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Sample records for gene drd4 exon

  1. ADHD candidate gene (DRD4 exon III affects inhibitory control in a healthy sample

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    Marco-Pallarés Josep

    2009-12-01

    Full Text Available Background Dopamine is believed to be a key neurotransmitter in the development of attention-deficit/hyperactivity disorder (ADHD. Several recent studies point to an association of the dopamine D4 receptor (DRD4 gene and this condition. More specifically, the 7 repeat variant of a variable number of tandem repeats (VNTR polymorphism in exon III of this gene is suggested to bear a higher risk for ADHD. In the present study, we investigated the role of this polymorphism in the modulation of neurophysiological correlates of response inhibition (Go/Nogo task in a healthy, high-functioning sample. Results Homozygous 7 repeat carriers showed a tendency for more accurate behavior in the Go/Nogo task compared to homozygous 4 repeat carriers. Moreover, 7 repeat carriers presented an increased nogo-related theta band response together with a reduced go-related beta decrease. Conclusions These data point to improved cognitive functions and prefrontal control in the 7 repeat carriers, probably due to the D4 receptor's modulatory role in prefrontal areas. The results are discussed with respect to previous behavioral data on this polymorphism and animal studies on the impact of the D4 receptor on cognitive functions.

  2. Identification and characterization of a tandem repeat in exon III of the dopamine receptor D4 (DRD4) gene in cetaceans

    DEFF Research Database (Denmark)

    Mogensen, Line; Kinze, Carl Christian; Werge, Thomas

    2006-01-01

    in exon III of their DRD4 gene. Consequently, the 18-bp tandem repeat appears to have originated prior to the differentiation of hoofed mammals into odd-toed and even-toed ungulates. The composition of the tandem repeat in cetaceans differed markedly from that in primates, which is composed of 48-bp...

  3. Hardy–Weinberg equilibrium analysis of the 48 bp VNTR in the III exon of the DRD4 gene in a sample of parents of ADHD cases

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    Trejo S

    2015-06-01

    Full Text Available Salvador Trejo, José J Toscano-Flores, Esmeralda Matute, María de Lourdes Ramírez-Dueñas Laboratorio de Neuropsicología y Neurolingüística, Instituto de Neurociencias CUCBA, Guadalajara, Jalisco, Mexico Abstract: The aim of this study was to obtain the genotype and gene frequency from parents of children with attention-deficit/hyperactivity disorder (ADHD and then assess the Hardy–Weinberg equilibrium of genotype frequency of the variable number tandem repeat (VNTR III exon of the dopamine receptor D4 (DRD4 gene. The genotypes of the III exon of 48 bp VNTR repeats of the DRD4 gene were determined by polymerase chain reaction in a sample of 30 parents of ADHD cases. In the 60 chromosomes analyzed, the following frequencies of DRD4 gene polymorphisms were observed: six chromosomes (c with two repeat alleles (r (10%; 1c with 3r (1.5%; 36c with 4r (60%; 1c with 5r (1.5%; and 16c with 7r (27%. The genotypic distribution of the 30 parents was two parents (p with 2r/2r (6.67%; 1p with 2r/4r (3.33%; 1p with 2r/5r (3.33%; 1p with 3r/4r (3.33%; 15p with 4r/4r (50%; 4p with 4r/7r (13.33; and 6p with 7r/7r (20%. A Hardy–Weinberg disequilibrium (χ2=13.03, P<0.01 was found due to an over-representation of the 7r/7r genotype. These results suggest that the 7r polymorphism of the DRD4 gene is associated with the ADHD condition in a Mexican population. Keywords: ADHD, parents, DRD4, HWE

  4. Hardy–Weinberg equilibrium analysis of the 48 bp VNTR in the III exon of the DRD4 gene in a sample of parents of ADHD cases

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    Trejo, Salvador; Toscano-Flores, José J; Matute, Esmeralda; Ramírez-Dueñas, María de Lourdes

