3. Genome instability in the context of chromatin structure and fragile sites

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Galiová-Šustáčková, Gabriela; Legartová, Soňa; Stixová, Lenka; Jugová, Alžbeta; Kozubek, Stanislav

    2010-01-01

    Roč. 20, č. 3 (2010), s. 181-194 ISSN 1045-4403 R&D Projects: GA MŠk ME 919; GA ČR(CZ) GAP302/10/1022 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * fragile sites * chromatin structure Subject RIV: BO - Biophysics Impact factor: 4.111, year: 2010

  4. Higher-order chromatin structure in DSB induction, repair and misrepair

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Kozubek, Stanislav

    2010-01-01

    Roč. 704, 1-3 (2010), s. 88-100 ISSN 1383-5742 R&D Projects: GA MŠk ME 919; GA AV ČR(CZ) IAA500040802; GA AV ČR(CZ) 1QS500040508 Grant - others:GA MŠk(CZ) LC535 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA double strand breaks * DSB repair * higher-order chromatin structure Subject RIV: BO - Biophysics Impact factor: 8.741, year: 2010

  5. Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy

    International Nuclear Information System (INIS)

    Terry, Samantha Y.A.; Vallis, Katherine A.

    2012-01-01

    Purpose: The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. Methods and Materials: Chromatin structure was altered in MDA-MB-468 and 231-H2N human breast cancer cells by suberoylanilide hydroxamic acid (SAHA), 5-aza-2-deoxycytidine, or hypertonic treatment. The extent and duration of chromatin structural changes were evaluated using the micrococcal nuclease assay. DNA damage (γH2AX assay) and clonogenic survival were evaluated after exposure to 111 In-DTPA-hEGF, an Auger electron-emitting radiopharmaceutical, or IR. The intracellular distribution of 111 In-DTPA-hEGF after chromatin modification was investigated in cell fractionation experiments. Results: Chromatin remained condensed for up to 20 minutes after NaCl and in a relaxed state 24 hours after SAHA treatment. The number of γH2AX foci per cell was greater in MDA-MB-468 and 231-H2N cells after IR (0.5 Gy) plus SAHA (1 μM) compared with IR alone (16 ± 0.6 and 14 ± 0.3 vs. 12 ± 0.4 and 11 ± 0.2, respectively). More γH2AX foci were observed in MDA-MB-468 and 231-H2N cells exposed to 111 In-DTPA-hEGF (6 MBq/μg) plus SAHA vs. 111 In-DTPA-hEGF alone (11 ± 0.3 and 12 ± 0.7 vs. 9 ± 0.4 and 7 ± 0.3, respectively). 5-aza-2-deoxycytidine enhanced the DNA damage caused by IR and 111 In-DTPA-hEGF. Clonogenic survival was reduced in MDA-MB-468 and 231-H2N cells after IR (6 Gy) plus SAHA (1 μM) vs. IR alone (0.6% ± 0.01 and 0.3% ± 0.2 vs. 5.8% ± 0.2 and 2% ± 0.1, respectively) and after 111 In-DTPA-hEGF plus SAHA compared to 111 In-DTPA-hEGF alone (21% ± 0.4% and 19% ± 4.6 vs. 33% ± 2.3 and 32% ± 3.7). SAHA did not affect 111 In-DTPA-hEGF nuclear localization. Hypertonic treatment resulted in fewer γH2AX foci per cell after IR and 111 In-DTPA-hEGF compared to controls but did not significantly alter clonogenic

  6. FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription

    International Nuclear Information System (INIS)

    Holmqvist, Per-Henrik; Belikov, Sergey; Zaret, Kenneth S.; Wrange, Oerjan

    2005-01-01

    Novel binding sites for the forkhead transcription factor family member Forkhead box A (FoxA), previously referred to as Hepatocyte Nuclear Factor 3 (HNF3), were found within the mouse mammary tumor virus long terminal repeat (MMTV LTR). The effect of FoxA1 on MMTV LTR chromatin structure, and expression was evaluated in Xenopus laevis oocytes. Mutagenesis of either of the two main FoxA binding sites showed that the distal site, -232/-221, conferred FoxA1-dependent partial inhibition of glucocorticoid receptor (GR) driven MMTV transcription. The proximal FoxA binding segment consisted of two individual FoxA sites at -57/-46 and -45/-34, respectively, that mediated an increased basal MMTV transcription. FoxA1 binding altered the chromatin structure of both the inactive- and the hormone-activated MMTV LTR. Hydroxyl radical foot printing revealed FoxA1-mediated changes in the nucleosome arrangement. Micrococcal nuclease digestion showed the hormone-dependent sub-nucleosome complex, containing ∼120 bp of DNA, to be expanded by FoxA1 binding to the proximal segment into a larger complex containing ∼200 bp. The potential function of the FoxA1-mediated expression of the MMTV provirus for maintenance of expression in different tissues is discussed

  7. Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    David eRoquis

    2014-07-01

    Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

  8. HDAC up-regulation in early colon field carcinogenesis is involved in cell tumorigenicity through regulation of chromatin structure.

    Directory of Open Access Journals (Sweden)

    Yolanda Stypula-Cyrus

    Full Text Available Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC. However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.

  9. Changes in chromatin structure during the aging of cell cultures as revealed by differential scanning calorimetry

    International Nuclear Information System (INIS)

    Almagor, M.; Cole, R.D.

    1989-01-01

    Nuclei from cultured human cells were examined by differential scanning calorimetry. Their melting profiles revealed four structural transitions at 60, 76, 88, and 105 degrees C (transitions I-IV, respectively). In immortalized (i.e., tumor) cell cultures and in normal cell cultures of low passage number, melting profiles were dominated by the 105 degrees C transition (transition IV), but in vitro aging of normal and Werner syndrome cells was associated with a marked decrease in transition IV followed by an increase in transition III at the expense of transition IV. At intermediate times in the aging process, much DNA melted at a temperature range (95-102 degrees C) intermediate between transitions III and IV, and this is consistent with the notion that aging of cell cultures is accompanied by an increase in single-strand character of the DNA. Calorimetric changes were observed in the melting profile of nuclei from UV-irradiated tumor cells that resembled the age-induced intermediate melting of chromatin. It is suggested that aging is accompanied by an increase in single-stranded character of the DNA in chromatin, which lowers its melting temperature, followed by strand breaks in the DNA that destroy its supercoiling potential

  10. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

    attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming...... and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors...

  11. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

    OpenAIRE

    Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li

    2007-01-01

    Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a high...

  12. Poly(ADP-ribosyl)ation of Methyl CpG Binding Domain Protein 2 Regulates Chromatin Structure*

    Science.gov (United States)

    Becker, Annette; Zhang, Peng; Allmann, Lena; Meilinger, Daniela; Bertulat, Bianca; Eck, Daniel; Hofstaetter, Maria; Bartolomei, Giody; Hottiger, Michael O.; Schreiber, Valérie; Leonhardt, Heinrich; Cardoso, M. Cristina

    2016-01-01

    The epigenetic information encoded in the genomic DNA methylation pattern is translated by methylcytosine binding proteins like MeCP2 into chromatin topology and structure and gene activity states. We have shown previously that the MeCP2 level increases during differentiation and that it causes large-scale chromatin reorganization, which is disturbed by MeCP2 Rett syndrome mutations. Phosphorylation and other posttranslational modifications of MeCP2 have been described recently to modulate its function. Here we show poly(ADP-ribosyl)ation of endogenous MeCP2 in mouse brain tissue. Consequently, we found that MeCP2 induced aggregation of pericentric heterochromatin and that its chromatin accumulation was enhanced in poly(ADP-ribose) polymerase (PARP) 1−/− compared with wild-type cells. We mapped the poly(ADP-ribosyl)ation domains and engineered MeCP2 mutation constructs to further analyze potential effects on DNA binding affinity and large-scale chromatin remodeling. Single or double deletion of the poly(ADP-ribosyl)ated regions and PARP inhibition increased the heterochromatin clustering ability of MeCP2. Increased chromatin clustering may reflect increased binding affinity. In agreement with this hypothesis, we found that PARP-1 deficiency significantly increased the chromatin binding affinity of MeCP2 in vivo. These data provide novel mechanistic insights into the regulation of MeCP2-mediated, higher-order chromatin architecture and suggest therapeutic opportunities to manipulate MeCP2 function. PMID:26772194

  13. Quantitative analysis of the chromatin of lymphocytes: an assay on comparative structuralism.

    Science.gov (United States)

    Meyer, F

    1980-01-01

    With 26 letters we can form all the words we use, and with a few words it is possible to form an infinite number of different meaningful sentences. In our case, the letters will be a few simple neighborhood image transformations and area measurements. The paper shows how, by iterating these transformations, it is possible to obtain a good quantitative description of the nuclear structure of Feulgen-stained lymphocytes (CLL and normal). The fact that we restricted ourselves to a small number of image transformations made it possible to construct an image analysis system (TAS) able to do these transformations very quickly. We will see, successively, how to segment the nucleus itself, the chromatin, and the interchromatinic channels, how openings and closings lead to size and spatial distribution curves, and how skeletons may be used for measuring the lengths of interchromatinic channels.

  14. The influence of chromatin structure on the frequency of radiation-induced DNA strand breaks: a study using nuclear and nucleoid monolayers

    International Nuclear Information System (INIS)

    Ljungman, M.

    1991-01-01

    To assess the influence of chromatin structure on the frequency of radiation-induced DNA strand breaks, the alkaline unwinding technique was applied to nuclear and nucleoid monolayers. These chromatin substrates were prepared by treating human fibroblasts grown as monolayers with the nonionic detergent Triton X-100 and varying concentrations of cations. The chromatin structure was modified either by a stepwise removal of DNA-bound proteins by extraction in increasing concentrations of monovalent salt, or by the addition or deletion of mono- and divalent cations to condense or decondense the chromatin, respectively. It was found that the stepwise removal of DNA-bound proteins from the chromatin dramatically increased the frequency of radiation-induced DNA strand breaks. The DNA-bound proteins showed a qualitative difference in their ability to protect the DNA where proteins removed by salt concentrations above 1.0 M exerted the greatest protection. Furthermore, the frequency of radiation-induced DNA strand breaks was found to be 6 times lower in condensed chromatin than in decondensed chromatin and about 80 times lower than in protein-depleted chromatin. It is concluded that the presence of DNA-bound proteins and the folding of the chromatin into higher-order structures protect the DNA against radiation-induced strand breaks

  15. Chromatin maturation depends on continued DNA-replication

    International Nuclear Information System (INIS)

    Schlaeger, E.J.; Puelm, W.; Knippers, R.

    1983-01-01

    The structure of [ 3 H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [ 3 H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. The authors conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation. (Auth.)

  16. The Correlation of Interphase Chromatin Structure with the Radiation-Induced Inter- and Intrachromosome Exchange Hotspots

    Science.gov (United States)

    Zhang, Ye; Mangala, Lingegowda S.; Purgason, Ashley M.; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    To investigate the relationship between chromosome aberrations induced by radiation and chromatin folding, we reconstructed three dimensional structure of chromosome 3 and measured the physical distances between different regions of the chromosome. Previously, we have investigated the location of breaks involved in inter- and intrachromosomal type exchange events in human chromosome 3, using the multicolor banding in situ hybridization (mBAND) technique. In human epithelial cells exposed to both low- and high-LET radiations in vitro, we reported that intra-chromosome exchanges occurred preferentially between a break in the 3p21 and one in the 3q11 regions, and the breaks involving in inter-chromosome exchanges occurred in two regions towards the telomeres of the chromosome. Exchanges were also observed between a break in 3p21 and one in 3q26, but few exchanges were observed between breaks in 3q11 and 3q26, even though the two regions are located on the same arm of the chromosome. In this study, human epithelial cells were fixed at G1 phase and the interphase cells were hybridized using the XCyte3 mBAND kit from MetaSystems. The z-section images of chromosome 3 were captured with a Leica and an LSM 510 Meta laser scanning confocal microscopes. A total of 100 chromosomes were analyzed. The reconstruction of three dimensional structure of interphase chromosome 3 with six different colored regions was achieved using the Imaris software. The relative distance between different regions was measured as well. We further analyzed fragile sites on the chromosome that have been identified in various types of cancers. The data showed that, in majority of the cells, the regions containing 3p21 and 3q11 are colocalized in the center of the chromosome, whereas, the regions towards the telomeres of the chromosome are either physically wrapping outside the chromosome center or with arms sticking out. Our results demonstrated that the distribution of breaks involved in radiation

  17. Applications of high-throughput sequencing to chromatin structure and function in mammals

    OpenAIRE

    Dunham, Ian

    2009-01-01

    High-throughput DNA sequencing approaches have enabled direct interrogation of chromatin samples from mammalian cells. We are beginning to develop a genome-wide description of nuclear function during development, but further data collection, refinement, and integration are needed.

  18. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

    DEFF Research Database (Denmark)

    Sarusi Portuguez, Avital; Schwartz, Michal; Siersbaek, Rasmus

    2017-01-01

    The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains...... by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis...

  19. Studies on sex-organ development. Changes in chromatin structure during spermatogenesis in maturing rooster testis as demonstrated by the initiation pattern of ribonucleic acid synthesis in vitro.

    Science.gov (United States)

    Mezquita, C; Teng, C S

    1978-01-01

    To probe the structural change in the genome of the differentiating germ cell of the maturing rooster testis, the chromatin from nuclei at various stages of differentiation were transcribed with prokaryotic RNA polymerase from Escherichia coli or with eukaryotic RNA polymerase II from wheat germ. The transcription was performed under conditions of blockage of RNA chain reinitiation in vitro with rifampicin or rifampicin AF/013. With the E. coli enzyme, the changes in (1) the titration curve for the enzyme-chromatin interaction, (2) the number of initiation sites, (3) the rate of elongation of RNA chains, and (4) the kinetics of the formation of stable initiation complexes revealed the unmasking of DNA in elongated spermatids and the masking of DNA in spermatozoa. In both cases the stability of the DNA duplex in the initiation region for RNA synthesis greatly increased. In contrast with the E. coli enzyme, the wheat-germ RNA polymerase II was relatively inefficient at transcribing chromatin of elongated spermatids. Such behaviour can be predicted if unmasked double-stranded DNA is present in elongated spermatids. PMID:346018

  20. Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei

    Science.gov (United States)

    Iashina, E. G.; Velichko, E. V.; Filatov, M. V.; Bouwman, W. G.; Duif, C. P.; Brulet, A.; Grigoriev, S. V.

    2017-07-01

    Small-angle neutron scattering (SANS) on nuclei of chicken erythrocytes demonstrates the cubic dependence of the scattering intensity Q-3 in the range of momentum transfer Q ∈10-3-10-2nm-1 . Independent spin-echo SANS measurements give the spin-echo function, which is well described by the exponential law in a range of sizes (3 ×102) -(3 ×104) nm. Both experimental dependences reflect the nature of the structural organization of chromatin in the nucleus of a living cell, which corresponds to the correlation function γ (r )=ln(ξ /r ) for r <ξ , where ξ =(3.69 ±0.07 ) ×103 nm, the size of the nucleus. It has the specific scaling property of the logarithmic fractal γ (r /a )=γ (r )+ln(a ), i.e., the scaling down by a gives an additive constant to the correlation function, which distinguishes it from the mass fractal, which is characterized by multiplicative constant.

  1. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Department of Molecular Genetics and Radiobiology, Babes National Institute, Bucharest (Romania)], E-mail: lilianajradu@yahoo.fr; Mihailescu, I. [Department of Lasers, Laser, Plasma and Radiation Physics Institute, Bucharest (Romania); Radu, S. [Department of Computer Science, Polytechnics University, Bucharest (Romania); Gazdaru, D. [Department of Biophysics, Bucharest University (Romania)

    2007-09-21

    The analysis of chromatin damage produced by a 248 nm excimer laser radiation, for doses of 0.3-3 MJ/m{sup 2} was carried out by time-resolved spectroscopy and fluorescence resonance energy transfer (FRET). The chromatin was extracted from a normal and a tumoral tissue of Wistar rats. The decrease with laser dose of the relative contribution of the excited state lifetimes of ethidium bromide (EtBr) bounded to chromatin constitutes an evidence of the reduction of chromatin deoxyribonucleic acid (DNA) double-strand structure. FRET was performed from dansyl chloride to acridine orange, both coupled to chromatin. The increase of the average distance between these ligands, under the action of laser radiation, reflects a loosening of the chromatin structure. The radiosensitivity of tumor tissue chromatin is higher than that of a normal tissue. The determination of the chromatin structure modification in an excimer laser field can be of interest in laser therapy.

  2. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    International Nuclear Information System (INIS)

    Radu, L.; Mihailescu, I.; Radu, S.; Gazdaru, D.

    2007-01-01

    The analysis of chromatin damage produced by a 248 nm excimer laser radiation, for doses of 0.3-3 MJ/m 2 was carried out by time-resolved spectroscopy and fluorescence resonance energy transfer (FRET). The chromatin was extracted from a normal and a tumoral tissue of Wistar rats. The decrease with laser dose of the relative contribution of the excited state lifetimes of ethidium bromide (EtBr) bounded to chromatin constitutes an evidence of the reduction of chromatin deoxyribonucleic acid (DNA) double-strand structure. FRET was performed from dansyl chloride to acridine orange, both coupled to chromatin. The increase of the average distance between these ligands, under the action of laser radiation, reflects a loosening of the chromatin structure. The radiosensitivity of tumor tissue chromatin is higher than that of a normal tissue. The determination of the chromatin structure modification in an excimer laser field can be of interest in laser therapy

  3. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures.

    Science.gov (United States)

    Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang

    2016-01-07

    Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for (60)Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with (60)Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.

  4. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures

    International Nuclear Information System (INIS)

    Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang

    2016-01-01

    Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for 60 Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60 Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage. (paper)

  5. Neuron-specific chromatin remodeling: a missing link in epigenetic mechanisms underlying synaptic plasticity, memory, and intellectual disability disorders.

    Science.gov (United States)

    Vogel-Ciernia, Annie; Wood, Marcelo A

    2014-05-01

    Long-term memory formation requires the coordinated regulation of gene expression. Until recently nucleosome remodeling, one of the major epigenetic mechanisms for controlling gene expression, had been largely unexplored in the field of neuroscience. Nucleosome remodeling is carried out by chromatin remodeling complexes (CRCs) that interact with DNA and histones to physically alter chromatin structure and ultimately regulate gene expression. Human exome sequencing and gene wide association studies have linked mutations in CRC subunits to intellectual disability disorders, autism spectrum disorder and schizophrenia. However, how mutations in CRC subunits were related to human cognitive disorders was unknown. There appears to be both developmental and adult specific roles for the neuron specific CRC nBAF (neuronal Brg1/hBrm Associated Factor). nBAF regulates gene expression required for dendritic arborization during development, and in the adult, contributes to long-term potentiation, a form of synaptic plasticity, and long-term memory. We propose that the nBAF complex is a novel epigenetic mechanism for regulating transcription required for long-lasting forms of synaptic plasticity and memory processes and that impaired nBAF function may result in human cognitive disorders. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Heterogeneous chromatin target model

    International Nuclear Information System (INIS)

    Watanabe, Makoto

    1996-01-01

    The higher order structure of the entangled chromatin fibers in a chromosome plays a key role in molecular control mechanism involved in chromosome mutation due to ionizing radiations or chemical mutagens. The condensed superstructure of chromatin is not so rigid and regular as has been postulated in general. We have proposed a rheological explanation for the flexible network system ('chromatin network') that consists of the fluctuating assembly of nucleosome clusters linked with supertwisting DNA in a chromatin fiber ('Supertwisting Particulate Model'). We have proposed a 'Heterosensitive Target Model' for cellular radiosensitivity that is a modification of 'Heterogeneous Target Model'. The heterogeneity of chromatin target is derived from the highly condensed organization of chromatin segments consist of unstable and fragile sites in the fluctuating assembly of nucleosome clusters, namely 'supranucleosomal particles' or 'superbeads'. The models have been principally supported by our electron microscopic experiments employing 'surface - spreading whole - mount technique' since 1967. However, some deformation and artifacts in the chromatin structure are inevitable with these electron microscopic procedures. On the contrary, the 'atomic force microscope (AFM)' can be operated in liquid as well as in the air. A living specimen can be examined without any preparative procedures. Micromanipulation of the isolated chromosome is also possible by the precise positional control of a cantilever on the nanometer scale. The living human chromosomes were submerged in a solution of culture medium and observed by AFM using a liquid immersion cell. The surface - spreading whole - mount technique was applicable for this observation. The particulate chromatin segments of nucleosome clusters were clearly observed within mitotic human chromosomes in a living hydrated condition. These findings support the heterogeneity of chromatin target in a living cell. (J.P.N.)

  7. Role of chromatin structure modulation by the histone deacetylase inhibitor trichostatin A on the radio-sensitivity of ataxia telangiectasia

    Energy Technology Data Exchange (ETDEWEB)

    Meschini, Roberta, E-mail: meschini@unitus.it; Morucci, Elisa; Berni, Andrea; Lopez-Martinez, Wilner; Palitti, Fabrizio

    2015-07-15

    Highlights: • Role of chromatin compaction on chromosomal instability. • Reduced radiation-induced clastogenicity in Ataxia telangiectasia cell lines. • Histone tails hyperacetylation reduces heterochromatin content favouring DSBs repair. - Abstract: At present, a lot is known about biochemical aspects of double strand breaks (DBS) repair but how chromatin structure affects this process and the sensitivity of DNA to DSB induction is still an unresolved question. Ataxia telangiectasia (A-T) patients are characterised by very high sensitivity to DSB-inducing agents such as ionising radiation. This radiosensitivity is revealed with an enhancement of chromosomal instability as a consequence of defective DNA repair for a small fraction of breaks located in the heterochromatin, where they are less accessible. Besides, recently it has been reported that Ataxia Telangiectasia Mutated (ATM) mediated signalling modifies chromatin structure. In order to study the impact of chromatin compaction on the chromosomal instability of A-T cells, the response to trichostatin-A, an histone deacetylase inhibitor, in normal and A-T lymphoblastoid cell lines was investigated testing its effect on chromosomal aberrations, cell cycle progression, DNA damage and repair after exposure to X-rays. The results suggest that the response to both trichostatin-A pre- and continuous treatments is independent of the presence of either functional or mutated ATM protein, as the reduction of chromosomal damage was found also in the wild-type cell line. The presence of trichostatin-A before exposure to X-rays could give rise to prompt DNA repair functioning on chromatin structure already in an open conformation. Differently, trichostatin-A post-treatment causing hyperacetylation of histone tails and reducing the heterochromatic DNA content might diminish the requirement for ATM and favour DSBs repair reducing chromosomal damage only in A-T cells. This fact could suggest that trichostatin-A post

  8. Global chromatin fibre compaction in response to DNA damage

    International Nuclear Information System (INIS)

    Hamilton, Charlotte; Hayward, Richard L.; Gilbert, Nick

    2011-01-01

    Highlights: ► Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. ► DNA repair foci are found in soluble chromatin. ► Biophysical analysis reveals global chromatin fibre compaction after DNA damage. ► DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation (γH2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and γH2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by linker histones. We suggest that following DSB formation, although there is localised chromatin unfolding to

  9. Chromatin Hydrodynamics

    Science.gov (United States)

    Bruinsma, Robijn; Grosberg, Alexander Y.; Rabin, Yitzhak; Zidovska, Alexandra

    2014-01-01

    Following recent observations of large scale correlated motion of chromatin inside the nuclei of live differentiated cells, we present a hydrodynamic theory—the two-fluid model—in which the content of a nucleus is described as a chromatin solution with the nucleoplasm playing the role of the solvent and the chromatin fiber that of a solute. This system is subject to both passive thermal fluctuations and active scalar and vector events that are associated with free energy consumption, such as ATP hydrolysis. Scalar events drive the longitudinal viscoelastic modes (where the chromatin fiber moves relative to the solvent) while vector events generate the transverse modes (where the chromatin fiber moves together with the solvent). Using linear response methods, we derive explicit expressions for the response functions that connect the chromatin density and velocity correlation functions to the corresponding correlation functions of the active sources and the complex viscoelastic moduli of the chromatin solution. We then derive general expressions for the flow spectral density of the chromatin velocity field. We use the theory to analyze experimental results recently obtained by one of the present authors and her co-workers. We find that the time dependence of the experimental data for both native and ATP-depleted chromatin can be well-fitted using a simple model—the Maxwell fluid—for the complex modulus, although there is some discrepancy in terms of the wavevector dependence. Thermal fluctuations of ATP-depleted cells are predominantly longitudinal. ATP-active cells exhibit intense transverse long wavelength velocity fluctuations driven by force dipoles. Fluctuations with wavenumbers larger than a few inverse microns are dominated by concentration fluctuations with the same spectrum as thermal fluctuations but with increased intensity. PMID:24806919

  10. [Correcting influence of vitamin E short chain derivatives on lipid peroxidation, liver cell membrane, and chromatin structure when rats are exposed to embichin].

    Science.gov (United States)

    Kovalenko, V M; Byshovets', T F; Hubs'kyĭ, Iu I; Levyts'kyĭ, Ie L; Shaiakhmetova, H M; Marchenko, O M; Voloshyna, O S; Saĭfetdinova, H A; Okhrimenko, V O; Donchenko, H V

    2000-01-01

    Embikhin causes activation of LPO processes in endoplasmic reticulum and in nuclear chromatine fractions of rat liver cells. The latter is accompanied by the impairment of repressive and active nuclear chromatine fractions structure. Derivate of vitamin E in these conditions renders correcting action on parameters of lipid peroxidation in the investigated subcellular structures, testifying its positive influence on the cell heredity apparatus state. The normalizing action of tocopherol derivative on cytochromes P450 and b5 levels is shown.

  11. APPLICATION OF THE SPERM CHROMATIN STRUCTURE ASSAY TO THE TEPLICE PROGRAM SEMEN STUDIES: A NEW METHOD FOR EVALUATING SPERM NUCLEAR CHROMATIN DAMAGE

    Science.gov (United States)

    ABSTRACTA measure of sperm chromatin integrity was added to the routine semen end points evaluated in the Teplice Program male reproductive health studies. To address the hypothesis that exposure to periods of elevated air pollution may be associated with abnormalities in sp...

  12. Impact of nuclear organization and chromatin structure on DNA repair and genome stability

    International Nuclear Information System (INIS)

    Batte, Amandine

    2016-01-01

    The non-random organization of the eukaryotic cell nucleus and the folding of genome in chromatin more or less condensed can influence many functions related to DNA metabolism, including genome stability. Double-strand breaks (DSBs) are the most deleterious DNA damages for the cells. To preserve genome integrity, eukaryotic cells thus developed DSB repair mechanisms conserved from yeast to human, among which homologous recombination (HR) that uses an intact homologous sequence to repair a broken chromosome. HR can be separated in two sub-pathways: Gene Conversion (GC) transfers genetic information from one molecule to its homologous and Break Induced Replication (BIR) establishes a replication fork than can proceed until the chromosome end. My doctorate work was focused on the contribution of the chromatin context and 3D genome organization on DSB repair. In S. cerevisiae, nuclear organization and heterochromatin spreading at sub-telomeres can be modified through the overexpression of the Sir3 or sir3A2Q mutant proteins. We demonstrated that reducing the physical distance between homologous sequences increased GC rates, reinforcing the notion that homology search is a limiting step for recombination. We also showed that hetero-chromatinization of DSB site fine-tunes DSB resection, limiting the loss of the DSB ends required to perform homology search and complete HR. Finally, we noticed that the presence of heterochromatin at the donor locus decreased both GC and BIR efficiencies, probably by affecting strand invasion. This work highlights new regulatory pathways of DNA repair. (author) [fr

  13. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.

    2000-01-01

    The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology...

  14. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate...... choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper...... organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  15. Chromatin dynamics in genome stability

    DEFF Research Database (Denmark)

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage....

  16. Chromatin structure with respect to histone signature changes during cell differentiation

    Czech Academy of Sciences Publication Activity Database

    Harničarová, Andrea; Bártová, Eva; Kozubek, Stanislav

    2010-01-01

    Roč. 35, č. 1 (2010), s. 31-44 ISSN 0386-7196 R&D Projects: GA MŠk ME 919; GA ČR(CZ) GAP302/10/1022 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin * gene expression * differentiation Subject RIV: BO - Biophysics Impact factor: 3.265, year: 2010

  17. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...... landscape may be stably maintained even in the face of dramatic changes in chromatin structure....

  18. Modulating chromatin structure and DNA accessibility by deacetylase inhibition enhances the anti-cancer activity of silver nanoparticles.

    Science.gov (United States)

    Igaz, Nóra; Kovács, Dávid; Rázga, Zsolt; Kónya, Zoltán; Boros, Imre M; Kiricsi, Mónika

    2016-10-01

    Histone deacetylase (HDAC) inhibitors are considered as novel therapeutic agents inducing cell cycle arrest and apoptotic cell death in various cancer cells. Inhibition of deacetylase activity results in a relaxed chromatin structure thereby rendering the genetic material more vulnerable to DNA targeting agents that could be exploited by combinational cancer therapy. The unique potential of silver nanoparticles (AgNPs) in tumor therapy relies on the generation of reactive radicals which trigger oxidative stress, DNA damage and apoptosis in cancer cells. The revolutionary application of AgNPs as chemotherapeutical drugs seems very promising, nevertheless the exact molecular mechanisms of AgNP action in combination with other anti-cancer agents have yet to be elucidated in details before clinical administrations. As a step towards this we investigated the combinational effect of HDAC inhibition and AgNP administration in HeLa cervical cancer cells. We identified synergistic inhibition of cancer cell growth and migration upon combinational treatments. Here we report that the HDAC inhibitor Trichostatin A enhances the DNA targeting capacity and apoptosis inducing efficacy of AgNPs most probably due to its effect on chromatin condensation. These results point to the potential benefits of combinational application of HDAC inhibitors and AgNPs in novel cancer medication protocols. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  20. Environmental toxicants cause sperm DNA fragmentation as detected by the Sperm Chromatin Structure Assay (SCSA[reg])

    International Nuclear Information System (INIS)

    Evenson, Donald P.; Wixon, Regina

    2005-01-01

    Studies over the past two decades have clearly shown that reproductive toxicants cause sperm DNA fragmentation. This DNA fragmentation can usually be detected prior to observing alterations of metaphase chromosomes in embryos. Thus, Sperm Chromatin Structure Assay (SCSA)-detected DNA damage is viewed as the molecular precursor to later gross chromosome damage observed under the light microscope. SCSA measurements of animal or human sperm consist of first obtaining a fresh or flash frozen neat semen sample in LN2 or dry ice. Samples are then sent to a SCSA diagnostic laboratory where the samples are thawed, diluted to ∼1-2 x 106 sperm/ml, treated for 30 s with a pH 1.2 detergent buffer and then stained with acridine orange (AO). The low pH partially denatures DNA at the sites of DNA strand breaks and the AO-ssDNA fluoresces red while the AO-dsDNA fluoresces green. Flow cytometry measurements of 5000 sperm/sample provide statistically robust data on the ratio of red to green sperm, the extent of the DNA fragmentation and the standard deviations of measures. Numerous experiments on rodents treated with reproductive toxicants clearly showed that SCSA measures are highly dose responsive and have a very low CV. Different agents that act on germ cells at various stages of development usually showed sperm DNA fragmentation when that germ cell fraction arrived in the epididymis or ejaculate. Some of these treated samples were capable of successful in vitro fertilization but with frequent embryo failure. A 2-year longitudinal study of men living a valley town with a reported abnormal level of infertility and spontaneous miscarriages and also a seasonal atmospheric smog pollution, showed, for the first time, that SCSA measurements of human sperm DNA fragmentation were detectable and correlated with dosage of air pollution while the classical semen measures were not correlated. Also, young men spraying pesticides without protective gear are at an increased risk for elevated

  1. Electron microscopic study on the initial effect of gamma-irradiation on the chromatin structure of L cells

    International Nuclear Information System (INIS)

    Kondo, Takashi; Nakanishi, Y.H.; Yoshii, Giichi

    1979-01-01

    Mouse L cells are gamma-irradiated at a dose of 1 Mrad, and ultrathin sections of the cells are examined by electron microscopy. The distance between chromatin fibers in diffused chromatin regions in the irradiated nuclei is essentially identical with the nonirradiated control. In contrast, an increase of the distance between the chromatin fibers is observed in the excess of Ca ions in irradiation. (author)

  2. Sperm DNA quality evaluated by comet assay and sperm chromatin structure assay in stallions after unilateral orchiectomy.

    Science.gov (United States)

    Serafini, R; Varner, D D; Bissett, W; Blanchard, T L; Teague, S R; Love, C C

    2015-09-15

    Unilateral orchiectomy (UO) may interfere with thermoregulation of the remaining testis caused by inflammation surrounding the incision site, thus altering normal spermatogenesis and consequently sperm quality. Two measures of sperm DNA quality (neutral comet assay and the sperm chromatin structure assay [SCSA]) were compared before UO (0 days) and at 14, 30, and 60 days after UO to determine whether sperm DNA changed after a mild testis stress (i.e., UO). The percent DNA in the comet tail was higher at 14 and 60 days compared to 0 days (P comet tail measures (i.e., length, moment, migration) were higher at all time periods after UO compared to 0 days (P comet assay and the SCSA, which was not identified using traditional measures of sperm quality. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: gamma-rays and protons in action

    Czech Academy of Sciences Publication Activity Database

    Ježková, L.; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, A.; Krasavin, E.; Kozubek, Stanislav

    2014-01-01

    Roč. 83, SI (2014), s. 128-136 ISSN 0969-8043 R&D Projects: GA MŠk(CZ) EE2.3.30.0030; GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GAP302/10/1022; GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LD12039; GA MŠk(CZ) LD12008 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double-strand breaks * Higher-order chromatin structure and DSB repair * Formation of chromosomal translocations Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014

  4. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

    Science.gov (United States)

    Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang

    2015-08-01

    Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

  5. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

    Directory of Open Access Journals (Sweden)

    Zing Tsung-Yeh Tsai

    2015-08-01

    Full Text Available Transcription factor (TF binding is determined by the presence of specific sequence motifs (SM and chromatin accessibility, where the latter is influenced by both chromatin state (CS and DNA structure (DS properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

  6. Chromatin modifications and the DNA damage response to ionizing radiation

    International Nuclear Information System (INIS)

    Kumar, Rakesh; Horikoshi, Nobuo; Singh, Mayank; Gupta, Arun; Misra, Hari S.; Albuquerque, Kevin; Hunt, Clayton R.; Pandita, Tej K.

    2013-01-01

    In order to survive, cells have evolved highly effective repair mechanisms to deal with the potentially lethal DNA damage produced by exposure to endogenous as well as exogenous agents. Ionizing radiation exposure induces highly lethal DNA damage, especially DNA double-strand breaks (DSBs), that is sensed by the cellular machinery and then subsequently repaired by either of two different DSB repair mechanisms: (1) non-homologous end joining, which re-ligates the broken ends of the DNA and (2) homologous recombination, that employs an undamaged identical DNA sequence as a template, to maintain the fidelity of DNA repair. Repair of DSBs must occur within the natural context of the cellular DNA which, along with specific proteins, is organized to form chromatin, the overall structure of which can impede DNA damage site access by repair proteins. The chromatin complex is a dynamic structure and is known to change as required for ongoing cellular processes such as gene transcription or DNA replication. Similarly, during the process of DNA damage sensing and repair, chromatin needs to undergo several changes in order to facilitate accessibility of the repair machinery. Cells utilize several factors to modify the chromatin in order to locally open up the structure to reveal the underlying DNA sequence but post-translational modification of the histone components is one of the primary mechanisms. In this review, we will summarize chromatin modifications by the respective chromatin modifying factors that occur during the DNA damage response.

  7. A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure

    DEFF Research Database (Denmark)

    Luijsterburg, Martijn S; Acs, Klara; Ackermann, Leena

    2012-01-01

    The ubiquitin ligases RNF8 and RNF168 orchestrate DNA damage signalling through the ubiquitylation of histone H2A and the recruitment of downstream repair factors. Here, we demonstrate that RNF8, but not RNF168 or the canonical H2A ubiquitin ligase RNF2, mediates extensive chromatin decondensation....... Our data show that CHD4, the catalytic subunit of the NuRD complex, interacts with RNF8 and is essential for RNF8-mediated chromatin unfolding. The chromatin remodelling activity of CHD4 promotes efficient ubiquitin conjugation and assembly of RNF168 and BRCA1 at DNA double-strand breaks....... Interestingly, RNF8-mediated recruitment of CHD4 and subsequent chromatin remodelling were independent of the ubiquitin-ligase activity of RNF8, but involved a non-canonical interaction with the forkhead-associated (FHA) domain. Our study reveals a new mechanism of chromatin remodelling-assisted ubiquitylation...

  8. Effect of Chromatin Structure on the Extent and Distribution of DNA Double Strand Breaks Produced by Ionizing Radiation; Comparative Study of hESC and Differentiated Cells Lines.

    Science.gov (United States)

    Venkatesh, Priyanka; Panyutin, Irina V; Remeeva, Evgenia; Neumann, Ronald D; Panyutin, Igor G

    2016-01-02

    Chromatin structure affects the extent of DNA damage and repair. Thus, it has been shown that heterochromatin is more protective against DNA double strand breaks (DSB) formation by ionizing radiation (IR); and that DNA DSB repair may proceed differently in hetero- and euchromatin regions. Human embryonic stem cells (hESC) have a more open chromatin structure than differentiated cells. Here, we study the effect of chromatin structure in hESC on initial DSB formation and subsequent DSB repair. DSB were scored by comet assay; and DSB repair was assessed by repair foci formation via 53BP1 antibody staining. We found that in hESC, heterochromatin is confined to distinct regions, while in differentiated cells it is distributed more evenly within the nuclei. The same dose of ionizing radiation produced considerably more DSB in hESC than in differentiated derivatives, normal human fibroblasts; and one cancer cell line. At the same time, the number of DNA repair foci were not statistically different among these cells. We showed that in hESC, DNA repair foci localized almost exclusively outside the heterochromatin regions. We also noticed that exposure to ionizing radiation resulted in an increase in heterochromatin marker H3K9me3 in cancer HT1080 cells, and to a lesser extent in IMR90 normal fibroblasts, but not in hESCs. These results demonstrate the importance of chromatin conformation for DNA protection and DNA damage repair; and indicate the difference of these processes in hESC.

  9. Chromatin in embryonic stem cell neuronal differentiation.

    Science.gov (United States)

    Meshorer, E

    2007-03-01

    Chromatin, the basic regulatory unit of the eukaryotic genetic material, is controlled by epigenetic mechanisms including histone modifications, histone variants, DNA methylation and chromatin remodeling. Cellular differentiation involves large changes in gene expression concomitant with alterations in genome organization and chromatin structure. Such changes are particularly evident in self-renewing pluripotent embryonic stem cells, which begin, in terms of cell fate, as a tabula rasa, and through the process of differentiation, acquire distinct identities. Here I describe the changes in chromatin that accompany neuronal differentiation, particularly of embryonic stem cells, and discuss how chromatin serves as the master regulator of cellular destiny.

  10. Radiation response and chromatin dynamics

    International Nuclear Information System (INIS)

    Ikura, Tsuyoshi

    2009-01-01

    Described is a recent progress in studies of chromatin structural alterations induced by DNA damage by radiation. DNA in eukaryotes exists in the chromatin structure and different mechanisms of response to damage and repair of DNA from those in prokaryotes have been recognized. Chromatin is composed from its unit structure of mono-nucleosome, which is formed from DNA and an octamer of core histones of H2A, H2B, H3 and H4. When DNA is damaged, histone structural alterations are required for repair factors and checkpoint proteins to access the damaged site. At the actual genome damage, chemical modification of histone to work as a code occurs dependently on the damage where chromatin remodeling factors and histone chaperone participate for structural alteration and remodeling. As well, the exchange of histone variants and fluidization of histones are recently reported. Known chemical modification involves phosphorylation, acetylation and ubiquitination of H2AX (a variant of H2A), and acetylation and methylation of H3. Each complex of TIP60, NuA4 and INO80 is known to be included in the regulation of chromatin with damaged/repaired DNA for remodeling, but little is known about recruitment of the factors concerned at the damage site. Regulatory mechanisms in above chromatin dynamics with consideration of quality and timing of radiation should be further elucidated for understanding the precise response to DNA damage. (K.T.)

  11. Heterochromatinization associated with cell differentiation as a model to study DNA double strand break induction and repair in the context of higher-order chromatin structure

    International Nuclear Information System (INIS)

    Falk, Martin; Lukášová, Emilie; Štefančíková, Lenka; Baranová, Elena; Falková, Iva; Ježková, Lucie; Davídková, Marie; Bačíková, Alena; Vachelová, Jana; Michaelidesová, Anna; Kozubek, Stanislav

    2014-01-01

    Cell differentiation is associated with extensive gene silencing, heterochromatinization and potentially decreasing need for repairing DNA double-strand breaks (DSBs). Differentiation stages of blood cells thus represent an excellent model to study DSB induction, repair and misrepair in the context of changing higher-order chromatin structure. We show that immature granulocytes form γH2AX and 53BP1 foci, contrary to the mature cells; however, these foci colocalize only rarely and DSB repair is inefficient. Moreover, specific chromatin structure of granulocytes probably influences DSB induction. - Highlights: ► DSB repair is absent in mature granulocytes with condensed chromatin. ► Repair proteins and γH2AX appear in immature stages but rarely colocalize. ► γH2AX persist long times in these cells and DSB repair is inefficient. ► Even though, γH2AX foci “move” out of the dense chromatin. ► 53BP1 enters HP1β domains only after their decondensation

  12. Alpha radiation-induced alterations of the proliferation kinetics, chromatin structure and gene expression in mammalian cells

    International Nuclear Information System (INIS)

    Hieber, L.

    1983-01-01

    Exponentially growing mammalian cells were exposed to 3.4 MeV alpha particles. The chromatin of cells arrested in G2 by alpha irradiation was severely damaged, though all cells were still capable to condensate their chromatin after fusion with mitotic cells. In addition to the common types of aberrations (breaks, gaps, dicentrics and exchanges) cells were found possessing one or more chromosomes with long stretches of undercondensed chromatin. Repair of these lesions was indicated by site specific unscheduled DNA synthesis and by the observation that condensation of these regions improved during G2 arrest. Furthermore, during G2 arrest the synthesis of two cellular proteins was stimulated. This was studied by two-dimensional gel electrophoresis of 35 S-methionine labeled cellular proteins. All these findings provided evidence that radiation-induced G2 arrest is caused by chromatin damage, which prevents regular chromosome condensation for mitosis. (orig./MG) [de

  13. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

    Ko, Myunggon; Sohn, Dong H.; Chung, Heekyoung; Seong, Rho H.

    2008-01-01

    Development is a stepwise process in which multi-potent progenitor cells undergo lineage commitment, differentiation, proliferation and maturation to produce mature cells with restricted developmental potentials. This process is directed by spatiotemporally distinct gene expression programs that allow cells to stringently orchestrate intricate transcriptional activation or silencing events. In eukaryotes, chromatin structure contributes to developmental progression as a blueprint for coordinated gene expression by actively participating in the regulation of gene expression. Changes in higher order chromatin structure or covalent modification of its components are considered to be critical events in dictating lineage-specific gene expression during development. Mammalian cells utilize multi-subunit nuclear complexes to alter chromatin structure. Histone-modifying complex catalyzes covalent modifications of histone tails including acetylation, methylation, phosphorylation and ubiquitination. ATP-dependent chromatin remodeling complex, which disrupts histone-DNA contacts and induces nucleosome mobilization, requires energy from ATP hydrolysis for its catalytic activity. Here, we discuss the diverse functions of ATP-dependent chromatin remodeling complexes during mammalian development. In particular, the roles of these complexes during embryonic and hematopoietic development are reviewed in depth. In addition, pathological conditions such as tumor development that are induced by mutation of several key subunits of the chromatin remodeling complex are discussed, together with possible mechanisms that underlie tumor suppression by the complex

  14. Structural changes in single chromatin fibers induced by tension and torsion

    NARCIS (Netherlands)

    Meng, He

    2014-01-01

    Since the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of the helical structure, called supercoiling, plays important roles in both DNA compaction and gene

  15. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

    Directory of Open Access Journals (Sweden)

    Nicole C Riddle

    2012-09-01

    Full Text Available Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs, HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low T(m downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.

  16. Higher-Order Chromatin Organisation in Cell Nuclei: Structure and Function

    Czech Academy of Sciences Publication Activity Database

    Kozubek, Stanislav; Lukášová, Emilie; Bártová, Eva; Kozubek, Michal; Skalníková, M.; Jirsová, Pavla; Koutná, I.

    2000-01-01

    Roč. 17, - (2000), s. 1145 ISSN 0739-1102. [Mendel - Brno 2000. DNA Structure and Interactions. Their Biological Roles and Implications in Biomedicine and Biotechnologies. 19.07.2000-23.07.2000, Brno] Institutional research plan: CEZ:A17/98:Z5-004-9-ii Subject RIV: BO - Biophysics

  17. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a

  18. Important hydrodynamic and spectroscopic techniques in the field of chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D. E.

    1978-01-01

    Combining hydrodynamic and spectroscopic techniques in the study of conformational states of ..nu../sub 1/ induced by a variety of perturbants has led us to a general coneption: the two structural domains of ..nu../sub 1/ (i.e., the DNA-rich outer shell and the ..cap alpha..-helix-rich apolar histone core) exhibit differential responsiveness. In general, the ..cap alpha..-helical regions are more resistant, than DNA conformation or ..nu../sub 1/ size and shape, to the perturbing effects of urea, decreased ionic strength and pH, trypsin treatment, or a variety of water-miscible organic solvents. There are a number of reasonable conceptual models to explain this differential responsiveness of the structural domains of ..nu../sub 1/.

  19. Salt and divalent cations affect the flexible nature of the natural beaded chromatin structure

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

    Cl or 0.6M NaCL, and is compact in 0.01 M NaCl solutions if histone H 1 is present. Even high concentrations of urea did not alter the fundamental beaded structure, consisting of 110A beads of 200 base pair content, each joined by thin DNA bridges of 50 base pairs. The physical bead observed by EM...

  20. Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

    Czech Academy of Sciences Publication Activity Database

    Fišerová, Jindřiška; Efenberková, Michaela; Sieger, T.; Maninová, Miloslava; Uhlířová, Jana; Hozák, Pavel

    2017-01-01

    Roč. 130, č. 12 (2017), s. 2066-2077 ISSN 0021-9533 R&D Projects: GA ČR GJ15-08835Y; GA MŠk(CZ) LM2015062 Institutional support: RVO:68378050 Keywords : Structured illumination * Image analysis * Chromation * Nucleus * Histone modification * Nuclear pore complexes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Cell biology Impact factor: 4.431, year: 2016

  1. The Drosophila melanogaster CHD1 chromatin remodeling factor modulates global chromosome structure and counteracts HP1a and H3K9me2.

    Science.gov (United States)

    Bugga, Lakshmi; McDaniel, Ivy E; Engie, Liana; Armstrong, Jennifer A

    2013-01-01

    CHD1 is a conserved chromatin remodeling factor that localizes to active genes and functions in nucleosome assembly and positioning as well as histone turnover. Mouse CHD1 is required for the maintenance of stem cell pluripotency while human CHD1 may function as a tumor suppressor. To investigate the action of CHD1 on higher order chromatin structure in differentiated cells, we examined the consequences of loss of CHD1 and over-expression of CHD1 on polytene chromosomes from salivary glands of third instar Drosophila melanogaster larvae. We observed that chromosome structure is sensitive to the amount of this remodeler. Loss of CHD1 resulted in alterations of chromosome structure and an increase in the heterochromatin protein HP1a, while over-expression of CHD1 disrupted higher order chromatin structure and caused a decrease in levels of HP1a. Over-expression of an ATPase inactive form of CHD1 did not result in severe chromosomal defects, suggesting that the ATPase activity is required for this in vivo phenotype. Interestingly, changes in CHD1 protein levels did not correlate with changes in the levels of the euchromatin mark H3K4me3 or elongating RNA Polymerase II. Thus, while CHD1 is localized to transcriptionally active regions of the genome, it can function to alter the levels of HP1a, perhaps through changes in methylation of H3K9.

  2. The Drosophila melanogaster CHD1 chromatin remodeling factor modulates global chromosome structure and counteracts HP1a and H3K9me2.

    Directory of Open Access Journals (Sweden)

    Lakshmi Bugga

    Full Text Available CHD1 is a conserved chromatin remodeling factor that localizes to active genes and functions in nucleosome assembly and positioning as well as histone turnover. Mouse CHD1 is required for the maintenance of stem cell pluripotency while human CHD1 may function as a tumor suppressor. To investigate the action of CHD1 on higher order chromatin structure in differentiated cells, we examined the consequences of loss of CHD1 and over-expression of CHD1 on polytene chromosomes from salivary glands of third instar Drosophila melanogaster larvae. We observed that chromosome structure is sensitive to the amount of this remodeler. Loss of CHD1 resulted in alterations of chromosome structure and an increase in the heterochromatin protein HP1a, while over-expression of CHD1 disrupted higher order chromatin structure and caused a decrease in levels of HP1a. Over-expression of an ATPase inactive form of CHD1 did not result in severe chromosomal defects, suggesting that the ATPase activity is required for this in vivo phenotype. Interestingly, changes in CHD1 protein levels did not correlate with changes in the levels of the euchromatin mark H3K4me3 or elongating RNA Polymerase II. Thus, while CHD1 is localized to transcriptionally active regions of the genome, it can function to alter the levels of HP1a, perhaps through changes in methylation of H3K9.

  3. A component of DNA double-strand break repair is dependent on the spatial orientation of the lesions within the higher-order structures of chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, P.J.; Bryant, P.E. (Saint Andrews Univ. (United Kingdom))

    1994-11-01

    By the use of a modified neutral filter elution procedure variations in the repair of DNA dsb have been observed between the ionising radiation sensitive mutant xrs-5 and the parent cell line CHO-K1. Conventional neutral filter elution requires harsh lysis conditions to remove higher-order chromatin structures which interfere with elution of DNA containing dsb. By lysing cells with non-ionic detergent in the presence of 2 mol dm[sup -3] salt, histone-depleted structures that retain the higher-order nuclear matrix organization, including chromatin loops, can be produced. Elution from these structures will only occur if two or more dsb lie within a single-looped domain delineated by points of attachment to the nuclear matrix. Repair experiments indicate that in CHO cells repair of dsb in loops containing multiple dsb are repaired with slow kinetics whilst dsb occurring in loops containing single dsb are repaired with fast kinetics. Xrs-5 cells are defective in the repair of multiply damaged loops. This work indicates that the spatial orientation of dsb in the higher-order structures of chromatin are a possible factor in the repair of these lesions. (Author).

  4. A component of DNA double-strand break repair is dependent on the spatial orientation of the lesions within the higher-order structures of chromatin

    International Nuclear Information System (INIS)

    Johnston, P.J.; Bryant, P.E.

    1994-01-01

    By the use of a modified neutral filter elution procedure variations in the repair of DNA dsb have been observed between the ionising radiation sensitive mutant xrs-5 and the parent cell line CHO-K1. Conventional neutral filter elution requires harsh lysis conditions to remove higher-order chromatin structures which interfere with elution of DNA containing dsb. By lysing cells with non-ionic detergent in the presence of 2 mol dm -3 salt, histone-depleted structures that retain the higher-order nuclear matrix organization, including chromatin loops, can be produced. Elution from these structures will only occur if two or more dsb lie within a single-looped domain delineated by points of attachment to the nuclear matrix. Repair experiments indicate that in CHO cells repair of dsb in loops containing multiple dsb are repaired with slow kinetics whilst dsb occurring in loops containing single dsb are repaired with fast kinetics. Xrs-5 cells are defective in the repair of multiply damaged loops. This work indicates that the spatial orientation of dsb in the higher-order structures of chromatin are a possible factor in the repair of these lesions. (Author)

  5. Chromatin structure influence of DNA damage measurements by four assays: pulsed- and constant-field gel electrophoresis, DNA precipitation and non-denaturing filter elution

    International Nuclear Information System (INIS)

    Wlodek, D.; Olive, P.L.

    1996-01-01

    The of elution of DNA during non-denaturing filter elution (NFE) often correlates with cell sensitivity to radiation. The elution rate is influenced by two cellular factors: chromatin structure and the number of DNA-strand breaks (DSBs) produced in an intact cell by ionizing radiation. To determine which of the above factors is relevant to cell radiosensitivity, four assays were used to measure induction of DNA damage in three cell lines varying in radiosensitivity (V79, CHO, and L5178Y-R). Each of the assays, neutral filter elution (NFE), DNA precipitation, constant (CFGE) and pulsed field gel electrophoresis (PFGE) have different physical basis for DNA damage measurement and might be differently affected by chromatin structure. Three of the methods used to measure DNA double-strand breaks gave different results: NFE was dependent on cell type and location of DNA relative to the replication fork, gel electrophoresis was independent of cell type but was affected by proximity to the replication fork, and the precipitation assay was independent of both cell type and replication status. Pulsed field gel electrophoresis produced the same results and constant field gel electrophoresis for 3 cell lines examined. Only NFE showed differences in sensitivity which correlated with cell survival following irradiation. The results suggest that three is the same initial amount of DSBs in cells from all three lines and that the sensitivity to radiation is determined by some additional factors, probably chromatin structure. (author). 18 refs, 5 figs

  6. Molecular basis for the redox control of nuclear transport of the structural chromatin protein Hmgb1

    International Nuclear Information System (INIS)

    Hoppe, George; Talcott, Katherine E.; Bhattacharya, Sanjoy K.; Crabb, John W.; Sears, Jonathan E.

    2006-01-01

    Oxidative stress can induce a covalent disulfide bond between protein and peptide thiols that is reversible through enzymatic catalysis. This process provides a post-translational mechanism for control of protein function and may also protect thiol groups from irreversible oxidation. High mobility group protein B1 (Hmgb1), a DNA-binding structural chromosomal protein and transcriptional co-activator was identified as a substrate of glutaredoxin. Hmgb1 contains 3 cysteines, Cys23, 45, and 106. In mild oxidative conditions, Cys23 and Cys45 readily form an intramolecular disulfide bridge, whereas Cys106 remains in the reduced form. The disulfide bond between Cys23 and Cys45 is a target of glutathione-dependent reduction by glutaredoxin. Endogenous Hmgb1 as well as GFP-tagged wild-type Hmgb1 co-localize in the nucleus of CHO cells. While replacement of Hmgb1 Cys23 and/or 45 with serines did not affect the nuclear distribution of the mutant proteins, Cys106-to-Ser and triple cysteine mutations impaired nuclear localization of Hmgb1. Our cysteine targeted mutational analysis suggests that Cys23 and 45 induce conformational changes in response to oxidative stress, whereas Cys106 appears to be critical for the nucleocytoplasmic shuttling of Hmgb1

  7. Retention of the Native Epigenome in Purified Mammalian Chromatin.

    Directory of Open Access Journals (Sweden)

    Andreas H Ehrensberger

    Full Text Available A protocol is presented for the isolation of native mammalian chromatin as fibers of 25-250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed.

  8. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  9. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    van Driel, R.

    2007-01-01

    Chromatin molecules have properties that set them aside from all other biomacromolecules in the cell. (i) Chromosomes, which are single chromatin molecules, are the largest macromolecules in eukaryotic cells. (ii) Chromatin molecules carry the cell's genetic and epigenetic information and all

  10. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases

  11. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    different proteins involved in the synthesis of mRNA from the. DNA template. ... CBP - CREB Binding Protein. CHRAC. Chromatin .... nucleosomal interactions, and thereby change the chromatin structure, as per the ..... methyltransferases in gene regulation is yet to be elucidated. .... Molecular Biology and. Genetics Unit.

  12. Map of open and closed chromatin domains in Drosophila genome.

    Science.gov (United States)

    Milon, Beatrice; Sun, Yezhou; Chang, Weizhong; Creasy, Todd; Mahurkar, Anup; Shetty, Amol; Nurminsky, Dmitry; Nurminskaya, Maria

    2014-11-18

    Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

  13. [The effect of structure of benzimidazoles on the character of forming intramolecular cross-links in DNA and chromatin].

    Science.gov (United States)

    Mil', E M; Zhil'tsova, V M; Biniukov, V I; Zhizhina, G P; Stoliarova, L G; Kuznetsov, Iu P

    1994-01-01

    An investigation of a number of benzimidazole class preparations, being distinguished by a position of aminomethyl substitutes, has been carried out. It has been shown, that the non-substituted preparation BIO-10 does not form UV-cross-links in DNA and chromatine; BIO-40, having one substitute in the position 2, causes the formation of inter-molecular cross-links DNA-DNA. The preparation BIO-50, having 2 aminomethyl groups in the imidazole nucleus positions 2 and 6, forms cross-links DNA-DNA and DNA-protein in chromatine. The generation of radicals by the preparations BIO-10 and BIO-50 has been studied by the EPR-method by use of spin trap. It has been demonstrated, that BIO-10, unlike BIO-50, actively generates superoxide. A supposition has been made, that an UV-formation of superoxide-radical in the presence of BIO-10 might be a reason of DNA-macromolecule destruction.

  14. [Biochemical characterization of fractionated rat liver chromatin in experimental D-hypovitaminosis and after administration of steroidal drugs].

    Science.gov (United States)

    Levitskiĭ, E L; Kholodova, Iu D; Gubskiĭ, Iu I; Primak, R G; Chabannyĭ, V N; Kindruk, N L; Mozzhukhina, T G; Lenchevskaia, L K; Mironova, V N; Saad, L M

    1993-01-01

    Marked changes in the structural and functional characteristics of liver nuclear chromatin fractions are observed under experimental D-hypovitaminosis, which differ in the degree of transcriptional activity. DNA-polymerase activity and activity of the fraction, enriched with RNA-polymerase I, increases in the active fraction. Free radical LPO reactions are modified in the chromatin fraction with low activity and to the less degree in the active one. Disturbances of chromatine structural properties are caused with the change in the protein and lipid components of chromatin. Administration of ecdysterone preparations (separately and together with vitamin D3) has a partial corrective effect on structural and functional organization of nuclear chromatine. At the action of ecdysterone normalization of LPO reactions modified by pathological changes is observed in the chromatin fraction with low activity and to the less degree in the active one. This kind of influence corrects to the less degree chromatin functional activity and quantitative and qualitative modifications of its protein component. Simultaneous influence of ecdysterone and vitamin D3 leads to the partial normalization of the biochemical indices studied (except for those which characterize LPO reactions) mainly in the active chromatin fraction.

  15. Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level.

    Science.gov (United States)

    Goswami, Sathi; Sanyal, Sulagna; Chakraborty, Payal; Das, Chandrima; Sarkar, Munna

    2017-08-01

    NSAIDs are the most common class of painkillers and anti-inflammatory agents. They also show other functions like chemoprevention and chemosuppression for which they act at the protein but not at the genome level since they are mostly anions at physiological pH, which prohibit their approach to the poly-anionic DNA. Complexing the drugs with bioactive metal obliterate their negative charge and allow them to bind to the DNA, thereby, opening the possibility of genome level interaction. To test this hypothesis, we present the interaction of a traditional NSAID, Piroxicam and its copper complex with core histone and chromatin. Spectroscopy, DLS, and SEM studies were applied to see the effect of the interaction on the structure of histone/chromatin. This was coupled with MTT assay, immunoblot analysis, confocal microscopy, micro array analysis and qRT-PCR. The interaction of Piroxicam and its copper complex with histone/chromatin results in structural alterations. Such structural alterations can have different biological manifestations, but to test our hypothesis, we have focused only on the accompanied modulations at the epigenomic/genomic level. The complex, showed alteration of key epigenetic signatures implicated in transcription in the global context, although Piroxicam caused no significant changes. We have correlated such alterations caused by the complex with the changes in global gene expression and validated the candidate gene expression alterations. Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Chromatin organization and cellular sensitivity to ionizing radiation

    International Nuclear Information System (INIS)

    Szumiel, I.; Walicka, M.

    1987-01-01

    The paper briefly describes chromatin organization in mammalian cells and reviews experimental work concerning relations between chromatin structure and accesibility of damaged DNA to repair enzymes. The ''contact effect'', the size of super-coiled DNA domains and ADP-ribosylation of chromatin proteins are discussed in relation to cellular radiosensitivity. 88 refs. (author)

  17. Chromatin Dynamics of the mouse β-globin locus

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); E. de Boer (Ernie); T.A. Knoch (Tobias); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractLately it has become more clear that (subtle) changes in 3D organization of chromatin can either trigger transcription or silence genes or gene clusters. It has also been postulated that due to changes in chromatin structure, a change in chromatin accessibility of transcription factors

  18. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    Directory of Open Access Journals (Sweden)

    Shieh Grace S

    2011-12-01

    Full Text Available Abstract Background The packaging of DNA into chromatin regulates transcription from initiation through 3' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. Results Here we provide evidence that H2B monoubiquitylation (H2BK123ub1 marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3, which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality. Conclusion These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.

  19. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    LENUS (Irish Health Repository)

    Shieh, Grace S.

    2011-12-22

    Abstract Background The packaging of DNA into chromatin regulates transcription from initiation through 3\\' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. Results Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality. Conclusion These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.

  20. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean; Rayapuram, Naganand; Pflieger, Delphine; Hirt, Heribert

    2014-01-01

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  1. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  2. DNA-repair, chromosome alterations and chromatin structure under environmental pollutions

    International Nuclear Information System (INIS)

    Altmann, H.

    1988-06-01

    54 abstracts, 20 of which are within the INIS scope, are presented. The papers are dealing with the influence of some chemicals, environmental pollutants as well as drugs, on the process of DNA repair after ionizing irradiation. Some advanced techniques of detecting genotoxic properties and some papers on the influence of DNA repair on cell differentiation were presented. Genetic changes in man, animals and plants as a consequence of the Chernobylsk accident were described

  3. Effect of hyperthermia on replicating chromatin

    International Nuclear Information System (INIS)

    Warters, R.L.; Roti Roti, J.L.

    1981-01-01

    The extent of heat-induced structural alterations in chromatin containing nascent (pulse-labeled) DNA was assayed using the enzyme micrococcal nuclease. The basic nucleosome structure in nascent and mature chromatin of S-phase cells appeared unaltered for up to 16 hr after exposure to hyperthermic temperatures as high as 48 0 C for 15 min. However, the rate of nuclease digestion of DNA in both nascent and mature chromatin is inhibited following exposure to hyperthermic temperatures. In unheated cells, pulse-labeled nascent DNA matured into mature chromatin structure with a half-time of 2.5 min. The half-time for the maturation of pulse-labeled DNA from nascent into mature chromatin increased in a linear manner as a function of increasing temperature of exposure with constant heating time at temperatures above 43 0 C. Both the reduced nuclease digestibility of nascent DNA and the increased time for chromatin structural changes could be due to the increased protein mass of chromatin following hyperthermia

  4. Chromatin Remodelers: From Function to Dysfunction

    Directory of Open Access Journals (Sweden)

    Gernot Längst

    2015-06-01

    Full Text Available Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.

  5. Chromatin damage induced by fast neutrons or UV laser radiation

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I

    2002-07-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m{sup -2}. The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  6. Chromatin damage induced by fast neutrons or UV laser radiation

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I.

    2002-01-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m -2 . The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  7. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

  8. Epigenetic regulation and chromatin remodeling in learning and memory.

    Science.gov (United States)

    Kim, Somi; Kaang, Bong-Kiun

    2017-01-13

    Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms.

  9. Chromatin meets its organizers.

    Science.gov (United States)

    Bodnar, Megan S; Spector, David L

    2013-06-06

    Chromatin organization and gene-gene interactions are critical components of carrying out developmental programs. Phillips-Cremins et al. identify a series of unexpected architectural proteins that work in a combinatorial manner to functionally organize chromatin in a cell-type-specific manner at the submegabase-length scale. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Extracellular Matrix, Nuclear and Chromatin Structure and GeneExpression in Normal Tissues and Malignant Tumors: A Work inProgress

    Energy Technology Data Exchange (ETDEWEB)

    Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.

    2006-08-01

    Almost three decades ago, we presented a model where theextracellular matrix (ECM) was postulated to influence gene expressionand tissue-specificity through the action of ECM receptors and thecytoskeleton. This hypothesis implied that ECM molecules could signal tothe nucleus and that the unit of function in higher organisms was not thecell alone, but the cell plus its microenvironment. We now know that ECMinvokes changes in tissue and organ architecture and that tissue, cell,nuclear, and chromatin structure are changed profoundly as a result ofand during malignant progression. Whereas some evidence has beengenerated for a link between ECM-induced alterations in tissuearchitecture and changes in both nuclear and chromatin organization, themanner by which these changes actively induce or repress gene expressionin normal and malignant cells is a topic in need of further attention.Here, we will discuss some key findings that may provide insights intomechanisms through which ECM could influence gene transcription and howtumor cells acquire the ability to overcome these levels ofcontrol.

  11. Condensins Exert Force on Chromatin-Nuclear Envelope Tethers to Mediate Nucleoplasmic Reticulum Formation in Drosophila melanogaster

    Science.gov (United States)

    Bozler, Julianna; Nguyen, Huy Q.; Rogers, Gregory C.; Bosco, Giovanni

    2014-01-01

    Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. PMID:25552604

  12. Condensins exert force on chromatin-nuclear envelope tethers to mediate nucleoplasmic reticulum formation in Drosophila melanogaster.

    Science.gov (United States)

    Bozler, Julianna; Nguyen, Huy Q; Rogers, Gregory C; Bosco, Giovanni

    2014-12-30

    Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. Copyright © 2015 Bozler et al.

  13. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure; Etude des cassures de l'ADN et des mecanismes de reparation dans les sequences telomeriques interstitielles: Influence de la structure chromatinienne

    Energy Technology Data Exchange (ETDEWEB)

    Revaud, D.

    2009-06-15

    Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)

  14. A transient ischemic environment induces reversible compaction of chromatin.

    Science.gov (United States)

    Kirmes, Ina; Szczurek, Aleksander; Prakash, Kirti; Charapitsa, Iryna; Heiser, Christina; Musheev, Michael; Schock, Florian; Fornalczyk, Karolina; Ma, Dongyu; Birk, Udo; Cremer, Christoph; Reid, George

    2015-11-05

    Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells.

  15. Concrete structures under projectile impact

    CERN Document Server

    Fang, Qin

    2017-01-01

    In this book, the authors present their theoretical, experimental and numerical investigations into concrete structures subjected to projectile and aircraft impacts in recent years. Innovative approaches to analyze the rigid, mass abrasive and eroding projectile penetration and perforation are proposed. Damage and failure analyses of nuclear power plant containments impacted by large commercial aircrafts are numerically and experimentally analyzed. Ultra-high performance concrete materials and structures against the projectile impact are developed and their capacities of resisting projectile impact are evaluated. This book is written for the researchers, engineers and graduate students in the fields of protective structures and terminal ballistics.

  16. ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition

    Directory of Open Access Journals (Sweden)

    Alexandra Lusser

    2011-10-01

    Full Text Available ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.

  17. Spectroscopic study of fast-neutron-irradiated chromatin

    International Nuclear Information System (INIS)

    Radu, L.; Gazdaru, D.; Constantinescu, B.

    2004-01-01

    The effects produced by fast neutrons (0-100 Gy) on chromatin structure were analyzed by (i) [ 1 H]-NMR spectroscopy, (ii) time resolved spectroscopy, and (iii) fluorescence resonance energy transfer (FRET). Two types of chromatin were tested: (i) a chromatin from a normal tissue (liver of Wistar rats) and (ii) a chromatin from a tumoral tissue (Guerin limphotrope epithelioma, a rat solid tumor). The fast-neutron action on chromatin determines greater values of the [ 1 H]-NMR transverse relaxation time, indicating a more injured structure. Time-resolved fluorescence measurements show that the relative contribution of the excited state lifetime of bound ethidium bromide to chromatin DNA diminishes with increasing irradiation doses. This reflects the damage that occurs in DNA structure: production of single- and double-strand breaks due to sugar and base modifications. By the FRET method, the distance between dansyl chloride and acridine orange coupled at chromatin was determined. This distance increases upon fast-neutron action. The radiosensitivity of the tumor tissue chromatin seems higher than that of the normal tissue chromatin, probably because of its higher (loose) euchromatin/(compact) heterochromatin ratio. As the values of the physical parameters analyzed are specific for a determined dose, the establishment of these parameters may constitute a criterion for the microdosimetry of chromatin radiolesions produced by fast neutrons. (author)

  18. Spectroscopic study of fast-neutron-irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [V. Babes National Inst., Dept. of Molecular Genetics, Bucharest (Romania)]. E-mail: serbanradu@pcnet.ro; Gazdaru, D. [Bucharest Univ., Dept. of Biophysics, Physics Faculty, Bucharest (Romania); Constantinescu, B. [H. Hulubei National Inst., Dept. of Cyclotron, Bucharest (Romania)

    2004-02-01

    The effects produced by fast neutrons (0-100 Gy) on chromatin structure were analyzed by (i) [{sup 1}H]-NMR spectroscopy, (ii) time resolved spectroscopy, and (iii) fluorescence resonance energy transfer (FRET). Two types of chromatin were tested: (i) a chromatin from a normal tissue (liver of Wistar rats) and (ii) a chromatin from a tumoral tissue (Guerin limphotrope epithelioma, a rat solid tumor). The fast-neutron action on chromatin determines greater values of the [{sup 1}H]-NMR transverse relaxation time, indicating a more injured structure. Time-resolved fluorescence measurements show that the relative contribution of the excited state lifetime of bound ethidium bromide to chromatin DNA diminishes with increasing irradiation doses. This reflects the damage that occurs in DNA structure: production of single- and double-strand breaks due to sugar and base modifications. By the FRET method, the distance between dansyl chloride and acridine orange coupled at chromatin was determined. This distance increases upon fast-neutron action. The radiosensitivity of the tumor tissue chromatin seems higher than that of the normal tissue chromatin, probably because of its higher (loose) euchromatin/(compact) heterochromatin ratio. As the values of the physical parameters analyzed are specific for a determined dose, the establishment of these parameters may constitute a criterion for the microdosimetry of chromatin radiolesions produced by fast neutrons. (author)

  19. The chromatin remodeler SPLAYED regulates specific stress signaling pathways.

    Directory of Open Access Journals (Sweden)

    Justin W Walley

    2008-12-01

    Full Text Available Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD is required for the expression of selected genes downstream of the jasmonate (JA and ethylene (ET signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.

  20. The Role of Chromatin-Associated Proteins in Cancer

    DEFF Research Database (Denmark)

    Helin, Kristian; Minucci, Saverio

    2017-01-01

    The organization of the chromatin structure is essential for maintaining cell-type-specific gene expression and therefore for cell identity. This structure is highly dynamic and is regulated by a large number of chromatin-associated proteins that are required for normal development...... and differentiation. Recurrent somatic mutations have been found with high frequency in genes coding for chromatin-associated proteins in cancer, and several of these are required for cancer maintenance. In this review, we discuss recent advances in understanding the role of chromatin-associated proteins...

  1. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.

    Science.gov (United States)

    Ulianov, Sergey V; Galitsyna, Aleksandra A; Flyamer, Ilya M; Golov, Arkadiy K; Khrameeva, Ekaterina E; Imakaev, Maxim V; Abdennur, Nezar A; Gelfand, Mikhail S; Gavrilov, Alexey A; Razin, Sergey V

    2017-07-11

    In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation. Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing

  2. Vibrational energy relaxation: proposed pathway of fast local chromatin denaturation

    International Nuclear Information System (INIS)

    Harder, D.; Greinert, R.

    2002-01-01

    The molecular mechanism responsible for the a component of exchange-type chromosome aberrations, of chromosome fragmentation and of reproductive cell death is one of the unsolved issues of radiation biology. Under review is whether vibrational energy relaxation in the constitutive biopolymers of chromatin, induced by inelastic energy deposition events and mediated via highly excited vibrational states, may provide a pathway of fast local chromatin denaturation, thereby producing the severe DNA lesion able to interact chemically with other, non-damaged chromatin. (author)

  3. Chromatin architecture and gene expression in Escherichia coli

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2004-01-01

    Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.......Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli....

  4. Cell- and stage-specific chromatin structure across the Complement receptor 2 (CR2/CD21) promoter coincide with CBF1 and C/EBP-beta binding in B cells.

    Science.gov (United States)

    Cruickshank, Mark N; Fenwick, Emily; Karimi, Mahdad; Abraham, Lawrence J; Ulgiati, Daniela

    2009-08-01

    Stringent developmental transcription requires multiple transcription factor (TF) binding sites, cell-specific expression of signaling molecules, TFs and co-regulators and appropriate chromatin structure. During B-lymphopoiesis, human Complement receptor 2 (CR2/CD21) is detected on immature and mature B cells but not on B cell precursors and plasma cells. We examined cell- and stage-specific human CR2 gene regulation using cell lines modeling B-lymphopoiesis. Chromatin accessibility assays revealed a region between -409 and -262 with enhanced accessibility in mature B cells and pre-B cells, compared to either non-lymphoid or plasma cell-types, however, accessibility near the transcription start site (TSS) was elevated only in CR2-expressing B cells. A correlation between histone acetylation and CR2 expression was observed, while histone H3K4 dimethylation was enriched near the TSS in both CR2-expressing B cells and non-expressing pre-B cells. Candidate sites within the CR2 promoter were identified which could regulate chromatin, including a matrix attachment region associated with CDP, SATB1/BRIGHT and CEBP-beta sites as well as two CBF1 sites. ChIP assays verified that both CBF1 and C/EBP-beta bind the CR2 promoter in B cells raising the possibility that these factors facilitate or respond to alterations in chromatin structure to control the timing and/or level of CR2 transcription.

  5. Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX.

    Science.gov (United States)

    Argentaro, Anthony; Yang, Ji-Chun; Chapman, Lynda; Kowalczyk, Monika S; Gibbons, Richard J; Higgs, Douglas R; Neuhaus, David; Rhodes, Daniela

    2007-07-17

    The chromatin-associated protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental retardation associated with alpha-thalassemia. Half of all of the disease-associated missense mutations cluster in a cysteine-rich region in the N terminus of ATRX. This region was named the ATRX-DNMT3-DNMT3L (ADD) domain, based on sequence homology with a family of DNA methyltransferases. Here, we report the solution structure of the ADD domain of ATRX, which consists of an N-terminal GATA-like zinc finger, a plant homeodomain finger, and a long C-terminal alpha-helix that pack together to form a single globular domain. Interestingly, the alpha-helix of the GATA-like finger is exposed and highly basic, suggesting a DNA-binding function for ATRX. The disease-causing mutations fall into two groups: the majority affect buried residues and hence affect the structural integrity of the ADD domain; another group affects a cluster of surface residues, and these are likely to perturb a potential protein interaction site. The effects of individual point mutations on the folding state and stability of the ADD domain correlate well with the levels of mutant ATRX protein in patients, providing insights into the molecular pathophysiology of ATR-X syndrome.

  6. Reprogramming the chromatin landscape

    DEFF Research Database (Denmark)

    Miranda, Tina B; Voss, Ty C; Sung, Myong-Hee

    2013-01-01

    , mechanistic details defining the cellular interactions between ER and GR are poorly understood. We investigated genome-wide binding profiles for ER and GR upon coactivation and characterized the status of the chromatin landscape. We describe a novel mechanism dictating the molecular interplay between ER...... and GR. Upon induction, GR modulates access of ER to specific sites in the genome by reorganization of the chromatin configuration for these elements. Binding to these newly accessible sites occurs either by direct recognition of ER response elements or indirectly through interactions with other factors...

  7. Chromatin organization regulated by EZH2-mediated H3K27me3 is required for OPN-induced migration of bone marrow-derived mesenchymal stem cells.

    Science.gov (United States)

    Liu, Lingling; Luo, Qing; Sun, Jinghui; Ju, Yang; Morita, Yasuyuki; Song, Guanbin

    2018-03-01

    Osteopontin (OPN) is a chemokine-like extracellular matrix-associated protein involved in the migration of bone marrow-derived mesenchymal stem cells (BMSCs). An increasing number of studies have found that chromatin organization may affect cellular migration. However, whether OPN regulates chromatin organization is not understood, nor are the underlying molecular mechanisms. In this study, we investigated the link between chromatin organization and BMSC migration and demonstrated that OPN-mediated BMSC migration leads to elevated levels of heterochromatin marker histone H3 lysine 27 trimethylation (H3K27me3) through the methyltransferase EZH2. The expression of EZH2 reorganizes the chromatin structure of BMSCs. Pharmacological inhibition or depletion of EZH2 blocks BMSC migration. Moreover, using an atomic force microscope (AFM), we found that chromatin decondensation alters the mechanical properties of the nucleus. In addition, inhibition of extracellular signal-regulated kinase 1/2 (ERK1/2) signals represses OPN-promoted chromatin condensation and cell migration. Thus, our results identify a mechanism by which ERK1/2 signalling drives specific chromatin modifications in BMSCs, which alters chromatin organization and thereby enables OPN-mediated BMSC migration. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Chromatin dynamics during DSB repair

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Gabrielová, Barbora; Ondřej, Vladan; Kozubek, Stanislav

    2007-01-01

    Roč. 1773, č. 10 (2007), s. 1534-1545 ISSN 0167-4889 R&D Projects: GA ČR(CZ) GP204/06/P349; GA ČR(CZ) 1QS500040508; GA AV ČR(CZ) IAA1065203; GA MŠk(CZ) 1P05OC084 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin structure * double- strand breaks (DSB) * DNA repair Subject RIV: BO - Biophysics Impact factor: 4.374, year: 2007

  9. Dynamics of Histone Tails within Chromatin

    Science.gov (United States)

    Bernier, Morgan; North, Justin; Page, Michael; Jaroniec, Christopher; Hammel, Christopher; Poirier, Michael

    2012-02-01

    Genetic information in humans is encoded within DNA molecules that is wrapped around histone octamer proteins and compacted into a highly conserved structural polymer, chromatin. The physical and material properties of chromatin appear to influence gene expression by altering the accessibility of proteins to the DNA. The tails of the histones are flexible domains that are thought to play a role in regulating DNA accessibility and compaction; however the molecular mechanisms for these phenomena are not understood. I will present CW-EPR studies on site directed spin labeled nucleosomes that probe the structure and dynamics of these histone tails within nucleosomes.

  10. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    Bradbury, E.M.; Baldwin, J.P.; Carpenter, B.G.; Hjelm, R.P.; Hancock, R.; Ibel, K.

    1976-01-01

    It is clear that a knowledge of the basic molecular structure of chromatin is a prerequisite for any progress toward an understanding of chromosome organization. With a two-component system, protein and nucleic acid, neutrons have a particularly powerful application to studies of the spatial arrangements of these components because of the ability, by contrast matching with H 2 O-D 2 O mixtures, to obtain neutron-scattering data on the individual components. With this approach it has been shown that the neutron diffraction of chromatin is consistent with a ''beads on a string'' model in which the bead consists of a protein core with DNA coiled on the outside. However, because chromatin is a gel and gives limited structural data, confirmation of such a model requires extension of the neutron studies by deuteration of specific chromatin components and the isolation of chromatin subunits. Although these studies are not complete, the neutron results so far obtained support the subunit model described above

  11. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

  12. Spin-echo small-angle neutron scattering study of the structure organization of the chromatin in biological cell

    NARCIS (Netherlands)

    Iashina, E.G.; Bouwman, W.G.; Duif, C.P.; Filatov, M.V.; Grigoriev, S. V.

    2017-01-01

    Spin-echo small-angle scattering (SESANS) technique is a method to measure the structure of materials from nano- to micrmeter length scales. This method could be important for studying the packaging of DNA in the eukaryotic cell. We measured the SESANS function from chicken erythrocyte nuclei

  13. Spin-echo small-angle neutron scattering study of the structure organization of the chromatin in biological cell

    International Nuclear Information System (INIS)

    Iashina, E G; Grigoriev, S V; Bouwman, W G; Duif, C P; Filatov, M V

    2017-01-01

    Spin-echo small-angle scattering (SESANS) technique is a method to measure the structure of materials from nano- to micrometer length scales. This method could be important for studying the packaging of DNA in the eukaryotic cell. We measured the SESANS function from chicken erythrocyte nuclei which is well fitted by the exponential function G ( z ) = exp(− z / ξ ), where ξ is the correlation length of a nucleus (in experimental data ξ = 3, 3 μ m). The exponential decay of G ( z ) corresponds to the logarithmic pair correlation function γ ( r ) = ln( ξ / r ). As the sensitivity of the SESANS signal depends on the neutron wavelength, we propose the SESANS setup with the changeable wavelength in the range from 2 to 12 Å. Such option allows one to study in great detail the internal structure of the biological cell in the length scale from 10 −2 μ m to 10 μ m. (paper)

  14. Spin-echo small-angle neutron scattering study of the structure organization of the chromatin in biological cell

    Science.gov (United States)

    Iashina, E. G.; Bouwman, W. G.; Duif, C. P.; Filatov, M. V.; Grigoriev, S. V.

    2017-06-01

    Spin-echo small-angle scattering (SESANS) technique is a method to measure the structure of materials from nano- to micrmeter length scales. This method could be important for studying the packaging of DNA in the eukaryotic cell. We measured the SESANS function from chicken erythrocyte nuclei which is well fitted by the exponential function G(z) = exp(-z/ξ), where ξ is the correlation length of a nucleus (in experimental data ξ = 3, 3 μm). The exponential decay of G(z) corresponds to the logarithmic pair correlation function γ(r) = ln(ξ/r). As the sensitivity of the SESANS signal depends on the neutron wavelength, we propose the SESANS setup with the changeable wavelength in the range from 2 to 12 Å. Such option allows one to study in great detail the internal structure of the biological cell in the length scale from 10-2 μm to 10 μm.

  15. Autism genes keep turning up chromatin.

    Science.gov (United States)

    Lasalle, Janine M

    2013-06-19

    Autism-spectrum disorders (ASD) are complex genetic disorders collectively characterized by impaired social interactions and language as well as repetitive and restrictive behaviors. Of the hundreds of genes implicated in ASD, those encoding proteins acting at neuronal synapses have been most characterized by candidate gene studies. However, recent unbiased genome-wide analyses have turned up a multitude of novel candidate genes encoding nuclear factors implicated in chromatin remodeling, histone demethylation, histone variants, and the recognition of DNA methylation. Furthermore, the chromatin landscape of the human genome has been shown to influence the location of de novo mutations observed in ASD as well as the landscape of DNA methylation underlying neurodevelopmental and synaptic processes. Understanding the interactions of nuclear chromatin proteins and DNA with signal transduction pathways and environmental influences in the developing brain will be critical to understanding the relevance of these ASD candidate genes and continued uncovering of the "roots" of autism etiology.

  16. CHD chromatin remodelers and the transcription cycle

    Science.gov (United States)

    Murawska, Magdalena

    2011-01-01

    It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by “opening” or “closing” chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but also are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts. PMID:22223048

  17. Modulation of chromatin access during adipocyte differentiation

    DEFF Research Database (Denmark)

    Mandrup, Susanne; Hager, Gordon L

    2012-01-01

    identified; however, it is not until recently that we have begun to understand how these factors act at a genome-wide scale. In a recent publication we have mapped the genome-wide changes in chromatin structure during differentiation of 3T3-L1 preadipocytes and shown that a major reorganization...... of the chromatin landscape occurs within few hours following the addition of the adipogenic cocktail. In addition, we have mapped the genome-wide profiles of several of the early adipogenic transcription factors and shown that they act in a highly cooperative manner to drive this dramatic remodeling process....