    2015-01-01

    The aim of this study was to obtain the genotype and gene frequency from parents of children with attention-deficit/hyperactivity disorder (ADHD) and then assess the Hardy–Weinberg equilibrium of genotype frequency of the variable number tandem repeat (VNTR) III exon of the dopamine receptor D4 (DRD4) gene. The genotypes of the III exon of 48 bp VNTR repeats of the DRD4 gene were determined by polymerase chain reaction in a sample of 30 parents of ADHD cases. In the 60 chromosomes analyzed, the following frequencies of DRD4 gene polymorphisms were observed: six chromosomes (c) with two repeat alleles (r) (10%); 1c with 3r (1.5%); 36c with 4r (60%); 1c with 5r (1.5%); and 16c with 7r (27%). The genotypic distribution of the 30 parents was two parents (p) with 2r/2r (6.67%); 1p with 2r/4r (3.33%); 1p with 2r/5r (3.33%); 1p with 3r/4r (3.33%); 15p with 4r/4r (50%); 4p with 4r/7r (13.33); and 6p with 7r/7r (20%). A Hardy–Weinberg disequilibrium (χ2=13.03, P<0.01) was found due to an over-representation of the 7r/7r genotype. These results suggest that the 7r polymorphism of the DRD4 gene is associated with the ADHD condition in a Mexican population. PMID:26082657

  5. Identification and characterization of a tandem repeat in exon III of the dopamine receptor D4 (DRD4) gene in cetaceans

    DEFF Research Database (Denmark)

    Mogensen, Line; Kinze, Carl Christian; Werge, Thomas

    2006-01-01

    , and these sequences differed by a maximum of two changes when compared to the remaining species. There was a high degree of similarity between the cetacean basic unit consensus sequences and those from members of the horse family and domestic cow, which also harbor a tandem repeat composed of 18-bp basic units...... in exon III of their DRD4 gene. Consequently, the 18-bp tandem repeat appears to have originated prior to the differentiation of hoofed mammals into odd-toed and even-toed ungulates. The composition of the tandem repeat in cetaceans differed markedly from that in primates, which is composed of 48-bp...

  6. Association of VNTR polymorphisms in DRD4, 5-HTT and DAT1 genes with obesity.

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    Uzun, Mustafa; Saglar, Emel; Kucukyildirim, Sibel; Erdem, Beril; Unlu, Hande; Mergen, Hatice

    2015-05-01

    To investigate the association between VNTR polymorphisms of DRD4, DAT1 and 5-HTT genes and obesity. Peripheral blood samples of 234 obese (BMI ≥ 30) and 148 healthy individuals (BMI ≤ 25) were objected to PCR to detect the VNTR of the 2nd intron of 5-HTT, 3rd exon of DRD4 and 3'UTR of DAT1 genes. The association between obesity and genotype distributions of 5-HTT, DAT1 and DRD4 genes and between obesity and distributions of allele frequencies were tested by Chi Square (χ(2)) test and were not found statistically significant. BMI values for genotype of obese and morbidly obese (BMI > 40) individuals were analyzed by Kruskal-Wallis and not found statistically significant differences between BMI values for the most frequent genotypes of 5-HTT, DAT1 and DRD4 genes. As a conclusion, there was no association between 5-HTT, DAT1 and DRD4 genes VNTR polymorphisms and obesity.

  7. Association study of MAO-A and DRD4 genes in schizophrenic patients with aggressive behavior.

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    Fresan, Ana; Camarena, Beatriz; Apiquian, Rogelio; Aguilar, Alejandro; Urraca, Nora; Nicolini, Humberto

    2007-01-01

    Genes involved in dopamine neurotransmission are interesting candidates to be analyzed in schizophrenia and aggressive behavior. Therefore, we analyzed the functional polymorphisms of the dopamine receptor D4 (DRD4) and monoamine oxidase A (MAO-A) genes in a sample of 71 schizophrenic patients assessed with the Overt Aggression Scale to measure aggressive behavior. CLUMP analysis of the DRD4 48-bp repeat-exon III polymorphism in schizophrenic patients showed significant differences between the aggressive behavior and the nonaggressive groups (T1 = 18.77, d.f. = 6, p = 0.0046; T3 = 6.54, p = 0.0195). However, analysis of the promoter polymorphism of the MAO-A gene revealed no significant association between aggressive and nonaggressive patients. Finally, analysis of Overt Aggression Scale dimensions exhibited significant differences for the DRD4 and MAO-A genes. Our preliminary findings suggest that the DRD4 and MAO-A genes may be involved in aggressive schizophrenic patients.

  8. DRD4-exonIII-VNTR moderates the effect of childhood adversities on emotional resilience in young-adults.

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    Debjani Das

    Full Text Available Most individuals successfully maintain psychological well-being even when exposed to trauma or adversity. Emotional resilience or the ability to thrive in the face of adversity is determined by complex interactions between genetic makeup, previous exposure to stress, personality, coping style, availability of social support, etc. Recent studies have demonstrated that childhood trauma diminishes resilience in adults and affects mental health. The Dopamine receptor D4 (DRD4 exon III variable number tandem repeat (VNTR polymorphism was reported to moderate the impact of adverse childhood environment on behaviour, mood and other health-related outcomes. In this study we investigated whether DRD4-exIII-VNTR genotype moderates the effect of childhood adversities (CA on resilience. In a representative population sample (n = 1148 aged 30-34 years, we observed an interactive effect of DRD4 genotype and CA (β = 0.132; p = 0.003 on resilience despite no main effect of the genotype when effects of age, gender and education were controlled for. The 7-repeat allele appears to protect against the adverse effect of CA since the decline in resilience associated with increased adversity was evident only in individuals without the 7-repeat allele. Resilience was also significantly associated with approach-/avoidance-related personality measures (behavioural inhibition/activation system; BIS/BAS measures and an interactive effect of DRD4-exIII-VNTR genotype and CA on BAS was observed. Hence it is possible that approach-related personality traits could be mediating the effect of the DRD4 gene and childhood environment interaction on resilience such that when stressors are present, the 7-repeat allele influences the development of personality in a way that provides protection against adverse outcomes.

  9. Dopamine receptor D4 (DRD4) gene modulates the influence of informational masking on speech recognition.

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    Xie, Zilong; Maddox, W Todd; Knopik, Valerie S; McGeary, John E; Chandrasekaran, Bharath

    2015-01-01

    Listeners vary substantially in their ability to recognize speech in noisy environments. Here we examined the role of genetic variation on individual differences in speech recognition in various noise backgrounds. Background noise typically varies in the levels of energetic masking (EM) and informational masking (IM) imposed on target speech. Relative to EM, release from IM is hypothesized to place greater demand on executive function to selectively attend to target speech while ignoring competing noises. Recent evidence suggests that the long allele variant in exon III of the DRD4 gene, primarily expressed in the prefrontal cortex, may be associated with enhanced selective attention to goal-relevant high-priority information even in the face of interference. We investigated the extent to which this polymorphism is associated with speech recognition in IM and EM conditions. In an unscreened adult sample (Experiment 1) and a larger screened replication sample (Experiment 2), we demonstrate that individuals with the DRD4 long variant show better recognition performance in noise conditions involving significant IM, but not in EM conditions. In Experiment 2, we also obtained neuropsychological measures to assess the underlying mechanisms. Mediation analysis revealed that this listening condition-specific advantage was mediated by enhanced executive attention/working memory capacity in individuals with the long allele variant. These findings suggest that DRD4 may contribute specifically to individual differences in speech recognition ability in noise conditions that place demands on executive function. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Lack of association of DRD4 exon 3 VNTR genotype with reactivity to dynamic smoking cues in movies

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    Lochbühler, K.C.; Verhagen, M.; Munafo, M.R.; Engels, R.C.M.E.

    2013-01-01

    Background: The objective of the present study was first to examine whether dynamic smoking cues in movies trigger craving, and second to explore whether the DRD4 48 bp variable number of tandem repeat (VNTR) exon 3 genotype modifies this relationship. Using an experimental design, daily adult smoke

  11. IDENTIFICATION AND CHARACTERIZATION OF DOPAMINE D4 RECEPTOR (DRD4 GENE SEQUENCE WITHIN AND AMONG NON MAMMALIAN SPECIES

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    Shikha Khandelwal

    2013-08-01

    Full Text Available A number of polymorphic tandem repeats in human dopamine D4 receptor (DRD4 have been identified in the exons, including a 12-bp repeat in the first exon and a 48-bp repeat in exon III located in the third cytoplasmic loop. However, to determine whether the tandem repeats is specific to humans or not, we have identified and characterized dopamine receptor D4 (DRD4 Exon III tandem repeats in public available nucleotide sequences from 13 different non mammalian species. We found that the tandem repeat was composed of 21-bp modules in sequences from the Mycobacterium smegmatis str. MC2 155, Salinibacter ruber DSM 13855, Danio rerio, Parus major, Corvus macrorhynchos, and Coturnix japonica. A tandem repeat consisting of 30-bp modules was identified in sequence from Melopsittacus undulates while in the Phalacrocorax capillatus and Numida meleagris we identified tandem repeats composed of 3-bp modules. Tandem repeats could not be identified in sequences from Carassius auratus, Phasianus colchicus and Gallus gallus. To understand the evolutionary history of the Exon I region of DRD4—which in humans contains a polymorphic 12bp tandem duplication, a polymorphic 13bp deletion, and other rare variants—we examined the homologous exon in these different species. There was a low degree of similarity between the sequences of bacterial species and those from members of the piscean and avian and with human sequence. We identified transmembrane domain of DRD4 gene and signature of G-protein coupled receptors in the amino acid sequences. The number of transmembrane segments varied pronouncedly between species from 0 to 7 and signature of G-protein coupled receptors was found only in piscean species and was also identified in one avian species (parus major. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the non mammalian and mammalian lineages. Furthermore, the analysis of