  18. Chromatin organisation during Arabidopsis root development

    NARCIS (Netherlands)

    Lorvellec, M.

    2007-01-01

    The genetic information is stored in a highly compact manner in every nucleus. About 150 bp of DNA is packed around a histone octamer constituting a nucleosome. Nucleosomes are linked together by histone H1 and further compaction of this "beads on a string" form higher-order chromatin structures.

  19. Dietary polyphenols and chromatin remodeling.

    Science.gov (United States)

    Russo, Gian Luigi; Vastolo, Viviana; Ciccarelli, Marco; Albano, Luigi; Macchia, Paolo Emidio; Ungaro, Paola

    2017-08-13

    Polyphenols are the most abundant phytochemicals in fruits, vegetables, and plant-derived beverages. Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer. Epigenetics, defined as heritable changes to the transcriptome, independent from those occurring in the genome, includes DNA methylation, histone modifications, and posttranscriptional gene regulation by noncoding RNAs. Sinergistically and cooperatively, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Such induced epigenetic changes can be inherited during cell division, resulting in permanent maintenance of the acquired phenotype, but they may also occur throughout an individual life-course and may ultimately influence phenotypic outcomes (health and disease risk). In the last decade, a number of studies have shown that nutrients can affect metabolic traits by altering the structure of chromatin and directly regulate both transcription and translational processes. In this context, dietary polyphenol-targeted epigenetics becomes an attractive approach for disease prevention and intervention. Here, we will review how polyphenols, including flavonoids, curcuminoids, and stilbenes, modulate the establishment and maintenance of key epigenetic marks, thereby influencing gene expression and, hence, disease risk and health.

  20. A model of photon cell killing based on the spatio-temporal clustering of DNA damage in higher order chromatin structures.

    Directory of Open Access Journals (Sweden)

    Lisa Herr

    Full Text Available We present a new approach to model dose rate effects on cell killing after photon radiation based on the spatio-temporal clustering of DNA double strand breaks (DSBs within higher order chromatin structures of approximately 1-2 Mbp size, so called giant loops. The main concept of this approach consists of a distinction of two classes of lesions, isolated and clustered DSBs, characterized by the number of double strand breaks induced in a giant loop. We assume a low lethality and fast component of repair for isolated DSBs and a high lethality and slow component of repair for clustered DSBs. With appropriate rates, the temporal transition between the different lesion classes is expressed in terms of five differential equations. These allow formulating the dynamics involved in the competition of damage induction and repair for arbitrary dose rates and fractionation schemes. Final cell survival probabilities are computable with a cell line specific set of three parameters: The lethality for isolated DSBs, the lethality for clustered DSBs and the half-life time of isolated DSBs. By comparison with larger sets of published experimental data it is demonstrated that the model describes the cell line dependent response to treatments using either continuous irradiation at a constant dose rate or to split dose irradiation well. Furthermore, an analytic investigation of the formulation concerning single fraction treatments with constant dose rates in the limiting cases of extremely high or low dose rates is presented. The approach is consistent with the Linear-Quadratic model extended by the Lea-Catcheside factor up to the second moment in dose. Finally, it is shown that the model correctly predicts empirical findings about the dose rate dependence of incidence probabilities for deterministic radiation effects like pneumonitis and the bone marrow syndrome. These findings further support the general concepts on which the approach is based.

  1. New insights into chromatin folding and dynamics from multi-scale modeling

    Science.gov (United States)

    Olson, Wilma

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

  2. HAMLET interacts with histones and chromatin in tumor cell nuclei.

    Science.gov (United States)

    Düringer, Caroline; Hamiche, Ali; Gustafsson, Lotta; Kimura, Hiroshi; Svanborg, Catharina

    2003-10-24

    HAMLET is a folding variant of human alpha-lactalbumin in an active complex with oleic acid. HAMLET selectively enters tumor cells, accumulates in their nuclei and induces apoptosis-like cell death. This study examined the interactions of HAMLET with nuclear constituents and identified histones as targets. HAMLET was found to bind histone H3 strongly and to lesser extent histones H4 and H2B. The specificity of these interactions was confirmed using BIAcore technology and chromatin assembly assays. In vivo in tumor cells, HAMLET co-localized with histones and perturbed the chromatin structure; HAMLET was found associated with chromatin in an insoluble nuclear fraction resistant to salt extraction. In vitro, HAMLET bound strongly to histones and impaired their deposition on DNA. We conclude that HAMLET interacts with histones and chromatin in tumor cell nuclei and propose that this interaction locks the cells into the death pathway by irreversibly disrupting chromatin organization.

  3. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    Chemical modifications to the DNA and histone protein components of chromatin can modulate gene expression and genome stability. Understanding the physiological impact of changes in chromatin structure remains an important question in biology. As one example, in order to generate antibody diversity...... with somatic hypermutation and class switch recombination, chromatin must be made accessible for activation-induced cytidine deaminase (AID)-mediated deamination of cytosines in DNA. These lesions are recognized and removed by various DNA repair pathways but, if not handled properly, can lead to formation...... of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct roles...

  4. Deoxyribonuclease probing of sea urchin embryo chromatin

    International Nuclear Information System (INIS)

    Landsman, D.

    1983-01-01

    The role that the sea urchin, Parechinus angulosus, embryo and sperm histone variants plays in chromatin structure has been investigated. Chromatin structure has been determined at different levels of resolution in sperm and in developing embryos using micrococcal nuclease, pancreatic deoxyribonuclease (DNase I) and restriction endonucleases. Micrococcal nuclease and restriction endonuclease digestions of sea urchin gastrula chromatin have been analysed and it is shown that it is not possible to isolate large polynucleosomal chromatin complexes which are soluble in low ionic strength buffers. The repeat length for sperm is significantly larger than blastula and gastrula repeat lengths whereas blastula and gastrula repeat lengths are not significantly different. Nucleosomal core particles have been isolated from early blastula, gastrula and sperm of sea urchins. After DNase I digestion of 5'-labelled core particles the rate constants of cutting of the DNA at the susceptible sites on these core particles have been determined. The DNase I digestion kinetics of blastula and gastrula core particles are similar whereas sperm core particles are digested at a slower rate, mainly at the sites which are closest to the ends of the core particle DNA

  5. Fatigue in Steel Structures under Random Loading

    DEFF Research Database (Denmark)

    Agerskov, Henning

    1999-01-01

    types of welded plate test specimens and full-scale offshore tubular joints. The materials that have been used are either conventional structural steel with a yield stress of ~ 360-410 MPa or high-strength steel with a yield stress of ~ 810-1010 MPa. The fatigue tests and the fracture mechanics analyses......Fatigue damage accumulation in steel structures under random loading is studied. The fatigue life of welded joints has been determined both experimentally and from a fracture mechanics analysis. In the experimental part of the investigation, fatigue test series have been carried through on various...... have been carried out using load histories, which are realistic in relation to the types of structures studied, i.e. primarily bridges, offshore structures and chimneys. In general, the test series carried through show a significant difference between constant amplitude and variable amplitude fatigue...

  6. Analysis of flexible structures under lateral impact

    International Nuclear Information System (INIS)

    Ramirez, D. F.; Razavi, H.

    2012-01-01

    Three methods for analysis of flexible structures under lateral impact are presented. The first proposed method (Method A) consists of: (1) modifying an available deceleration on a rigid target with conservation principles to account for structural flexibility; and (2) transient nonlinear analysis of the structure with the corrected forcing function. The second proposed method (Method B) is similar to Method A in obtaining the forcing function but it solves the equations of motion of an idealized two-degree-of-freedom system instead of directly using conservation principles. The last method simply provides the maximum force in the structure using the conservation of energy and linear momentum. A coupled simulation is also performed in LS-DYNA and compared against the proposed methods. A case study is presented to illustrate the applicability of all three methods and the LS-DYNA simulation. (authors)

  7. The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

    Science.gov (United States)

    Agarwal, Poonam; Miller, Kyle M

    2016-10-01

    DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

  8. A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP–Chip

    Directory of Open Access Journals (Sweden)

    Weishaupt Holger

    2010-01-01

    Full Text Available Abstract Dynamic chromatin structure is a fundamental property of gene transcriptional regulation, and has emerged as a critical modulator of physiological processes during cellular differentiation and development. Analysis of chromatin structure using molecular biology and biochemical assays in rare somatic stem and progenitor cells is key for understanding these processes but poses a great challenge because of their reliance on millions of cells. Through the development of a miniaturized genome-scale chromatin immunoprecipitation method (miniChIP–chip, we have documented the genome-wide chromatin states of low abundant populations that comprise hematopoietic stem cells and immediate progeny residing in murine bone marrow. In this report, we describe the miniChIP methodology that can be used for increasing an understanding of the epigenetic mechanisms underlying hematopoietic stem and progenitor cell function. Application of this method will reveal the contribution of dynamic chromatin structure in regulating the function of other somatic stem cell populations, and how this process becomes perturbed in pathological conditions. Additional file 1 Click here for file

  9. Aberrant Chromatin Modification as a Mechanism of Prostate Cancer Progression

    National Research Council Canada - National Science Library

    Chen, Hongwu

    2004-01-01

    .... However, the underlying mechanism is still unclear. The purpose of this study is to test the hypothesis that aberrant chromatin modification plays a critical role in prostate cancer progression...

  10. Chromatin Flavors: Chromatin composition and domain organization in Drosophila melanogaster

    NARCIS (Netherlands)

    J.G. van Bemmel (Joke)

    2012-01-01

    textabstractChromatin was originally identified by W. Flemming in 1882 as not much more than the stainable substance of the cell nucleus. Flemming named this substance according to the Greek word “chroma”, meaning color. In 1911 chromatin was characterized as proteins, named histones, that

  11. [The biological aspects of chromatin diminution].

    Science.gov (United States)

    Akif'ev, A P; Grishanin, A K

    1993-01-01

    The chromatine diminution (CD), first discovered by Boveri (1887) in ascarids, represents programmed elimination of a part of genetic material in the nuclei of the somatic cells in cyclops and ascarids, and in the protist macronuclei. The CD can be considered as a macromutation sharply changing chromosomal structure, though minimally effecting the phenotype. The analysis of CD is of significance for discussing mechanisms of origin of chromosomal organization, transformation of genome molecular structure in eucaryote evolution, role of the extra DNA.

  12. Estimation of structural reliability under combined loads

    International Nuclear Information System (INIS)

    Shinozuka, M.; Kako, T.; Hwang, H.; Brown, P.; Reich, M.

    1983-01-01

    For the overall safety evaluation of seismic category I structures subjected to various load combinations, a quantitative measure of the structural reliability in terms of a limit state probability can be conveniently used. For this purpose, the reliability analysis method for dynamic loads, which has recently been developed by the authors, was combined with the existing standard reliability analysis procedure for static and quasi-static loads. The significant parameters that enter into the analysis are: the rate at which each load (dead load, accidental internal pressure, earthquake, etc.) will occur, its duration and intensity. All these parameters are basically random variables for most of the loads to be considered. For dynamic loads, the overall intensity is usually characterized not only by their dynamic components but also by their static components. The structure considered in the present paper is a reinforced concrete containment structure subjected to various static and dynamic loads such as dead loads, accidental pressure, earthquake acceleration, etc. Computations are performed to evaluate the limit state probabilities under each load combination separately and also under all possible combinations of such loads

  13. Thermomechanics of composite structures under high temperatures

    CERN Document Server

    Dimitrienko, Yu I

    2016-01-01

    This pioneering book presents new models for the thermomechanical behavior of composite materials and structures taking into account internal physico-chemical transformations such as thermodecomposition, sublimation and melting at high temperatures (up to 3000 K). It is of great importance for the design of new thermostable materials and for the investigation of reliability and fire safety of composite structures. It also supports the investigation of interaction of composites with laser irradiation and the design of heat-shield systems. Structural methods are presented for calculating the effective mechanical and thermal properties of matrices, fibres and unidirectional, reinforced by dispersed particles and textile composites, in terms of properties of their constituent phases. Useful calculation methods are developed for characteristics such as the rate of thermomechanical erosion of composites under high-speed flow and the heat deformation of composites with account of chemical shrinkage. The author expan...

  14. The Latest Twists in Chromatin Remodeling.

    Science.gov (United States)

    Blossey, Ralf; Schiessel, Helmut

    2018-01-05

    In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Optical tweezers stretching of chromatin

    NARCIS (Netherlands)

    Pope, L.H.; Bennink, Martin L.; Greve, Jan

    2003-01-01

    Recently significant success has emerged from exciting research involving chromatin stretching using optical tweezers. These experiments, in which a single chromatin fibre is attached by one end to a micron-sized bead held in an optical trap and to a solid surface or second bead via the other end,

  16. Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins.

    Science.gov (United States)

    Borysov, Sergiy; Bryant, Victoria L; Alexandrow, Mark G

    2015-01-01

    Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze

  17. Estimation of structural reliability under combined loads

    International Nuclear Information System (INIS)

    Shinozuka, M.; Kako, T.; Hwang, H.; Brown, P.; Reich, M.

    1983-01-01

    For the overall safety evaluation of seismic category I structures subjected to various load combinations, a quantitative measure of the structural reliability in terms of a limit state probability can be conveniently used. For this purpose, the reliability analysis method for dynamic loads, which has recently been developed by the authors, was combined with the existing standard reliability analysis procedure for static and quasi-static loads. The significant parameters that enter into the analysis are: the rate at which each load (dead load, accidental internal pressure, earthquake, etc.) will occur, its duration and intensity. All these parameters are basically random variables for most of the loads to be considered. For dynamic loads, the overall intensity is usually characterized not only by their dynamic components but also by their static components. The structure considered in the present paper is a reinforced concrete containment structure subjected to various static and dynamic loads such as dead loads, accidental pressure, earthquake acceleration, etc. Computations are performed to evaluate the limit state probabilities under each load combination separately and also under all possible combinations of such loads. Indeed, depending on the limit state condition to be specified, these limit state probabilities can indicate which particular load combination provides the dominant contribution to the overall limit state probability. On the other hand, some of the load combinations contribute very little to the overall limit state probability. These observations provide insight into the complex problem of which load combinations must be considered for design, for which limit states and at what level of limit state probabilities. (orig.)

  18. Concrete structures under impact and impulsive loading

    International Nuclear Information System (INIS)

    Plauk, G.

    1982-05-01

    This book contains papers contributed to the RILEM/CEB/IABSE/IASS-Interassociation Symposium on 'Concrete Structures under Impact and Impulsive Loading'. The essential aim of this symposium is to provide an international forum for the exchange of information on existing and current research relating to impact problems as well as to identify areas to which further research activities should be directed. The subject of the symposium is far ranging. Fifty five papers were proposed and arranged in six technical sessions, a task which sometimes posed difficulties for the Organization Committee and the Advisory Group, because some of the papers touched several topics and were difficult to integrate. However, we are confident that these minor difficulties were solved to the satisfaction of everyone involved. Each session of the symposium is devoted to a major subject area and introduced by a distinguished Introductory Reporter. The large international attendance, some 21 countries are represented, and the large number of excellent papers will certainly produce a lively discussion after each session and thus help to further close the gaps in our knowledge about the behaviour of structures and materials under impact and impulsive loading. (orig./RW)

  19. Histone chaperone networks shaping chromatin function

    DEFF Research Database (Denmark)

    Hammond, Colin; Strømme, Caroline Bianchi; Huang, Hongda

    2017-01-01

    and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone...... chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin....

  20. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

    Science.gov (United States)

    Bandaria, Jigar N.; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

    2016-01-01

    SUMMARY Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, and not by DNA methylation, histone deacetylation or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres become more accessible to telomere-associated proteins and accumulate DDR signals. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

  1. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    Energy Technology Data Exchange (ETDEWEB)

    Uppal, Timsy [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Jha, Hem C. [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States); Verma, Subhash C. [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Robertson, Erle S., E-mail: erle@mail.med.upenn.edu [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States)

    2015-01-14

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle.

  2. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    International Nuclear Information System (INIS)

    Uppal, Timsy; Jha, Hem C.; Verma, Subhash C.; Robertson, Erle S.

    2015-01-01

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle

  3. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  4. Tracking the mechanical dynamics of human embryonic stem cell chromatin

    Directory of Open Access Journals (Sweden)

    Hinde Elizabeth

    2012-12-01

    Full Text Available Abstract Background A plastic chromatin structure has emerged as fundamental to the self-renewal and pluripotent capacity of embryonic stem (ES cells. Direct measurement of chromatin dynamics in vivo is, however, challenging as high spatiotemporal resolution is required. Here, we present a new tracking-based method which can detect high frequency chromatin movement and quantify the mechanical dynamics of chromatin in live cells. Results We use this method to study how the mechanical properties of chromatin movement in human embryonic stem cells (hESCs are modulated spatiotemporally during differentiation into cardiomyocytes (CM. Notably, we find that pluripotency is associated with a highly discrete, energy-dependent frequency of chromatin movement that we refer to as a ‘breathing’ state. We find that this ‘breathing’ state is strictly dependent on the metabolic state of the cell and is progressively silenced during differentiation. Conclusions We thus propose that the measured chromatin high frequency movements in hESCs may represent a hallmark of pluripotency and serve as a mechanism to maintain the genome in a transcriptionally accessible state. This is a result that could not have been observed without the high spatial and temporal resolution provided by this novel tracking method.

  5. The role of proteins and metal ions in the protection of chromatin DNA at fast neutrons action

    International Nuclear Information System (INIS)

    Radu, L.; Preoteasa, V.; Radulescu, I.; Constantinescu, B.

    1997-01-01

    The role of chromatin proteins and of some ions on the fast neutrons actions on chromatin DNA from rat Walker tumors was analysed. The DNA in chromatin is effectively protected against fast neutrons actions by DNA bound proteins and specially by histones, because of the limited accessibility of the condensed chromatin DNA to hydroxyl radicals and of the scavenging of radicals by the chromatin proteins. The ions utilised protect chromatin DNA against the damage produced ed by fast neutrons, through the induction of structural DNA changes with a less accessibility to OH radicals. (authors)

  6. Structural behavior of supercritical fluids under confinement

    Science.gov (United States)

    Ghosh, Kanka; Krishnamurthy, C. V.

    2018-01-01

    The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P =5000 bar, 240 K ≤T ≤1500 K ) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features

  7. Sleep duration is associated with sperm chromatin integrity among young men in Chongqing, China.

    Science.gov (United States)

    Wang, Xiaogang; Chen, Qing; Zou, Peng; Liu, Taixiu; Mo, Min; Yang, Huan; Zhou, Niya; Sun, Lei; Chen, Hongqiang; Ling, Xi; Peng, Kaige; Ao, Lin; Yang, Huifang; Cao, Jia; Cui, Zhihong

    2017-10-09

    This study explores whether sleep duration is associated with sperm chromatin integrity. To do so, we conducted a three-phase panel study of 796 male volunteers from colleges in Chongqing (China) from 2013 to 2015. Sleep duration was measured using a modified Munich Chronotype Questionnaire. Sperm DNA integrity was examined via Sperm Chromatin Structure Assay and Comet assay. Setting 7-7.5 h day -1 of sleep duration as a reference, either longer or shorter sleep duration was associated negatively with high DNA stainability (HDS) (P = 0.009), which reflected the immaturity of sperm chromatin. The volunteers with > 9.0 h day -1 sleep and those with ≤ 6.5 h day -1 sleep had 40.7 and 30.3% lower HDS than did volunteers with 7-7.5 h day -1 sleep. No association was found between sleep duration and DNA fragmentation index or Comet assay parameters. This study suggests that sleep duration is associated with sperm chromatin integrity. Further studies are required to validate these findings and investigate the mechanism underlying this association. © 2017 European Sleep Research Society.

  8. Higher order chromatin organization in cancer

    Science.gov (United States)

    Reddy, Karen L.; Feinberg, Andrew P.

    2013-01-01

    In spite of our increased understanding of how genomes are dysregulated in cancer and a plethora of molecular diagnostic tools, the front line and ‘gold standard’ detection of cancer remains the pathologist’s detection of gross changes in cellular and tissue structure, most strikingly nuclear dis-organization. In fact, for over 140 years it has been noted that nuclear morphology is often disrupted in cancer. Even today, nuclear morphology measures include nuclear size, shape, DNA content (ploidy) and ‘chromatin organization’. Given the importance of nuclear shape to diagnoses of cancer phenotypes, it is surprising and frustrating that we currently lack a detailed understanding to explain these changes and how they might arise and relate to molecular events in the cell. It is an implicit hypothesis that perturbation of chromatin and epigenetic signatures may lead to alterations in nuclear structure (or vice versa) and that these perturbations lie at the heart of cancer genesis. In this review, we attempt to synthesize research leading to our current understanding on how chromatin interactions at the nuclear lamina, epigenetic modulation and gene regulation may intersect in cancer and offer a perspective on critical experiments that would help clarify how nuclear architecture may contribute to the cancerous phenotype. We also discuss the historical understanding of nuclear structure in normal cells and as a diagnostic in cancer. PMID:23266653

  9. Structural modifications of spinels under radiation

    International Nuclear Information System (INIS)

    Quentin, A.

    2010-12-01

    This work is devoted to the study of spinel structure materials under radiation. For that purpose, samples of polycrystalline ZnAl 2 O 4 and monocrystalline MgAl 2 O 4 were irradiated by different heavy ions with different energies. Samples of ZnAl 2 O 4 were studied par electron transmission microscopy, and by grazing incidence X-Ray diffraction and Rietveld analysis. Samples of MgAl 2 O 4 were studied by optical spectroscopy. Most of the results concern amorphization and crystalline structure modification of ZnAl 2 O 4 especially the inversion. We were able to determine a stopping power threshold for amorphization, between 11 keV/nm and 12 keV/nm, and also the amorphization process, which is a multiple impacts process. We studied the evolution of the amorphous phase by TEM and showed a nano-patterning phenomenon. Concerning the inversion, we determined that it did happen by a single impact process, and the saturation value did not reach the random cation distribution value. Inversion and amorphization have different, but close, stopping power threshold. However, amorphization seems to be conditioned by a pre-damage of the material which consists in inversion. (author)

  10. Processing of DNA double strand breaks by alternative non-homologous end-joining in hyperacetylated chromatin.

    Science.gov (United States)

    Manova, Vasilissa; Singh, Satyendra K; Iliakis, George

    2012-08-22

    Mammalian cells employ at least two subpathways of non-homologous end-joining for the repair of ionizing radiation induced DNA double strand breaks: The canonical DNA-PK-dependent form of non-homologous end-joining (D-NHEJ) and an alternative, slowly operating, error-prone backup pathway (B-NHEJ). In contrast to D-NHEJ, which operates with similar efficiency throughout the cell cycle, B-NHEJ operates more efficiently in G2-phase. Notably, B-NHEJ also shows strong and as of yet unexplained dependency on growth activity and is markedly compromised in serum-deprived cells, or in cells that enter the plateau-phase of growth. The molecular mechanisms underpinning this response remain unknown. Since chromatin structure or changes in chromatin structure are prime candidate-B-NHEJ-modulators, we study here the role of chromatin hyperacetylation, either by HDAC2 knockdown or treatment with the HDAC inhibitor TSA, on the repair by B-NHEJ of IR-induced DSBs. siRNA-mediated knockdown of HDAC2 fails to provoke histone hyperacetylation in Lig4-/- MEFs and has no detectable effect on B-NHEJ function. Treatment with TSA that inhibits multiple HDACs causes efficient, reversible chromatin hyperacetylation in Lig4-/- MEFs, as well as in human HCT116 Lig4-/- cells and the human glioma cell line M059K. The IR yield of DSBs in TSA-treated cells remains similar to that of untreated cells despite the expected chromatin relaxation. In addition, chromatin hyperacetylation leaves unchanged repair of DSBs by B-NHEJ in irradiated exponentially growing, or plateau-phase cells. Notably, under the experimental conditions employed here, chromatin hyperacetylation fails to detectably modulate B-NHEJ in M059K cells as well. In summary, the results show that chromatin acetylation or deacetylation does not affect the kinetics of alternative NHEJ in all types of cells examined both in exponentially growing and serum deprived cultures. We conclude that parameters beyond chromatin acetylation determine B

  11. Chromatin Regulation of Neuronal Maturation and Plasticity.

    Science.gov (United States)

    Gallegos, David A; Chan, Urann; Chen, Liang-Fu; West, Anne E

    2018-05-01

    Neurons are dynamic cells that respond and adapt to stimuli throughout their long postmitotic lives. The structural and functional plasticity of neurons requires the regulated transcription of new gene products, and dysregulation of transcription in either the developing or adult brain impairs cognition. We discuss how mechanisms of chromatin regulation help to orchestrate the transcriptional programs that underlie the maturation of developing neurons and the plasticity of adult neurons. We review how chromatin regulation acts locally to modulate the expression of specific genes and more broadly to coordinate gene expression programs during transitions between cellular states. These data highlight the importance of epigenetic transcriptional mechanisms in postmitotic neurons. We suggest areas where emerging methods may advance understanding in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Determination of local chromatin composition by CasID.

    Science.gov (United States)

    Schmidtmann, Elisabeth; Anton, Tobias; Rombaut, Pascaline; Herzog, Franz; Leonhardt, Heinrich

    2016-09-02

    Chromatin structure and function are determined by a plethora of proteins whose genome-wide distribution is typically assessed by immunoprecipitation (ChIP). Here, we developed a novel tool to investigate the local chromatin environment at specific DNA sequences. We combined the programmable DNA binding of dCas9 with the promiscuous biotin ligase BirA* (CasID) to biotinylate proteins in the direct vicinity of specific loci. Subsequent streptavidin-mediated precipitation and mass spectrometry identified both known and previously unknown chromatin factors associated with repetitive telomeric, major satellite and minor satellite DNA. With super-resolution microscopy, we confirmed the localization of the putative transcription factor ZNF512 at chromocenters. The versatility of CasID facilitates the systematic elucidation of functional protein complexes and locus-specific chromatin composition.

  13. FACT facilitates chromatin transcription by RNA polymerases I and III

    DEFF Research Database (Denmark)

    Birch, Joanna L; Tan, Bertrand C-M; Panov, Kostya I

    2009-01-01

    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle....... The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results...... in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III...

  14. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

    Dayarian, Adel; Sengupta, Anirvan M

    2013-01-01

    Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of this paper is to examine how the perturbations altering the activity of histone modifying enzymes affect the epigenetic states. We analyze the implications of having the total number of silencing proteins, given by the sum of proteins bound to the nucleosomes and the ones available in the ambient, to be constant. This constraint couples different regions of chromatin through the shared reservoir of ambient silencing proteins. We show that the response of the system to perturbations depends dramatically on the titration effect caused by the above constraint. In particular, for a certain range of overall abundance of silencing proteins, the hysteresis loop changes qualitatively with certain jump replaced by continuous merger of different states. In addition, we find a nonmonotonic dependence of gene expression on the rate of histone deacetylation activity of Sir2. We discuss how these qualitative predictions of our model could be compared with experimental studies of the yeast system under anti-silencing drugs. (paper)

  15. Default assembly of early adenovirus chromatin

    International Nuclear Information System (INIS)

    Spector, David J.

    2007-01-01

    In adenovirus particles, the viral nucleoprotein is organized into a highly compacted core structure. Upon delivery to the nucleus, the viral nucleoprotein is very likely to be remodeled to a form accessible to the transcription and replication machinery. Viral protein VII binds to intra-nuclear viral DNA, as do at least two cellular proteins, SET/TAF-Iβ and pp32, components of a chromatin assembly complex that is implicated in template remodeling. We showed previously that viral DNA-protein complexes released from infecting particles were sensitive to shearing after cross-linking with formaldehyde, presumably after transport of the genome into the nucleus. We report here the application of equilibrium-density gradient centrifugation to the analysis of the fate of these complexes. Most of the incoming protein VII was recovered in a form that was not cross-linked to viral DNA. This release of protein VII, as well as the binding of SET/TAF-Iβ and cellular transcription factors to the viral chromatin, did not require de novo viral gene expression. The distinct density profiles of viral DNA complexes containing protein VII, compared to those containing SET/TAF-Iβ or transcription factors, were consistent with the notion that the assembly of early viral chromatin requires both the association of SET/TAF-1β and the release of protein VII

  16. MRN1 implicates chromatin remodeling complexes and architectural factors in mRNA maturation

    DEFF Research Database (Denmark)

    Düring, Louis; Thorsen, Michael; Petersen, Darima

    2012-01-01

    A functional relationship between chromatin structure and mRNA processing events has been suggested, however, so far only a few involved factors have been characterized. Here we show that rsc nhp6¿¿ mutants, deficient for the function of the chromatin remodeling factor RSC and the chromatin....... Genetic interactions are observed between 2 µm-MRN1 and the splicing deficient mutants snt309¿, prp3, prp4, and prp22, and additional genetic analyses link MRN1, SNT309, NHP6A/B, SWI/SNF, and RSC supporting the notion of a role of chromatin structure in mRNA processing....

  17. DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance.

    Science.gov (United States)

    Rother, Magdalena B; van Attikum, Haico

    2017-10-05

    Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Authors.

  18. Epigenetic regulation of open chromatin in pluripotent stem cells

    Science.gov (United States)

    Kobayashi, Hiroshi; Kikyo, Nobuaki

    2014-01-01

    The recent progress in pluripotent stem cell research has opened new avenues of disease modeling, drug screening, and transplantation of patient-specific tissues that had been unimaginable until a decade ago. The central mechanism underlying pluripotency is epigenetic gene regulation; the majority of cell signaling pathways, both extracellular and cytoplasmic, eventually alter the epigenetic status of their target genes during the process of activating or suppressing the genes to acquire or maintain pluripotency. It has long been thought that the chromatin of pluripotent stem cells is globally open to enable the timely activation of essentially all genes in the genome during differentiation into multiple lineages. The current article reviews descriptive observations and the epigenetic machinery relevant to what is supposed to be globally open chromatin in pluripotent stem cells. This includes microscopic appearance, permissive gene transcription, chromatin remodeling complexes, histone modifications, DNA methylation, noncoding RNAs, dynamic movement of chromatin proteins, nucleosome accessibility and positioning, and long-range chromosomal interactions. Detailed analyses of each element, however, have revealed that the globally open chromatin hypothesis is not necessarily supported by some of the critical experimental evidence, such as genome-wide nucleosome accessibility and nucleosome positioning. Further understanding of the epigenetic gene regulation is expected to determine the true nature of the so-called globally open chromatin in pluripotent stem. PMID:24695097

  19. Riparian vegetation structure under desertification scenarios

    Science.gov (United States)

    Rosário Fernandes, M.; Segurado, Pedro; Jauch, Eduardo; Ferreira, M. Teresa

    2015-04-01

    Riparian areas are responsible for many ecological and ecosystems services, including the filtering function, that are considered crucial to the preservation of water quality and social benefits. The main goal of this study is to quantify and understand the riparian variability under desertification scenario(s) and identify the optimal riparian indicators for water scarcity and droughts (WS&D), henceforth improving river basin management. This study was performed in the Iberian Tâmega basin, using riparian woody patches, mapped by visual interpretation on Google Earth imagery, along 130 Sampling Units of 250 m long river stretches. Eight riparian structural indicators, related with lateral dimension, weighted area and shape complexity of riparian patches were calculated using Patch Analyst extension for ArcGis 10. A set of 29 hydrological, climatic, and hydrogeomorphological variables were computed, by a water modelling system (MOHID), using monthly meteorological data between 2008 and 2014. Land-use classes were also calculated, in a 250m-buffer surrounding each sampling unit, using a classification based system on Corine Land Cover. Boosted Regression Trees identified Mean-width (MW) as the optimal riparian indicator for water scarcity and drought, followed by the Weighted Class Area (WCA) (classification accuracy =0.79 and 0.69 respectively). Average Flow and Strahler number were consistently selected, by all boosted models, as the most important explanatory variables. However, a combined effect of hidrogeomorphology and land-use can explain the high variability found in the riparian width mainly in Tâmega tributaries. Riparian patches are larger towards Tâmega river mouth although with lower shape complexity, probably related with more continuous and almost monospecific stands. Climatic, hydrological and land use scenarios, singly and combined, were used to quantify the riparian variability responding to these changes, and to assess the loss of riparian

  20. Magnetic structures of erbium under high pressure

    DEFF Research Database (Denmark)

    Kawano, S.; Lebech, B.; Achiwa, N.

    1993-01-01

    Neutron diffraction studies of the magnetic structures of erbium metal at 4.5 K and 11.5 kbar hydrostatic pressure have revealed that the transition to a conical structure at low temperatures is suppressed and that the cycloidal structure, with modulation vector Q congruent-to (2/7 2pi/c)c persists...

  1. Electronic structure of Ca, Sr, and Ba under pressure.

    Science.gov (United States)

    Animalu, A. O. E.; Heine, V.; Vasvari, B.

    1967-01-01

    Electronic band structure calculations phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure electronic band structure calculations for fcc phase of Ca, Sr and Ba over wide range of atomic volumes under pressure

  2. Chromatin Remodeling and Plant Immunity.

    Science.gov (United States)

    Chen, W; Zhu, Q; Liu, Y; Zhang, Q

    Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance? © 2017 Elsevier Inc. All rights reserved.

  3. Response of masonry structure under impact load

    International Nuclear Information System (INIS)

    Makovicka, D.

    1993-01-01

    The paper deals with interaction of a short gaseous impact wave with a plate structure. Analyses of dynamic bending, depending on the parameters of the structure and the impact wave (i.e. the stress and displacement field produced by the resulting incident and reflected wave) have been made by FEM. The calculated data was based on the real material properties of this structure. Pressures greater than computed limit pressures result in the failure of the structure. The calculated and experimental data are compared. (author)

  4. Concurrent Structural Fatigue Damage Prognosis Under Uncertainty

    Science.gov (United States)

    2014-04-30

    Piascik, R.S., "Local Crack Closure Measurements: Development and Application of a Measurement System Using Computer Vision and a Far-Field Microscope...aircraft structural health monitoring. Structural Health Monitoring, 2002. 1(1): p. 41-61. 16. Constantin , N., S. Sorohan, and M. Gavan, Efficient and

  5. Maize histone H2B-mCherry: a new fluorescent chromatin marker for somatic and meiotic chromosome research.

    Science.gov (United States)

    Howe, Elizabeth S; Clemente, Thomas E; Bass, Hank W

    2012-06-01

    Cytological studies of fluorescent proteins are rapidly yielding insights into chromatin structure and dynamics. Here we describe the production and cytological characterization of new transgenic maize lines expressing a fluorescent histone fusion protein, H2B-mCherry. The transgene is expressed under the control of the maize ubiquitin1 promoter, including its first exon and intron. Polymerase chain reaction-based genotyping and root-tip microscopy showed that most of the lines carrying the transgene also expressed it, producing bright uniform staining of nuclei. Further, plants showing expression in root tips at the seedling stage also showed expression during meiosis, late in the life cycle. Detailed high-resolution three-dimensional imaging of cells and nuclei from various somatic and meiotic cell types showed that H2B-mCherry produced remarkably clear images of chromatin and chromosome fiber morphology, as seen in somatic, male meiotic prophase, and early microgametophyte cells. H2B-mCherry also yielded distinct nucleolus staining and was shown to be compatible with fluorescence in situ hybridization. We found several instances where H2B-mCherry was superior to DAPI as a generalized chromatin stain. Our study establishes these histone H2B-mCherry lines as new biological reagents for visualizing chromatin structure, chromosome morphology, and nuclear dynamics in fixed and living cells in a model plant genetic system.

  6. A Poly-ADP-Ribose Trigger Releases the Auto-Inhibition of a Chromatin Remodeling Oncogene

    DEFF Research Database (Denmark)

    Singh, Hari R; Nardozza, Aurelio P; Möller, Ingvar R

    2017-01-01

    DNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to DNA-damage-mediated PARP1 induction. We show that the interaction of the ALC1 macrodomain......-macrodomain interactions, promotes an ungated conformation, and activates the remodeler's ATPase. ALC1 fragments lacking the regulatory macrodomain relax chromatin in vivo without requiring PARP1 activation. Further, the ATPase restricts the macrodomain's interaction with PARP1 under non-DNA damage conditions. Somatic...... cancer mutants disrupt ALC1's auto-inhibition and activate chromatin remodeling. Our data show that the NAD+-metabolite and nucleic acid PAR triggers ALC1 to drive chromatin relaxation. Modular allostery in this oncogene tightly controls its robust, DNA-damage-dependent activation....

  7. Restoring chromatin after replication: How new and old histone marks come together

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    In dividing cells genome stability and function rely on faithful transmission of both DNA sequence and its organization into chromatin. In the course of DNA replication chromatin undergoes transient genome-wide disruption followed by restoration on new DNA. This involves tight coordination of DNA...... replication and chromatin assembly processes in time and space. Dynamic recycling and de novo deposition of histones are fundamental for chromatin restoration. Histone post-translational modifications (PTMs) are thought to have a causal role in establishing distinct chromatin structures. Here we discuss PTMs...... present on new and parental histones and how they influence genome stability and restoration of epigenetically defined domains. Newly deposited histones must change their signature in the process of chromatin restoration, this may occur in a step-wise fashion involving replication-coupled processes...

  8. Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection.

    Science.gov (United States)

    Rogge, Ryan A; Hansen, Jeffrey C

    2015-01-01

    Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system. © 2015 Elsevier Inc. All rights reserved.

  9. Superconductivity and structure of gallium under nanoconfinement

    Energy Technology Data Exchange (ETDEWEB)

    Charnaya, E V; Tien, Cheng; Lee, Min Kai [Department of Physics, National Cheng Kung University, Tainan 70101, Taiwan (China); Kumzerov, Yu A [A F Ioffe Physico-Technical Institute RAS, St Petersburg, 194021 (Russian Federation)

    2009-11-11

    Superconductivity and crystalline structure were studied for two nanocomposites consisting of gallium loaded porous glasses with different pore sizes. The superconducting transition temperatures were found to differ from those in known bulk gallium modifications. The transition temperatures 7.1 and 6.7 K were ascribed to two new confined gallium structures, iota- and kappa-Ga, observed by synchrotron radiation x-ray powder diffraction. The evolution of superconductivity on decreasing the pore filling with gallium was also studied.

  10. A Long-Distance Chromatin Affair

    NARCIS (Netherlands)

    Denker, Annette; de Laat, Wouter

    2015-01-01

    Changes in transcription factor binding sequences result in correlated changes in chromatin composition locally and at sites hundreds of kilobases away. New studies demonstrate that this concordance is mediated via spatial chromatin interactions that constitute regulatory modules of the human

  11. Guarding against Collateral Damage during Chromatin Transactions

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Lukas, Jiri

    2013-01-01

    Signal amplifications are vital for chromatin function, yet they also bear the risk of transforming into unrestrained, self-escalating, and potentially harmful responses. Examples of inbuilt limitations are emerging, revealing how chromatin transactions are confined within physiological boundaries....

  12. Concrete structures under impact loading: general aspects

    Directory of Open Access Journals (Sweden)

    Cornelia Baeră

    2016-09-01

    Full Text Available Dynamic loading conditions distress the structural integrity of a structure differently than the static ones. Such actions transfer high rate strains and instant energy waves to the structure, inducing the possibility of imminent collapse and casualties as a direct consequence. In the latest years, considering the dramatic increase of terrorist threats and global warming, the structural safety criteria imply more than ever the need to withstand this kind of loading (e.g., missiles and blast, projectiles, strong winds, tornados and earthquakes in addition to the static ones. The aim of this paper is to provide a general overview with regard to impact loading in terms of defining the phenomenon from physical and mechanical perspective, its complex local or global effect on the targeted structure, relevant material characteristics, main research approaches, namely theoretical studies and experimental procedures developed for improving the predictability of the dynamic loads and their effects. New directions in developing superior cementitious composites, with better characteristics in terms of dynamic loading performance are also emphasized.

  13. Multiplant strategy under core-periphery structure

    OpenAIRE

    Tsubota, Kenmei

    2012-01-01

    A typical implicit assumption on monopolistic competition models for trade and economic geography is that firms can produce and sell only at one place. This paper fallows endogenous determination of the number of plants in a new economic geography model and examine the stable outcomes of organization choice between single-plant and multi-plant in two regions. We explicitly consider the firms' trade-off between larger economies of scale under single plant configuration and the saving in interr...

  14. Anatomic Pathology Structured Report Under FHIR

    Directory of Open Access Journals (Sweden)

    T. Schrader

    2016-06-01

    A first FHIR based structured report was created and validated against a public available FHIR server (http:// spark.furore.com/fhir. FHIR allows to create different document structures for any type of document: a document only with inside resources or a document with inside and outside (linked resources. Our example consists of resources embedded in the main document file and linked resources. The FHIR document allows a great flexibility related to the document resources as well as data files. It is possible FHIR documents as XML, JSON (JavaScript Object Notation or RDF (Resource Description Framework. Due to these various possibilities FHIR documents can be used in a web based application context easily.

  15. Prediction of highly expressed genes in microbes based on chromatin accessibility

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2007-01-01

    BACKGROUND: It is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed...