  12. Drd4 gene polymorphisms are associated with personality variation in a passerine bird.

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    Fidler, Andrew E; van Oers, Kees; Drent, Piet J; Kuhn, Sylvia; Mueller, Jakob C; Kempenaers, Bart

    2007-07-22

    Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour. However, genetic epistasis, genotype-environment interactions and confounding environmental factors all act to obscure genotype-personality relationships. Such problems can be addressed by measuring personality under standardized conditions and by selection experiments, with both approaches only feasible with non-human animals. Looking for similar Drd4 genotype-personality associations in a free-living bird, the great tit (Parus major), we detected 73 polymorphisms (66 SNPs, 7 indels) in the P. major Drd4 orthologue. Two of the P. major Drd4 gene polymorphisms were investigated for evidence of association with novelty-seeking behaviour: a coding region synonymous single nucleotide polymorphism (SNP830) and a 15bp indel (ID15) located 5' to the putative transcription initiation site. Frequencies of the three Drd4 SNP830 genotypes, but not the ID15 genotypes, differed significantly between two P. major lines selected over four generations for divergent levels of 'early exploratory behaviour' (EEB). Strong corroborating evidence for the significance of this finding comes from the analysis of free-living, unselected birds where we found a significant association between SNP830 genotypes and differing mean EEB levels. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the avian and mammalian lineages. Furthermore, this work heralds the possibility of following microevolutionary changes in frequencies of behaviourally relevant Drd4 polymorphisms within populations where natural selection acts differentially on different personality types.

  13. Linking gene, brain, and behavior: DRD4, frontal asymmetry, and temperament.

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    Schmidt, Louis A; Fox, Nathan A; Perez-Edgar, Koraly; Hamer, Dean H

    2009-07-01

    Gene-environment interactions involving exogenous environmental factors are known to shape behavior and personality development. Although gene-environment interactions involving endogenous environmental factors are hypothesized to play an equally important role, this conceptual approach has not been empirically applied in the study of early-developing temperament in humans. Here we report evidence for a gene-endoenvironment (i.e., resting frontal brain electroencephalogram, EEG, asymmetry) interaction in predicting child temperament. The dopamine D4 receptor (DRD4) gene (long allele vs. short allele) moderated the relation between resting frontal EEG asymmetry (left vs. right) at 9 months and temperament at 48 months. Children who exhibited left frontal EEG asymmetry at 9 months and who possessed the DRD4 long allele were significantly more soothable at 48 months than other children. Among children with right frontal EEG asymmetry at 9 months, those with the DRD4 long allele had significantly more difficulties focusing and sustaining attention at 48 months than those with the DRD4 short allele. Resting frontal EEG asymmetry did not influence temperament in the absence of the DRD4 long allele. We discuss how the interaction of genetic and endoenvironmental factors may confer risk and protection for different behavioral styles in children.

  14. Thyroid hormone and adrenergic signaling interact to control pineal expression of the dopamine receptor D4 gene (Drd4)

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    Kim, Jong-So; Bailey, Michael J; Weller, Joan L;

    2009-01-01

    . Our studies indicate that Drd4 is the dominant dopamine receptor gene expressed in the pineal gland. The gene is expressed in pinealocytes at levels which are approximately 100-fold greater than in other tissues, except the retina, in which transcript levels are similar. Pineal Drd4 expression...... and whether thyroid hormone controls expression of other genes in the pineal gland.......Dopamine plays diverse and important roles in vertebrate biology, impacting behavior and physiology through actions mediated by specific G-protein-coupled receptors, one of which is the dopamine receptor D4 (Drd4). Here we present studies on the >100-fold daily rhythm in rat pineal Drd4 expression...

  15. The Dopamine Receptor D4 Gene ("DRD4") Moderates Family Environmental Effects on ADHD

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    Martel, Michelle M.; Nikolas, Molly; Jernigan, Katherine; Friderici, Karen; Waldman, Irwin; Nigg, Joel T.