  16. Materials and structures under shock and impact

    CERN Document Server

    Bailly, Patrice

    2013-01-01

    In risk studies, engineers often have to consider the consequences of an accident leading to a shock on a construction. This can concern the impact of a ground vehicle or aircraft, or the effects of an explosion on an industrial site.This book presents a didactic approach starting with the theoretical elements of the mechanics of materials and structures, in order to develop their applications in the cases of shocks and impacts. The latter are studied on a local scale at first. They lead to stresses and strains in the form of waves propagating through the material, this movement then extending

  17. Nucleolar chromatin organization at different activities of soybean root meristematic cell nucleoli.

    Science.gov (United States)

    Stępiński, Dariusz

    2013-06-01

    Nucleolar chromatin, including nucleolus-associated chromatin as well as active and inactive condensed ribosomal DNA (rDNA) chromatin, derives mostly from secondary constrictions known as nucleolus organizer regions containing rDNA genes on nucleolus-forming chromosomes. This chromatin may occupy different nucleolar positions being in various condensation states which may imply different rDNA transcriptional competence. Sections of nucleoli originating from root meristematic cells of soybean seedlings grown at 25 °C (the control), then subjected to chilling stress (10 °C), and next transferred again to 25 °C (the recovery) were used to measure profile areas occupied by nucleolar condensed chromatin disclosed with sodium hydroxide methylation-acetylation plus uranyl acetate technique. The biggest total area of condensed chromatin was found in the nucleoli of chilled plants, while the smallest was found in those of recovered plants in relation to the amounts of chromatin in the control nucleoli. The condensed nucleolar chromatin, in the form of different-sized and different-shaped clumps, was mainly located in fibrillar centers. One can suppose that changes of condensed rDNA chromatin amounts might be a mechanism controlling the number of transcriptionally active rDNA genes as the nucleoli of plants grown under these experimental conditions show different transcriptional activity and morphology.

  18. Histone modifications influence mediator interactions with chromatin

    Science.gov (United States)

    Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.

    2011-01-01

    The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760

  19. Factor structure underlying components of allostatic load.

    Directory of Open Access Journals (Sweden)

    Jeanne M McCaffery

    Full Text Available Allostatic load is a commonly used metric of health risk based on the hypothesis that recurrent exposure to environmental demands (e.g., stress engenders a progressive dysregulation of multiple physiological systems. Prominent indicators of response to environmental challenges, such as stress-related hormones, sympatho-vagal balance, or inflammatory cytokines, comprise primary allostatic mediators. Secondary mediators reflect ensuing biological alterations that accumulate over time and confer risk for clinical disease but overlap substantially with a second metric of health risk, the metabolic syndrome. Whether allostatic load mediators covary and thus warrant treatment as a unitary construct remains to be established and, in particular, the relation of allostatic load parameters to the metabolic syndrome requires elucidation. Here, we employ confirmatory factor analysis to test: 1 whether a single common factor underlies variation in physiological systems associated with allostatic load; and 2 whether allostatic load parameters continue to load on a single common factor if a second factor representing the metabolic syndrome is also modeled. Participants were 645 adults from Allegheny County, PA (30-54 years old, 82% non-Hispanic white, 52% female who were free of confounding medications. Model fitting supported a single, second-order factor underlying variance in the allostatic load components available in this study (metabolic, inflammatory and vagal measures. Further, this common factor reflecting covariation among allostatic load components persisted when a latent factor representing metabolic syndrome facets was conjointly modeled. Overall, this study provides novel evidence that the modeled allostatic load components do share common variance as hypothesized. Moreover, the common variance suggests the existence of statistical coherence above and beyond that attributable to the metabolic syndrome.

  20. Chromatin remodelling: the industrial revolution of DNA around histones.

    Science.gov (United States)

    Saha, Anjanabha; Wittmeyer, Jacqueline; Cairns, Bradley R

    2006-06-01

    Chromatin remodellers are specialized multi-protein machines that enable access to nucleosomal DNA by altering the structure, composition and positioning of nucleosomes. All remodellers have a catalytic ATPase subunit that is similar to known DNA-translocating motor proteins, suggesting DNA translocation as a unifying aspect of their mechanism. Here, we explore the diversity and specialization of chromatin remodellers, discuss how nucleosome modifications regulate remodeller activity and consider a model for the exposure of nucleosomal DNA that involves the use of directional DNA translocation to pump 'DNA waves' around the nucleosome.

  1. Oxidative stress signaling to chromatin in health and disease

    KAUST Repository

    Kreuz, Sarah

    2016-06-20

    Oxidative stress has a significant impact on the development and progression of common human pathologies, including cancer, diabetes, hypertension and neurodegenerative diseases. Increasing evidence suggests that oxidative stress globally influences chromatin structure, DNA methylation, enzymatic and non-enzymatic post-translational modifications of histones and DNA-binding proteins. The effects of oxidative stress on these chromatin alterations mediate a number of cellular changes, including modulation of gene expression, cell death, cell survival and mutagenesis, which are disease-driving mechanisms in human pathologies. Targeting oxidative stress-dependent pathways is thus a promising strategy for the prevention and treatment of these diseases. We summarize recent research developments connecting oxidative stress and chromatin regulation.

  2. Design methods for structures under thermal ratchet

    International Nuclear Information System (INIS)

    Branca, T.R.; McLean, J.L.

    1975-01-01

    Previous work on the thermal ratchet analysis of a simple pipe is extended to the case of an intersection of a pipe with a spherical shell. The chosen nozzle configuration is subjected to an internal pressure which remains constant, and a cyclic thermal transient which is representative of the type of transient that might be expected for components of a LMFBR. A number of cross-sections through the nozzle were examined, each yielding a different combination of elastic primary and secondary stress. These stresses, together with their associated cyclic strain growth, as determined from an elastic-plastic-creep analysis of the nozzle, were then plotted on a Miller or Bree-type diagram. Thus, a number of points, one for each cross-section considered, were available for comparison with the data obtained from the ratchet analysis of simple pipe sections. Both the elastic and inelastic analyses on the nozzle were performed using the finite element method of structural analysis of the ANSYS computer code. The pipe ratchetting cases were computed using the Oak Ridge National Laboratory PLACRE code. For a simple pipe ratchet case, a brief comparison is given between the version of ANSYS used in this study, the ANSYS version used in previous work and PLACRE code. The three programs did not yield identical results. Further study is needed to resolve the discrepancies that were observed. The results of the comparison between the nozzle ratchet and pipe ratchet solutions indicate that reasonable predictions can be made for the nozzle ratchet strains based on elastic parameters and design curves developed from pipe ratchetting solutions. (author)

  3. Trichostatin A induced histone acetylation causes decondensation of interphase chromatin.

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Wachsmuth (Malte); M. Frank-Stöhr (Monika); M. Stöhr (Michael); C.P. Bacher (Christian); K. Rippe (Karsten)

    2004-01-01

    textabstractThe effect of trichostatin A (TSA)-induced histone acetylation on the interphase chromatin structure was visualized in vivo with a HeLa cell line stably expressing histone H2A, which was fused to enhanced yellow fluorescent protein. The globally increased histone acetylation caused a

  4. Pharmacologic Targeting of Chromatin Modulators As Therapeutics of Acute Myeloid Leukemia.

    Science.gov (United States)

    Lu, Rui; Wang, Gang Greg

    2017-01-01

    Acute myeloid leukemia (AML), a common hematological cancer of myeloid lineage cells, generally exhibits poor prognosis in the clinic and demands new treatment options. Recently, direct sequencing of samples from human AMLs and pre-leukemic diseases has unveiled their mutational landscapes and significantly advanced the molecular understanding of AML pathogenesis. The newly identified recurrent mutations frequently "hit" genes encoding epigenetic modulators, a wide range of chromatin-modifying enzymes and regulatory factors involved in gene expression regulation, supporting aberration of chromatin structure and epigenetic modification as a main oncogenic mechanism and cancer-initiating event. Increasing body of evidence demonstrates that chromatin modification aberrations underlying the formation of blood cancer can be reversed by pharmacological targeting of the responsible epigenetic modulators, thus providing new mechanism-based treatment strategies. Here, we summarize recent advances in development of small-molecule inhibitors specific to chromatin factors and their potential applications in the treatment of genetically defined AMLs. These compounds selectively inhibit various subclasses of "epigenetic writers" (such as histone methyltransferases MLL/KMT2A, G9A/KMT1C, EZH2/KMT6A, DOT1L/KMT4, and PRMT1), "epigenetic readers" (such as BRD4 and plant homeodomain finger proteins), and "epigenetic erasers" (such as histone demethylases LSD1/KDM1A and JMJD2C/KDM4C). We also discuss about the molecular mechanisms underpinning therapeutic effect of these epigenetic compounds in AML and favor their potential usage for combinational therapy and treatment of pre-leukemia diseases.

  5. Pharmacologic Targeting of Chromatin Modulators As Therapeutics of Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Rui Lu

    2017-10-01

    Full Text Available Acute myeloid leukemia (AML, a common hematological cancer of myeloid lineage cells, generally exhibits poor prognosis in the clinic and demands new treatment options. Recently, direct sequencing of samples from human AMLs and pre-leukemic diseases has unveiled their mutational landscapes and significantly advanced the molecular understanding of AML pathogenesis. The newly identified recurrent mutations frequently “hit” genes encoding epigenetic modulators, a wide range of chromatin-modifying enzymes and regulatory factors involved in gene expression regulation, supporting aberration of chromatin structure and epigenetic modification as a main oncogenic mechanism and cancer-initiating event. Increasing body of evidence demonstrates that chromatin modification aberrations underlying the formation of blood cancer can be reversed by pharmacological targeting of the responsible epigenetic modulators, thus providing new mechanism-based treatment strategies. Here, we summarize recent advances in development of small-molecule inhibitors specific to chromatin factors and their potential applications in the treatment of genetically defined AMLs. These compounds selectively inhibit various subclasses of “epigenetic writers” (such as histone methyltransferases MLL/KMT2A, G9A/KMT1C, EZH2/KMT6A, DOT1L/KMT4, and PRMT1, “epigenetic readers” (such as BRD4 and plant homeodomain finger proteins, and “epigenetic erasers” (such as histone demethylases LSD1/KDM1A and JMJD2C/KDM4C. We also discuss about the molecular mechanisms underpinning therapeutic effect of these epigenetic compounds in AML and favor their potential usage for combinational therapy and treatment of pre-leukemia diseases.

  6. Do chromatin changes around a nascent double strand DNA break spread spherically into linearly non-adjacent chromatin?

    Science.gov (United States)

    Savic, Velibor

    2013-01-01

    In the last decade, a lot has been done in elucidating the sequence of events that occur at the nascent double strand DNA break. Nevertheless, the overall structure formed by the DNA damage response (DDR) factors around the break site, the repair focus, remains poorly understood. Although most of the data presented so far only address events that occur in chromatin in cis around the break, there are strong indications that in mammalian systems it may also occur in trans, analogous to the recent findings showing this if budding yeast. There have been attempts to address the issue but the final proof is still missing due to lack of a proper experimental system. If found to be true, the spatial distribution of DDR factors would have a major impact on the neighboring chromatin both in cis and in trans, significantly affecting local chromatin function; gene transcription and potentially other functions.

  7. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Jenna [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); Ekwall, Karl, E-mail: karl.ekwall@ki.se [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); School of Life Sciences, University College Sodertorn, NOVUM, Huddinge (Sweden)

    2010-05-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  8. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    International Nuclear Information System (INIS)

    Persson, Jenna; Ekwall, Karl

    2010-01-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  9. Electronic structure and optical properties of AIN under high pressure

    International Nuclear Information System (INIS)

    Li Zetao; Dang Suihu; Li Chunxia

    2011-01-01

    We have calculated the electronic structure and optical properties of Wurtzite structure AIN under different high pressure with generalized gradient approximation (GGA) in this paper. The total energy, density of state, energy band structure and optical absorption and reflection properties under high pressure are calculated. By comparing the changes of the energy band structure, we obtained AIN phase transition pressure for 16.7 GPa, which is a direct band structure transforming to an indirect band structure. Meanwhile, according to the density of states distribution and energy band structure, we analyzed the optical properties of AIN under high-pressure, the results showed that the absorption spectra moved from low-energy to high-energy. (authors)

  10. Empirical Analysis of Farm Credit Risk under the Structure Model

    Science.gov (United States)

    Yan, Yan

    2009-01-01

    The study measures farm credit risk by using farm records collected by Farm Business Farm Management (FBFM) during the period 1995-2004. The study addresses the following questions: (1) whether farm's financial position is fully described by the structure model, (2) what are the determinants of farm capital structure under the structure model, (3)…

  11. Physical and chemical properties of chromatin and its fragments formed in the rat thymus during postirradiation autolysis and under the influence of DNA-ase and protease on DNP preparations

    International Nuclear Information System (INIS)

    Ermolaeva, N.V.; Vodolazskaya, N.A.

    1978-01-01

    It has been shown that the thymus chromatin degradation 2-8 hr after irradiation is followed by its cross-splitting and accumulation of several types of fragments differing in the degree of DNA association with the protein. Participation of proteases in the formation of fragments is hardly probable. Acid DNAase is involved in the autolysis perhaps in his maximum later 6 hr after irradiation

  12. Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins.

    Science.gov (United States)

    Culurgioni, Simone; Muñoz, Inés G; Moreno, Alberto; Palacios, Alicia; Villate, Maider; Palmero, Ignacio; Montoya, Guillermo; Blanco, Francisco J

    2012-03-30

    The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.

  13. Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

    Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for

  14. High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation

    DEFF Research Database (Denmark)

    Mouaikel, John; Causse, Sébastien Z; Rougemaille, Mathieu

    2013-01-01

    The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes...... (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single......-molecule fluorescence insitu hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase...

  15. Thermal behavior of spatial structures under solar irradiation

    International Nuclear Information System (INIS)

    Liu, Hongbo; Liao, Xiangwei; Chen, Zhihua; Zhang, Qian

    2015-01-01

    The temperature, particularly the non-uniform temperature under solar irradiation, is the main load for large-span steel structures. Due the shortage of in-site temperature test in previous studies, an in-site test was conducted on the large-span steel structures under solar irradiation, which was covered by glass roof and light roof, to gain insight into the temperature distribution of steel members under glass roof or light roof. A numerical method also was presented and verified to forecast the temperature of steel member under glass roof or light roof. Based on the on-site measurement and numerical analyses conducted, the following conclusions were obtained: 1) a remarkable temperature difference exists between the steel member under glass roof and that under light roof, 2) solar irradiation has a significant effect on the temperature distribution and thermal behavior of large-span spatial structures, 3) negative thermal load is the controlling factor for member stress, and the positive thermal load is the controlling factor for nodal displacement. - Highlights: • Temperature was measured for a steel structures under glass roof and light roof. • Temperature simulation method was presented and verified. • The thermal behavior of steel structures under glass or light roof was presented

  16. Induction of stable protein-deoxyribonucleic acid adducts in Chinese hamster cell chromatin by ultraviolet light

    International Nuclear Information System (INIS)

    Strniste, G.F.; Rall, S.C.

    1976-01-01

    Ultraviolet (uv)-light-mediated formation of protein-DNA adducts in Chinese hamster cell chromatin was investigated in an attempt to compare chromatin alterations induced in vitro with those observed in vivo. Three independent methods of analysis indicated stable protein-DNA associations: a membrane filter assay which retained DNA on the filter in the presence of high salt-detergent; a Sepharose 4B column assay in which protein eluted coincident with DNA; and a CsCl density gradient equilibrium assay which showed both protein and DNA banding at densities other than their respective native densities. Treatment of the irradiated chromatin with DNase provided further evidence that protein--DNA and not protein-protein adducts were being observed in the column assay. There is a fluence-dependent response of protein-DNA adduct formation when the chromatin is irradiated at low ionic strength and is linear for protein over the range studied. When the chromatin is exposed to differing conditions of pH, ionic strength, or divalent metal ion concentration, the quantity of adduct formed upon uv irradiation varies. Susceptibility to adduct formation can be partially explained in terms of the condensation state of the chromatin and other factors such as rearrangement, denaturation, and dissociation of the chromatin components. Besides providing information on the biological significance of these types of uv-induced lesions, this technique may be useful as a probe of chromatin structure

  17. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    International Nuclear Information System (INIS)

    Lesne, Annick; Victor, Jean–Marc; Bécavin, Christophe

    2012-01-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity. (perspective)

  18. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    Science.gov (United States)

    Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc

    2012-02-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.

  19. Effect of benzimidazol-derivatives on the DNA-protein binding formation after UV-radiation of chromatin

    International Nuclear Information System (INIS)

    Mil', E.M.; Binyukov, V.I.; Zhil'tsova, V.M.; Stolyarova, L.G.; Kuznetsov, Yu.V.

    1991-01-01

    Effect of benzimidazol-derivatives on the DNA-protein binding formation was studied after UV-radiation of chromatin. These derivatives were shown to protect chromatin from UV-induced DNA-protein binding formation. Structural analog contained two aminomethyl residuals sensibilized additional binding formation in chromatin. Results suggested, that benzimidazol interacted with DNA, while aminomethyl groups interacted with protein and sensibilized binding of DNA, whilt aminomethyl groups interacted with protein and sensibilized binding of DNA with histone H1

  20. The architects of crenarchaeal chromatin : A biophysical characterization of chromatin proteins from Sulfolobus solfataricus

    NARCIS (Netherlands)

    Driessen, Rosalie Paula Catharina

    2014-01-01

    Understanding of chromatin organization and compaction in Archaea is currently limited. The genome of several megabasepairs long is folded by a set of small chromatin proteins to fit into the micron-sized cell. A first step in understanding archaeal chromatin organization is to study the action of

  1. Reliability analysis of structures under periodic proof tests in service

    Science.gov (United States)

    Yang, J.-N.

    1976-01-01

    A reliability analysis of structures subjected to random service loads and periodic proof tests treats gust loads and maneuver loads as random processes. Crack initiation, crack propagation, and strength degradation are treated as the fatigue process. The time to fatigue crack initiation and ultimate strength are random variables. Residual strength decreases during crack propagation, so that failure rate increases with time. When a structure fails under periodic proof testing, a new structure is built and proof-tested. The probability of structural failure in service is derived from treatment of all the random variables, strength degradations, service loads, proof tests, and the renewal of failed structures. Some numerical examples are worked out.

  2. Chromatin-bound RNA and the neurobiology of psychiatric disease.

    Science.gov (United States)

    Tushir, J S; Akbarian, S

    2014-04-04

    A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

    Fog, Cathrine K; Jensen, Klaus T; Lund, Anders Henrik

    2007-01-01

    -despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic...... alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins....

  4. A microscopic analysis of Arabidopsis chromatin

    NARCIS (Netherlands)

    Willemse, J.J.

    2007-01-01

    Genetic information of eukaryotic organisms is stored as DNA in the nuclei of their cells. Nuclear DNA is associated with several proteins, which together form chromatin. The most abundant chromatin proteins arehistones,they arrange the initial packaging step of the DNA. DNA

  5. [The influence of N-, S-containing chinasolone derivatives (NC-224) on the biochemical and physicochemical parameters of membrane endoplasmatic reticulum and nuclear chromatine fractions of rats liver cells in conditions of its injury by tetrachloromethane].

    Science.gov (United States)

    Gubs'kyî, Iu I; Goriushko, G G; Belenichev, I F; Kovalenko, S I; Litvinova, N V; Marchenko, O M; Kurapova, T M; Babenko, L P; Velychko, O M

    2010-01-01

    Using biochemical and physicochemical methods of investigation in vivo, the effect of the substance NC-224, N-, S-chinasolone-derivative, on the lipoperoxidation activity in rat liver endoplasmatic reticulum membranes and nuclear chromatin fractions under tetrachloromethane intoxication have been studied. It was shown that NC-224 has pronounced antioxidant activity which is the biochemical basis of the substance membrane- and genome-protective effects and its ability to restore physicochemical properties of the surface and hydrophobic zones of hepatocyte membranes and structural parameter nuclear chromatin fractions in the conditions of chemical liver injury.

  6. The integrity of cracked structures under thermal loading

    International Nuclear Information System (INIS)

    Townley, C.H.A.

    1976-01-01

    Previous work by Dowling and Townley on the load-carrying capacity of a cracked structure is extended so that quantitative predictions can be made about failure under thermal loading. Residual stresses can be dealt with in the same way as thermal stresses. It is shown that the tolerance of the structure to thermal stress can be quantified in terms of a parameter which defines the state of the structure. This state parameter can be deduced from the calculated performance of the structure when subjected to an external load. (author)

  7. Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; John, Sam

    2011-01-01

    hypersensitive site analysis to investigate the genome-wide changes in chromatin structure that accompany the binding of adipogenic transcription factors. These analyses revealed a dramatic and dynamic modulation of the chromatin landscape during the first hours of adipocyte differentiation that coincides...... and chromatin remodelling and is required for their establishment. Furthermore, a subset of early remodelled C/EBP-binding sites persists throughout differentiation and is later occupied by PPARγ, indicating that early C/EBP family members, in addition to their well-established role in activation of PPARγ...

  8. Numerical Analysis of Vibrations of Structures under Moving Inertial Load

    CERN Document Server

    Bajer, Czeslaw I

    2012-01-01

    Moving inertial loads are applied to structures in civil engineering, robotics, and mechanical engineering. Some fundamental books exist, as well as thousands of research papers. Well known is the book by L. Frýba, Vibrations of Solids and Structures Under Moving Loads, which describes almost all problems concerning non-inertial loads. This book presents broad description of numerical tools successfully applied to structural dynamic analysis. Physically we deal with non-conservative systems. The discrete approach formulated with the use of the classical finite element method results in elemental matrices, which can be directly added to global structure matrices. A more general approach is carried out with the space-time finite element method. In such a case, a trajectory of the moving concentrated parameter in space and time can be simply defined. We consider structures described by pure hyperbolic differential equations such as strings and structures described by hyperbolic-parabolic differential equations ...

  9. Structural Analysis of Cabinet Support under Static and Seismic Loads

    International Nuclear Information System (INIS)

    Jung, Kwangsub; Lee, Sangjin; Oh, Jinho

    2014-01-01

    The cabinet support consists of frames including steel channels and steel square tubes. Four tap holes for screw bolts are located on the support frame of a steel channel to fix the cabinet on the support. The channels and square tubes are assembled by welded joints. The cabinet supports are installed on the outer walls of the reactor concrete island. The KEPIC code, MNF, is used for the design of the cabinet support. In this work, the structural integrity of the cabinet support is analyzed under consideration of static and seismic loads. A 3-D finite element model of the cabinet support was developed. The structural integrity of the cabinet support under postulated service loading conditions was evaluated through a static analysis, modal analysis, and response spectrum analysis. From the structural analysis results, it was concluded that the structural integrity of the cabinet support is guaranteed

  10. Circular chromatin complexes in human lymphocytes high-resolution autoradiography

    International Nuclear Information System (INIS)

    Becak, M.L.; Fukuda-Pizzocaro, K.; Santos, R. de C.S. dos; Brunner, O.

    1985-01-01

    Transcriptionally active chromatin fibers were observed in chromosomes presenting the loops/scaffold configuration. The active fibers showed altered nucleosomes and presented multiforked aspects which led to the formation of ring complexes. The ribonucleoprotein transcripts (RNP) appeared as networks of 0.1 μm or multiples tandemly disposed along the fiber. It is suggested that the ring complexes belong to the human genome. The possibility that these circular structures come from a prokaryote is also considered. (author) [pt

  11. Introducing enteral feeding induces intestinal subclinical inflammation and respective chromatin changes in preterm pigs

    DEFF Research Database (Denmark)

    Willems, Rhea; Krych, Lukasz; Rybicki, Verena

    2015-01-01

    AIM: To analyze how enteral food introduction affects intestinal gene regulation and chromatin structure in preterm pigs. MATERIALS & METHODS: Preterm pigs were fed parenteral nutrition plus/minus slowly increasing volumes of enteral nutrition. Intestinal gene-expression and chromatin structure......; no significant differences for colostrum) with corresponding decondensed chromatin configurations. On histology this correlated with mild mucosal lesions, particularly in formula-fed pigs. In CaCo-2 cells, histone hyperacetylation led to a marked increase in TLR4 mRNA and increased IL8 expression upon...... stimulation with lipopolysaccharide (median: 7.0; interquartile range: 5.63-8.85) compared with naive cells (median 4.2; interquartile range: 2.45-6.33; p = 0.03). CONCLUSION: Enteral feeding, particular with formula, induces subclinical inflammation in the premature intestine and more open chromatin...

  12. Two independent modes of chromatin organization revealed by cohesin removal.

    Science.gov (United States)

    Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois

    2017-11-02

    Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.

  13. Safety margins associated with containment structures under dynamic loading

    International Nuclear Information System (INIS)

    Lu, S.C.

    1978-01-01

    A technical basis for assessing the true safety margins of containment structures involved with MARK I boiling water reactor reevaluation activities is presented. It is based on the results of a plane-strain, large displacement, elasto-plastic, finite-element analysis of a thin cylindrical shell subjected to external and internal pressure pulses. An analytical procedure is presented for estimating the ultimate load capacity of the thin shell structure, and subsequently, for quantifying the design margins of safety for the type of loads under consideration. For defining failure of structures, a finite strain failure criterion is derived that accounts for multiaxiality effects

  14. Studies on the Chromatin Isolated from the Organs of Animals Received Whole-body X-ray Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Han, Su Nam [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1967-09-15

    Within experimental chromatin, the total protein: DNA ratio did not vary in the same organs of control and irradiated rats. However, the amount of RNA and total protein associated with the DNA varied considerably among the different types of chromatin. In particular, the content of chromatin was the highest in the irradiated tissue, and the lowest in the chromatin control tissue. RNA and total protein ratio of chromatins from brain, liver, testis and spleen declined with experimental organs. 2) There was the same quantitative relationship between the amount of RNA and the amount histone-protein associated with DNA in each chromatin. 3) RNA:DNA ratio of chromatin showed a 1.5-2 times increase in the irradiated organs except brain. However, RNA:DNA ratio was decreased in chromatin by irradiation. 4) Histone-protein: Residual protein ratio was greatly varied among the organs. However, the effect was not found by irradiation. 5) Priming activity of chromatins showed a higher value in testis and the activity was greater in organs with higher metabolic activity. 6) Inhibition of Actinomycin D observable in chromatin for testis, liver, spleen and brain declined without relationship between irradiated and non-irradiated conditions. Ammonium sulfate in DNA of chromatin from histone showed increased priming activity with dissociation by Electrostatics. It may give different effect of ammonium sulfate on stimulation by property of chromatins. 7) It is suggested that the results support a proposal that the higher sensitivity of radioactive in testis, spleen by irradiated showed a increase and decrease lower-sensitivity of radioactive from brain, liver than did priming activity under the radioactive conditions.

  15. Studies on the Chromatin Isolated from the Organs of Animals Received Whole-body X-ray Irradiation

    International Nuclear Information System (INIS)

    Han, Su Nam

    1967-01-01

    Within experimental chromatin, the total protein: DNA ratio did not vary in the same organs of control and irradiated rats. However, the amount of RNA and total protein associated with the DNA varied considerably among the different types of chromatin. In particular, the content of chromatin was the highest in the irradiated tissue, and the lowest in the chromatin control tissue. RNA and total protein ratio of chromatins from brain, liver, testis and spleen declined with experimental organs. 2) There was the same quantitative relationship between the amount of RNA and the amount histone-protein associated with DNA in each chromatin. 3) RNA:DNA ratio of chromatin showed a 1.5-2 times increase in the irradiated organs except brain. However, RNA:DNA ratio was decreased in chromatin by irradiation. 4) Histone-protein: Residual protein ratio was greatly varied among the organs. However, the effect was not found by irradiation. 5) Priming activity of chromatins showed a higher value in testis and the activity was greater in organs with higher metabolic activity. 6) Inhibition of Actinomycin D observable in chromatin for testis, liver, spleen and brain declined without relationship between irradiated and non-irradiated conditions. Ammonium sulfate in DNA of chromatin from histone showed increased priming activity with dissociation by Electrostatics. It may give different effect of ammonium sulfate on stimulation by property of chromatins. 7) It is suggested that the results support a proposal that the higher sensitivity of radioactive in testis, spleen by irradiated showed a increase and decrease lower-sensitivity of radioactive from brain, liver than did priming activity under the radioactive conditions.

  16. Role of chromatin structure in telomere maintenance

    Czech Academy of Sciences Publication Activity Database

    Kunická, Zuzana; Muselíková Polanská, Eva; Dvořáčková, Martina; Štros, Michal; Fajkus, Jiří

    2008-01-01

    Roč. 28, 5C (2008), s. 193 ISSN 0250-7005. [Eighth International Conference of Anticancer Research. 17.10.2008-22.10.2008, Kos] R&D Projects: GA ČR(CZ) GA204/08/1530 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : telomeres * epigenetics * heterochromatin Subject RIV: BO - Biophysics

  17. Behaviour of cellular structures with fluid fillers under impact loading

    Directory of Open Access Journals (Sweden)

    Matej Vesenjak

    2007-03-01

    Full Text Available The paper investigates the behaviour of closed- and open-cell cellular structures under uniaxial impact loading by means of computational simulations using the explicit nonlinear finite element code LS-DYNA. Simulations also consider the influence of pore fillers and the base material strain rate sensitivity. The behaviour of closed-cell cellular structure has been evaluated with use of the representative volume element, where the influence of residual gas inside the closed pores has been studied. Open- cell cellular structure was modelled as a whole to properly account for considered fluid flow through the cells, which significantly influences macroscopic behaviour of the cellular structure. The fluid has been modelled by applying a meshless Smoothed Particle Hydrodynamics (SPH method. Parametric computational simulations provide grounds for optimization of cellular structures to satisfy different requirements, which makes them very attractive for use in general engineering applications.

  18. Reliability analysis of RC containment structures under combined loads

    International Nuclear Information System (INIS)

    Hwang, H.; Reich, M.; Kagami, S.

    1984-01-01

    This paper discusses a reliability analysis method and load combination design criteria for reinforced concrete containment structures under combined loads. The probability based reliability analysis method is briefly described. For load combination design criteria, derivations of the load factors for accidental pressure due to a design basis accident and safe shutdown earthquake (SSE) for three target limit state probabilities are presented

  19. Assessing the performance of reinforced concrete structures under impact loads

    International Nuclear Information System (INIS)

    Sharma, Akanshu; Reddy, G.R.; Vaze, K.K.; Ozbolt, Josko; Hofmann, J.

    2011-01-01

    Reinforced concrete (RC) structures housing nuclear facilities must qualify against much stringent requirements of operating and accidental loads than conventional structures. One such accidental load that must be considered while assessing the performance of safety related RC structures is impact load. It is known that the behavior of concrete/reinforced concrete structures is strongly influenced by the loading rate. The RC structural members subjected to impact loads behave quite differently as compared to the same subjected to quasi-static loading due to the strain-rate influence on strength, stiffness, and ductility as well as to the activation of inertia forces. Moreover, for concrete structures, which exhibit damage and fracture phenomena, the failure mode and cracking pattern depend significantly on loading rate. In general, there is a tendency that with the increase of loading rate the failure mode changes from mode-I to mixed mode. In order to assess the performance of existing structures against impact loads that may be generated mainly due to man-made accidental conditions, it is important to have models that can realistically predict the impact behavior of concrete structures. The present paper focuses on a relatively new approach for 3D finite element analysis of RC structures under impact loads. The approach uses rate sensitive micro-plane model as constitutive law for concrete, while the strain-rate influence is captured by the activation energy. Inertia forces are implicitly accounted for through dynamic finite element analysis. It is shown with the help of different examples that the approach can very well simulate the behavior of RC structural elements under high rate loading. (author)

  20. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  1. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.; Kyriazopoulou-Panagiotopoulou, S.; Grubert, F.; Zaugg, J. B.; Kundaje, A.; Liu, Y.; Boyle, A. P.; Zhang, Q. C.; Zakharia, F.; Spacek, D. V.; Li, J.; Xie, D.; Olarerin-George, A.; Steinmetz, L. M.; Hogenesch, J. B.; Kellis, M.; Batzoglou, S.; Snyder, M.

    2013-01-01

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  2. Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin

    OpenAIRE

    Freidkin, Ilya; Katcoff, Don J.

    2001-01-01

    In virtually all eukaryotic organisms, linker DNA between nucleosomes is associated with a histone termed linker histone or histone H1. In Saccharomyces cerevisiae, HHO1 encodes a putative linker histone with very significant homology to histone H1. The encoded protein is expressed in the nucleus, but has not been shown to affect global chromatin structure, nor has its deletion shown any detectable phenotype. In vitro chromatin assembly experiments with recombinant HHO1p have shown that it is...

  3. Structural phase transitions in boron carbide under stress

    International Nuclear Information System (INIS)

    Korotaev, P; Pokatashkin, P; Yanilkin, A

    2016-01-01

    Structural transitions in boron carbide B 4 C under stress were studied by means of first-principles molecular dynamics in the framework of density functional theory. The behavior depends strongly on degree of non-hydrostatic stress. Under hydrostatic stress continuous bending of the three-atom C–B–C chain was observed up to 70 GPa. The presence of non-hydrostatic stress activates abrupt reversible chain bending, which is displacement of the central boron atom in the chain with the formation of weak bonds between this atom and atoms in the nearby icosahedra. Such structural change can describe a possible reversible phase transition in dynamical loading experiments. High non-hydrostatic stress achieved in uniaxial loading leads to disordering of the initial structure. The formation of carbon chains is observed as one possible transition route. (paper)

  4. The Fatigue Behavior of Steel Structures under Random Loading

    DEFF Research Database (Denmark)

    Agerskov, Henning

    2009-01-01

    of the investigation, fatigue test series with a total of 540 fatigue tests have been carried through on various types of welded plate test specimens and full-scale offshore tubular joints. The materials that have been used are either conventional structural steel or high-strength steel. The fatigue tests......Fatigue damage accumulation in steel structures under random loading has been studied in a number of investigations at the Technical University of Denmark. The fatigue life of welded joints has been determined both experimentally and from a fracture mechanics analysis. In the experimental part...... and the fracture mechanics analyses have been carried out using load histories, which are realistic in relation to the types of structures studied, i.e. primarily bridges, offshore structures and chimneys. In general, the test series carried through show a significant difference between constant amplitude...

  5. Constitutive model and electroplastic analysis of structures under cyclic loading

    International Nuclear Information System (INIS)

    Wang, X.; Lei, Y; Du, Q.

    1989-01-01

    Many engineering structures in nuclear reactors, thermal power stations, chemical plants and aerospace vehicles are subjected to cyclic mechanic-thermal loading, which is the main cause of structural fatigue failure. Over the past twenty years, designers and researchers have paid great attention to the research on life prediction and elastoplastic analysis of structures under cyclic loading. One of the key problems in elastoplastic analysis is to construct a reasonable constitutive model for cyclic plasticity. In the paper, the constitutive equations are briefly outlined. Then, the model is implemented in a finite element code to predict the response of cyclic loaded structural components such as a double-edge-notched plate, a grooved bar and a nozzle in spherical shell. Numerical results are compared with those from other theories and experiments

  6. Quasi-static structural optimization under the seismic loads

    International Nuclear Information System (INIS)

    Choi, W. S.; Lee, K. M.; Kim, T. W.

    2001-01-01

    For preliminaries to optimization of SMART under the seismic loads, a quasi-static structural optimization for elastic structures under dynamic loads is presented. An equivalent static load (ESL) set is defined as a static load set, which generates the same displacement field as that from a dynamic load at a certain time. Multiple ESL sets calculated at all the time intervals are employed to represent the various states of the structure under the dynamic load. They can cover all the critical states that might happen at arbitrary times. The continuous characteristics of a dynamic load are considered by multiple static load sets. The calculated sets of ESLs are utilized as a multiple loading condition in the optimization process. A design cycle is defined as a circulated process between an analysis domain and a design domain. The analysis domain gives the loading condition needed in the design domain. The design domain gives a new updated design to be verified by the analysis domain in the next design cycle. The design cycles are iterated until the design converges. Structural optimization with dynamic loads is tangible by the proposed method. Standard example problems are solved to verify the validity of the method

  7. Models of chromatin spatial organisation in the cell nucleus

    Science.gov (United States)

    Nicodemi, Mario

    2014-03-01

    In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Recent experiments have started unveiling the interaction map of DNA sites genome-wide, revealing different levels of organisation at different scales. The principles, though, which orchestrate such a complex 3D structure remain still mysterious. I will overview the scenario emerging from some classical polymer physics models of the general aspect of chromatin spatial organisation. The available experimental data, which can be rationalised in a single framework, support a picture where chromatin is a complex mixture of differently folded regions, self-organised across spatial scales according to basic physical mechanisms. I will also discuss applications to specific DNA loci, e.g. the HoxB locus, where models informed with biological details, and tested against targeted experiments, can help identifying the determinants of folding.

  8. Atomic force microscopy on chromosomes, chromatin and DNA: a review.

    Science.gov (United States)

    Kalle, Wouter; Strappe, Padraig

    2012-12-01

    The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  9. Chromatin Pioneers | Center for Cancer Research

    Science.gov (United States)

    Taking advantage of their ability to explore provocative ideas, NCI investigators pioneered the study of chromatin to demonstrate its functional importance and lay the groundwork for understanding its role in cancer and other diseases.

  10. Band structure of CdTe under high pressure

    International Nuclear Information System (INIS)

    Jayam, Sr. Gerardin; Nirmala Louis, C.; Amalraj, A.

    2005-01-01

    The band structures and density of states of cadmium telluride (CdTe) under various pressures ranging from normal to 4.5 Mbar are obtained. The electronic band structure at normal pressure of CdTe (ZnS structure) is analyzed and the direct band gap value is found to be 1.654 eV. CdTe becomes metal and superconductor under high pressure but before that it undergoes structural phase transition from ZnS phase to NaCl phase. The equilibrium lattice constant, bulk modulus and the phase transition pressure at which the compounds undergo structural phase transition from ZnS to NaCl are predicted from the total energy calculations. The density of states at the Fermi level (N(E F )) gets enhanced after metallization, which leads to the superconductivity in CdTe. In our calculation, the metallization pressure (P M = 1.935 Mbar) and the corresponding reduced volume ((V/V 0 ) M = 0.458) are estimated. Metallization occurs via direct closing of band gap at Γ point. (author)

  11. Effect of support conditions on structural response under dynamic loading

    International Nuclear Information System (INIS)

    Akram, T.; Memon, S.A.

    2008-01-01

    In design practice, dynamic structural analysis is carried out with base of structure considered as fixed; this means that foundation is placed on rock like soil material. While conducting this type of analyses the role of foundation and soil behaviour is totally neglected. The actions in members and loads transferred at foundation level obtained in this manner do not depict the true structural behaviour. FEM (Finite Element Methods) analysis where both superstructure and foundation soil are coupled together is quite complicated and expensive for design environments. A simplified model is required to depict dynamic response of structures with foundations based on flexible soils. The primary purpose of this research is to compare the superstructure dynamic responses of structural systems with fixed base to that of simple soil model base. The selected simple soil model is to be suitable for use in a design environment to give more realistic results. For this purpose building models are idealized with various heights and structural systems in both 2D (Two Dimensional) and 3D (Three Dimensional) space. These models are then provided with visco-elastic supports representing three soil bearing capacities and the analysis results are compared to that of fixed supports models. The results indicate that fixed support system underestimates natural time period of the structures. Dynamic behavior and force response of visco-elastic support is different from fixed support model. Fixed support models result in over designed base columns and under designed beams. (author)

  12. The Fatigue Behavior of Steel Structures under Random Loading

    DEFF Research Database (Denmark)

    Agerskov, Henning

    2008-01-01

    Fatigue damage accumulation in steel structures under random loading has been studied in a number of investigations at the Technical University of Denmark. The fatigue life of welded joints has been determined both experimentally and from a fracture mechanics analysis. In the experimental part...... and variable amplitude fatigue test results. Both the fracture mechanics analysis and the fatigue test results indicate that Miner’s rule, which is normally used in the design against fatigue in steel structures, may give results, which are unconservative, and that the validity of the results obtained from...

  13. Macrogenomic engineering via modulation of the scaling of chromatin packing density.

    Science.gov (United States)

    Almassalha, Luay M; Bauer, Greta M; Wu, Wenli; Cherkezyan, Lusik; Zhang, Di; Kendra, Alexis; Gladstein, Scott; Chandler, John E; VanDerway, David; Seagle, Brandon-Luke L; Ugolkov, Andrey; Billadeau, Daniel D; O'Halloran, Thomas V; Mazar, Andrew P; Roy, Hemant K; Szleifer, Igal; Shahabi, Shohreh; Backman, Vadim

    2017-11-01

    Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment. We show that the regulation of the chromatin nanoenvironment allows for the predictable modulation of global patterns in gene expression. In particular, we show that the rational modulation of chromatin density fluctuations can lead to a decrease in global transcriptional activity and intercellular transcriptional heterogeneity in cancer cells during chemotherapeutic responses to achieve near-complete cancer cell killing in vitro. Our findings represent a 'macrogenomic engineering' approach to modulating the physical structure of chromatin for whole-scale transcriptional modulation.

  14. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

    Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin -- a dynamic complex of nucleic acids and proteins -- is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.

  15. Structural Evaluation on HIC Transport Packaging under Accident Conditions

    International Nuclear Information System (INIS)

    Chung, Sung Hwan; Kim, Duck Hoi; Jung, Jin Se; Yang, Ke Hyung; Lee, Heung Young

    2005-01-01

    HIC transport packaging to transport a high integrity container(HIC) containing dry spent resin generated from nuclear power plants is to comply with the regulatory requirements of Korea and IAEA for Type B packaging due to the high radioactivity of the content, and to maintain the structural integrity under normal and accident conditions. It must withstand 9 m free drop impact onto an unyielding surface and 1 m drop impact onto a mild steel bar in a position causing maximum damage. For the conceptual design of a cylindrical HIC transport package, three dimensional dynamic structural analysis to ensure that the integrity of the package is maintained under all credible loads for 9 m free drop and 1 m puncture conditions were carried out using ABAQUS code.

  16. Nonlinear system identification of smart structures under high impact loads

    Science.gov (United States)

    Sarp Arsava, Kemal; Kim, Yeesock; El-Korchi, Tahar; Park, Hyo Seon

    2013-05-01

    The main purpose of this paper is to develop numerical models for the prediction and analysis of the highly nonlinear behavior of integrated structure control systems subjected to high impact loading. A time-delayed adaptive neuro-fuzzy inference system (TANFIS) is proposed for modeling of the complex nonlinear behavior of smart structures equipped with magnetorheological (MR) dampers under high impact forces. Experimental studies are performed to generate sets of input and output data for training and validation of the TANFIS models. The high impact load and current signals are used as the input disturbance and control signals while the displacement and acceleration responses from the structure-MR damper system are used as the output signals. The benchmark adaptive neuro-fuzzy inference system (ANFIS) is used as a baseline. Comparisons of the trained TANFIS models with experimental results demonstrate that the TANFIS modeling framework is an effective way to capture nonlinear behavior of integrated structure-MR damper systems under high impact loading. In addition, the performance of the TANFIS model is much better than that of ANFIS in both the training and the validation processes.

  17. Portfolio optimization with structured products under return constraint

    Directory of Open Access Journals (Sweden)

    Baweja Meena

    2015-01-01

    Full Text Available A new approach for optimizing risk in a portfolio of financial instruments involving structured products is presented. This paper deals with a portfolio selection model which uses optimization methodology to minimize conditional Value-at-Risk (CVaR under return constraint. It focuses on minimizing CVaR rather than on minimizing value-at-Risk VaR, as portfolios with low CVaR necessarily have low VaR as well. We consider a simple investment problem where besides stocks and bonds, the investor can also include structured products into the investment portfolio. Due to possible intermediate payments from structured product, we have to deal with a re-investment problem modeled as a linear optimization problem.

  18. Structural and electronic properties of carbon nanotubes under hydrostatic pressures

    International Nuclear Information System (INIS)

    Zhang Ying; Cao Juexian; Yang Wei

    2008-01-01

    We studied the structural and electronic properties of carbon nanotubes under hydrostatic pressures based on molecular dynamics simulations and first principles band structure calculations. It is found that carbon nanotubes experience a hard-to-soft transition as external pressure increases. The bulk modulus of soft phase is two orders of magnitude smaller than that of hard phase. The band structure calculations show that band gap of (10, 0) nanotube increases with the increase of pressure at low pressures. Above a critical pressure (5.70GPa), band gap of (10, 0) nanotube drops rapidly and becomes zero at 6.62GPa. Moreover, the calculated charge density shows that a large pressure can induce an sp 2 -to-sp 3 bonding transition, which is confirmed by recent experiments on deformed carbon nanotubes

  19. Structural pounding of concrete frame structure with masonry infill wall under seismic loading

    Science.gov (United States)

    Ismail, Rozaina; Hasnan, Mohd Hafizudin; Shamsudin, Nurhanis

    2017-10-01

    Structural pounding is additional problem than the other harmful damage that may occurs due to the earthquake vibrations. A lot of study has been made by past researcher but most of them did not include the walls. The infill masonry walls are rarely involved analysis of structural systems but it does contribute to earthquake response of the structures. In this research, a comparison between adjacent building of 10-storey and 7-storey concrete frame structure without of masonry infill walls and the same dynamic properties of buildings. The diagonal strut approach is adopted for modeling masonry infill walls. This research also focused on finding critical building separation in order to prevent the adjacent structures from pounding. LUSAS FEA v14.03 software has been used for modeling analyzing the behavior of structures due to seismic loading and the displacement each floor of the building has been taken in order to determine the critical separation distance between the buildings. From the analysis that has been done, it is found that masonry infill walls do affect the structures behavior under seismic load. Structures without masonry infill walls needs more distance between the structures to prevent structural pounding due to higher displacement of the buildings when it sways under seismic load compared to structures with masonry infill walls. This shows that contribution of masonry infill walls to the analysis of structures cannot be neglected.

  20. Relationship between chromatin complexity and nuclear envelope circularity in hippocampal pyramidal neurons

    International Nuclear Information System (INIS)

    Pantic, Igor; Basailovic, Milos; Paunovic, Jovana; Pantic, Senka

    2015-01-01

    Highlights: •We analyzed chromatin structure and nuclear envelope of 200 hippocampal pyramidal neurons. •Fractal and GLCM mathematical parameters were calculated each chromatin structure. •Nuclear shape was quantified by calculating circularity of the nuclear envelope. •Circularity was in significant relationship with chromatin fractal dimension. •Strong correlation was detected between circularity and some GLCM parameters. -- Abstract: In this study we tested the existence and strength of the relationship between circularity of nuclear envelope and mathematical parameters of chromatin structure. Coronal sections of the brain were made in 10 male albino mice. The brain tissue was stained using a modification of Feulgen method for DNA visualization. A total of 200 hippocampal pyramidal neurons (20 per animal) were visualized using DEM 200 High-Speed Color CMOS Chip and Olympus CX21FS1 microscope. Circularity of the nuclear membrane was calculated in ImageJ (NIH, USA) after the nuclear segmentation, based on the freehand selection of the nuclear regions of interest. Circularity was determined from the values of area and perimeter. For each chromatin structure, using fractal and grey level co-occurrence matrix (GLCM) algorithms, we determined the values of fractal dimension, lacunarity, angular second moment, GLCM entropy, inverse difference moment, GLCM correlation, and GLCM contrast. It was found that circularity is in a significant correlation (p < 0.05) with fractal dimension as the main parameter of fractal complexity analysis. Also, circularity was in a very strong relationship (p < 0.001) with certain parameters of grey level co-occurrence matrix such as the angular second moment and GLCM correlation. This is the first study to indicate that nuclear shape is significantly related to mathematical parameters of higher chromatin organization. Also, it seems that circularity of the nuclear envelope is a good predictor of certain features of chromatin

  1. The alteration of chromatin domains during damage repair induced by ionizing radiation

    International Nuclear Information System (INIS)

    Cress, A.E.; Olson, K.M.; Olson, G.B.

    1995-01-01

    Several groups previously have reported the ability of chromatin structure to influence the production of damage induced by ionizing radiation. The authors' interest has been to determine whether chromatin structural alterations exist after ionizing radiation during a repair interval. The earlier work investigated this question using biochemical techniques. The crosslinking of nuclear structural proteins to DNA after ionizing radiation was observed. In addition, they found that the chromatin structure in vitro as measured by sucrose density gradient sedimentation, was altered after ionizing radiation. These observations added to earlier studies in which digital imaging techniques showed an alteration in feulgen-positive DNA after irradiation prompted the present study. The object of this study was to detect whether the higher order structure of DNA into chromatin domains within interphase human cells was altered in interphase cells in response to a radiation induced damage. The present study takes advantage of the advances in the detection of chromatin domains in situ using DNA specific dyes and digital image processing of established human T and B cell lines

  2. The use of ultraviolet light in the fractionation of chromatin containing unsubstituted and bromodeoxyuridine-substituted DNA

    International Nuclear Information System (INIS)

    Taichman, L.B.

    1979-01-01

    Two procedures are described for the fractionation of chromatin containing unsubstituted (LL) DNA and DNA unifilarly substituted with bromodeoxyuridine (HL). The two procedures rely upon the sensitivity of bromodeoxyuridine-containing DNA to UV light to induce either strand breakage or protein crosslinking. When a mixture of LL and HL chromatin is irradiated with UV light, the HL DNA fragments into molecules of smaller molecular weight than the LL DNA and crosslinks more chromosomal protein than the LL DNA. LL and HL chromatin can be fractionated on the basis of size by centrifuging through a neutral sucrose gradient. The HL DNA-protein adducts that are generated by the UV light have a unique buoyant density and may be isolated by isopycnic centrifugation in Cs 2 S0 4 . The ability to fractionate LL and HL chromatin permits certain studies on the structure of replicating chromatin. (author)

  3. A Poly-ADP-Ribose Trigger Releases the Auto-Inhibition of a Chromatin Remodeling Oncogene.

    Science.gov (United States)

    Singh, Hari R; Nardozza, Aurelio P; Möller, Ingvar R; Knobloch, Gunnar; Kistemaker, Hans A V; Hassler, Markus; Harrer, Nadine; Blessing, Charlotte; Eustermann, Sebastian; Kotthoff, Christiane; Huet, Sébastien; Mueller-Planitz, Felix; Filippov, Dmitri V; Timinszky, Gyula; Rand, Kasper D; Ladurner, Andreas G

    2017-12-07

    DNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to DNA-damage-mediated PARP1 induction. We show that the interaction of the ALC1 macrodomain with the ATPase module mediates auto-inhibition. PARP1 activation suppresses this inhibitory interaction. Crucially, release from auto-inhibition requires a poly-ADP-ribose (PAR) binding macrodomain. We identify tri-ADP-ribose as a potent PAR-mimic and synthetic allosteric effector that abrogates ATPase-macrodomain interactions, promotes an ungated conformation, and activates the remodeler's ATPase. ALC1 fragments lacking the regulatory macrodomain relax chromatin in vivo without requiring PARP1 activation. Further, the ATPase restricts the macrodomain's interaction with PARP1 under non-DNA damage conditions. Somatic cancer mutants disrupt ALC1's auto-inhibition and activate chromatin remodeling. Our data show that the NAD + -metabolite and nucleic acid PAR triggers ALC1 to drive chromatin relaxation. Modular allostery in this oncogene tightly controls its robust, DNA-damage-dependent activation. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

    Directory of Open Access Journals (Sweden)

    Gary Hon

    2008-10-01

    Full Text Available Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory elements. But the vast majority of regulatory elements have yet to be discovered, and it has become increasingly apparent that their discovery will not come from using genetic information alone. Recently, high-throughput technologies have enabled the creation of information-rich epigenetic maps, most notably for histone modifications. However, tools that search for functional elements using this epigenetic information have been lacking. Here, we describe an unsupervised learning method called ChromaSig to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known patterns associated with transcriptional promoters and enhancers. Interestingly, we observe that the distinct chromatin signatures found at enhancers mark distinct functional classes of enhancers in terms of transcription factor and coactivator binding. In addition, we identify three clusters of novel chromatin signatures that contain evolutionarily conserved sequences and potential cis-regulatory elements. Applying ChromaSig to a panel of 21 chromatin marks mapped genomewide by ChIP-Seq reveals 16 classes of genomic elements marked by distinct chromatin signatures. Interestingly, four classes containing enrichment for repressive histone modifications appear to be locally heterochromatic sites and are enriched in quickly evolving regions of the genome. The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications.

  5. Basic concept on the responses of structural members and structures under impact or impulsive loadings

    International Nuclear Information System (INIS)

    Takeda, J.I.; Tachikawa, H.; Fujimoto, K.

    1982-01-01

    The responses of structural members and structures subjected to impact or impulsive loadings are generated by the interaction between acting bodies and structures, and the interaction is affected by many factors, e.g. the relations of masses, sizes, rigidities, etc. between acting bodies and structures and especially by relative velocity. The development of the responses of structural members and structures are controlled by the constitutive equations and failure criteria of constituent materials, the relationships of cowork system between the constituent materials and existing stress waves. Furthermore, the first two are influenced by rate effects and they all widely change by the speeds of impact and impulsive loadings. This paper deals with the physical meaning of the responses of structures under impact and impulsive loadings. (orig.) [de

  6. New mitotic regulators released from chromatin

    Directory of Open Access Journals (Sweden)

    Hideki eYokoyama

    2013-12-01

    Full Text Available Faithful action of the mitotic spindle segregates duplicated chromosomes into daughter cells. Perturbations of this process result in chromosome mis-segregation, leading to chromosomal instability and cancer development. Chromosomes are not simply passengers segregated by spindle microtubules but rather play a major active role in spindle assembly. The GTP bound form of the Ran GTPase (RanGTP, produced around chromosomes, locally activates spindle assembly factors. Recent studies have uncovered that chromosomes organize mitosis beyond spindle formation. They distinctly regulate other mitotic events, such as spindle maintenance in anaphase, which is essential for chromosome segregation. Furthermore, the direct function of chromosomes is not only to produce RanGTP but, in addition, to release key mitotic regulators from chromatin. Chromatin-remodeling factors and nuclear pore complex proteins, which have established functions on chromatin in interphase, dissociate from mitotic chromatin and function in spindle assembly or maintenance. Thus, chromosomes actively organize their own segregation using chromatin-releasing mitotic regulators as well as RanGTP.

  7. Capital Structure Arbitrage under a Risk-Neutral Calibration

    Directory of Open Access Journals (Sweden)

    Peter J. Zeitsch

    2017-01-01

    Full Text Available By reinterpreting the calibration of structural models, a reassessment of the importance of the input variables is undertaken. The analysis shows that volatility is the key parameter to any calibration exercise, by several orders of magnitude. To maximize the sensitivity to volatility, a simple formulation of Merton’s model is proposed that employs deep out-of-the-money option implied volatilities. The methodology also eliminates the use of historic data to specify the default barrier, thereby leading to a full risk-neutral calibration. Subsequently, a new technique for identifying and hedging capital structure arbitrage opportunities is illustrated. The approach seeks to hedge the volatility risk, or vega, as opposed to the exposure from the underlying equity itself, or delta. The results question the efficacy of the common arbitrage strategy of only executing the delta hedge.

  8. CARIBBEAN OFFSHORE CORPORATE STRUCTURES UNDER A SWOT ANALYSIS

    Directory of Open Access Journals (Sweden)

    Ana-Maria GEAMÃNU

    2015-04-01

    Full Text Available Tax havens have long been under the attention of numerous Governments and International Organizations which triggered the concern of an uneven playing field in the taxation area. As a result numerous amendments have been made to both their commercial and tax legislations in order to be in line with the internationally agreed tax standards. The aim of this article is to conduct a SWOT analysis on the offshore corporate structures found in the Caribbean landscape. Based on a selection process of the most commonly recognized tax havens in the Caribbean region and an analysis of their offshore companies at the level of incorporation, administration, activities conducted and costs, a set of frequently met characteristics have been identified which stand at the basis of the SWOT analysis. The results stand to present a comprehensive four dimension framework of the offshore corporate structures in regards to their strengths, weaknesses, opportunities and threats.

  9. Structure of high-density amorphous ice under pressure

    International Nuclear Information System (INIS)

    Klotz, S.; Hamel, G.; Loveday, J.S.; Nelmes, R.J.; Guthrie, M.; Soper, A.K.

    2002-01-01

    We report in situ neutron diffraction studies of high-density amorphous ice (HDA) at 100 K at pressures up to 2.2 GPa. We find that the compression is achieved by a strong contraction (∼20%) of the second neighbor coordination shell, so that at 2.2 GPa it closely approaches the first coordination shell, which itself remains intact in both structure and size. The hydrogen bond orientations suggest an absence of hydrogen bonding between first and second shells and that HDA has increasingly interpenetrating hydrogen bond networks under pressure

  10. Probabilistic analysis of flaw distribution on structure under cyclic load

    International Nuclear Information System (INIS)

    Kwak, Sang Log; Choi, Young Hwan; Kim, Hho Jung

    2003-01-01

    Flaw geometries, applied stress, and material properties are major input variables for the fracture mechanics analysis. Probabilistic approach can be applied for the consideration of uncertainties within these input variables. But probabilistic analysis requires many assumptions due to the lack of initial flaw distributions data. In this study correlations are examined between initial flaw distributions and in-service flaw distributions on structures under cyclic load. For the analysis, LEFM theories and Monte Carlo simulation are applied. Result shows that in-service flaw distributions are determined by initial flaw distributions rather than fatigue crack growth rate. So initial flaw distribution can be derived from in-service flaw distributions

  11. Structural assessment of TAPS core shroud under accident loads

    International Nuclear Information System (INIS)

    Bhasin, Vivek; Kushwaha, H.S.; Mahajan, S.C.; Kakodkar, A.

    1996-09-01

    Over the last few years, the Core Shroud of Boiling Water Reactors (BWRs) operating in foreign countries, have developed cracks at weld locations. As a first step for assessment of structural safety of Tarapur Atomic Power Station (TAPS) core shroud, its detailed stress analysis was done for postulated accident loads. This report is concerned with structural assessment of core shroud, of BWR at TAPS, subjected to loads resulting from main steam line break (MSLB), recirculation line break (RLB) and safe shut down earthquake. The stress analysis was done for core shroud in healthy condition and without any crack since, visual examination conducted till now, do not indicate presence of any flaw. Dynamic structural analysis for MSLB and RLB events was done using dynamic load factor (DLF) method. The complete core shroud and its associated components were modelled and analysed using 3D plate/shell elements. Since, the components of core shroud are submerged in water, hence, hydrodynamic added mass was also considered for evaluation of natural frequencies. It was concluded that from structural point of view, adequate safety margin is available under all the accident loads. Nonlinear analysis was done to evaluate buckling/collapse load. The collapse/buckling load have sufficient margin against the allowable limits. The displacements are low hence, the insertion of control rod may not be affected. (author)

  12. The influence of ionizing irradiation on functional state of chromatin neurons in mice living at the territory of the Chernobylsk NPP

    International Nuclear Information System (INIS)

    Mustafin, A.G.; Yarygin, V.N.; Vakhtel', N.M.; Bibaeva, L.V.

    1996-01-01

    Daily variations in activity of endo-RNA-polymerases were studied in neurocyte nuclei of the L v -cerebrospinal node, α-motoneurons of spinal cord, neurons of sensomotor and visual areas of the mice crust, subjected to radiation impact in the Chernobyl NPP zone. Changes in circadian time organization of nerve cells genetic apparatus functioning in various nerve system sections were observed in the irradiated mice. Shift of acrophases of nucleoplasmatic and nucleolus tracing was observed during daily cycle after 40-day exposure under conditions of increased radioactive background. Degree of synchronization of ribosome and structural genes transcription in the studied cell populations decreased. Mesors and amplitudes of circadian rhythms of chromatin matrix activity was reduced. The chromatin histon state in irradiated animals also changed. 8 refs.; 2 tabs

  13. Plant cell plasma membrane structure and properties under clinostatting

    Science.gov (United States)

    Polulakh, Yu. A.; Zhadko, S. I.; Klimchuk, D. A.; Baraboy, V. A.; Alpatov, A. N.; Sytnik, K. M.

    Structural-functional organization of plasma membrane of pea roots seedling was investigated by methods of chemiluminescence, fluorescence probes, chromatography and freeze-fracture studies under normal conditions and clinostatting. Phase character of lipid peroxidation intensity was fixed. The initial phase of this process is characterized by lipid peroxidation decreasing with its next induction. The primary changes depending on free-radical mechanisms of lipid peroxidation were excellently revealed by chemiluminescence. Plasmalemma microviscosity increased on the average of 15-20 % under microgravity at the initial stages of its phenomenon. There were major changes of phosphatidilcholine and phosphatidilethanolamine contents. The total quantity of phospholipids remained rather stable. Changes of phosphatide acid concentration point to degradation and phospholipids biosynthesis. There were increases of unsaturated fatty acids mainly at the expense of linoleic and linolenic acids and also a decrease of saturated fatty acid content at the expense of palmitic and stearic acids. Unsaturation index of fatty acids increased as well. On the whole fatty acid composition was variable in comparison with phospholipids. Probably it is one of mechanisms of maintaining of microviscosity within definite limits. Considerable structural changes in organization of plasmalemma protein-lipid complex were not revealed by the freeze-fracture studies.

  14. Structural Health Monitoring under Nonlinear Environmental or Operational Influences

    Directory of Open Access Journals (Sweden)

    Jyrki Kullaa

    2014-01-01

    Full Text Available Vibration-based structural health monitoring is based on detecting changes in the dynamic characteristics of the structure. It is well known that environmental or operational variations can also have an influence on the vibration properties. If these effects are not taken into account, they can result in false indications of damage. If the environmental or operational variations cause nonlinear effects, they can be compensated using a Gaussian mixture model (GMM without the measurement of the underlying variables. The number of Gaussian components can also be estimated. For the local linear components, minimum mean square error (MMSE estimation is applied to eliminate the environmental or operational influences. Damage is detected from the residuals after applying principal component analysis (PCA. Control charts are used for novelty detection. The proposed approach is validated using simulated data and the identified lowest natural frequencies of the Z24 Bridge under temperature variation. Nonlinear models are most effective if the data dimensionality is low. On the other hand, linear models often outperform nonlinear models for high-dimensional data.

  15. Nonlinear system identification of smart structures under high impact loads

    International Nuclear Information System (INIS)

    Sarp Arsava, Kemal; Kim, Yeesock; El-Korchi, Tahar; Park, Hyo Seon

    2013-01-01

    The main purpose of this paper is to develop numerical models for the prediction and analysis of the highly nonlinear behavior of integrated structure control systems subjected to high impact loading. A time-delayed adaptive neuro-fuzzy inference system (TANFIS) is proposed for modeling of the complex nonlinear behavior of smart structures equipped with magnetorheological (MR) dampers under high impact forces. Experimental studies are performed to generate sets of input and output data for training and validation of the TANFIS models. The high impact load and current signals are used as the input disturbance and control signals while the displacement and acceleration responses from the structure–MR damper system are used as the output signals. The benchmark adaptive neuro-fuzzy inference system (ANFIS) is used as a baseline. Comparisons of the trained TANFIS models with experimental results demonstrate that the TANFIS modeling framework is an effective way to capture nonlinear behavior of integrated structure–MR damper systems under high impact loading. In addition, the performance of the TANFIS model is much better than that of ANFIS in both the training and the validation processes. (paper)

  16. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during...... replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors...... such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment...

  17. Chromatin proteins and modifications as drug targets

    DEFF Research Database (Denmark)

    Helin, Kristian; Dhanak, Dashyant

    2013-01-01

    A plethora of groundbreaking studies have demonstrated the importance of chromatin-associated proteins and post-translational modifications of histones, proteins and DNA (so-called epigenetic modifications) for transcriptional control and normal development. Disruption of epigenetic control...... is a frequent event in disease, and the first epigenetic-based therapies for cancer treatment have been approved. A generation of new classes of potent and specific inhibitors for several chromatin-associated proteins have shown promise in preclinical trials. Although the biology of epigenetic regulation...

  18. Size-dependent structure of silver nanoparticles under high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Koski, Kristie Jo [Univ. of California, Berkeley, CA (United States)

    2008-12-31

    Silver noble metal nanoparticles that are<10 nm often possess multiply twinned grains allowing them to adopt shapes and atomic structures not observed in bulk materials. The properties exhibited by particles with multiply twinned polycrystalline structures are often far different from those of single-crystalline particles and from the bulk. I will present experimental evidence that silver nanoparticles<10 nm undergo a reversible structural transformation under hydrostatic pressures up to 10 GPa. Results for nanoparticles in the intermediate size range of 5 to 10 nm suggest a reversible linear pressure-dependent rhombohedral distortion which has not been previously observed in bulk silver. I propose a mechanism for this transitiion that considers the bond-length distribution in idealized multiply twinned icosahedral particles. Results for nanoparticles of 3.9 nm suggest a reversible linear pressure-dependent orthorhombic distortion. This distortion is interpreted in the context of idealized decahedral particles. In addition, given these size-dependent measurements of silver nanoparticle compression with pressure, we have constructed a pressure calibration curve. Encapsulating these silver nanoparticles in hollow metal oxide nanospheres then allows us to measure the pressure inside a nanoshell using x-ray diffraction. We demonstrate the measurement of pressure gradients across nanoshells and show that these nanoshells have maximum resolved shear strengths on the order of 500 MPa to IGPa.

  19. Structure of a financial cross-correlation matrix under attack

    Science.gov (United States)

    Lim, Gyuchang; Kim, SooYong; Kim, Junghwan; Kim, Pyungsoo; Kang, Yoonjong; Park, Sanghoon; Park, Inho; Park, Sang-Bum; Kim, Kyungsik

    2009-09-01

    We investigate the structure of a perturbed stock market in terms of correlation matrices. For the purpose of perturbing a stock market, two distinct methods are used, namely local and global perturbation. The former involves replacing a correlation coefficient of the cross-correlation matrix with one calculated from two Gaussian-distributed time series while the latter reconstructs the cross-correlation matrix just after replacing the original return series with Gaussian-distributed time series. Concerning the local case, it is a technical study only and there is no attempt to model reality. The term ‘global’ means the overall effect of the replacement on other untouched returns. Through statistical analyses such as random matrix theory (RMT), network theory, and the correlation coefficient distributions, we show that the global structure of a stock market is vulnerable to perturbation. However, apart from in the analysis of inverse participation ratios (IPRs), the vulnerability becomes dull under a small-scale perturbation. This means that these analysis tools are inappropriate for monitoring the whole stock market due to the low sensitivity of a stock market to a small-scale perturbation. In contrast, when going down to the structure of business sectors, we confirm that correlation-based business sectors are regrouped in terms of IPRs. This result gives a clue about monitoring the effect of hidden intentions, which are revealed via portfolios taken mostly by large investors.

  20. Saccharomyces cerevisiae Linker Histone—Hho1p Maintains Chromatin Loop Organization during Ageing

    Directory of Open Access Journals (Sweden)

    Katya Uzunova

    2013-01-01

    Full Text Available Intricate, dynamic, and absolutely unavoidable ageing affects cells and organisms through their entire lifetime. Driven by diverse mechanisms all leading to compromised cellular functions and finally to death, this process is a challenge for researchers. The molecular mechanisms, the general rules that it follows, and the complex interplay at a molecular and cellular level are yet little understood. Here, we present our results showing a connection between the linker histones, the higher-order chromatin structures, and the process of chronological lifespan of yeast cells. By deleting the gene for the linker histone in Saccharomyces cerevisiae we have created a model for studying the role of chromatin structures mainly at its most elusive and so far barely understood higher-order levels of compaction in the processes of yeast chronological lifespan. The mutant cells demonstrated controversial features showing slower growth than the wild type combined with better survival during the whole process. The analysis of the global chromatin organization during different time points demonstrated certain loss of the upper levels of chromatin compaction in the cells without linker histone. The results underlay the importance of this histone for the maintenance of the chromatin loop structures during ageing.

  1. Osmotic stress alters chromatin condensation and nucleocytoplasmic transport

    Energy Technology Data Exchange (ETDEWEB)

    Finan, John D.; Leddy, Holly A. [Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC (United States); Department of Biomedical Engineering, Duke University, Durham, NC (United States); Guilak, Farshid, E-mail: guilak@duke.edu [Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC (United States); Department of Biomedical Engineering, Duke University, Durham, NC (United States)

    2011-05-06

    Highlights: {yields} The rate of nucleocytoplasmic transport increases under hyper-osmotic stress. {yields} The mechanism is a change in nuclear geometry, not a change in permeability of the nuclear envelope. {yields} Intracytoplasmic but not intranuclear diffusion is sensitive to osmotic stress. {yields} Pores in the chromatin of the nucleus enlarge under hyper-osmotic stress. -- Abstract: Osmotic stress is a potent regulator of biological function in many cell types, but its mechanism of action is only partially understood. In this study, we examined whether changes in extracellular osmolality can alter chromatin condensation and the rate of nucleocytoplasmic transport, as potential mechanisms by which osmotic stress can act. Transport of 10 kDa dextran was measured both within and between the nucleus and the cytoplasm using two different photobleaching methods. A mathematical model was developed to describe fluorescence recovery via nucleocytoplasmic transport. As osmolality increased, the diffusion coefficient of dextran decreased in the cytoplasm, but not the nucleus. Hyper-osmotic stress decreased nuclear size and increased nuclear lacunarity, indicating that while the nucleus was getting smaller, the pores and channels interdigitating the chromatin had expanded. The rate of nucleocytoplasmic transport was increased under hyper-osmotic stress but was insensitive to hypo-osmotic stress, consistent with the nonlinear osmotic properties of the nucleus. The mechanism of this osmotic sensitivity appears to be a change in the size and geometry of the nucleus, resulting in a shorter effective diffusion distance for the nucleus. These results may explain physical mechanisms by which osmotic stress can influence intracellular signaling pathways that rely on nucleocytoplasmic transport.

  2. Keeping it quiet: chromatin control of gammaherpesvirus latency.

    Science.gov (United States)

    Lieberman, Paul M

    2013-12-01

    The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) establish long-term latent infections associated with diverse human cancers. Viral oncogenesis depends on the ability of the latent viral genome to persist in host nuclei as episomes that express a restricted yet dynamic pattern of viral genes. Multiple epigenetic events control viral episome generation and maintenance. This Review highlights some of the recent findings on the role of chromatin assembly, histone and DNA modifications, and higher-order chromosome structures that enable gammaherpesviruses to establish stable latent infections that mediate viral pathogenesis.

  3. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templates

    National Research Council Canada - National Science Library

    Nordeen, Steven

    2000-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  4. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templaces

    National Research Council Canada - National Science Library

    Nordeen, Steve

    2001-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  5. Chromatin Repressive Complexes in Stem Cells, Development, and Cancer

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles...

  6. Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Saera Hihara

    2012-12-01

    Full Text Available Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms, which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.

  7. The possible role of chromatin conformation changes in adaptive responses to ionizing radiation

    International Nuclear Information System (INIS)

    Ekhtiar, A.; Ammer, A.; Jbawi, A.; Othman, A.

    2012-05-01

    Organisms are affected by different DNA damaging agents naturally present in the environment or released as a result of human activity. Many defense mechanisms have evolved in organisms to minimize genotoxic damage. One of them is induced radioresistance or adaptive response. The adaptive response could be considered as a nonspecific phenomenon in which exposure to minimal stress could result in increased resistance to higher levels of the same or to other types of stress some hours later. A better understanding of the molecular mechanism underlying the adaptive response may lead to an improvement of cancer treatment, risk assessment and risk management strategies, radiation protection. The aim of current study was to study the possible role of chromatin conformation changes induced by ionizing radiation on the adaptive responses in human lymphocyte. For this aim the chromatin conformation have been studied in human lymphocytes from three non-smoking and three smoking healthy volunteers prior, and after espouser to gamma radiation (adaptive dose 0.1 Gy, challenge dose 1.5 Gy and adaptive + dose challenge). Chromosomal aberrations and micronucleus have been used as end point to study radio cytotoxicity and adaptive response. Our results indicated individual differences in radio adaptive response and the level of this response was dependent of chromatin de condensation induced by a adaptive small dose.The results showed that different dose of gamma rays induce a chromatin de condensation in human lymphocyte. The maximum chromatin relaxation were record when lymphocyte exposed to adaptive dose (0.1 Gy.). Results also showed that Adaptive dose have affected on the induction of challenge dose (1.5 Gy) of chromosome aberration and micronucleus . The comparison of results of chromatin de condensation induction as measured by flow cytometry and cytogenetic damages measured by chromosomal aberrations or micronucleus, was showed a proportionality of adaptive response with

  8. Chromatin organisation and cancer prognosis: a pan-cancer study.

    Science.gov (United States)

    Kleppe, Andreas; Albregtsen, Fritz; Vlatkovic, Ljiljana; Pradhan, Manohar; Nielsen, Birgitte; Hveem, Tarjei S; Askautrud, Hanne A; Kristensen, Gunnar B; Nesbakken, Arild; Trovik, Jone; Wæhre, Håkon; Tomlinson, Ian; Shepherd, Neil A; Novelli, Marco; Kerr, David J; Danielsen, Håvard E

    2018-03-01

    cohort (HR 1·7, 95% CI 1·1-2·5, in the discovery cohort; 1·9, 1·1-3·2, in the Gloucester validation cohort; 2·6, 1·2-5·6, in the QUASAR 2 cohort; 1·8, 1·1-3·0, for ovarian carcinoma; 1·6, 1·0-2·4, for uterine sarcoma; 1·43, 0·68-2·99, for prostate carcinoma; and 1·9, 1·1-3·1, for endometrial carcinoma). Chromatin heterogeneity was a significant predictor of cancer-specific survival in microsatellite unstable (HR 2·9, 95% CI 1·0-8·4) and microsatellite stable (1·8, 1·2-2·7) stage II colorectal cancer, but microsatellite instability was not a significant predictor of outcome in chromatin homogeneous (1·3, 0·7-2·4) or chromatin heterogeneous (0·8, 0·3-2·0) stage II colorectal cancer. The consistent prognostic prediction of Nucleotyping in different biological and technical circumstances suggests that the marker of chromatin heterogeneity can be reliably assessed in routine clinical practice and could be used to objectively assist decision making in a range of clinical settings. An immediate application would be to identify high-risk patients with stage II colorectal cancer who might have greater absolute benefit from adjuvant chemotherapy. Clinical trials are warranted to evaluate the survival benefit and cost-effectiveness of using Nucleotyping to guide treatment decisions in multiple clinical settings. The Research Council of Norway, the South-Eastern Norway Regional Health Authority, the National Institute for Health Research, and the Wellcome Trust. Copyright © 2018 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC-BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.

  9. Chromatin conformation capture strategies in molecular diagnostics

    NARCIS (Netherlands)

    de Vree, Pauline J.P.

    2015-01-01

    In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or

  10. EBV Latency Types Adopt Alternative Chromatin Conformations

    Science.gov (United States)

    Tempera, Italo; Klichinsky, Michael; Lieberman, Paul M.

    2011-01-01

    Epstein-Barr Virus (EBV) can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C) assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp) or type III (Cp) gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer. PMID:21829357

  11. EBV latency types adopt alternative chromatin conformations.

    Directory of Open Access Journals (Sweden)

    Italo Tempera

    2011-07-01

    Full Text Available Epstein-Barr Virus (EBV can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp or type III (Cp gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer.

  12. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively...

  13. On the underlying gauge group structure of D=11 supergravity

    International Nuclear Information System (INIS)

    Bandos, I.A.; Azcarraga, J.A. de; Izquierdo, J.M.; Picon, M.; Varela, O.

    2004-01-01

    The underlying gauge group structure of D=11 supergravity is revisited. It may be described by a one-parametric family of Lie supergroups Σ-bar (s)x-bar SO(1,10), s 0. The family of superalgebras E-bar (s) associated to Σ-bar (s) is given by a family of extensions of the M-algebra {Pa,Qα,Zab,Za1...a5} by an additional fermionic central charge Qα'. The Chevalley-Eilenberg four-cocycle ω4∼Πα-bar Πβ-bar Πa-bar ΠbΓabαβ on the standard D=11 supersymmetry algebra may be trivialized on E-bar (s), and this implies that the three-form field A3 of D=11 supergravity may be expressed as a composite of the Σ-bar (s) one-form gauge fields ea, ψα, Bab, Ba1...a5 and ηα. Two superalgebras of E-bar (s) recover the two earlier D'Auria and Fre decompositions of A3. Another member of E-bar (s) allows for a simpler composite structure for A3 that does not involve the Ba1...a5 field. Σ-bar (s) is a deformation of Σ-bar (0), which is singularized by having an enhanced Sp(32) (rather than just SO(1,10)) automorphism symmetry and by being an expansion of OSp(1 vertical bar 32)

  14. Analysis of Dynamic Properties of Piezoelectric Structure under Impact Load

    Directory of Open Access Journals (Sweden)

    Taotao Zhang

    2015-10-01

    Full Text Available An analytical model of the dynamic properties is established for a piezoelectric structure under impact load, without considering noise and perturbations in this paper. Based on the general theory of piezo-elasticity and impact mechanics, the theoretical solutions of the mechanical and electrical fields of the smart structure are obtained with the standing and traveling wave methods, respectively. The comparisons between the two methods have shown that the standing wave method is better for studying long-time response after an impact load. In addition, good agreements are found between the theoretical and the numerical results. To simulate the impact load, both triangle and step pulse loads are used and comparisons are given. Furthermore, the influence of several parameters is discussed so as to provide some advices for practical use. It can be seen that the proposed analytical model would benefit, to some extent, the design and application (especially the airport runway of the related smart devices by taking into account their impact load performance.

  15. Quantitative analysis of nucleolar chromatin distribution in the complex convoluted nucleoli of Didinium nasutum (Ciliophora).

    Science.gov (United States)

    Leonova, Olga G; Karajan, Bella P; Ivlev, Yuri F; Ivanova, Julia L; Skarlato, Sergei O; Popenko, Vladimir I

    2013-01-01

    We have earlier shown that the typical Didinium nasutum nucleolus is a complex convoluted branched domain, comprising a dense fibrillar component located at the periphery of the nucleolus and a granular component located in the central part. Here our main interest was to study quantitatively the spatial distribution of nucleolar chromatin structures in these convoluted nucleoli. There are no "classical" fibrillar centers in D.nasutum nucleoli. The spatial distribution of nucleolar chromatin bodies, which play the role of nucleolar organizers in the macronucleus of D.nasutum, was studied using 3D reconstructions based on serial ultrathin sections. The relative number of nucleolar chromatin bodies was determined in macronuclei of recently fed, starved D.nasutum cells and in resting cysts. This parameter is shown to correlate with the activity of the nucleolus. However, the relative number of nucleolar chromatin bodies in different regions of the same convoluted nucleolus is approximately the same. This finding suggests equal activity in different parts of the nucleolar domain and indicates the existence of some molecular mechanism enabling it to synchronize this activity in D. nasutum nucleoli. Our data show that D. nasutum nucleoli display bipartite structure. All nucleolar chromatin bodies are shown to be located outside of nucleoli, at the periphery of the fibrillar component.

  16. Evaluation of chromatin integrity of motile bovine spermatozoa capacitated in vitro.

    Science.gov (United States)

    Reckova, Z; Machatkova, M; Rybar, R; Horakova, J; Hulinska, P; Machal, L

    2008-08-01

    The efficiency of in vitro embryo production is highly variable amongst individual sires in cattle. To eliminate that this variability is not caused by sperm chromatin damage caused by separation or capacitacion, chromatin integrity was evaluated. Seventeen of AI bulls with good NRRs but variable embryo production efficiency were used. For each bull, motile spermatozoa were separated on a Percoll gradient, resuspended in IVF-TALP medium and capacitated with or incubated without heparin for 6 h. Samples before and after separation and after 3-h and 6-h capacitacion or incubation were evaluated by the Sperm Chromatin Structure Assay (SCSA) and the proportion of sperm with intact chromatin structure was calculated. Based on changes in the non-DFI-sperm proportion, the sires were categorized as DNA-unstable (DNA-us), DNA-stable (DNA-s) and DNA-most stable (DNA-ms) bulls (n=3, n=5 and n=9, respectively). In DNA-us bulls, separation produced a significant increase of the mean non-DFI-sperm proportion (p Capacitacion produced a significant decrease in the mean non-DFI-sperm proportion in H+ sperm (p capacitacion, the mean non-DFI-sperm proportion remained almost unchanged. In DNA-ms bulls, neither separation nor capacitacion had any effect on the mean non-DFI-sperm proportion. It can be concluded that, although separation and capacitacion may produce some changes in sperm chromatin integrity, these are not associated with different in vitro fertility of the bulls involved.

  17. The Chromatin Scaffold Protein SAFB1 Renders Chromatin Permissive for DNA Damage Signaling

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Toledo Lazaro, Luis Ignacio; Gudjonsson, Thorkell

    2013-01-01

    Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify...... the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly......(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological...

  18. Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts.

    Science.gov (United States)

    Babbitt, G A

    2010-10-15

    The spurious (or nonfunctional) binding of transcription factors (TF) to the wrong locations on DNA presents a formidable challenge to genomes given the relatively low ceiling for sequence complexity within the short lengths of most binding motifs. The high potential for the occurrence of random motifs and subsequent nonfunctional binding of many transcription factors should theoretically lead to natural selection against the occurrence of spurious motif throughout the genome. However, because of the active role that chromatin can influence over eukaryotic gene regulation, it may also be expected that many supposed spurious binding sites could escape purifying selection if (A) they simply occur in regions of high nucleosome occupancy or (B) their surrounding chromatin was dynamically involved in their identity and function. We compared nucleosome occupancy and the presence/absence of functionally conserved chromatin context to the strength of selection against spurious binding of various TF binding motifs in Saccharomyces yeast. While we find no direct relationship with nucleosome occupancy, we find strong evidence that transcription factors spatially associated with evolutionarily conserved chromatin states are under relaxed selection against accidental binding. Transcription factors (with/without) a conserved chromatin context were found to occur on average, (87.7%/49.3%) of their expected frequencies. Functional binding motifs with conserved chromatin contexts were also significantly shorter in length and more often clustered. These results indicate a role of chromatin context dependency in relaxing selection against spurious binding in nearly half of all TF binding motifs throughout the yeast genome. 2010 Elsevier B.V. All rights reserved.

  19. FGF signalling regulates chromatin organisation during neural differentiation via mechanisms that can be uncoupled from transcription.

    Directory of Open Access Journals (Sweden)

    Nishal S Patel

    Full Text Available Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset. Conversely, down-regulation of Fgf8 as neural differentiation commences correlates with a more peripheral nuclear position of this locus. During normal neural differentiation, fibroblast growth factor (FGF signalling is repressed by retinoic acid, and this vitamin A derivative is further required for transcription of neural genes. We show here that exposure to retinoic acid or inhibition of FGF signalling promotes precocious decompaction and central nuclear positioning of differentiation gene loci. Using the Raldh2 mutant as a model for retinoid deficiency, we further find that such changes in higher order chromatin organisation are dependent on retinoid signalling. In this retinoid deficient condition, FGF signalling persists ectopically in the elongating body, and importantly, we find that inhibiting FGF receptor (FGFR signalling in Raldh2-/- embryos does not rescue differentiation gene transcription, but does elicit both chromatin decompaction and nuclear position change. These findings demonstrate that regulation of higher order chromatin organisation during differentiation in the embryo can be uncoupled from the machinery that promotes transcription and, for the first time, identify FGF as an extrinsic signal that

  20. A comparison of the effect of lead nitrate on rat liver chromatin, DNA and histone proteins in solution.

    Science.gov (United States)

    Rabbani-Chadegani, Azra; Abdosamadi, Sayeh; Fani, Nesa; Mohammadian, Shayesteh

    2009-06-01

    Although lead is widely recognized as a toxic substance in the environment and directly damage DNA, no studies are available on lead interaction with chromatin and histone proteins. In this work, we have examined the effect of lead nitrate on EDTA-soluble chromatin (SE chromatin), DNA and histones in solution using absorption and fluorescence spectroscopy, thermal denaturation and gel electrophoresis techniques. The results demonstrate that lead nitrate binds with higher affinity to chromatin than to DNA and produces an insoluble complex as monitored at 400 nm. Binding of lead to DNA decreases its Tm, increases its fluorescence intensity and exhibits hypochromicity at 210 nm which reveal that both DNA bases and the backbone participate in the lead-DNA interaction. Lead also binds strongly to histone proteins in the absence of DNA. The results suggest that although lead destabilizes DNA structure, in the chromatin, the binding of lead introduces some sort of compaction and aggregation, and the histone proteins play a key role in this aspect. This chromatin condensation, upon lead exposure, in turn may decrease fidelity of DNA, and inhibits DNA and RNA synthesis, the process that introduces lead toxicity at the chromatin level.