    2011-01-01

    Attention-Deficit/Hyperactivity Disorder (ADHD) is a prime candidate for exploration of gene-by-environment interaction (i.e., G x E), particularly in relation to dopamine system genes, due to strong evidence that dopamine systems are dysregulated in the disorder. Using a G x E design, we examined whether the "DRD4" promoter 120-bp tandem repeat…

  16. The Dopamine Receptor D4 Gene ("DRD4") Moderates Family Environmental Effects on ADHD

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    Martel, Michelle M.; Nikolas, Molly; Jernigan, Katherine; Friderici, Karen; Waldman, Irwin; Nigg, Joel T.

    2011-01-01

    Attention-Deficit/Hyperactivity Disorder (ADHD) is a prime candidate for exploration of gene-by-environment interaction (i.e., G x E), particularly in relation to dopamine system genes, due to strong evidence that dopamine systems are dysregulated in the disorder. Using a G x E design, we examined whether the "DRD4" promoter 120-bp tandem repeat…

  17. Drd4 gene polymorphisms are associated with personality variation in a passerine bird

    NARCIS (Netherlands)

    Fidler, A.E.; Van Oers, K.; Drent, P.J.; Kuhn, S.; Mueller, J.C.; Kempenaers, B.

    2007-01-01

    Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour. However, genetic epistasis, gen

  18. Drd4 gene polymorphisms are associated with personality variation in a passerine bird

    NARCIS (Netherlands)

    Fidler, A.E.; Van Oers, K.; Drent, P.J.; Kuhn, S.; Mueller, J.C.; Kempenaers, B.

    2007-01-01

    Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour. However, genetic epistasis, gen

  19. Family-based association study of DRD4 gene in methylphenidate-responded Attention Deficit/Hyperactivity Disorder.

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    Leung, Patrick Wing-Leung; Chan, Janice Ka Yan; Chen, Lu Hua; Lee, Chi Chiu; Hung, Se Fong; Ho, Ting Pong; Tang, Chun Pan; Moyzis, Robert K; Swanson, James M

    2017-01-01

    The 48-basepair (48-bp) variable number tandem repeat (VNTR) polymorphism in exon 3 of the dopamine receptor D4 gene (DRD4) is implicated in the etiology of attention-deficit/ hyperactivity disorder (ADHD). In particular, ADHD in European-ancestry population is associated with an increased prevalence of the 7-repeat (7R) allele of the exon 3 VNTR. However, it is intriguing to note that the 7R allele has been found to be of very low prevalence in the Chinese general population. In a previous case-control study, our research team had found that the 7R allele was similarly absent in Chinese ADHD children in Hong Kong. Instead, there was an increased prevalence of the 2R allele in Chinese ADHD children. Interestingly, in Asian samples, the 2R allele had been found to be an evolutionary derivative of the 7R allele with equivalent biochemical functionality. So, the finding of an association between ADHD and 2R allele in Chinese population does not exactly contradict the original 7R allele finding in European-ancestry population. However, given the potential pitfall of population stratification in the previous case-control design, this current study tested the 2R allele and ADHD association using a methodologically more rigorous family-based approach on 33 Chinese ADHD probands who had favorable clinical responses to stimulant medication (methylphenidate). Haplotype Relative Risk (HRR) analysis and Transmission Disequilibrium Test (TDT) both showed a significant preferential transmission of the 2R allele from the biological parents to ADHD probands (pone-tailed = 0.038, OR = 2.04; pone-tailed = 0.048, OR = 2.29, respectively). A second hypothesis speculates that it is the deviation, including 7R and 2R alleles, from the conserved ancestral 4R allele which confers risk to ADHD. Thus, a preferential transmission of non-4R alleles, against the 4R allele, from biological parents to their ADHD probands is predicted. Both HRR analysis and TDT confirmed such prediction (pone

  20. The association between creativity and 7R polymorphism in the dopamine receptor D4 gene (DRD4).

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    Mayseless, Naama; Uzefovsky, Florina; Shalev, Idan; Ebstein, Richard P; Shamay-Tsoory, Simone G

    2013-01-01

    Creativity can be defined as the ability to produce responses that are both novel and appropriate. One way to assess creativity is to measure divergent thinking (DT) abilities that involve generating multiple novel and meaningful responses to open-ended questions. DT abilities have been shown to be associated with dopaminergic (DA) activity, and impaired DT has been reported in populations with DA dysfunctions. Given the strong association between DT and the DA system, the current study examined a group of healthy individuals (N = 185) to determine the role of repeat polymorphism in exon3 of the DRD4 gene in creativity. The results show that individuals carrying the DRD4-7R allele scored significantly lower on tests of DT, particularly on the flexibility dimension of DT, compared to non-carriers. The current findings link creative cognition to the DA system and suggest that DA dysfunctions in neurological and psychiatric disorders may account for impaired creativity and cognitive flexibility in these individuals.