  1. The N-terminal domain determines the affinity and specificity of H1 binding to chromatin

    International Nuclear Information System (INIS)

    Öberg, Christine; Belikov, Sergey

    2012-01-01

    Highlights: ► wt Human histone H1.4 and hH1.4 devoid of N-terminal domain, ΔN-hH1.4, were compared. ► Both histones bind to chromatin, however, ΔN-hH1.4 displays lower binding affinity. ► Interaction of ΔN-hH1.4 with chromatin includes a significant unspecific component. ► N-terminal domain is a determinant of specificity of histone H1 binding to chromatin. -- Abstract: Linker histone H1, one of the most abundant nuclear proteins in multicellular eukaryotes, is a key component of the chromatin structure mainly due to its role in the formation and maintenance of the 30 nm chromatin fiber. It has a three-domain structure; a central globular domain flanked by a short N-terminal domain and a long, highly basic C-terminal domain. Previous studies have shown that the binding abilities of H1 are at large determined by the properties of the C-terminal domain; much less attention has been paid to role of the N-terminal domain. We have previously shown that H1 can be reconstituted via cytoplasmic mRNA injection in Xenopus oocytes, cells that lack somatic H1. The heterologously expressed H1 proteins are incorporated into in vivo assembled chromatin at specific sites and the binding event is monitored as an increase in nucleosomal repeat length (NRL). Using this setup we have here compared the binding properties of wt-H1.4 and hH1.4 devoid of its N-terminal domain (ΔN-hH1.4). The ΔN-hH1.4 displays a drastically lower affinity for chromatin binding as compared to the wild type hH1.4. Our data also indicates that ΔN-hH1.4 is more prone to unspecific chromatin binding than the wild type. We conclude that the N-terminal domain of H1 is an important determinant of affinity and specificity of H1-chromatin interactions.

  2. Oriented matroids—combinatorial structures underlying loop quantum gravity

    Science.gov (United States)

    Brunnemann, Johannes; Rideout, David

    2010-10-01

    We analyze combinatorial structures which play a central role in determining spectral properties of the volume operator (Ashtekar A and Lewandowski J 1998 Adv. Theor. Math. Phys. 1 388) in loop quantum gravity (LQG). These structures encode geometrical information of the embedding of arbitrary valence vertices of a graph in three-dimensional Riemannian space and can be represented by sign strings containing relative orientations of embedded edges. We demonstrate that these signature factors are a special representation of the general mathematical concept of an oriented matroid (Ziegler G M 1998 Electron. J. Comb.; Björner A et al 1999 Oriented Matroids (Cambridge: Cambridge University Press)). Moreover, we show that oriented matroids can also be used to describe the topology (connectedness) of directed graphs. Hence, the mathematical methods developed for oriented matroids can be applied to the difficult combinatorics of embedded graphs underlying the construction of LQG. As a first application we revisit the analysis of Brunnemann and Rideout (2008 Class. Quantum Grav. 25 065001 and 065002), and find that enumeration of all possible sign configurations used there is equivalent to enumerating all realizable oriented matroids of rank 3 (Ziegler G M 1998 Electron. J. Comb.; Björner A et al 1999 Oriented Matroids (Cambridge: Cambridge University Press)), and thus can be greatly simplified. We find that for 7-valent vertices having no coplanar triples of edge tangents, the smallest non-zero eigenvalue of the volume spectrum does not grow as one increases the maximum spin jmax at the vertex, for any orientation of the edge tangents. This indicates that, in contrast to the area operator, considering large jmax does not necessarily imply large volume eigenvalues. In addition we give an outlook to possible starting points for rewriting the combinatorics of LQG in terms of oriented matroids.

  3. Fragmentation of chromatin DNA in mouse thymus cells after whole body γ-irradiation

    International Nuclear Information System (INIS)

    Wei Kang; Liu Xueying; Zhu Xuefen

    1984-01-01

    The characteristics of soluble chromatin in mouse thymus nuclei after whole body γ-irradiation were investigated by means of polyacrylamide gel electrophoresis. After deproteinization and electrophoresis eight regular DNA bands were revealed. The molecular weights of these bands were estimated by comparing their migration rates with those of the standard fragments obtained from PBR 322 digested completely by restrictive endonuclease Hae III. The molecular weight of the first band was calculated to be 186 base pairs corresponding approximately to the size of DNA fragment from a single nucleosome, and those of other bands appeared to be its multiples. The results suggested that the disintegration of chromatin DNA after γ-irradiation might have occurred at the linkage regions of chromatin. The autolysis product of normal thymus chromatin under sterile condition were also analyzed and its electrophoretic pattern was found to be just the same as that of the postirradiation product. It seems, therefore, that the endonuclease existing in normal tissues might be responsible for the postirradiation chromatin degradation. The mechanism of this kind of enzymatic digestion remains to be elucidated in further investigation. (author)

  4. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells.

    Science.gov (United States)

    Daer, René M; Cutts, Josh P; Brafman, David A; Haynes, Karmella A

    2017-03-17

    In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.

  5. The Network Structure Underlying the Earth Observation Assessment

    Science.gov (United States)

    Vitkin, S.; Doane, W. E. J.; Mary, J. C.

    2017-12-01

    The Earth Observations Assessment (EOA 2016) is a multiyear project designed to assess the effectiveness of civil earth observation data sources (instruments, sensors, models, etc.) on societal benefit areas (SBAs) for the United States. Subject matter experts (SMEs) provided input and scored how data sources inform products, product groups, key objectives, SBA sub-areas, and SBAs in an attempt to quantify the relationships between data sources and SBAs. The resulting data were processed by Integrated Applications Incorporated (IAI) using MITRE's PALMA software to create normalized relative impact scores for each of these relationships. However, PALMA processing obscures the natural network representation of the data. Any network analysis that might identify patterns of interaction among data sources, products, and SBAs is therefore impossible. Collaborating with IAI, we cleaned and recreated a network from the original dataset. Using R and Python we explore the underlying structure of the network and apply frequent itemset mining algorithms to identify groups of data sources and products that interact. We reveal interesting patterns and relationships in the EOA dataset that were not immediately observable from the EOA 2016 report and provide a basis for further exploration of the EOA network dataset.

  6. Structure activity relationships to assess new chemicals under TSCA

    Energy Technology Data Exchange (ETDEWEB)

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  7. Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction.

    Science.gov (United States)

    Dukowic-Schulze, Stefanie; Liu, Chang; Chen, Changbin

    2018-01-01

    DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.

  8. ATP-dependent chromatin remodeling in the DNA-damage response

    Directory of Open Access Journals (Sweden)

    Lans Hannes

    2012-01-01

    Full Text Available Abstract The integrity of DNA is continuously challenged by metabolism-derived and environmental genotoxic agents that cause a variety of DNA lesions, including base alterations and breaks. DNA damage interferes with vital processes such as transcription and replication, and if not repaired properly, can ultimately lead to premature aging and cancer. Multiple DNA pathways signaling for DNA repair and DNA damage collectively safeguard the integrity of DNA. Chromatin plays a pivotal role in regulating DNA-associated processes, and is itself subject to regulation by the DNA-damage response. Chromatin influences access to DNA, and often serves as a docking or signaling site for repair and signaling proteins. Its structure can be adapted by post-translational histone modifications and nucleosome remodeling, catalyzed by the activity of ATP-dependent chromatin-remodeling complexes. In recent years, accumulating evidence has suggested that ATP-dependent chromatin-remodeling complexes play important, although poorly characterized, roles in facilitating the effectiveness of the DNA-damage response. In this review, we summarize the current knowledge on the involvement of ATP-dependent chromatin remodeling in three major DNA repair pathways: nucleotide excision repair, homologous recombination, and non-homologous end-joining. This shows that a surprisingly large number of different remodeling complexes display pleiotropic functions during different stages of the DNA-damage response. Moreover, several complexes seem to have multiple functions, and are implicated in various mechanistically distinct repair pathways.

  9. Acetylation-Dependent Chromatin Reorganization by BRDT, a Testis-Specific Bromodomain-Containing Protein

    Science.gov (United States)

    Pivot-Pajot, Christophe; Caron, Cécile; Govin, Jérôme; Vion, Alexandre; Rousseaux, Sophie; Khochbin, Saadi

    2003-01-01

    The association between histone acetylation and replacement observed during spermatogenesis prompted us to consider the testis as a source for potential factors capable of remodelling acetylated chromatin. A systematic search of data banks for open reading frames encoding testis-specific bromodomain-containing proteins focused our attention on BRDT, a testis-specific protein of unknown function containing two bromodomains. BRDT specifically binds hyperacetylated histone H4 tail depending on the integrity of both bromodomains. Moreover, in somatic cells, the ectopic expression of BRDT triggered a dramatic reorganization of the chromatin only after induction of histone hyperacetylation by trichostatin A (TSA). We then defined critical domains of BRDT involved in its activity. Both bromodomains of BRDT, as well as flanking regions, were found indispensable for its histone acetylation-dependent remodelling activity. Interestingly, we also observed that recombinant BRDT was capable of inducing reorganization of the chromatin of isolated nuclei in vitro only when the nuclei were from TSA-treated cells. This assay also allowed us to show that the action of BRDT was ATP independent, suggesting a structural role for the protein in the remodelling of acetylated chromatin. This is the first demonstration of a large-scale reorganization of acetylated chromatin induced by a specific factor. PMID:12861021

  10. Effect of ultraviolet irradiation on chromatin and its components from Yoshida ascites tumour cells

    International Nuclear Information System (INIS)

    Ramakrishnan, N.; Patil, M.S.; Pradhan, D.S.

    1981-01-01

    A study has been made of the effect of U.V. irradiation on Yoshida ascites tumour chromatin and its non-DNA components. The extractability of total histones was increased from 6% to 17% with an increase in U.V. incident radiation dose from 500J/m 2 to 2000J/m 2 . The polyacrylamide gel electrophoresis pattern of chromosomal proteins was examined after irradiation of the chromatin, and the effect of U.V. irradiation of chromatin on histones was also investigated. The results indicated that cross-linking of DNA with chromosomal proteins is an important category of U.V. radiation-induced lesions discerned in U.V. irradiated chromatin. Histones and several non-histone proteins seemed to undergo U.V. radiation-induced cross-linking with DNA, which was taken as indicative of their close association with DNA in the chromatin structure. It is suggested that the cross-link formation between DNA and non-histone proteins may be due to sequence-specific association of non-histone proteins with DNA. (U.K.)

  11. Chromatin dynamics in Pollen Mother Cells underpin a common scenario at the somatic-to-reproductive fate transition of both the male and female lineages in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Wenjing eShe

    2015-04-01

    Full Text Available Unlike animals, where the germline is established early during embryogenesis, plants set aside their reproductive lineage late in development in dedicated floral organs. The specification of pollen mother cells (PMCs committed to meiosis takes place in the sporogenous tissue in anther locules and marks the somatic-to-reproductive cell fate transition towards the male reproductive lineage. Here we show that Arabidopsis PMCs differentiation is accompanied by large-scale changes in chromatin organization. This is characterized by significant increase in nuclear volume, chromatin decondensation, reduction in heterochromatin, eviction of linker histones and the H2AZ histone variant. These structural alterations are accompanied by dramatic, quantitative changes in histone modifications levels compared to that of surrounding somatic cells that do not share a sporogenic fate. All these changes are highly reminiscent of those we have formerly described in female megaspore mother cells (MMCs. This indicates that chromatin reprogramming is a common underlying scenario in the somatic-to-reproductive cell fate transition in both male and female lineages.

  12. Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations.

    Directory of Open Access Journals (Sweden)

    Ashwat Visvanathan

    Full Text Available The organisation of the large volume of mammalian genomic DNA within cell nuclei requires mechanisms to regulate chromatin compaction involving the reversible formation of higher order structures. The compaction state of chromatin varies between interphase and mitosis and is also subject to rapid and reversible change upon ATP depletion/repletion. In this study we have investigated mechanisms that may be involved in promoting the hyper-condensation of chromatin when ATP levels are depleted by treating cells with sodium azide and 2-deoxyglucose. Chromatin conformation was analysed in both live and permeabilised HeLa cells using FLIM-FRET, high resolution fluorescence microscopy and by electron spectroscopic imaging microscopy. We show that chromatin compaction following ATP depletion is not caused by loss of transcription activity and that it can occur at a similar level in both interphase and mitotic cells. Analysis of both live and permeabilised HeLa cells shows that chromatin conformation within nuclei is strongly influenced by the levels of divalent cations, including calcium and magnesium. While ATP depletion results in an increase in the level of unbound calcium, chromatin condensation still occurs even in the presence of a calcium chelator. Chromatin compaction is shown to be strongly affected by small changes in the levels of polyamines, including spermine and spermidine. The data are consistent with a model in which the increased intracellular pool of polyamines and divalent cations, resulting from depletion of ATP, bind to DNA and contribute to the large scale hyper-compaction of chromatin by a charge neutralisation mechanism.

  13. Chromatin changes in response to drought, salinity, heat, and cold stresses in plants

    Directory of Open Access Journals (Sweden)

    Jong-Myong eKim

    2015-03-01

    Full Text Available Chromatin regulation is essential to regulate genes and genome activities. In plants, the alteration of histone modification and DNA methylation are coordinated with changes in the expression of stress-responsive genes to adapt to environmental changes. Several chromatin regulators have been shown to be involved in the regulation of stress-responsive gene networks under abiotic stress conditions. Specific histone modification sites and the histone modifiers that regulate key stress-responsive genes have been identified by genetic and biochemical approaches, revealing the importance of chromatin regulation in plant stress responses. Recent studies have also suggested that histone modification plays an important role in plant stress memory. In this review, we summarize recent progress on the regulation and alteration of histone modification (acetylation, methylation, phosphorylation, and SUMOylation in response to the abiotic stresses, drought, high-salinity, heat, and cold in plants.

  14. Undifferentiated embryonic cell transcription factor 1 regulates ESC chromatin organization and gene expression

    DEFF Research Database (Denmark)

    Kooistra, Susanne M; van den Boom, Vincent; Thummer, Rajkumar P

    2010-01-01

    Previous reports showed that embryonic stem (ES) cells contain hyperdynamic and globally transcribed chromatin-properties that are important for ES cell pluripotency and differentiation. Here, we demonstrate a role for undifferentiated embryonic cell transcription factor 1 (UTF1) in regulating ES...... cell chromatin structure. Using chromatin immunoprecipitation-on-chip analysis, we identified >1,700 UTF1 target genes that significantly overlap with previously identified Nanog, Oct4, Klf-4, c-Myc, and Rex1 targets. Gene expression profiling showed that UTF1 knock down results in increased expression...... of a large set of genes, including a significant number of UTF1 targets. UTF1 knock down (KD) ES cells are, irrespective of the increased expression of several self-renewal genes, Leukemia inhibitory factor (LIF) dependent. However, UTF1 KD ES cells are perturbed in their differentiation in response...

  15. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  16. Studies on Pounding Response Considering Structure-Soil-Structure Interaction under Seismic Loads

    Directory of Open Access Journals (Sweden)

    Peizhen Li

    2017-12-01

    Full Text Available Pounding phenomena considering structure–soil–structure interaction (SSSI under seismic loads are investigated in this paper. Based on a practical engineering project, this work presents a three-dimensional finite element numerical simulation method using ANSYS software. According to Chinese design code, the models of adjacent shear wall structures on Shanghai soft soil with the rigid foundation, box foundation and pile foundation are built respectively. In the simulation, the Davidenkov model of the soil skeleton curve is assumed for soil behavior, and the contact elements with Kelvin model are adopted to simulate pounding phenomena between adjacent structures. Finally, the dynamic responses of adjacent structures considering the pounding and SSSI effects are analyzed. The results show that pounding phenomena may occur, indicating that the seismic separation requirement for adjacent buildings of Chinese design code may not be enough to avoid pounding effect. Pounding and SSSI effects worsen the adjacent buildings’ conditions because their acceleration and shear responses are amplified after pounding considering SSSI. These results are significant for studying the effect of pounding and SSSI phenomena on seismic responses of structures and national sustainable development, especially in earthquake prevention and disaster reduction.

  17. Interface stability of granular filter structures under currents

    NARCIS (Netherlands)

    Verheij, H.J.; Hoffmans, G.; Dorst, K.; Van de Sande, S.

    2012-01-01

    Granular filters are used for protection of structures against scour and erosion. For a proper functioning it is necessary that the interfaces between the filter structure, the subsoil and the water flowing above the filter structure are stable. Stability means that there is no transport of subsoil

  18. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

    KAUST Repository

    Jé gu, Teddy; Domenichini, Sé verine; Blein, Thomas; Ariel, Federico; Christ, Auré lie; Kim, SoonKap; Crespi, Martin; Boutet-Mercey, Sté phanie; Mouille, Gré gory; Bourge, Mickaë l; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cé cile; Benhamed, Moussa

    2015-01-01

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

  19. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

    KAUST Repository

    Jégu, Teddy

    2015-10-12

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

  20. Flow cytometric method for measuring chromatin fragmentation in fixed sperm from yellow perch (Perca flavescens).

    Science.gov (United States)

    Jenkins, J A; Draugelis-Dale, R O; Pinkney, A E; Iwanowicz, L R; Blazer, V S

    2015-03-15

    Declining harvests of yellow perch, Perca flavescens, in urbanized watersheds of Chesapeake Bay have prompted investigations of their reproductive fitness. The purpose of this study was to establish a flow cytometric technique for DNA analysis of fixed samples sent from the field to provide reliable gamete quality measurements. Similar to the sperm chromatin structure assay, measures were made on the susceptibility of nuclear DNA to acid-induced denaturation, but used fixed rather than live or thawed cells. Nuclei were best exposed to the acid treatment for 1 minute at 37 °C followed by the addition of cold (4 °C) propidium iodide staining solution before flow cytometry. The rationale for protocol development is presented graphically through cytograms. Field results collected in 2008 and 2009 revealed DNA fragmentation up to 14.5%. In 2008, DNA fragmentation from the more urbanized watersheds was significantly greater than from reference sites (P = 0.026) and in 2009, higher percentages of haploid testicular cells were noted from the less urbanized watersheds (P = 0.032) indicating better reproductive condition at sites with less urbanization. For both years, total and progressive live sperm motilities by computer-assisted sperm motion analysis ranged from 19.1% to 76.5%, being significantly higher at the less urbanized sites (P < 0.05). This flow cytometric method takes advantage of the propensity of fragmented DNA to be denatured under standard conditions, or 1 minute at 37 °C with 10% buffered formalin-fixed cells. The study of fixed sperm makes possible the restrospective investigation of germplasm fragmentation, spermatogenic ploidy patterns, and chromatin compaction levels from samples translocated over distance and time. The protocol provides an approach that can be modified for other species across taxa. Published by Elsevier Inc.

  1. Structural changes and intermolecular interactions of filled ice Ic structure for hydrogen hydrate under high pressure

    International Nuclear Information System (INIS)

    Machida, S; Hirai, H; Kawamura, T; Yamamoto, Y; Yagi, T

    2010-01-01

    High-pressure experiments of hydrogen hydrate were performed using a diamond anvil cell under conditions of 0.1-44.2 GPa and at room temperature. Also, high pressure Raman studies of solid hydrogen were performed in the pressure range of 0.1-43.7 GPa. X-ray diffractometry (XRD) for hydrogen hydrate revealed that a known high-pressure structure, filled ice Ic structure, of hydrogen hydrate transformed to a new high-pressure structure at approximately 35-40 GPa. A comparison of the Raman spectroscopy of a vibron for hydrogen molecules between hydrogen hydrate and solid hydrogen revealed that the extraction of hydrogen molecules from hydrogen hydrate occurred above 20 GPa. Also, the Raman spectra of a roton revealed that the rotation of hydrogen molecules in hydrogen hydrate was suppressed at around 20 GPa and that the rotation recovered under higher pressure. These results indicated that remarkable intermolecular interactions in hydrogen hydrate between neighboring hydrogen molecules and between guest hydrogen molecules and host water molecules might occur. These intermolecular interactions could produce the stability of hydrogen hydrate.

  2. Local structure and structural signature underlying properties in metallic glasses and supercooled liquids

    Science.gov (United States)

    Ding, Jun

    Metallic glasses (MGs), discovered five decades ago as a newcomer in the family of glasses, are of current interest because of their unique structures and properties. There are also many fundamental materials science issues that remain unresolved for metallic glasses, as well as their predecessor above glass transition temperature, the supercooled liquids. In particular, it is a major challenge to characterize the local structure and unveil the structure-property relationship for these amorphous materials. This thesis presents a systematic study of the local structure of metallic glasses as well as supercooled liquids via classical and ab initio molecular dynamics simulations. Three typical MG models are chosen as representative candidate, Cu64 Zr36, Pd82Si18 and Mg65Cu 25Y10 systems, while the former is dominant with full icosahedra short-range order and the prism-type short-range order dominate for latter two. Furthermore, we move to unravel the underlying structural signature among several properties in metallic glasses. Firstly, the temperature dependence of specific heat and liquid fragility between Cu-Zr and Mg-Cu-Y (also Pd-Si) in supercooled liquids are quite distinct: gradual versus fast evolution of specific heat and viscosity/relaxation time with undercooling. Their local structural ordering are found to relate with the temperature dependence of specific heat and relaxation time. Then elastic heterogeneity has been studied to correlate with local structure in Cu-Zr MGs. Specifically, this part covers how the degree of elastic deformation correlates with the internal structure at the atomic level, how to quantitatively evaluate the local solidity/liquidity in MGs and how the network of interpenetrating connection of icosahedra determine the corresponding shear modulus. Finally, we have illustrated the structure signature of quasi-localized low-frequency vibrational normal modes, which resides the intriguing vibrational properties in MGs. Specifically, the

  3. [Effect of irradiation on the degradation of rat thymocyte chromatin].

    Science.gov (United States)

    Tsudzevich, B O; Parkhomets', Iu P; Andriĭchuk, T R; Iurkina, V V

    1998-01-01

    Genome instability of adaptive nature is formed under the experimental influence on a cell. Under critical conditions, strategy of organism is to damage the cells that cannot be restored and controlled by including the program of apoptosis. The ordered internucleosomal DNA degradation is considered to be one of the proof attributes of immunocompetent cell apoptosis. We investigated the effects of various doses of irradiation on the thymocytes chromatine fragmentation in 1,2,3 hours after a single X-ray exposure or after chronic influence in conditions of Chernobyl research base. By the means of electrophoresis in agarose and judging by polydeoxyribonucleotides accumulation we observed the "ladder pattern" of degradation in 3 hr after single 1 Gr irradiation (the smallest dose displaying the effect). We suppose that the influence of both chronic low-intensity irradiation taking place in Chernobyl and single X-ray exposure result in intensifying of DNA fragmentation in the cells of immunocompetent organs.

  4. Structural integrity of a reinforced concrete structure and a pipe outlet under hydrogen detonation conditions

    International Nuclear Information System (INIS)

    Saarenheimo, A.; Silde, A.; Calonius, K.

    2002-05-01

    Structural integrity of a reinforced concrete wall and a pipe penetration under detonation conditions in a selected reactor building room of Olkiluoto BWR were studied. Hydrogen leakage from the pressurised containment to the sur rounding reactor building is possible during a severe accident. Leaked hydrogen tends to accumulate in the reactor building rooms where the leak is located leading to a stable stratification and locally very high hydrogen concentration. If ignited, a possibility to flame acceleration and detonation cannot be ruled out. The structure may survive the peak detonation transient because the eigenperiod of the structure is considerably longer than the duration of the peak detonation. However, the relatively slowly decreasing static type pressure after a peak detonation damages the wall more severely. Elastic deformations in reinforcement are recoverable and cracks in these areas will close after the pressure decrease. But there will be remarkable compression crushing and the static type slowly decreasing over pressure clearly exceeds the loading capacity of the wall. Structural integrity of a pipe outlet was considered also under detonation conditions. The effect of drag forces was taken into account. Damping and strain rate dependence of yield strength were not taken into consideration. The boundary condition at the end of the pipe line model was varied in order to find out the effect of the stiffness of the pipeline outside the calculation model. The calculation model where the lower pipe end is free to move axially, is conservative from the pipe penetration integrity point of view. Even in this conservative study, the highest peak value for the maximum plastic deformation is 3.5%. This is well below the success criteria found in literature. (au)

  5. Optimization and anti-optimization of structures under uncertainty

    National Research Council Canada - National Science Library

    Elishakoff, Isaac; Ohsaki, Makoto

    2010-01-01

    The volume presents a collaboration between internationally recognized experts on anti-optimization and structural optimization, and summarizes various novel ideas, methodologies and results studied over 20 years...

  6. Structural convergence under reversible and irreversible monetary unification

    NARCIS (Netherlands)

    Beetsma, R.M.W.J.; Jensen, H.

    2003-01-01

    We explore endogenous monetary unification in the context of a model in which a country with serious structural distortions (and, hence, high inflation) is admitted into a monetary union once its economic structure has converged sufficiently towards that of the existing participants. If unification

  7. Structural convergence under reversible and irreversible monetary unification

    NARCIS (Netherlands)

    Beetsma, R.M.W.J.; Jensen, H.

    1999-01-01

    We explore endogenous monetary unification in the context of a model in which a country with serious structural distortions (and, hence, high inflation) is admitted into a monetary union once its economic structure has converged sufficiently towards that of the existing participants. If unification

  8. Tuned mass absorbers on damped structures under random load

    DEFF Research Database (Denmark)

    Krenk, Steen; Høgsberg, Jan Becker

    2008-01-01

    the mass ratio alone, and the damping can be determined subsequently. Only approximate results are available for the influence of damping in the original structure, typically in the form of series expansions. In the present paper it is demonstrated that for typical mass ratios in the order of a few percent......A substantial literature exists on the optimal choice of parameters of a tuned mass absorber on a structure excited by a force or by ground acceleration with random characteristics in the form of white noise. In the absence of structural damping the optimal frequency tuning is determined from...... for the response variance of a structure with initial damping in terms of the mass ratio and both damping ratios. Within this format the optimal tuning of the absorber turns out to be independent of the structural damping, and a simple explicit expression is obtained for the equivalent total damping....

  9. Analysis Of Masonry Infilled RC Frame Structures Under Lateral Loading

    Directory of Open Access Journals (Sweden)

    Barnaure Mircea

    2015-03-01

    Full Text Available Partition walls are often made of masonry in Romania. Although they are usually considered non-structural elements in the case of reinforced concrete framed structures, the infill panels contribute significantly to the seismic behaviour of the building. Their impact is difficult to assess, mainly because the interaction between the bounding frame and the infill is an intricate issue. This paper analyses the structural behaviour of a masonry infilled reinforced concrete frame system subjected to in - plane loading. Three numerical models are proposed and their results are compared in terms of stiffness and strength of the structure. The role of the openings in the infill panel on the behaviour is analysed and discussed. The effect of gaps between the frame and the infill on the structural behaviour is also investigated. Comparisons are made with the in-force Romanian and European regulations provisions.

  10. Submerged Fixed Floating Structure under the Action of Surface Current

    Directory of Open Access Journals (Sweden)

    Zhen Cui

    2018-01-01

    Full Text Available The implementation of floating structures has increased with the construction of new sluices for flood control. The overturning moment of floating structure and its influencing factors are the important parameters that determine the structural safety. It is essential to understand the overturning characteristics of these structures in currents. Based on hydrodynamic theory and equilibrium analysis, the hydraulic characteristics of a floating structure are discussed by means of theoretical analysis and experiments. A formula for the overturning moment is developed in terms of the time-averaged pressure on the structure. The corresponding parametric study aims to assess the effects of flow velocities, vertical positions, shape ratios and water levels on the overturning moment. The experimental results show that hydrodynamic factors have a significant influence on the overturning of the structure. Furthermore, a relationship is obtained between the overturning moment and the contributing parameters according to dimensional analysis and the linear fitting method of multidimensional ordinary least squares (OLS. The results predicted by the formula agree with the experimental results, demonstrating the potential for general applicability.

  11. Optimal Design of Composite Structures Under Manufacturing Constraints

    DEFF Research Database (Denmark)

    Marmaras, Konstantinos

    determination of the appropriate laminate thickness and the material choice in the structure. The optimal design problems that arise are stated as nonconvex mixed integer programming problems. We resort to different reformulation techniques to state the optimization problems as either linear or nonlinear convex....... The continuous relaxation of the mixed integer programming problems is being solved by an implementation of a primal–dual interior point method for nonlinear programming that updates the barrier parameter adaptively. The method is chosen for its excellent convergence properties and the ability of the method...... design phase results in structures with better structural performance reducing the need of manually post–processing the found designs....

  12. A role for chromatin topology in imprinted domain regulation.

    Science.gov (United States)

    MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

    2016-02-01

    Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

  13. Vacuum ultraviolet (VUV) absorption spectra of chromatin and its components

    International Nuclear Information System (INIS)

    Dodonova, N.Y.; Kiseleva, M.N.; Petrov, M.Y.; Tsyganenko, N.M.; Bubyakina, V.V.; Chikhirzhina, G.I.

    1984-01-01

    The electron absorption spectra of thin films of chromatin and chromatin components in the ultraviolet region (140-280 nm) were investigated. The absorption coefficients μ(lambda) of chromatin, nucleosomes with and without histone H1, total histones (TH), and DNA were compared. The spectra of nucleosomes differ from the sum-spectrum of DNA plus TH. The chromatin and nucleosome spectra are not similar in the spectral region of 190-160 nm. The lack of additivity of absorption coefficients at different wavelengths may be explained by different conformational changes of DNA, TH in nucleosomes and chromatin during the process of drying aqueous solutions for the preparation of thin films. The μ(lambda) values are useful for an estimate of the DNA and TH absorption in chromatin and nucleosomes in discussing UV and VUV irradiation damages. (Auth.)

  14. Harvesting Energy from Vibrations of the Underlying Structure

    DEFF Research Database (Denmark)

    Han, Bo; Vssilaras, S; Papadias, C.B.

    2013-01-01

    to the long-term structural health of a building or bridge, but at the same time they can be exploited as a power source to power the wireless sensors that are monitoring this structural health. This paper presents a new energy harvesting method based on a vibration driven electromagnetic harvester. By using......The use of wireless sensors for structural health monitoring offers several advantages such as small size, easy installation and minimal intervention on existing structures. However the most significant concern about such wireless sensors is the lifetime of the system, which depends heavily...... on the type of power supply. No matter how energy efficient the operation of a battery operated sensor is, the energy of the battery will be exhausted at some point. In order to achieve a virtually unlimited lifetime, the sensor node should be able to recharge its battery in an easy way. Energy harvesting...

  15. Structural analysis of reinforced concrete structures under monotonous and cyclic loadings: numerical aspects

    International Nuclear Information System (INIS)

    Lepretre, C.; Millard, A.; Nahas, G.

    1989-01-01

    The structural analysis of reinforced concrete structures is usually performed either by means of simplified methods of strength of materials type i.e. global methods, or by means of detailed methods of continuum mechanics type, i.e. local methods. For this second type, some constitutive models are available for concrete and rebars in a certain number of finite element systems. These models are often validated on simple homogeneous tests. Therefore, it is important to appraise the validity of the results when applying them to the analysis of a reinforced concrete structure, in order to be able to make correct predictions of the actual behaviour, under normal and faulty conditions. For this purpose, some tests have been performed at I.N.S.A. de Lyon on reinforced concrete beams, subjected to monotonous and cyclic loadings, in order to generate reference solutions to be compared with the numerical predictions given by two finite element systems: - CASTEM, developed by C.E.A./.D.E.M.T. - ELEFINI, developed by I.N.S.A. de Lyon

  16. Behavior of auxetic structures under compression and impact forces

    Science.gov (United States)

    Yang, Chulho; Vora, Hitesh D.; Chang, Young

    2018-02-01

    In recent years, various auxetic material structures have been designed and fabricated for diverse applications that utilize normal materials that follow Hooke’s law but still show the properties of negative Poisson’s ratios (NPR). One potential application is body protection pads that are comfortable to wear and effective in protecting body parts by reducing impact force and preventing injuries in high-risk individuals such as elderly people, industrial workers, law enforcement and military personnel, and athletes. This paper reports an integrated theoretical, computational, and experimental investigation conducted for typical auxetic materials that exhibit NPR properties. Parametric 3D CAD models of auxetic structures such as re-entrant hexagonal cells and arrowheads were developed. Then, key structural characteristics of protection pads were evaluated through static analyses of FEA models. Finally, impact analyses were conducted through dynamic simulations of FEA models to validate the results obtained from the static analyses. Efforts were also made to relate the individual and/or combined effect of auxetic structures and materials to the overall stiffness and shock-absorption performance of the protection pads. An advanced additive manufacturing (3D printing) technique was used to build prototypes of the auxetic structures. Three different materials typically used for fused deposition modeling technology, namely polylactic acid (PLA) and thermoplastic polyurethane material (NinjaFlex® and SemiFlex®), were used for different stiffness and shock-absorption properties. The 3D printed prototypes were then tested and the results were compared to the computational predictions. The results showed that the auxetic material could be effective in reducing the shock forces. Each structure and material combination demonstrated unique structural properties such as stiffness, Poisson’s ratio, and efficiency in shock absorption. Auxetic structures showed better shock

  17. Oxide glass structure evolution under swift heavy ion irradiation

    International Nuclear Information System (INIS)

    Mendoza, C.; Peuget, S.; Charpentier, T.; Moskura, M.; Caraballo, R.; Bouty, O.; Mir, A.H.; Monnet, I.; Grygiel, C.; Jegou, C.

    2014-01-01

    Highlights: • Structure of SHI irradiated glass is similar to the one of a hyper quenched glass. • D2 Raman band associated to 3 members ring is only observed in irradiated glass. • Irradiated state seems slightly different to an equilibrated liquid quenched rapidly. - Abstract: The effects of ion tracks on the structure of oxide glasses were examined by irradiating a silica glass and two borosilicate glass specimens containing 3 and 6 oxides with krypton ions (74 MeV) and xenon ions (92 MeV). Structural changes in the glass were observed by Raman and nuclear magnetic resonance spectroscopy using a multinuclear approach ( 11 B, 23 Na, 27 Al and 29 Si). The structure of irradiated silica glass resembles a structure quenched at very high temperature. Both borosilicate glass specimens exhibited depolymerization of the borosilicate network, a lower boron coordination number, and a change in the role of a fraction of the sodium atoms after irradiation, suggesting that the final borosilicate glass structures were quenched from a high temperature state. In addition, a sharp increase in the concentration of three membered silica rings and the presence of large amounts of penta- and hexacoordinate aluminum in the irradiated 6-oxide glass suggest that the irradiated glass is different from a liquid quenched at equilibrium, but it is rather obtained from a nonequilibrium liquid that is partially relaxed by very rapid quenching within the ion tracks

  18. Structural integrity analysis of an INPP building under external loading

    International Nuclear Information System (INIS)

    Dundulis, G.; Karalevicius, R.; Uspuras, E.; Kulak, R.F.; Marchertas, A.

    2005-01-01

    After the terrorist attacks in New York and Washington D. C. using civil airplanes, the evaluation of civil airplane crashes into civil and NPP structures has become very important. The interceptions of many terrorists' communications reveal that the use of commandeered commercial aircraft is still a major part of their plans for destruction. Aircraft crash or other flying objects in the territory of the Ignalina Nuclear Power Plant (INPP) represents a concern to the plant. Aircraft traveling at high velocity have a destructive potential. The aircraft crash may damage the roof and walls of buildings, pipelines, electric motors, cases of power supplies, power cables of electricity transmission and other elements and systems, which are important for safety. Therefore, the evaluation of the structural response to an of aircraft crash is important and was selected for analysis. The structural integrity analysis due to the effects of an aircraft crash on an NPP building structure is the subject of this paper. The finite element method was used for the structural analysis of a typical Ignalina NPP building. The structural integrity analysis was performed for a portion of the ALS using the dynamic loading of an aircraft crash impact model. The computer code NEPTUNE was used for this analysis. The local effects caused by impact of the aircraft's engine on the building wall were evaluated independently by using an empirical formula. (authors)

  19. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  20. Predicted crystal structures of molybdenum under high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bing; Zhang, Guang Biao [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China); Wang, Yuan Xu, E-mail: wangyx@henu.edu.cn [Institute for Computational Materials Science, School of Physics and Electronics, Henan University, Kaifeng 475004 (China); Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang 550018 (China)

    2013-04-15

    Highlights: ► A double-hexagonal close-packed (dhcp) structure of molybdenum is predicted. ► Calculated acoustic velocity confirms the bcc–dhcp phase transition at 660 GPa. ► The valence electrons of dhcp Mo are mostly localized in the interstitial sites. -- Abstract: The high-pressure structures of molybdenum (Mo) at zero temperature have been extensively explored through the newly developed particle swarm optimization (PSO) algorithm on crystal structural prediction. All the experimental and earlier theoretical structures were successfully reproduced in certain pressure ranges, validating our methodology in application to Mo. A double-hexagonal close-packed (dhcp) structure found by Mikhaylushkin et al. (2008) [12] is confirmed by the present PSO calculations. The lattice parameters and physical properties of the dhcp phase were investigated based on first principles calculations. The phase transition occurs only from bcc phase to dhcp phase at 660 GPa and at zero temperature. The calculated acoustic velocities also indicate a transition from the bcc to dhcp phases for Mo. More intriguingly, the calculated density of states (DOS) shows that the dhcp structure remains metallic. The calculated electron density difference (EDD) reveals that its valence electrons are localized in the interstitial regions.

  1. Training set optimization under population structure in genomic selection.

    Science.gov (United States)

    Isidro, Julio; Jannink, Jean-Luc; Akdemir, Deniz; Poland, Jesse; Heslot, Nicolas; Sorrells, Mark E

    2015-01-01

    Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

  2. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  3. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus.

    Science.gov (United States)

    Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F

    2017-07-07

    The cell nucleus must continually resist and respond to intercellular and intracellular mechanical forces to transduce mechanical signals and maintain proper genome organization and expression. Altered nuclear mechanics is associated with many human diseases, including heart disease, progeria, and cancer. Chromatin and nuclear envelope A-type lamin proteins are known to be key nuclear mechanical components perturbed in these diseases, but their distinct mechanical contributions are not known. Here we directly establish the separate roles of chromatin and lamin A/C and show that they determine two distinct mechanical regimes via micromanipulation of single isolated nuclei. Chromatin governs response to small extensions (<3 μm), and euchromatin/heterochromatin levels modulate the stiffness. In contrast, lamin A/C levels control nuclear strain stiffening at large extensions. These results can be understood through simulations of a polymeric shell and cross-linked polymer interior. Our results provide a framework for understanding the differential effects of chromatin and lamin A/C in cell nuclear mechanics and their alterations in disease. © 2017 Stephens et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  4. Chromatin- and temperature-dependent modulation of radiation-induced double-strand breaks.

    Science.gov (United States)

    Elmroth, K; Nygren, J; Stenerlöw, B; Hultborn, R

    2003-10-01

    To investigate the influence of chromatin organization and scavenging capacity in relation to irradiation temperature on the induction of double-strand breaks (DSB) in structures derived from human diploid fibroblasts. Agarose plugs with different chromatin structures (intact cells+/-wortmannin, permeabilized cells with condensed chromatin, nucleoids and DNA) were prepared and irradiated with X-rays at 2 or 37 degrees C and lysed using two different lysis protocols (new ice-cold lysis or standard lysis at 37 degrees C). Induction of DSB was determined by constant-field gel electrophoresis. The dose-modifying factor (DMF(temp)) for irradiation at 37 compared with 2 degrees C was 0.92 in intact cells (i.e. more DSB induced at 2 degrees C), but gradually increased to 1.5 in permeabilized cells, 2.2 in nucleoids and 2.6 in naked DNA, suggesting a role of chromatin organization for temperature modulation of DNA damage. In addition, DMF(temp) was influenced by the presence of 0.1 M DMSO or 30 mM glutathione, but not by post-irradiation temperature. The protective effect of low temperature was correlated to the indirect effects of ionizing radiation and was not dependent on post-irradiation temperature. Reasons for a dose modifying factor <1 in intact cells are discussed.

  5. Is there a relationship between the chromatin status and DNA fragmentation of boar spermatozoa following freezing-thawing?