  1. The dopamine D4 receptor gene (DRD4) moderates cultural difference in independent versus interdependent social orientation.

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    Kitayama, Shinobu; King, Anthony; Yoon, Carolyn; Tompson, Steve; Huff, Sarah; Liberzon, Israel

    2014-06-01

    Prior research suggests that cultural groups vary on an overarching dimension of independent versus interdependent social orientation, with European Americans being more independent, or less interdependent, than Asians. Drawing on recent evidence suggesting that the dopamine D4 receptor gene (DRD4) plays a role in modulating cultural learning, we predicted that carriers of DRD4 polymorphisms linked to increased dopamine signaling (7- or 2-repeat alleles) would show higher levels of culturally dominant social orientations, compared with noncarriers. European Americans and Asian-born Asians (total N = 398) reported their social orientation on multiple scales. They were also genotyped for DRD4. As in earlier work, European Americans were more independent, and Asian-born Asians more interdependent. This cultural difference was significantly more pronounced for carriers of the 7- or 2-repeat alleles than for noncarriers. Indeed, no cultural difference was apparent among the noncarriers. Implications for potential coevolution of genes and culture are discussed.

  2. Relationship between dopamine receptor D4 exon Ⅲ polymorphism and aggressive behavior and psychiatric symptoms in schizophrenia%DRD4 exon Ⅲ基因多态性与精神分裂症患者攻击行为及精神症状的关联研究

    Institute of Scientific and Technical Information of China (English)

    陈玄玄; 杨道良; 陈剑华; 季卫东

    2016-01-01

    Objective To investigate the relationship between the polymorphism of repeatable sequence of DRD4 exon Ⅲ 48 bp gene and psychiatric symptoms and aggressive behavior in schizophrenia. Methods 302 patients who were diagnosed as schizophrenia according to the criteria of the International classification of diseases (ICD-10) were divided into two groups according to the score of modified overt aggression scale (MOAS): group with aggressive behavior (research group) and group without aggressive behavior (control group). All objects were evaluated with general demographic data and positive and negative syndrome scale (PANSS). The polymorphous points of DRD4 gene were genotyped by the amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) genotyping assay method. The test for Hardy-Weinberg equilibrium and the difference of genotype frequency between groups were performed using SHEsis software, the significance for the association was estimated by chi-square and t test. Results In those common items, there were no significantly differences between the two groups (P>0.05). The DRD4 genotype frequencies of the two groups were consistent with the Hardy-Weinberg genetic equilibrium law (P>0.05). Six alleles and eight genetypes of 48 bp polymorphism had been detected in the exonⅢof DRD4. In all the groups, the most common allele was 4. There were statistical differences on the frequencies of genotypes and alleles of DRD4 exon Ⅲbp VNTR among the two groups (P0.05). The factor scores of thought disorder and aggressivity were statistically significant (P<0.05). The scores in patients who carried long repeat allele group were higher than that in short repeat allele group. Conclusions (1) The results suggest that the DRD4 exon Ⅲ 48 bp VNTR is associated with aggressive schizophrenic patients. (2) The DRD4 exonⅢ48 bp VNTR is associated with thought disorder and aggressivity in aggressive schizophrenic patients. The aggressive schizophrenic

  3. The association between creativity and 7R polymorphism in the dopamine receptor D4 gene (DRD4

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    Naama eMayseless

    2013-08-01

    Full Text Available Creativity can be defined as the ability to produce responses that are both novel and appropriate. One way to assess creativity is to measure divergent thinking (DT abilities that involve generating multiple novel and meaningful responses to open-ended questions. DT abilities have been shown to be associated with dopaminergic activity, and impaired DT has been reported in populations with dopaminergic dysfunctions. Given the strong association between DT and the dopaminergic system, the current study examined a group of healthy individuals (N=185 to determine the role of the repeat polymorphism in exon3 of the DRD4 in creativity. The results show that individuals carrying the DRD4-7R allele scored significantly lower on tests of DT, particularly on the flexibility dimension of DT, compared to non-carriers. The current findings link creative cognition to the dopaminergic system and suggest that dopaminergic dysfunctions in neurological and psychiatric disorders may account for impaired creativity and cognitive flexibility in these individuals.

  4. The association between dopamine receptor (DRD4) gene polymorphisms and second language learning style and behavioral variability in undergraduate students in Turkey.