    Science.gov (United States)

    Fraser, L; Strzezek, J

    2007-07-15

    In this study a radioisotope method, which is based on the quantitative measurements of tritiated-labeled actinomycin D ((3)H-AMD) incorporation into the sperm nuclei ((3)H-AMD incorporation assay), was used to assess the chromatin status of frozen-thawed boar spermatozoa. This study also tested the hypothesis that frozen-thawed spermatozoa with altered chromatin were susceptible to DNA fragmentation measured with the neutral comet assay (NCA). Boar semen was diluted in lactose-hen egg yolk-glycerol extender (L-HEY) or lactose ostrich egg yolk lipoprotein fractions-glycerol extender (L-LPFo), packaged into aluminum tubes or plastic straws and frozen in a controlled programmable freezer. In Experiment 1, the chromatin status and DNA fragmentation were measured in fresh and frozen-thawed spermatozoa from the same ejaculates. There was a significant increase in sperm chromatin destabilization and DNA fragmentation in frozen-thawed semen as compared with fresh semen. The proportions of spermatozoa labeled with (3)H-AMD were concurrent with elevated levels of sperm DNA fragmentation in K-3 extender, without cryoprotective substances, compared with L-HEY or L-LPFo extender. Regression analysis revealed that the results of the (3)H-AMD incorporation assay and NCA for frozen-thawed spermatozoa were correlated. Boars differed significantly in terms of post-thaw sperm DNA damage. In Experiment 2, the susceptibility of sperm chromatin to decondensation was assessed using a low concentration of heparin. Treatment of frozen-thawed spermatozoa with heparin revealed enhanced (3)H-AMD binding, suggesting nuclear chromatin decondensation. The deterioration in post-thaw sperm viability, such as motility, mitochondrial function and plasma membrane integrity, was concurrent with increased chromatin instability and DNA fragmentation. This is the first report to show that freezing-thawing procedure facilitated destabilization in the chromatin structure of boar spermatozoa, resulting in

  6. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Bowen Xu

    2018-03-01

    Full Text Available Summary: Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF, a component of the nucleosome remodeling factor (NURF chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs, including long-term hematopoietic stem cells (HSCs. Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia. Genome-wide transcriptome profiling revealed that BPTF loss caused downregulation of HSC-specific gene-expression programs, which contain several master transcription factors (Meis1, Pbx1, Mn1, and Lmo2 required for HSC maintenance and self-renewal. Furthermore, we show that BPTF potentiates the chromatin accessibility of key HSC “stemness” genes. These results demonstrate an essential requirement of the chromatin remodeler BPTF and NURF for activation of “stemness” gene-expression programs and proper function of adult HSCs. : Wang and colleagues show that a chromatin remodeler, BPTF, sustains appropriate functions of hematopoietic stem/progenitor cells (HSPCs. BPTF loss causes bone marrow failure and anemia. The authors further define a BPTF-dependent gene-expression program in HSPCs, which contains key HSC stemness factors. These results demonstrate an essential requirement of the BPTF-associated chromatin remodelers for HSC functionality and adult hematopoiesis. Keywords: Bptf, hematopoietic stem cells, chromatin remodeler, Meis1, Pbx1, Mn1, DNA accessibility, NURF, AP1 complex

  7. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    International Nuclear Information System (INIS)

    Boulos, Rasha E; Julienne, Hanna; Baker, Antoine; Jensen, Pablo; Arneodo, Alain; Audit, Benjamin; Chen, Chun-Long; D'Aubenton-Carafa, Yves; Thermes, Claude; Petryk, Nataliya; Kahli, Malik; Hyrien, Olivier; Goldar, Arach

    2014-01-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. (paper)

  8. [Mechanisms of genoprotective action of a phytoecdysteroid drug(BTK-8L) in chromatin damage by tetrachloromethane].

    Science.gov (United States)

    Gubskiĭ, Iu I; Levitskiĭ, E L; Kholodova, Iu D; Goriushko, A G; Primak, R G; Vistunova, I E; Sachenko, L G

    1993-01-01

    Hepatoprotective action of prophylactic injection of aqueous solution of preparation BTK-8L from plant ecdysteroids to experimental animals with the liver damage by tetrachloromethane was revealed. This effect at least partially was connected with the genoprotective action of the given preparation. As a result, normalization of free radical chromatin lipid peroxidation reaction, modified at the intoxication, as well as partial correction of physical and chemical properties of chromatin protein-lipid complex were those molecular mechanisms of genoprotective action of BTK-8L, which were manifested by the influence of the preparation on such indices which characterized the depth structure of the complex as microviscosity and energy transfer from the protein to the lipid probe. Investigation of the interaction of the preparation with chromatin fractions in vitro and comparison of this interaction with the analogous process in model systems allowed revealing determinative participation of chromatin proteins and lipids in the given process. The preparation interacted more intensively with the active chromatin fraction, which contained a more marked protein-lipid complex, as comparing to the repressed one. Injection of the preparation also normalized such indices as relation between the chromatine fractions and protein/DNA ratio in them. On the contrary, injection of the alcoholic solution of the preparation to experimental animals, aggravated genotoxic tetrachloromethane action.

  9. Control of Genome Integrity by RFC Complexes; Conductors of PCNA Loading onto and Unloading from Chromatin during DNA Replication

    Directory of Open Access Journals (Sweden)

    Yasushi Shiomi

    2017-01-01

    Full Text Available During cell division, genome integrity is maintained by faithful DNA replication during S phase, followed by accurate segregation in mitosis. Many DNA metabolic events linked with DNA replication are also regulated throughout the cell cycle. In eukaryotes, the DNA sliding clamp, proliferating cell nuclear antigen (PCNA, acts on chromatin as a processivity factor for DNA polymerases. Since its discovery, many other PCNA binding partners have been identified that function during DNA replication, repair, recombination, chromatin remodeling, cohesion, and proteolysis in cell-cycle progression. PCNA not only recruits the proteins involved in such events, but it also actively controls their function as chromatin assembles. Therefore, control of PCNA-loading onto chromatin is fundamental for various replication-coupled reactions. PCNA is loaded onto chromatin by PCNA-loading replication factor C (RFC complexes. Both RFC1-RFC and Ctf18-RFC fundamentally function as PCNA loaders. On the other hand, after DNA synthesis, PCNA must be removed from chromatin by Elg1-RFC. Functional defects in RFC complexes lead to chromosomal abnormalities. In this review, we summarize the structural and functional relationships among RFC complexes, and describe how the regulation of PCNA loading/unloading by RFC complexes contributes to maintaining genome integrity.

  10. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.

    Science.gov (United States)

    Gürsoy, Gamze; Xu, Yun; Liang, Jie

    2017-07-01

    Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization. With significantly improved sampling of genome structures, both intra- and inter-chromosomal interaction patterns from genome-wide 3C studies are accurately captured in our model at higher resolution than previous studies. We show that nuclear confinement is a key determinant of the intra-chromosomal interactions, and centromere tethering is responsible for the inter-chromosomal interactions. In addition, important genomic elements such as fragile sites and tRNA genes are found to be clustered spatially, largely due to centromere tethering. We uncovered previously unknown interactions that were not captured by genome-wide 3C studies, which are found to be enriched with tRNA genes, RNAPIII and TFIIS binding. Moreover, we identified specific high-frequency genome-wide 3C interactions that are unaccounted for by polymer effects under landmark constraints. These interactions are enriched with important genes and likely play biological roles.

  11. Modeling of fracture of protective concrete structures under impact loads

    Energy Technology Data Exchange (ETDEWEB)

    Radchenko, P. A., E-mail: radchenko@live.ru; Batuev, S. P.; Radchenko, A. V.; Plevkov, V. S. [Tomsk State University of Architecture and Building, Tomsk, 634003 (Russian Federation)

    2015-10-27

    This paper presents results of numerical simulation of interaction between a Boeing 747-400 aircraft and the protective shell of a nuclear power plant. The shell is presented as a complex multilayered cellular structure consisting of layers of concrete and fiber concrete bonded with steel trusses. Numerical simulation was performed three-dimensionally using the original algorithm and software taking into account algorithms for building grids of complex geometric objects and parallel computations. Dynamics of the stress-strain state and fracture of the structure were studied. Destruction is described using a two-stage model that allows taking into account anisotropy of elastic and strength properties of concrete and fiber concrete. It is shown that wave processes initiate destruction of the cellular shell structure; cells start to destruct in an unloading wave originating after the compression wave arrival at free cell surfaces.

  12. Modeling of fracture of protective concrete structures under impact loads

    Science.gov (United States)

    Radchenko, P. A.; Batuev, S. P.; Radchenko, A. V.; Plevkov, V. S.

    2015-10-01

    This paper presents results of numerical simulation of interaction between a Boeing 747-400 aircraft and the protective shell of a nuclear power plant. The shell is presented as a complex multilayered cellular structure consisting of layers of concrete and fiber concrete bonded with steel trusses. Numerical simulation was performed three-dimensionally using the original algorithm and software taking into account algorithms for building grids of complex geometric objects and parallel computations. Dynamics of the stress-strain state and fracture of the structure were studied. Destruction is described using a two-stage model that allows taking into account anisotropy of elastic and strength properties of concrete and fiber concrete. It is shown that wave processes initiate destruction of the cellular shell structure; cells start to destruct in an unloading wave originating after the compression wave arrival at free cell surfaces.

  13. A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber

    DEFF Research Database (Denmark)

    Comet, Itys; Schuettengruber, Bernd; Sexton, Tom

    2011-01-01

    to insulate genes from regulatory elements or to take part in long-distance interactions. Using a high-resolution chromatin conformation capture (H3C) method, we show that the Drosophila gypsy insulator behaves as a conformational chromatin border that is able to prohibit contacts between a Polycomb response...... element (PRE) and a distal promoter. On the other hand, two spaced gypsy elements form a chromatin loop that is able to bring an upstream PRE in contact with a downstream gene to mediate its repression. Chromatin immunoprecipitation (ChIP) profiles of the Polycomb protein and its associated H3K27me3...... histone mark reflect this insulator-dependent chromatin conformation, suggesting that Polycomb action at a distance can be organized by local chromatin topology....

  14. Chromatin Dynamics in Vivo: A Game of Musical Chairs

    Directory of Open Access Journals (Sweden)

    Daniël P. Melters

    2015-08-01

    Full Text Available Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.

  15. Optimization and anti-optimization of structures under uncertainty

    National Research Council Canada - National Science Library

    Elishakoff, Isaac; Ohsaki, Makoto

    2010-01-01

    ..., architecture, civil, mechanical or ocean engineering, invariably adopt the either/or style. Namely, they devote themselves either to linear or to nonlinear analysis of the structure they are dealing with, they are engaged in analyzing it either in the elastic or in the inelastic range; they deal either with its static or with its dynamic behavior. Al...

  16. Occupational structure in the Czech lands under the second serfdom

    Czech Academy of Sciences Publication Activity Database

    Klein, Alexander; Ogilvie, S.

    2016-01-01

    Roč. 69, č. 2 (2016), s. 493-521 ISSN 0013-0117 R&D Projects: GA ČR GA13-13848S Institutional support: RVO:67985998 Keywords : occupational structure * Czech lands * Bohemia Subject RIV: AH - Economics OBOR OECD: Applied Economics, Econometrics Impact factor: 1.233, year: 2016

  17. Structural performance of HEPA filters under simulated tornado conditions

    International Nuclear Information System (INIS)

    Horak, H.L.; Gregory, W.S.; Ricketts, C.I.; Smith, P.R.

    1982-02-01

    This report contains the results of structural tests to determine the response of High Efficiency Particulate Air filters to simulated tornado conditions. The data include the structural limits of the filters, their resistance at high flow rates, and the effects of filter design features and tornado parameters. Considering all the filters tested, the mean break pressure or structural limit was found to be 2.35 pse (16.2 kPa). The maximum value was 2.87 psi (19.8 kPa), and the low value found was 1.31 psi (9.0 kPa). The type of failure was usually a medium break of the downstream filter fold. The type of filters that were evaluated were nuclear grade with design flow rates of 1000 cfm (0.472 m 3 /s), standard separators, and folded medium design. The parameters evaluated that are characteristic of the filter included manufacturer, separator type, faceguards, pack tightness, and aerosol loading. Manufacturer and medium properties were found to have a large effect on the structural limits

  18. Structures of water molecules in carbon nanotubes under electric fields

    International Nuclear Information System (INIS)

    Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji

    2015-01-01

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate

  19. Influence of amendments on soil structure and soil loss under ...

    African Journals Online (AJOL)

    Macromolecule polymers are significant types of chemical amendments because of their special structure, useful functions and low cost. Macromolecule polymers as soil amendment provide new territory for studying China's agricultural practices and for soil and water conservation, because polymers have the ability to ...

  20. Profit Tax Evasion Under Oligopoly With Endogenous Market Structure

    OpenAIRE

    Goerke, Laszlo; Runkel, Marco

    2006-01-01

    This note investigates the impact of profit tax evasion on firms' output decisions in a Cournot oligopoly setting in which the market structure is determined endogenously. It is shown that tax evasion intensifies market entry and raises aggregate output, while production of each incumbent firm decreases. Therefore, tax evasion choices affect activity decisions and an evadable profit tax distorts the market outcome.

  1. Structural analyses of ITER toroidal field coils under fault conditions

    International Nuclear Information System (INIS)

    Jong, C.T.J.

    1992-04-01

    ITER (International Thermonuclear Experimental Reactor) is intended to be an experimental thermonuclear tokamak reactor testing the basic physics performance and technologies essential to future fusion reactors. The magnet system of ITER consists essentially of 4 sub-systems, i.e. toroidal field coils (TFCs), poloidal field coils (PFCs), power supplies, and cryogenic supplies. These subsystems do not contain significant radioactivity inventories, but the large energy inventory is a potential accident initiator. The aim of the structural analyses is to prevent accidents from propagating into vacuum vessel, tritium system and cooling system, which all contain significant amounts of radioactivity. As part of design process 3 conditions are defined for PF and TF coils, at which mechanical behaviour has to be analyzed in some detail, viz: normal operating conditions, upset conditions and fault conditions. This paper describes the work carried out by ECN to create a detailed finite element model of 16 TFCs as well as results of some fault condition analyses made with the model. Due to fault conditions, either electrical or mechanical, magnetic loading of TFCs becomes abnormal and further mechanical failure of parts of the overall structure might occur (e.g. failure of coil, gravitational supports, intercoil structure). The analyses performed consist of linear elastic stress analyses and electro-magneto-structural analyses (coupled field analyses). 8 refs.; 5 figs.; 5 tabs

  2. The electronic structure of core states under extreme compressions

    International Nuclear Information System (INIS)

    Straub, G.K.

    1992-01-01

    At normal density and for modest compressions, the electronic structure of a metal can be accurately described by treating the conduction electrons and their interactions with the usual methods of band theory. The core electrons remain essentially the same as for an isolated free atom and do not participate in the bonding forces responsible for creating a condensed phase. As the density increases, the core electrons begin to ''see'' one another as the overlap of the tails of wave functions can no longer be neglected. The electronic structure of the core electrons is responsible for an effective repulsive interaction that eventually becomes free-electron-like at very high compressions. The electronic structure of the interacting core electrons may be treated in a simple manner using the Atomic Surface Method (ASM). The ASM is a first-principles treatment of the electronic structure involving a rigorous integration of the Schroedinger equation within the atomic-sphere approximation. Solid phase wave functions are constructed from isolated atom wave functions and the band width W l and the center of gravity of the band C l are obtained from simple formulas. The ASM can also utilize analytic forms of the atomic wave functions and thus provide direct functional dependence of various aspects of the electronic structure. Of particular use in understanding the behavior of the core electrons, the ASM provides the ability to analytically determine the density dependence of the band widths and positions. The process whereby core states interact with one another is best viewed as the formation of narrow electron bands formed from atomic states. As the core-core overlap increases, the bands increase in width and mean energy. In Sec.3 this picture is further developed and from the ASM one obtains the analytic dependence on density of the relative motion of the different bands. Also in Sec. 3 is a discussion of the transition to free electron bands

  3. Structural analysis under the Blanket Comparison and Selection Study

    International Nuclear Information System (INIS)

    Majumdar, S.

    1985-01-01

    Structural design procedures followed in the Blanket Comparison and Selection Study are briefly reviewed. The American Society of Mechanical Engineers Boilers and Pressure Vessels Code, Section III, Code Case N47 has been used as a design guide. Its relevance to fusion reactor applications, however, is open to question and needs to be evaluated in the future. The primary structural problem encountered in tokamak blanket designs is the high thermal stress due to surface heat flux, with fatigue being an additional concern for pulsed systems. The conflicting requirements of long erosion life and high surface heat flux capability imply that some form of stress relief in the first-wall region will be necessary. Simplified stress and fatigue crack growth analyses are presented to show that the use of orthogonally grooved first wall may be a potential solution for mitigating the thermal stress problem. A comparison of three structural alloys on the basis of both grooved and nongrooved first-wall designs is also presented. Other structural problems encountered in tokamak designs include stresses due to plasma disruptions, and magnetohydrodynamic (MHD) pressure drop in liquid-metal-cooled systems. In particular, it is shown that the maximum stress in the side wall of a uniform duct generated by MHD pressure drop cannot be reduced by increasing the wall thickness or by decreasing the span. In contract to tokamak blankets, tandem mirror blankets are far less severely stressed because of a much lower surface heat flux, coolant pressure, and also because of their axisymmetric geometry. Both blankets, however, will require detailed structural dynamics analysis to verify their ability to withstand seismic loadings if the heavy 17Li-83Pb is used as a coolant

  4. Exploiting risk-reward structures in decision making under uncertainty.

    Science.gov (United States)

    Leuker, Christina; Pachur, Thorsten; Hertwig, Ralph; Pleskac, Timothy J

    2018-06-01

    People often have to make decisions under uncertainty-that is, in situations where the probabilities of obtaining a payoff are unknown or at least difficult to ascertain. One solution to this problem is to infer the probability from the magnitude of the potential payoff and thus exploit the inverse relationship between payoffs and probabilities that occurs in many domains in the environment. Here, we investigated how the mind may implement such a solution: (1) Do people learn about risk-reward relationships from the environment-and if so, how? (2) How do learned risk-reward relationships impact preferences in decision-making under uncertainty? Across three experiments (N = 352), we found that participants can learn risk-reward relationships from being exposed to choice environments with a negative, positive, or uncorrelated risk-reward relationship. They were able to learn the associations both from gambles with explicitly stated payoffs and probabilities (Experiments 1 & 2) and from gambles about epistemic events (Experiment 3). In subsequent decisions under uncertainty, participants often exploited the learned association by inferring probabilities from the magnitudes of the payoffs. This inference systematically influenced their preferences under uncertainty: Participants who had been exposed to a negative risk-reward relationship tended to prefer the uncertain option over a smaller sure option for low payoffs, but not for high payoffs. This pattern reversed in the positive condition and disappeared in the uncorrelated condition. This adaptive change in preferences is consistent with the use of the risk-reward heuristic. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. ERDBEBEN, Structure Displacements and Forces Under Earthquake Conditions

    International Nuclear Information System (INIS)

    Brandhuber, F.

    1977-01-01

    1 - Nature of physical problem solved: ERDBEBEN calculates the displacements and forces of a structure, excited by an earthquake. 2 - Method of solution: The mathematical method is the 'response spectrum modal analysis'. Before calculation, the user of ERDBEBEN has to idealize the structure with finite elements and to calculate its eigenfrequencies with the program NASTRAN (level 15). The superposition of the Eigen-forms will be done by the 'root mean square method'. 3 - Restrictions on the complexity of the problem: The length of the arrays can be variable (parameter card). Only the number of the different types of finite elements cannot be more than 5. The program calculates the element forces only for beam and spring elements

  6. Optical properties of a multibarrier structure under intense laser fields

    Science.gov (United States)

    Ospina, D. A.; Akimov, V.; Mora-Ramos, M. E.; Morales, A. L.; Tulupenko, V.; Duque, C. A.

    2015-11-01

    Using the diagonalization method and within the effective mass and parabolic band approximations, the energy spectrum and the wave functions are investigated in biased multibarrier structure taking into account the effects of nonresonant intense laser fields. We calculated the optical properties from the susceptibility using a nonperturbative formalism recently reported. We study the changes in the intersubband optical absorption coefficients and refraction index for several values of the dressing laser parameter and for some specific values of the electric field applied along the growth direction of the heterostructure. It is concluded from our study that the peaks in the optical absorption spectrum have redshifts or blueshifts as a function of the laser parameter and the electric field. These parameters could be suitable tools for tuning the electronic and optical properties of the multibarrier structure.

  7. Analysis of ADU structure obtained under different precipitation conditions

    International Nuclear Information System (INIS)

    Ramella, Jose L.; Esteban, Adolfo; Mendez De Leo, Lucia P.; Sassone, Ariel; Novara, Oscar E.; Boero, Norma L.; Leyva, Ana G.

    1999-01-01

    ADU is the nominal name for ammonium poly uranate. It is a very complex compound of polymeric structure, which may have, according to precipitation conditions, different chemical composition and crystallographic structure. ADU is used as uranium oxide precursor in the manufacture of fuel elements. In former papers it was proved that if ultrasound is applied during precipitation and digestion the characteristics of the final product (U 3 O 8 UO 2 ) improve. By studying ADU thermal decomposition obtained by ultrasonic application, it was intended to obtain its composition. Therefore, differential thermal gravimetric and differential thermal analyses were performed. Samples were taken from special points and analyzed by X-ray diffraction, infra-red spectroscopy and scanning. An experiment was also designed to identify the products released during heating. Results and conclusions obtained are presented in this work. (author)

  8. Optimal Design of Composite Structures Under Manufacturing Constraints

    DEFF Research Database (Denmark)

    Marmaras, Konstantinos

    algorithms to perform the global optimization. The efficiency of the proposed models is examined on a set of well–defined discrete multi material and thickness optimization problems originating from the literature. The inclusion of manufacturing limitations along with structural considerations in the early...... mixed integer 0–1 programming problems. The manufacturing constraints have been treated by developing explicit models with favorable properties. In this thesis we have developed and implemented special purpose global optimization methods and heuristic techniques for solving this class of problems......This thesis considers discrete multi material and thickness optimization of laminated composite structures including local failure criteria and manufacturing constraints. Our models closely follow an immediate extension of the Discrete Material Optimization scheme, which allows simultaneous...

  9. Fiscal reaction under endogenous structural changes in Brazil

    Directory of Open Access Journals (Sweden)

    Andrei G. Simonassi

    2014-01-01

    Full Text Available Regarding the importance of fiscal policy in smoothing the impact of shocks such as the international financial and economic crises, the paper analyzes the sustainability of the Brazilian fiscal policy by taking into consideration the possibility of multiple endogenous structural breaks on the coefficients of government reaction function. From monthly data in the period 1991–2008, tests on the reliable estimates dictate the occurrence of structural change in May 1994, and another in February 2003. There has been a situation of fiscal solvency in Brazil, but only from May 1994 the hitherto innocuous actions of government to formulate policies on public debt turn out to be significant, as it rose twofold after February 2003. This reinforces the existence of a more flexible alternative to implement strategic policy in Brazil, if an eventual alternative for increasing public spending is a way of hindering the effects of international financial crises without compromising the fiscal targets.

  10. Structural studies on serum albumins under green light irradiation.

    Science.gov (United States)

    Comorosan, Sorin; Polosan, Silviu; Popescu, Irinel; Ionescu, Elena; Mitrica, Radu; Cristache, Ligia; State, Alina Elena

    2010-10-01

    This paper presents two new experimental results: the protective effect of green light (GL) on ultraviolet (UV) denaturation of proteins, and the effect of GL on protein macromolecular structures. The protective effect of GL was revealed on two serum albumins, bovine (BSA) and human (HSA), and recorded by electrophoresis, absorption, and circular dichroism spectra. The effect of GL irradiation on protein structure was recorded by using fluorescence spectroscopy and electrophoresis. These new effects were modeled by quantum-chemistry computation using Gaussian 03 W, leading to good fit between theoretical and experimental absorption and circular dichroism spectra. A mechanism for these phenomena is suggested, based on a double-photon absorption process. This nonlinear effect may lead to generation of long-lived Rydberg macromolecular systems, capable of long-range interactions. These newly suggested systems, with macroscopic quantum coherence behaviors, may block the UV denaturation processes.

  11. Spray structure as generated under homogeneous flash boiling nucleation regime

    International Nuclear Information System (INIS)

    Levy, M.; Levy, Y.; Sher, E.

    2014-01-01

    We show the effect of the initial pressure and temperature on the spatial distribution of droplets size and their velocity profile inside a spray cloud that is generated by a flash boiling mechanism under homogeneous nucleation regime. We used TSI's Phase Doppler Particle Analyzer (PDPA) to characterize the spray. We conclude that the homogeneous nucleation process is strongly affected by the initial liquid temperature while the initial pressure has only a minor effect. The spray shape is not affected by temperature or pressure under homogeneous nucleation regime. We noted that the only visible effect is in the spray opacity. Finally, homogeneous nucleation may be easily achieved by using a simple atomizer construction, and thus is potentially suitable for fuel injection systems in combustors and engines. - Highlights: • We study the characteristics of a spray that is generated by a flash boiling process. • In this study, the flash boiling process occurs under homogeneous nucleation regime. • We used Phase Doppler Particle Analyzer (PDPA) to characterize the spray. • The SMD has been found to be strongly affected by the initial liquid temperature. • Homogeneous nucleation may be easily achieved by using a simple atomizer unit

  12. Structure and morphology of mythimna pupa under diffraction enhanced imaging

    International Nuclear Information System (INIS)

    Huang Wanxia; Yuan Qingxi; Zhu Peiping; Wang Junyue; Liu Yijin; Chen Bo; Shu Hang; Hu Tiandou; Wu Ziyu; Ge Siqin

    2007-01-01

    As a technique of X-ray phase contrast imaging, the diffraction enhanced imaging (DEI) attracts much interest due to its high resolution and contrast. The top images of DEI were used to study the growth of a complete metamorphic mythimna in the period of pupa. Clear images about the pupa structure were obtained. The entire growth process of the pupa was observed, including the evolvement of part of organs and tissues from larva to imago. (authors)

  13. Modeling amorphization of tetrahedral structures under local approaches

    International Nuclear Information System (INIS)

    Jesurum, C.E.; Pulim, V.; Berger, B.; Hobbs, L.W.

    1997-01-01

    Many crystalline ceramics can be topologically disordered (amorphized) by disordering radiation events involving high-energy collision cascades or (in some cases) successive single-atom displacements. The authors are interested in both the potential for disorder and the possible aperiodic structures adopted following the disordering event. The potential for disordering is related to connectivity, and among those structures of interest are tetrahedral networks (such as SiO 2 , SiC and Si 3 N 4 ) comprising corner-shared tetrahedral units whose connectivities are easily evaluated. In order to study the response of these networks to radiation, the authors have chosen to model their assembly according to the (simple) local rules that each corner obeys in connecting to another tetrahedron; in this way they easily erect large computer models of any crystalline polymorphic form. Amorphous structures can be similarly grown by application of altered rules. They have adopted a simple model of irradiation in which all bonds in the neighborhood of a designated tetrahedron are destroyed, and they reform the bonds in this region according to a set of (possibly different) local rules appropriate to the environmental conditions. When a tetrahedron approaches the boundary of this neighborhood, it undergoes an optimization step in which a spring is inserted between two corners of compatible tetrahedra when they are within a certain distance of one another; component forces are then applied that act to minimize the distance between these corners and minimize the deviation from the rules. The resulting structure is then analyzed for the complete adjacency matrix, irreducible ring statistics, and bond angle distributions

  14. The Value of Distributed Generation under Different Tariff Structures

    OpenAIRE

    Firestone, Ryan; Magnus Maribu, Karl; Marnay, Chris

    2006-01-01

    Distributed generation (DG) may play a key role in a modern energy system because it can improve energy efficiency. Reductions in the energy bill, and therefore DG attractiveness, depend on the electricity tariff structure; a system created before widespread adoption of distributed generation. Tariffs have been designed to recover costs equitably amongst customers with similar consumption patterns. Recently, electric utilities began to question the equity of this electricity pricing stru...

  15. The Response of Simple Polymer Structures Under Dynamic Loading

    Science.gov (United States)

    Proud, William; Ellison, Kay; Yapp, Su; Cole, Cloe; Galimberti, Stefano; Institute of Shock Physics Team

    2017-06-01

    The dynamic response of polymeric materials has been widely studied with the effects of degree of crystallinity, strain rate, temperature and sample size being commonly reported. This study uses a simple PMMA structure, a right cylindrical sample, with structural features such as holes. The features are added an varied in a systematic fashion. Samples were dynamically loaded using a Split Hopkinson Pressure Bar up to failure. The resulting stress-strain curves are presented showing the change in sample response. The strain to failure is shown to increase initially with the presence of holes, while failure stress is relatively unaffected. The fracture patterns seen in the failed samples change, with tensile cracks, Hertzian cones, shear effects being dominant for different holes sizes and geometries. The sample were prepared by laser cutting and checked for residual stress before experiment. The data is used to validate predictive model predictions where material, structure and damage are included.. The Institute of Shock Physics acknowledges the support of Imperial College London and the Atomic Weapons Establishment.

  16. Disrupted white matter structure underlies cognitive deficit in hypertensive patients

    International Nuclear Information System (INIS)

    Li, Xin; Ma, Chao; Zhang, Junying; Chen, Yaojing; Zhang, Zhanjun; Sun, Xuan; Chen, Kewei

    2016-01-01

    Hypertension is considered a risk factor of cognitive impairments and could result in white matter changes. Current studies on hypertension-related white matter (WM) changes focus only on regional changes, and the information about global changes in WM structure network is limited. We assessed the cognitive function in 39 hypertensive patients and 37 healthy controls with a battery of neuropsychological tests. The WM structural networks were constructed by utilizing diffusion tensor tractography and calculated topological properties of the networks using a graph theoretical method. The direct and indirect correlations among cognitive impairments, brain WM network disruptions and hypertension were analyzed with structural equation modelling (SEM). Hypertensive patients showed deficits in executive function, memory and attention compared with controls. An aberrant connectivity of WM networks was found in the hypertensive patients (P Eglob = 0.005, P Lp = 0.005), especially in the frontal and parietal regions. Importantly, SEM analysis showed that the decline of executive function resulted from aberrant WM networks in hypertensive patients (p = 0.3788, CFI = 0.99). These results suggest that the cognitive decline in hypertensive patients was due to frontal and parietal WM disconnections. Our findings highlight the importance of brain protection in hypertension patients. (orig.)

  17. Probabilistic SSME blades structural response under random pulse loading

    Science.gov (United States)

    Shiao, Michael; Rubinstein, Robert; Nagpal, Vinod K.

    1987-01-01

    The purpose is to develop models of random impacts on a Space Shuttle Main Engine (SSME) turbopump blade and to predict the probabilistic structural response of the blade to these impacts. The random loading is caused by the impact of debris. The probabilistic structural response is characterized by distribution functions for stress and displacements as functions of the loading parameters which determine the random pulse model. These parameters include pulse arrival, amplitude, and location. The analysis can be extended to predict level crossing rates. This requires knowledge of the joint distribution of the response and its derivative. The model of random impacts chosen allows the pulse arrivals, pulse amplitudes, and pulse locations to be random. Specifically, the pulse arrivals are assumed to be governed by a Poisson process, which is characterized by a mean arrival rate. The pulse intensity is modelled as a normally distributed random variable with a zero mean chosen independently at each arrival. The standard deviation of the distribution is a measure of pulse intensity. Several different models were used for the pulse locations. For example, three points near the blade tip were chosen at which pulses were allowed to arrive with equal probability. Again, the locations were chosen independently at each arrival. The structural response was analyzed both by direct Monte Carlo simulation and by a semi-analytical method.

  18. Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization.

    Science.gov (United States)

    González-Romero, Rodrigo; Eirín-López, José M; Ausió, Juan

    2015-01-01

    High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Term Structure of Credit Spreads of A Firm When Its Underlying Assets are Discontinuous

    Directory of Open Access Journals (Sweden)

    Budhi Arta Surya

    2012-01-01

    Full Text Available We revisit the previous works of Leland [12], Leland and Toft [11] andHilberink and Rogers [7] on optimal capital structure and show that thecredit spreads of short-maturity corporate bonds can have nonzero valueswhen the underlying of the firm’s assets value has downward jumps. We givean analytical treatment of this fact under a general Levy process and discusssome numerical examples under pure jump processes.Keywords: Optimal capital structure, credit risk, term structure of creditspread

  20. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.; Jé gu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Auré lie; Benhamed, Moussa; Crespi, Martí n D.

    2014-01-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  1. Put your 3D glasses on: plant chromatin is on show

    KAUST Repository

    Rodriguez Granados, Natalia Yaneth; Ramirez Prado, Juan Sebastian; Veluchamy, Alaguraj; Latrasse, David; Raynaud, Cé cile; Crespi, Martin; Ariel, Federico; Benhamed, Moussa

    2016-01-01

    The three-dimensional organization of the eukaryotic nucleus and its chromosomal conformation have emerged as important features in the complex network of mechanisms behind gene activity and genome connectivity dynamics, which can be evidenced in the regionalized chromosomal spatial distribution and the clustering of diverse genomic regions with similar expression patterns. The development of chromatin conformation capture (3C) techniques has permitted the elucidation of commonalities between the eukaryotic phyla, as well as important differences among them. The growing number of studies in the field performed in plants has shed light on the structural and regulatory features of these organisms. For instance, it has been proposed that plant chromatin can be arranged into different conformations such as Rabl, Rosette-like, and Bouquet, and that both short- and long-range chromatin interactions occur in Arabidopsis. In this review, we compile the current knowledge about chromosome architecture characteristics in plants, as well as the molecular events and elements (including long non-coding RNAs, histone and DNA modifications, chromatin remodeling complexes, and transcription factors) shaping the genome three-dimensional conformation. Furthermore, we discuss the developmental outputs of genome topology-mediated gene expression regulation. It is becoming increasingly clear that new tools and techniques with higher resolution need to be developed and implemented in Arabidopsis and other model plants in order to better understand chromosome architecture dynamics, from an integrative perspective with other fields of plant biology such as development, stress biology, and finally agriculture. © 2016 The Author 2016.

  2. Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Amrita; Sanyal, Sulagna; Majumder, Parijat [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India); Chakraborty, Payal [Bionivid Technology Pvt Ltd, Kasturi Nagar, Bangalore 560043 (India); Jana, Kuladip [Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal (India); Das, Chandrima, E-mail: chandrima.das@saha.ac.in [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India); Dasgupta, Dipak, E-mail: dipak.dasgupta@saha.ac.in [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India)

    2015-07-10

    Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a ‘dual binder’. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. - Highlights: • Ellipticine acts a dual binder binding to both DNA and core histone(s). • It induces structural perturbations in chromatin, chromatosome and histone octamer. • It alters histones acetylation and affects global gene expression.

  3. Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder

    International Nuclear Information System (INIS)

    Banerjee, Amrita; Sanyal, Sulagna; Majumder, Parijat; Chakraborty, Payal; Jana, Kuladip; Das, Chandrima; Dasgupta, Dipak

    2015-01-01

    Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a ‘dual binder’. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. - Highlights: • Ellipticine acts a dual binder binding to both DNA and core histone(s). • It induces structural perturbations in chromatin, chromatosome and histone octamer. • It alters histones acetylation and affects global gene expression

  4. Put your 3D glasses on: plant chromatin is on show

    KAUST Repository

    Rodriguez Granados, Natalia Yaneth

    2016-04-30

    The three-dimensional organization of the eukaryotic nucleus and its chromosomal conformation have emerged as important features in the complex network of mechanisms behind gene activity and genome connectivity dynamics, which can be evidenced in the regionalized chromosomal spatial distribution and the clustering of diverse genomic regions with similar expression patterns. The development of chromatin conformation capture (3C) techniques has permitted the elucidation of commonalities between the eukaryotic phyla, as well as important differences among them. The growing number of studies in the field performed in plants has shed light on the structural and regulatory features of these organisms. For instance, it has been proposed that plant chromatin can be arranged into different conformations such as Rabl, Rosette-like, and Bouquet, and that both short- and long-range chromatin interactions occur in Arabidopsis. In this review, we compile the current knowledge about chromosome architecture characteristics in plants, as well as the molecular events and elements (including long non-coding RNAs, histone and DNA modifications, chromatin remodeling complexes, and transcription factors) shaping the genome three-dimensional conformation. Furthermore, we discuss the developmental outputs of genome topology-mediated gene expression regulation. It is becoming increasingly clear that new tools and techniques with higher resolution need to be developed and implemented in Arabidopsis and other model plants in order to better understand chromosome architecture dynamics, from an integrative perspective with other fields of plant biology such as development, stress biology, and finally agriculture. © 2016 The Author 2016.

  5. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.

    2014-08-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  6. Structural characterization of lipidic systems under nonequilibrium conditions

    DEFF Research Database (Denmark)

    Yaghmur, Anan; Rappolt, Michael

    2012-01-01

    This review covers recent studies on the characterization of the dynamics of lipidic nanostructures formed via self-assembly processes. The focus is placed on two main topics: First, an overview of advanced experimental small-angle X-ray scattering (SAXS) setups combined with various sample...... negatively charged vesicles with calcium ions, and in situ hydration-induced formation of inverted-type liquid-crystalline phases loaded with the local anesthetic bupivacaine are summarized. These in situ time-resolved experiments allow real-time monitoring of the dynamics of the structural changes...

  7. Spatially periodic structures, under femtosecond pulsed excitation of crystals

    International Nuclear Information System (INIS)

    Martynovitch, Evgueni F.; Petite, Guillaume; Dresvianski, Vladimir P.; Starchenko, Anton A.

    2004-01-01

    Measuring the luminescence intensity of specially prepared irradiation defects induced in crystals, we observe that the longitudinal structure of quasi-interferences induced by two orthogonally polarized femtosecond pulses propagating together with different velocities is insensitive to the spatial broadening due to velocity dispersion in the crystals. On the contrary, it does depend on the pulse duration when it is changed by varying the spectral width of the radiation. It thus allows a direct measurement of the coherence time of such pulses. Stability of the axial selectivity is a good sign, taking away a number of serious limitations concerning possible applications

  8. Structural behavior of human lumbar intervertebral disc under direct shear.

    Science.gov (United States)

    Schmidt, Hendrik; Häussler, Kim; Wilke, Hans-Joachim; Wolfram, Uwe

    2015-03-18

    The intervertebral disc (IVD) is a complex, flexible joint between adjacent vertebral bodies that provides load transmission while permitting movements of the spinal column. Finite element models can be used to help clarify why and how IVDs fail or degenerate. To do so, it is of importance to validate those models against controllable experiments. Due to missing experimental data, shear properties are not used thus far in validating finite element models. This study aimed to investigate the structural shear properties of human lumbar IVDs in posteroanterior (PA) and laterolateral (LL) loading directions. Fourteen lumbar IVDs (median age: 49 years) underwent direct shear in PA and LL loading directions. A custom-build shear device was used in combination with a materials testing machine to load the specimens until failure. Shear stiffness, ultimate shear force and displacement, and work to failure were determined. Each specimen was tested until complete or partial disruption. Median stiffness in PA direction was 490 N/mm and in LL direction 568 N/mm. Median ultimate shear force in the PA direction was 2,877 N and in the LL direction 3,199 N. Work to failure was 12 Nm in the PA and 9 Nm in the LL direction. This study was an experiment to subject IVDs to direct shear. The results could help us to understand the structure and function of IVDs with regard to mechanical spinal stability, and they can be used to validate finite element models of the IVD.

  9. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwang Won, E-mail: kwjeong@gachon.ac.kr

    2014-04-04

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators.

  10. Chromatin relaxation-mediated induction of p19INK4d increases the ability of cells to repair damaged DNA.

    Science.gov (United States)

    Ogara, María F; Sirkin, Pablo F; Carcagno, Abel L; Marazita, Mariela C; Sonzogni, Silvina V; Ceruti, Julieta M; Cánepa, Eduardo T

    2013-01-01

    The maintenance of genomic integrity is of main importance to the survival and health of organisms which are continuously exposed to genotoxic stress. Cells respond to DNA damage by activating survival pathways consisting of cell cycle checkpoints and repair mechanisms. However, the signal that triggers the DNA damage response is not necessarily a direct detection of the primary DNA lesion. In fact, chromatin defects may serve as initiating signals to activate those mechanisms. If the modulation of chromatin structure could initiate a checkpoint response in a direct manner, this supposes the existence of specific chromatin sensors. p19INK4d, a member of the INK4 cell cycle inhibitors, plays a crucial role in regulating genomic stability and cell viability by enhancing DNA repair. Its expression is induced in cells injured by one of several genotoxic treatments like cis-platin, UV light or neocarzinostatin. Nevertheless, when exogenous DNA damaged molecules are introduced into the cell, this induction is not observed. Here, we show that p19INK4d is enhanced after chromatin relaxation even in the absence of DNA damage. This induction was shown to depend upon ATM/ATR, Chk1/Chk2 and E2F activity, as is the case of p19INK4d induction by endogenous DNA damage. Interestingly, p19INK4d improves DNA repair when the genotoxic damage is caused in a relaxed-chromatin context. These results suggest that changes in chromatin structure, and not DNA damage itself, is the actual trigger of p19INK4d induction. We propose that, in addition to its role as a cell cycle inhibitor, p19INK4d could participate in a signaling network directed to detecting and eventually responding to chromatin anomalies.

  11. Chromatin relaxation-mediated induction of p19INK4d increases the ability of cells to repair damaged DNA.

    Directory of Open Access Journals (Sweden)

    María F Ogara

    Full Text Available The maintenance of genomic integrity is of main importance to the survival and health of organisms which are continuously exposed to genotoxic stress. Cells respond to DNA damage by activating survival pathways consisting of cell cycle checkpoints and repair mechanisms. However, the signal that triggers the DNA damage response is not necessarily a direct detection of the primary DNA lesion. In fact, chromatin defects may serve as initiating signals to activate those mechanisms. If the modulation of chromatin structure could initiate a checkpoint response in a direct manner, this supposes the existence of specific chromatin sensors. p19INK4d, a member of the INK4 cell cycle inhibitors, plays a crucial role in regulating genomic stability and cell viability by enhancing DNA repair. Its expression is induced in cells injured by one of several genotoxic treatments like cis-platin, UV light or neocarzinostatin. Nevertheless, when exogenous DNA damaged molecules are introduced into the cell, this induction is not observed. Here, we show that p19INK4d is enhanced after chromatin relaxation even in the absence of DNA damage. This induction was shown to depend upon ATM/ATR, Chk1/Chk2 and E2F activity, as is the case of p19INK4d induction by endogenous DNA damage. Interestingly, p19INK4d improves DNA repair when the genotoxic damage is caused in a relaxed-chromatin context. These results suggest that changes in chromatin structure, and not DNA damage itself, is the actual trigger of p19INK4d induction. We propose that, in addition to its role as a cell cycle inhibitor, p19INK4d could participate in a signaling network directed to detecting and eventually responding to chromatin anomalies.