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    Maras Atabay, Meltem; Safi Oz, Zehra; Kurtman, Elvan

    2014-08-01

    The dopamine D4 receptor gene (DRD4) encodes a receptor for dopamine, a chemical messenger used in the brain. One variant of the DRD4 gene, the 7R allele, is believed to be associated with attention deficit hyperactivity disorder (ADHD). The aim of this study was to investigate the relationships between repeat polymorphisms in dopamine DRD4 and second language learning styles such as visual (seeing), tactile (touching), auditory (hearing), kinesthetic (moving) and group/individual learning styles, as well as the relationships among DRD4 gene polymorphisms and ADHD in undergraduate students. A total of 227 students between the ages of 17-21 years were evaluated using the Wender Utah rating scale and DSM-IV diagnostic criteria for ADHD. Additionally, Reid's perceptual learning style questionnaire for second language learning style was applied. In addition, these students were evaluated for social distress factors using the list of Threatening Events (TLE); having had no TLE, having had just one TLE or having had two or more TLEs within the previous 6 months before the interview. For DRD4 gene polymorphisms, DNA was extracted from whole blood using the standard phenol/chloroform method and genotyped using polymerase chain reaction. Second language learners with the DRD4.7+ repeats showed kinaesthetic and auditory learning styles, while students with DRD4.7-repeats showed visual, tactile and group learning, and also preferred the more visual learning styles [Formula: see text]. We also demonstrated that the DRD4 polymorphism significantly affected the risk effect conferred by an increasing level of exposure to TLE.

  5. Polymorphisms of the dopamine D4 receptor gene (DRD4 VNTR) and cannabinoid CB1 receptor gene (CNR1) are not strongly related to cue-reactivity after alcohol exposure.

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    van den Wildenberg, Esther; Janssen, Rob G J H; Hutchison, Kent E; van Breukelen, Gerard J P; Wiers, Reinout W

    2007-06-01

    Polymorphisms in the D4 dopamine receptor gene (DRD4) and the CB1 cannabinoid receptor gene (CNR1) have been associated with a differential response to alcohol after consumption. The goal of the present study was to investigate whether heavy drinkers with these polymorphisms would respond with enhanced cue-reactivity after alcohol exposure. Eighty-eight male heavy drinkers were genotyped for the DRD4 variable number of tandem repeats (VNTR) [either DRD4 long (L) or short (S)] and the CNR1 rs2023239 polymorphism (either CT/CC or TT). Participants were exposed to water and beer in 3-minute trials. Dependent variables of main interest were subjective craving for alcohol, subjective arousal and salivary reactivity. Overall, no strong evidence was found for stronger cue-reactivity (= outcome difference between beer and water trial) in the DRD4 L and CNR1 C allele groups. The DRD4 VNTR polymorphism tended to moderate salivary reactivity such that DRD4 L participants showed a larger beverage effect than the DRD4 S participants. Unexpectedly, the DRD4 L participants reported, on average, less craving for alcohol and more subjective arousal during cue exposure, compared with the DRD4 S participants. As weekly alcohol consumption increased, the CNR1 C allele group tended to report more craving for alcohol during the alcohol exposure than the T allele group. The DRD4 and CNR1 polymorphisms do not appear to strongly moderate cue-reactivity after alcohol cue exposure, in male heavy drinkers.

  6. A DRD4 Gene by Maternal Sensitivity Interaction Predicts Risk for Overweight or Obesity in Two Independent Cohorts of Preschool Children

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    Levitan, Robert D.; Jansen, Pauline; Wendland, Barbara; Tiemeier, Henning; Jaddoe, Vincent W.; Silveira, Patricia P.; Kennedy, James L.; Atkinson, Leslie; Fleming, Alison; Sokolowski, Marla; Gaudreau, Helene; Steiner, Meir; Dubé, Laurette; Hamilton, Jill; Moss, Ellen; Wazana, Ashley; Meaney, Michael

    2017-01-01

    Background: Recent evidence suggests that early exposure to low maternal sensitivity is a risk factor for obesity in children and adolescents. A separate line of study shows that the seven-repeat (7R) allele of the dopamine-4 receptor gene (DRD4) increases susceptibility to environmental factors including maternal sensitivity. The current study…

  7. A DRD4 Gene by Maternal Sensitivity Interaction Predicts Risk for Overweight or Obesity in Two Independent Cohorts of Preschool Children

    Science.gov (United States)

    Levitan, Robert D.; Jansen, Pauline; Wendland, Barbara; Tiemeier, Henning; Jaddoe, Vincent W.; Silveira, Patricia P.; Kennedy, James L.; Atkinson, Leslie; Fleming, Alison; Sokolowski, Marla; Gaudreau, Helene; Steiner, Meir; Dubé, Laurette; Hamilton, Jill; Moss, Ellen; Wazana, Ashley; Meaney, Michael