  12. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    International Nuclear Information System (INIS)

    Jeong, Kwang Won

    2014-01-01

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators

  13. Homoeologous chromatin exchange in a radiation-induced gene transfer

    International Nuclear Information System (INIS)

    Dvorak, J.; Knott, D.R.

    1977-01-01

    Some of the ionizing-radiation-induced translocations between alien and wheat chromosomes show no deleterious effects and are transmitted normally through the pollen. Translocations of this type will be called ''compensating''. In one such compensating translocation, designated T4, it was found that chromatin in the long arm of wheat chromosome 7D was replaced with homoeologous chromatin of the Agropyron chromosome

  14. Chromatin Immunoprecipitation (ChIP) using Drosophila tissue

    OpenAIRE

    Tran, Vuong; Gan, Qiang; Chen, Xin

    2012-01-01

    Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at different developmental stages. Epigenetic regulation contributes to a broad spectrum of biological processes, including cellular differentiation during embryonic development and homeostasis in adulthood. A critical strategy in epigenetic studies is to examine how various histone modifications and chromatin factors regulate gene expression. ...

  15. Homoeologous chromatin exchange in a radiation-induced gene transfer

    Energy Technology Data Exchange (ETDEWEB)

    Dvorak, J; Knott, D R [Department of Crop Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    1977-03-01

    Some of the ionizing-radiation-induced translocations between alien and wheat chromosomes show no deleterious effects and are transmitted normally through the pollen. Translocations of this type will be called ''compensating''. In one such compensating translocation, designated T4, it was found that chromatin in the long arm of wheat chromosome 7D was replaced with homologous chromatin of the Agropyron chromosome.

  16. Structural evaluation of electrosleeved tubes under severe accident transients

    International Nuclear Information System (INIS)

    Majumdar, S.

    1999-01-01

    A flow stress model was developed for predicting failure of Electrosleeved PWR steam generator tubing under severe accident transients. The Electrosleeve, which is nanocrystalline pure nickel, loses its strength at temperatures greater than 400 C during severe accidents because of grain growth. A grain growth model and the Hall-Petch relationship were used to calculate the loss of flow stress as a function of time and temperature during the accident. Available tensile test data as well as high temperature failure tests on notched Electrosleeved tube specimens were used to derive the basic parameters of the failure model. The model was used to predict the failure temperatures of Electrosleeved tubes with axial cracks in the parent tube during postulated severe accident transients

  17. Principles underlying the Fourth Power Nature of Structured Shock Waves

    Science.gov (United States)

    Grady, Dennis

    2017-06-01

    Steady structured shock waves in materials including metals, glasses, compounds and solid mixtures, when represented through plots of Hugoniot stress against a measure of the strain rate through which the Hugoniot state is achieved, have consistently demonstrated a dependence to the fourth power. A perhaps deeper observation is that the product of the energy dissipated through the transition to the Hugoniot state and the time duration of the Hugoniot state event exhibits invariance independent of the Hugoniot amplitude. Invariance of the energy-time product and the fourth-power trend are to first order equivalent. Further, constancy of this energy-time product is observed in other dynamic critical state failure events including spall fracture, dynamic compaction and adiabatic shear failure. The presentation pursues the necessary background exposing the foregoing shock physics observations and explores possible statistical physics principals that may underlie the collective dynamic observations.

  18. Durability reliability analysis for corroding concrete structures under uncertainty

    Science.gov (United States)

    Zhang, Hao

    2018-02-01

    This paper presents a durability reliability analysis of reinforced concrete structures subject to the action of marine chloride. The focus is to provide insight into the role of epistemic uncertainties on durability reliability. The corrosion model involves a number of variables whose probabilistic characteristics cannot be fully determined due to the limited availability of supporting data. All sources of uncertainty, both aleatory and epistemic, should be included in the reliability analysis. Two methods are available to formulate the epistemic uncertainty: the imprecise probability-based method and the purely probabilistic method in which the epistemic uncertainties are modeled as random variables. The paper illustrates how the epistemic uncertainties are modeled and propagated in the two methods, and shows how epistemic uncertainties govern the durability reliability.

  19. Structural attributes of stand overstory and light under the canopy

    Directory of Open Access Journals (Sweden)

    Alice Angelini

    2015-02-01

    Full Text Available  This paper reviews the literature relating to the relationship between light availability in the understory and the main qualitative and quantitative attributes of stand overstory usually considered in forest management and planning (species composition, density, tree sizes, etc. as well as their changes as consequences of harvesting. The paper is divided in two sections: the first one reviews studies which investigated the influence of species composition on understory light conditions; the second part examines research on the relationships among stand parameters determined from dendrometric field data and the radiation on understory layer. The objective was to highlight which are the most significant stand traits and management features to build more practical models for predicting light regimes in any forest stand and, in more general terms, to support forest managers in planning and designing silvicultural treatments that retain structure in different way in order to meet different objectives.

  20. Finite element modeling of Balsa wood structures under severe loadings

    International Nuclear Information System (INIS)

    Toson, B.; Pesque, J.J.; Viot, P.

    2014-01-01

    In order to compute, in various situations, the requirements for transporting packages using Balsa wood as an energy absorber, a constitutive model is needed that takes into account all of the specific characteristics of the wood, such as its anisotropy, compressibility, softening, densification, and strain rate dependence. Such a model must also include the treatment of rupture of the wood when it is in traction. The complete description of wood behavior is not sufficient: robustness is also necessary because this model has to work in presence of large deformations and of many other external nonlinear phenomena in the surrounding structures. We propose such a constitutive model that we have developed using the commercial finite element package ABAQUS. The necessary data were acquired through an extensive compilation of the existing literature with the augmentation of personal measurements. Numerous validation tests are presented that represent different impact situations that a transportation cask might endure. (authors)

  1. Reliability prediction for structures under cyclic loads and recurring inspections

    Directory of Open Access Journals (Sweden)

    Alberto W. S. Mello Jr

    2009-06-01

    Full Text Available This work presents a methodology for determining the reliability of fracture control plans for structures subjected to cyclic loads. It considers the variability of the parameters involved in the problem, such as initial flaw and crack growth curve. The probability of detection (POD curve of the field non-destructive inspection method and the condition/environment are used as important factors for structural confidence. According to classical damage tolerance analysis (DTA, inspection intervals are based on detectable crack size and crack growth rate. However, all variables have uncertainties, which makes the final result totally stochastic. The material properties, flight loads, engineering tools and even the reliability of inspection methods are subject to uncertainties which can affect significantly the final maintenance schedule. The present methodology incorporates all the uncertainties in a simulation process, such as Monte Carlo, and establishes a relationship between the reliability of the overall maintenance program and the proposed inspection interval, forming a “cascade” chart. Due to the scatter, it also defines the confidence level of the “acceptable” risk. As an example, the damage tolerance analysis (DTA results are presented for the upper cockpit longeron splice bolt of the BAF upgraded F-5EM. In this case, two possibilities of inspection intervals were found: one that can be characterized as remote risk, with a probability of failure (integrity nonsuccess of 1 in 10 million, per flight hour; and other as extremely improbable, with a probability of nonsuccess of 1 in 1 billion, per flight hour, according to aviation standards. These two results are compared with the classical military airplane damage tolerance requirements.

  2. Structural changes in elastically stressed crystallites under irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Zolnikov, K.P., E-mail: kost@ispms.ru [Institute of Strength Physics and Materials Science SB RAS, 2/4, pr. Akademicheskii, Tomsk (Russian Federation); Tomsk State University, 36 Lenin Ave., Tomsk (Russian Federation); Korchuganov, A.V. [Institute of Strength Physics and Materials Science SB RAS, 2/4, pr. Akademicheskii, Tomsk (Russian Federation); Kryzhevich, D.S. [Institute of Strength Physics and Materials Science SB RAS, 2/4, pr. Akademicheskii, Tomsk (Russian Federation); Tomsk State University, 36 Lenin Ave., Tomsk (Russian Federation); Chernov, V.M. [Tomsk State University, 36 Lenin Ave., Tomsk (Russian Federation); A.A. Bochvar High-Technology Scientific Research Institute for Inorganic Materials, 5a Rogova St., Moscow (Russian Federation); Psakhie, S.G. [Institute of Strength Physics and Materials Science SB RAS, 2/4, pr. Akademicheskii, Tomsk (Russian Federation); Tomsk Polytechnic University, 30 Lenin Ave., Tomsk (Russian Federation); Skolkovo Institute of Science and Technology, 100 Novaya St., Skolkovo (Russian Federation)

    2015-06-01

    The response of elastically stressed iron and vanadium crystallites to atomic displacement cascades was investigated by molecular dynamics simulation. Interatomic interaction in vanadium was described by a many-body potential calculated in the Finnis–Sinclair approximation of the embedded atom method. Interatomic interaction in iron was described by a many-body potential constructed in the approximation of valence-electron gas. The crystallite temperature in the calculations was varied from 100 to 600 K. The elastically stressed state in the crystallites was formed through uniaxial tension by 4–8% such that their volume remained unchanged. The energy of a primary knock-on atom was varied from 0.5 to 50 keV. It is shown that the lower the temperature and the higher the strain degree of an initial crystallite, the lower the threshold primary knock-on atom energy for plastic deformation generation in the crystallite. The structural rearrangements induced in the crystallites by an atomic displacement cascade are similar to those induced by mechanical loading. It is found that the rearrangements are realized through twinning.

  3. Rheological, structural and chemical evolution of bitumen under gamma irradiation

    International Nuclear Information System (INIS)

    Mouazen, M.; Poulesquen, A.; Bart, F.; Masson, J.; Charlot, M.; Vergnes, B.

    2013-01-01

    Bitumen derived from crude oil by fractional distillation has been used in the nuclear industry as a radioactive waste encapsulation matrix. When subjected to α, β and γ self-irradiation, this organic matrix undergoes radiolysis, generating hydrogen bubbles and modifying the physical and chemical properties of the material. In this paper, the effects of irradiation on bitumen materials, especially in terms of its physical, chemical, structural and rheological properties, were characterized at radiation doses ranging from 1 to 7 MGy. An increase in the shear viscosity and melt yield stress was observed with increasing doses. Similarly, the elastic and viscous moduli (G' and G'') increase with the dose, with a more pronounced increase for G' that reflects enhanced elasticity arising from radiation-induced cross-linking. In addition, a low-frequency plateau is observed for G', reflecting pseudo-solid behavior and leading to an increase of the complex viscosity. This behavior is due to increased interactions between asphaltene particles, and to aromatization of the bitumen by γ-radiations. Cross-linking of bitumen enhances its strength, as confirmed by various techniques (modulated DSC, DTA/TGA, SEC, FTIR and XRD). (authors)

  4. Structural changes in elastically stressed crystallites under irradiation

    International Nuclear Information System (INIS)

    Zolnikov, K.P.; Korchuganov, A.V.; Kryzhevich, D.S.; Chernov, V.M.; Psakhie, S.G.

    2015-01-01

    The response of elastically stressed iron and vanadium crystallites to atomic displacement cascades was investigated by molecular dynamics simulation. Interatomic interaction in vanadium was described by a many-body potential calculated in the Finnis–Sinclair approximation of the embedded atom method. Interatomic interaction in iron was described by a many-body potential constructed in the approximation of valence-electron gas. The crystallite temperature in the calculations was varied from 100 to 600 K. The elastically stressed state in the crystallites was formed through uniaxial tension by 4–8% such that their volume remained unchanged. The energy of a primary knock-on atom was varied from 0.5 to 50 keV. It is shown that the lower the temperature and the higher the strain degree of an initial crystallite, the lower the threshold primary knock-on atom energy for plastic deformation generation in the crystallite. The structural rearrangements induced in the crystallites by an atomic displacement cascade are similar to those induced by mechanical loading. It is found that the rearrangements are realized through twinning

  5. Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice.

    Directory of Open Access Journals (Sweden)

    Atsushi Fukuda

    2016-10-01

    Full Text Available In female mammals, activation of Xist (X-inactive specific transcript is essential for establishment of X chromosome inactivation. During early embryonic development in mice, paternal Xist is preferentially expressed whereas maternal Xist (Xm-Xist is silenced. Unlike autosomal imprinted genes, Xist imprinting for Xm-Xist silencing was erased in cloned or parthenogenetic but not fertilized embryos. However, the molecular mechanism underlying the variable nature of Xm-Xist imprinting is poorly understood. Here, we revealed that Xm-Xist silencing depends on chromatin condensation states at the Xist/Tsix genomic region and on Rnf12 expression levels. In early preimplantation, chromatin decondensation via H3K9me3 loss and histone acetylation gain caused Xm-Xist derepression irrespective of embryo type. Although the presence of the paternal genome during pronuclear formation impeded Xm-Xist derepression, Xm-Xist was robustly derepressed when the maternal genome was decondensed before fertilization. Once Xm-Xist was derepressed by chromatin alterations, the derepression was stably maintained and rescued XmXpΔ lethality, indicating that loss of Xm-Xist imprinting was irreversible. In late preimplantation, Oct4 served as a chromatin opener to create transcriptional permissive states at Xm-Xist/Tsix genomic loci. In parthenogenetic embryos, Rnf12 overdose caused Xm-Xist derepression via Xm-Tsix repression; physiological Rnf12 levels were essential for Xm-Xist silencing maintenance in fertilized embryos. Thus, chromatin condensation and fine-tuning of Rnf12 dosage were crucial for Xist imprint maintenance by silencing Xm-Xist.

  6. Modification of DNA bases in mammalian chromatin by radiation-generated free radicals

    International Nuclear Information System (INIS)

    Gajewski, E.; Rao, G.; Nackerdien, Z.; Dizdaroglu, M.

    1990-01-01

    Modification of DNA bases in mammalian chromatin in aqueous suspension by ionizing radiation generated free radicals was investigated. Argon, air, N2O, and N2O/O2 were used for saturation of the aqueous system in order to provide different radical environments. Radiation doses ranging from 20 to 200 Gy (J.kg-1) were used. Thirteen products resulting from radical interactions with pyrimidines and purines in chromatin were identified and quantitated by using the technique of gas chromatography/mass spectrometry with selected-ion monitoring after acidic hydrolysis and trimethylsilylation of chromatin. The methodology used permitted analysis of the modified bases directly in chromatin without the necessity of isolation of DNA from chromatin first. The results indicate that the radical environment provided by the presence of different gases in the system had a substantial effect on the types of products and their quantities. Some products were produced only in the presence of oxygen, whereas other products were detected only in the absence of oxygen. Products produced under all four gaseous conditions were also observed. Generally, the presence of oxygen in the system increased the yields of the products with the exception of formamidopyrimidines. Superoxide radical formed in the presence of air, and to a lesser extent in the presence of N2O/O2, had no effect on product formation. The presence of oxygen dramatically increased the yields of 8-hydroxypurines, whereas the yields of formamidopyrimidines were not affected by oxygen, although these products result from respective oxidation and reduction of the same hydroxyl-adduct radicals of purines. The yields of the products were much lower than those observed previously with DNA

  7. Nanoscale changes in chromatin organization represent the initial steps of tumorigenesis: a transmission electron microscopy study

    International Nuclear Information System (INIS)

    Cherkezyan, Lusik; Backman, Vadim; Stypula-Cyrus, Yolanda; Subramanian, Hariharan; White, Craig; Dela Cruz, Mart; Wali, Ramesh K; Goldberg, Michael J; Bianchi, Laura K; Roy, Hemant K

    2014-01-01

    Nuclear alterations are a well-known manifestation of cancer. However, little is known about the early, microscopically-undetectable stages of malignant transformation. Based on the phenomenon of field cancerization, the tissue in the field of a tumor can be used to identify and study the initiating events of carcinogenesis. Morphological changes in nuclear organization have been implicated in the field of colorectal cancer (CRC), and we hypothesize that characterization of chromatin alterations in the early stages of CRC will provide insight into cancer progression, as well as serve as a biomarker for early detection, risk stratification and prevention. For this study we used transmission electron microscopy (TEM) images of nuclei harboring pre-neoplastic CRC alterations in two models: a carcinogen-treated animal model of early CRC, and microscopically normal-appearing tissue in the field of human CRC. We quantify the chromatin arrangement using approaches with two levels of complexity: 1) binary, where chromatin is separated into areas of dense heterochromatin and loose euchromatin, and 2) grey-scale, where the statistics of continuous mass-density distribution within the nucleus is quantified by its spatial correlation function. We established an increase in heterochromatin content and clump size, as well as a loss of its characteristic peripheral positioning in microscopically normal pre-neoplastic cell nuclei. Additionally, the analysis of chromatin density showed that its spatial distribution is altered from a fractal to a stretched exponential. We characterize quantitatively and qualitatively the nanoscale structural alterations preceding cancer development, which may allow for the establishment of promising new biomarkers for cancer risk stratification and diagnosis. The findings of this study confirm that ultrastructural changes of chromatin in field carcinogenesis represent early neoplastic events leading to the development of well

  8. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation

    OpenAIRE

    Metzger, Eric; Yin, Na; Wissmann, Melanie; Kunowska, Natalia; Fischer, Kristin; Friedrichs, Nicolaus; Patnaik, Debasis; Higgins, Jonathan M.G.; Potier, Noelle; Scheidtmann, Karl-Heinz; Buettner, Reinhard; Schüle, Roland

    2007-01-01

    Posttranslational modifications of histones such as methylation, acetylation, and phosphorylation regulate chromatin structure and gene expression. Here we show that protein kinase C-related kinase 1 (PRK1) phosphorylates histone H3 at threonine 11 (H3T11) upon ligand-dependent recruitment to androgen receptor (AR) target genes. PRK1 is pivotal to AR function since PRK1 knockdown or inhibition impedes AR-dependent transcription. Blocking PRK1 function abrogates androgen-induced H3T11 phosphor...

  9. Neutron activation analysis of antimony in chromatin and nucleoids of HeLa cells

    International Nuclear Information System (INIS)

    Ashry, H.A.; Topaloglou, A.; Altmann, H.

    1988-02-01

    Antimony seems to be cancerogenic in men. In the present investigations we tried to find out if Sb +++ are also bound to the cell nucleus. HeLa cells were incubated with SbCl 3 and after a 18 h incubation time cells were lysed and crude chromatin isolated. In this preparation Sb was determined by neutron activation analysis. From the same cell culture nucleoids were prepared by ultracentrifugation and also Sb detected in these structures. 12 refs., 2 tabs. (Author)

  10. Organisation de la chromatine et signalisation par les oestrogènes

    OpenAIRE

    Quintin , Justine

    2013-01-01

    A given cell has to be able to adapt its fate and homeostasis in response to endogenous and exogenous signals. This adaptation occurs through finely tuned regulations of genes' expressions leading to the variation of their transcriptomes. Multiple parameters have to be integrated in order to provide such mechanisms of regulation. First, the primary sequence of the genome and its organization into chromatin are major regulatory components that harbor genetic, structural and epigenetic informat...

  11. Microcystin-LR and Cylindrospermopsin Induced Alterations in Chromatin Organization of Plant Cells

    OpenAIRE

    Máthé, Csaba; Mikóné Hamvas, Márta; Vasas, Gábor

    2013-01-01

    Cyanobacteria produce metabolites with diverse bioactivities, structures and pharmacological properties. The effects of microcystins (MCYs), a family of peptide type protein-phosphatase inhibitors and cylindrospermopsin (CYN), an alkaloid type of protein synthesis blocker will be discussed in this review. We are focusing mainly on cyanotoxin-induced changes of chromatin organization and their possible cellular mechanisms. The particularities of plant cells explain the importance of such studi...

  12. Rapid and reversible epigenome editing by endogenous chromatin regulators.

    Science.gov (United States)

    Braun, Simon M G; Kirkland, Jacob G; Chory, Emma J; Husmann, Dylan; Calarco, Joseph P; Crabtree, Gerald R

    2017-09-15

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

  13. Chromatin decondensed by acetylation shows an elevated radiation response

    International Nuclear Information System (INIS)

    Nackerdien, Z.; Michie, J.; Boehm, L.

    1989-01-01

    V-79 Chinese hamster lung fibroblasts exposed to 5 mM n-sodium butyrate were irradiated with 60Co gamma rays and cell survival was determined by the cell colony assay. In a separate set of experiments the acetylated chromatin obtained from these cells was irradiated and the change of molecular weight of the DNA was evaluated by alkaline sucrose density centrifugation. At a survival level of 10(-2) to 10(-4) cells exposed to butyrate were found to be 1.3-1.4 times more radiosensitive than control cells. Exposure of isolated chromatin to 100 Gy of 60Co gamma irradiation generated 0.9 +/- 0.03 single-strand breaks (ssb) per 10 Gy per 10(8) Da and 2.0 +/- 0.3 ssb/10 Gy/10(8) Da for control and acetylated chromatin, respectively. The elevated radiation sensitivity of chromatin relaxed by acetylation is in good agreement with previous results on chromatin expanded by histone H1 depletion. Packing and accessibility of DNA in chromatin appear to be major factors which influence the radiation sensitivity. The intrinsic radiation sensitivity of chromatin in various packing states is discussed in light of the variation of radiation sensitivity of whole cells in the cell cycle which incorporates repair

  14. Anti-chromatin antibodies in juvenile rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    V. Gerloni

    2011-09-01

    Full Text Available Objective: to evaluate the prevalence and clinical significance of anti-chromatin antibodies (Abs in juvenile rheumatoid arthritis (JRA. Methods: IgG anti-chromatin Abs were detected by an enzyme-linked immunosorbent assay (ELISA, in sera of 94 children with JRA (10 children with systemic, 38 with polyarticular and 46 with oligoarticular disease onset. As control group, 33 age- and-sex-matched healthy children (HC were also examined. Results: Abs to chromatin were detected in 24/94 (25,5% of children suffering from JRA. Particularly, the higher prevalence of anti-chromatin Abs has been found in children with oligoarticular (30,4% and polyarticular (23,7% onset JRA. In these groups Abs titers were significantly higher compared to systemic JRA and HC (p=0.003. Anti-chromatin Abs were observed more frequently in patients with oligoarticular disease and chronic uveitis (21,7%. Furthermore, higher levels of anti-chromatin Abs has been found in all the patients treated with anti-TNFα therapy (p<0.0001. Conclusions: our results confirm previous data about the prevalence of anti-chromatin Abs in JRA. These Abs were significantly higher in the group of patients with oligoarticular onset with past or present hystory of ocular involvement and in the group with polyarticular JRA treated with biologic therapy. A long-term follow-up study could be useful to evaluate the potential utility of these autoantibodies.

  15. Chromatin regulation at the frontier of synthetic biology

    Science.gov (United States)

    Keung, Albert J.; Joung, J. Keith; Khalil, Ahmad S.; Collins, James J.

    2016-01-01

    As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including `epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication. PMID:25668787

  16. SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Treffers, Louise W; Verlaan-de Vries, Matty

    2015-01-01

    dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO......-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4....

  17. DNA packing in chromatine, a manifestation of the Bonnet transformation.

    Science.gov (United States)

    Blum, Z; Lidin, S

    1988-08-01

    The packing of DNA is described using the formalism of differential geometry. Winding of the DNA double helix around the histone 2-5 octamer forming a nucleosome and the condensation of the so-formed bead-on-a-string chromatine aided by histone 1 is interpreted as two consecutive isometric, i.e. Bonnet, transformations. The DNA double helix can be approximated to a helicoid which can be transformed isometrically to a catenoid, an approximation of the nucleosome. Owing to the organization of the histone octamer the extended chromatine takes a helicoidal shape allowing a second Bonnet transformation to consummate the condensation into a chromatine fibre.

  18. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Zotova, R.N.; Umanskij, S.R.; Tokarskaya, V.I.

    1983-01-01

    A biphase change in poly (ADP-ribose) polymerase activity of the thymocyte chromatin was observed after 10 Gy irradiation of rats: during the first minutes the incorporation of 14 C-NAD increased by 40% then started decreasing to make 110, 60 and 35% after 1, 2 and 3 h, respectively. Irradiation of rat thymus chromatin in vitro sharply decreased poly (ADP-ribose) polymerase activity. The possible role of changes in the poly (ADP-ribose) synthesis in the activation of nuclear Ca/Mg-dependent endonuclease and in the postirradiation degradation of the thymocyte chromatin is discussed

  19. Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C.

    Science.gov (United States)

    Hitrik, Anna; Popliker, Malka; Gancz, Dana; Mukamel, Zohar; Lifshitz, Aviezer; Schwartzman, Omer; Tanay, Amos; Gilboa, Lilach

    2016-11-01

    The development of niches for tissue-specific stem cells is an important aspect of stem cell biology. Determination of niche size and niche numbers during organogenesis involves precise control of gene expression. How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein Combgap (Cg) supports correct ovarian niche formation in Drosophila by controlling ecdysone-Receptor (EcR)- mediated transcription and long-range chromatin contacts in the broad locus (BR-C). Both cg and BR-C promote ovarian growth and the development of niches for germ line stem cells. BR-C levels were lower when Combgap was either reduced or over-expressed, indicating an intricate regulation of the BR-C locus by Combgap. Polytene chromosome stains showed that Cg co-localizes with EcR, the major regulator of BR-C, at the BR-C locus and that EcR binding to chromatin was sensitive to changes in Cg levels. Proximity ligation assay indicated that the two proteins could reside in the same complex. Finally, chromatin conformation analysis revealed that EcR-bound regions within BR-C, which span ~30 KBs, contacted each other. Significantly, these contacts were stabilized in an ecdysone- and Combgap-dependent manner. Together, these results highlight Combgap as a novel regulator of chromatin structure that promotes transcription of ecdysone target genes and ovarian niche formation.

  20. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells.

    Science.gov (United States)

    Xu, Bowen; Cai, Ling; Butler, Jason M; Chen, Dongliang; Lu, Xiongdong; Allison, David F; Lu, Rui; Rafii, Shahin; Parker, Joel S; Zheng, Deyou; Wang, Gang Greg

    2018-03-13

    Self-renewal and differentiation of adult stem cells are tightly regulated partly through configuration of chromatin structure by chromatin remodelers. Using knockout mice, we here demonstrate that bromodomain PHD finger transcription factor (BPTF), a component of the nucleosome remodeling factor (NURF) chromatin-remodeling complex, is essential for maintaining the population size of hematopoietic stem/progenitor cells (HSPCs), including long-term hematopoietic stem cells (HSCs). Bptf-deficient HSCs are defective in reconstituted hematopoiesis, and hematopoietic-specific knockout of Bptf caused profound defects including bone marrow failure and anemia. Genome-wide transcriptome profiling revealed that BPTF loss caused downregulation of HSC-specific gene-expression programs, which contain several master transcription factors (Meis1, Pbx1, Mn1, and Lmo2) required for HSC maintenance and self-renewal. Furthermore, we show that BPTF potentiates the chromatin accessibility of key HSC "stemness" genes. These results demonstrate an essential requirement of the chromatin remodeler BPTF and NURF for activation of "stemness" gene-expression programs and proper function of adult HSCs. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Higher order magnetic modulation structures in rare earth metal, alloys and compounds under extreme conditions

    International Nuclear Information System (INIS)

    Kawano, S.

    2003-01-01

    Magnetic materials consisting of rare earth ions form modulation structures such as a helical or sinusoidal structure caused by the oscillating magnetic interaction between rare earth ions due to RKKY magnetic interaction. These modulation structures, in some cases, develop further to higher order modulation structures by additional modulations caused by higher order crystalline electric field, magnetic interactions such as spin-lattice interaction, external magnetic field and pressure. The higher order modulation structures are observed in a spin-slip structure or a helifan structure in Ho, and a tilt helix structure in a TbEr alloy. Paramagnetic ions originated from frustration generate many magnetic phases under applied external magnetic field. KUR neutron diffraction groups have performed the development and adjustment of high-pressure instruments and external magnetic fields for neutron diffraction spectrometers. The studies of 'neutron diffraction under extreme conditions' by the seven groups are described in this report. (Y. Kazumata)

  2. Experimental Study on the Structural Behavior of HSC Slab under out of plane load

    International Nuclear Information System (INIS)

    Ham, K. W.; Lee, K. J.; Park, D. S.

    2009-01-01

    HSC(Half Steel plate Concrete) Slab is a kind of SC(Steel plate Concrete) structure, so it has a similar advantage of SC structures (short construction period, lower cost and good quality control compared to RC). To apply HSC to the slab of containment building of NPP, several test with different test condition (shear span ratio, shear bar, loading type) were conducted to verify structural behavior of HSC slab structure under out of plane loading

  3. Wettability, soil organic matter and structure-properties of typical chernozems under the forest and under the arable land

    Science.gov (United States)

    Bykova, Galina; Umarova, Aminat; Tyugai, Zemfira; Milanovskiy, Evgeny; Shein, Evgeny

    2017-04-01

    Intensive tillage affects the properties of soil: decrease in content of soil organic matter and in hydrophobicity of the soil's solid phase, the reduction of amount of water stable aggregates - all this leads to deterioration of the structure of the soil and affects the process of movement of moisture in the soil profile. One of the hypotheses of soil's structure formation ascribes the formation of water stable aggregates with the presence of hydrophobic organic substances on the surface of the soil's solid phase. The aim of this work is to study the effect of tillage on properties of typical chernozems (pachic Voronic Chernozems, Haplic Chernozems) (Russia, Kursk region), located under the forest and under the arable land. The determination of soil-water contact angle was performed by a Drop Shape Analyzer DSA100 (Krüss GmbH, Germany) by the static sessile drop method. For all samples the content of total and organic carbon by dry combustion in oxygen flow and the particle size distribution by the laser diffraction method on the device Analysette 22 comfort, FRITCH, Germany were determined. The estimation of aggregate composition was performed by dry sieving (AS 200, Retsch, Germany), the content of water stable aggregates was estimated by the Savvinov method. There was a positive correlation between the content of organic matter and soil's wettability in studied soils, a growth of contact angle with the increasing the content of organic matter. Under the forest the content of soil organic matter was changed from 6,41% on the surface up to 1,9% at the depth of 100 cm. In the Chernozem under the arable land the organic carbon content in arable horizon is almost two times less. The maximum of hydrophobicity (78.1o) was observed at the depth of 5 cm under the forest. In the profile under the arable land the contact angle value at the same depth was 50o. The results of the structure analysis has shown a decrease in the content of agronomically valuable and water

  4. SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair

    DEFF Research Database (Denmark)

    McCord, Ronald A; Michishita, Eriko; Hong, Tao

    2009-01-01

    -PKcs) to chromatin in response to DNA damage and stabilizes DNA-PKcs at chromatin adjacent to an induced site-specific DSB. Abrogation of these SIRT6 activities leads to impaired resolution of DSBs. Together, these findings elucidate a mechanism whereby regulation of dynamic interaction of a DNA repair factor......-dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetylation levels on histone H3 Lysine 9. Moreover, SIRT6 is required for mobilization of the DNA-PK catalytic subunit (DNA......, and SIRT6 knockout cells exhibit genomic instability and DNA damage hypersensitivity. However, the molecular mechanisms underlying these defects are not fully understood. Here, we show that SIRT6 forms a macromolecular complex with the DNA double-strand break (DSB) repair factor DNA-PK (DNA...

  5. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Yupeng; Levendosky, Robert F.; Chakravarthy, Srinivas; Patel, Ashok; Bowman, Gregory D.; Myong, Sua

    2017-10-01

    Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.

  6. Phosphorylated SAP155, the spliceosomal component, is localized to chromatin in postnatal mouse testes

    Energy Technology Data Exchange (ETDEWEB)

    Eto, Ko, E-mail: etoko@gpo.kumamoto-u.ac.jp [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555 (Japan); Sonoda, Yoshiyuki [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555 (Japan); Jin, Yuji [School of Basic Medicine, Jilin Medical College, Jilin 132013 (China); Abe, Shin-ichi [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555 (Japan)

    2010-03-19

    SAP155 is an essential component of the spliceosome and its phosphorylation is required for splicing catalysis, but little is known concerning its expression and regulation during spermatogenesis in postnatal mouse testes. We report that SAP155 is ubiquitously expressed in nuclei of germ and Sertoli cells within the seminiferous tubules of 6- and 35-day postpartum (dpp) testes. Analyses by fractionation of testes revealed that (1) phosphorylated SAP155 was found in the fraction containing nuclear structures at 6 dpp in amounts much larger than that at other ages; (2) non-phosphorylated SAP155 was detected in the fraction containing nucleoplasm; and (3) phosphorylated SAP155 was preferentially associated with chromatin. Our findings suggest that the active spliceosome, containing phosphorylated SAP155, performs pre-mRNA splicing on chromatin concomitant with transcription during testicular development.

  7. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang

    2016-02-04

    Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.

  8. HACking the centromere chromatin code: insights from human artificial chromosomes.

    Science.gov (United States)

    Bergmann, Jan H; Martins, Nuno M C; Larionov, Vladimir; Masumoto, Hiroshi; Earnshaw, William C

    2012-07-01

    The centromere is a specialized chromosomal region that serves as the assembly site of the kinetochore. At the centromere, CENP-A nucleosomes form part of a chromatin landscape termed centrochromatin. This chromatin environment conveys epigenetic marks regulating kinetochore formation. Recent work sheds light on the intricate relationship between centrochromatin state, the CENP-A assembly pathway and the maintenance of centromere function. Here, we review the emerging picture of how chromatin affects mammalian kinetochore formation. We place particular emphasis on data obtained from Human Artificial Chromosome (HAC) biology and the targeted engineering of centrochromatin using synthetic HACs. We discuss implications of these findings, which indicate that a delicate balance of histone modifications and chromatin state dictates both de novo centromere formation and the maintenance of centromere identity in dividing cell populations.

  9. histone H3 predominantly mark the pericentromeric chromatin

    Indian Academy of Sciences (India)

    SANTOSH KUMAR SHARMA

    pericentromeric chromatin during mitosis in monokinetic plants. J. Genet. .... bigger), cytological preparations (easy to difficult) as well as their habitat ... Poaceae. Monocot. Land. 14. Triticum aestivum. Common wheat. Poaceae. Monocot. Land.

  10. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang; Schwarzer, Dirk

    2016-01-01

    and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites

  11. Citrullination regulates pluripotency and histone H1 binding to chromatin

    DEFF Research Database (Denmark)

    Christophorou, Maria A; Castelo-Branco, Gonçalo; Halley-Stott, Richard P

    2014-01-01

    citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune...... and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel...... PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic...

  12. histone H3 predominantly mark the pericentromeric chromatin

    Indian Academy of Sciences (India)

    SANTOSH KUMAR SHARMA

    packaging of eukaryotic DNA in nucleoprotein complex known as .... The plant material used in the present study has ... materials (root tips/flower buds) were fixed in PHEMES ..... fications that mark active chromatin, while there are no data.

  13. Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Holmberg, S

    2000-01-01

    The Saccharomyces cerevisiae NHP6A and NHP6B proteins are chromatin architectural factors, functionally and structurally related to the mammalian high mobility group (HMG)-1 and -2 proteins, a family of non-sequence-specific DNA binding proteins. nhp6a nhp6b mutants have various morphological...

  14. Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data.

    Science.gov (United States)

    Kustatscher, Georg; Grabowski, Piotr; Rappsilber, Juri

    2016-02-01

    Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. © 2015 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Dual mechanism of chromatin remodeling in the common shrew sex trivalent (XY 1Y 2

    Directory of Open Access Journals (Sweden)

    Sergey N. Matveevsky

    2017-11-01

    Full Text Available Here we focus on the XY1Y2 condition in male common shrew Sorex araneus Linnaeus, 1758, applying electron microscopy and immunocytochemistry for a comprehensive analysis of structure, synapsis and behaviour of the sex trivalent in pachytene spermatocytes. The pachytene sex trivalent consists of three distinct parts: short and long synaptic SC fragments (between the X and Y1 and between the X and Y2, respectively and a long asynaptic region of the X in-between. Chromatin inactivation was revealed in the XY1 synaptic region, the asynaptic region of the X and a very small asynaptic part of the Y2. This inactive part of the sex trivalent, that we named the ‘head’, forms a typical sex body and is located at the periphery of the meiotic nucleus at mid pachytene. The second part or ‘tail’, a long region of synapsis between the X and Y2 chromosomes, is directed from the periphery into the nucleus. Based on the distribution patterns of four proteins involved in chromatin inactivation, we propose a model of meiotic silencing in shrew sex chromosomes. Thus, we conclude that pachytene sex chromosomes are structurally and functionally two different chromatin domains with specific nuclear topology: the peripheral inactivated ‘true’ sex chromosome regions (part of the X and the Y1 and more centrally located transcriptionally active autosomal segments (part of the X and the Y2.

  16. Cytogenetic abnormality in man, wider implications of theories of sex chromatin origin.

    Science.gov (United States)

    MILES, C P

    1962-01-01

    Female nuclei may be identified by means of sex chromatin. In general the number of sex chromatin bodies is one less than the number of X chromosomes. An exception to this rule is a case of sex chromatin-positive XO Turner's syndrome. This case suggests the possibility of sex chromatin-positive XY males, and it may be evidence for chromosomal differentiation.

  17. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Nikonova, L.V.; Nelipovich, P.A.; Umanskij, S.R.

    1983-01-01

    Chromatin digestion in isolated thymocyte nuclei with DNAase I, micrococcal nuclease and nuclease from Serratia marcescens was studied. It was shown that 3 h after irradiation (10 Gy), the kinetics of accumulation of acid soluble and salt soluble products of DNA degradation, caused by exogenous nucleases, remains unchanged. The administration of cycloheximide does not influence the sensitivity of chromatin to DNAase I and somewhat increases the rate of salt soluble products formation upon the nuclease from S, marcescens treatment

  18. Fragmentation of chromatin with 125I radioactive disintegrations

    International Nuclear Information System (INIS)

    Turner, G.N.; Nobis, P.; Dewey, W.C.

    1976-01-01

    The DNA in Chinese hamster cells was labeled first for 3 h with [ 3 H]TdR and then for 3 h with [ 125 I]UdR. Chromatin was extracted, frozen, and stored at -30 0 C until 1.0 x 10 17 and 1.25 x 10 17 disintegrations/g of labeled DNA occurred for 125 I and 3 H, respectively. Velocity sedimentation of chromatin (DNA with associated chromosomal proteins) in neutral sucrose gradients indicated that the localized energy from the 125 I disintegrations, which gave about 1 double-strand break/disintegration plus an additional 1.3 single strand breaks, selectively fragmented the [ 125 I] chromatin into pieces smaller than the [ 3 H] chromatin. In other words, 125 I disintegrations caused much more localized damage in the chromatin labeled with 125 I than in the chromatin labeled with 3 H, and fragments induced in DNA by 125 I disintegrations were not held together by the associated chromosomal proteins. Use of this 125 I technique for studying chromosomal proteins associated with different regions in the cellular DNA is discussed. For these studies, the number of disintegrations required for fragmenting DNA molecules of different sizes is illustrated

  19. Cytoplasmic chromatin triggers inflammation in senescence and cancer.

    Science.gov (United States)

    Dou, Zhixun; Ghosh, Kanad; Vizioli, Maria Grazia; Zhu, Jiajun; Sen, Payel; Wangensteen, Kirk J; Simithy, Johayra; Lan, Yemin; Lin, Yanping; Zhou, Zhuo; Capell, Brian C; Xu, Caiyue; Xu, Mingang; Kieckhaefer, Julia E; Jiang, Tianying; Shoshkes-Carmel, Michal; Tanim, K M Ahasan Al; Barber, Glen N; Seykora, John T; Millar, Sarah E; Kaestner, Klaus H; Garcia, Benjamin A; Adams, Peter D; Berger, Shelley L

    2017-10-19

    Chromatin is traditionally viewed as a nuclear entity that regulates gene expression and silencing. However, we recently discovered the presence of cytoplasmic chromatin fragments that pinch off from intact nuclei of primary cells during senescence, a form of terminal cell-cycle arrest associated with pro-inflammatory responses. The functional significance of chromatin in the cytoplasm is unclear. Here we show that cytoplasmic chromatin activates the innate immunity cytosolic DNA-sensing cGAS-STING (cyclic GMP-AMP synthase linked to stimulator of interferon genes) pathway, leading both to short-term inflammation to restrain activated oncogenes and to chronic inflammation that associates with tissue destruction and cancer. The cytoplasmic chromatin-cGAS-STING pathway promotes the senescence-associated secretory phenotype in primary human cells and in mice. Mice deficient in STING show impaired immuno-surveillance of oncogenic RAS and reduced tissue inflammation upon ionizing radiation. Furthermore, this pathway is activated in cancer cells, and correlates with pro-inflammatory gene expression in human cancers. Overall, our findings indicate that genomic DNA serves as a reservoir to initiate a pro-inflammatory pathway in the cytoplasm in senescence and cancer. Targeting the cytoplasmic chromatin-mediated pathway may hold promise in treating inflammation-related disorders.

  20. A Role for Histone Deacetylases in the Cellular and Behavioral Mechanisms Underlying Learning and Memory

    Science.gov (United States)

    Mahgoub, Melissa; Monteggia, Lisa M.

    2014-01-01

    Histone deacetylases (HDACs) are a family of chromatin remodeling enzymes that restrict access of transcription factors to the DNA, thereby repressing gene expression. In contrast, histone acetyltransferases (HATs) relax the chromatin structure allowing for an active chromatin state and promoting gene transcription. Accumulating data have…