    2017-01-01

    Background: Recent evidence suggests that early exposure to low maternal sensitivity is a risk factor for obesity in children and adolescents. A separate line of study shows that the seven-repeat (7R) allele of the dopamine-4 receptor gene (DRD4) increases susceptibility to environmental factors including maternal sensitivity. The current study…

  8. Genetic variation in the dopamine D4 receptor (DRD4) gene and smoking cessation: follow-up of a randomised clinical trial of transdermal nicotine patch.

    Science.gov (United States)

    David, S P; Munafò, M R; Murphy, M F G; Proctor, M; Walton, R T; Johnstone, E C

    2008-04-01

    Smokers of European ancestry (n=720) who participated in a double-blind, randomised, placebo-controlled trial of transdermal nicotine replacement therapy, were genotyped for two functional polymorphisms (variable number of tandem repeats (VNTR) and a C to T transition at position -521 (C-521T)) in the dopamine D4 receptor gene (DRD4) gene. Logistic regression models of abstinence at 12- and 26-week follow-ups were carried out separately for each polymorphism. For the DRD4 VNTR models, the main effect of treatment was significant at both 12-week (P=0.001) and 26-week (P=0.006) follow-ups, indicating an increased likelihood of successful cessation on active nicotine replacement therapy transdermal patch relative to placebo. The main effect of DRD4 VNTR genotype was associated with abstinence at 12-week follow-up (P=0.034), with possession of one or more copies of the long allele associated with reduced likelihood of cessation (17 vs 23%), but this effect was not observed at 26-week follow-up. For the DRD4 C-521T models, no main effect or interaction terms involving genotype were retained in the models at either 12- or 26-week follow-up. These data are consistent with observations from studies of the DRD2 gene that genetic variants related to relatively decreased dopaminergic tone in the mesocorticolimbic system are associated with increased risk for relapse to smoking following a cessation attempt.

  9. Anorexia nervosa, perfectionism, and dopamine D4 receptor (DRD4).

    Science.gov (United States)

    Bachner-Melman, Rachel; Lerer, Elad; Zohar, Ada H; Kremer, Ilana; Elizur, Yoel; Nemanov, Lubov; Golan, Moria; Blank, Shulamit; Gritsenko, Inga; Ebstein, Richard P

    2007-09-05

    The dopamine D4 receptor (DRD4), a well-characterized, polymorphic gene, is an attractive candidate for contributing risk to disordered eating and anorexia nervosa (AN). We tested association using UNPHASED for 5 DRD4 polymorphic loci, 3 promoter region SNPs (C-521T, C-616G, A-809G), the 120 bp promoter region tandem duplication and the exon III repeat, in 202 AN trios and 418 control families. Since perfectionism characterizes AN, we tested these five loci for association with the Child and Adolescent Perfectionism Scale (CAPS) in the AN and control groups. Single locus analysis showed significant association between the 'C' C-521T allele and AN. Haplotype analysis also showed significant association, particularly a 4-locus haplotype (exon III&120 bp repeat&C-521T&A-809G). Association was also observed between DRD4 and CAPS scores both for AN and control subjects. The insulin-like growth factor 2 (IGF2) and the arginine vasopressin 1a receptor (AVPR1a), previously shown to be associated with disordered eating, were also associated with CAPS scores. Three genes associated with AN were also associated with perfectionism. Personality traits are potential endophenotypes for understanding the etiology of eating disorders and one of the several pathways to eating pathology may be mediated by the impact of DNA sequences on perfectionism.

  10. The polymorphism of dopamine receptor D4 (DRD4) and dopamine transporter (DAT) genes in the men with antisocial behaviour and mixed martial arts fighters.

    Science.gov (United States)

    Cherepkova, Elena V; Maksimov, Vladimir N; Kushnarev, Alexandr P; Shakhmatov, Igor I; Aftanas, Lyubomir I

    2017-09-12

    Variable-number tandem repeat (VNTR) polymorphisms of DRD4 and DAT genes were studied in the Russian and Chechen men convicted of crimes, and two control groups comprised of the MMA fighters and a sample of general population. A group of MMA fighters included only the subjects without history of antisocial behaviour. DNA was isolated by phenol-chloroform extraction from the blood. Genotyping VNTR polymorphisms of the DRD4 and DAT genes were performed by PCR on published methods. Among those convicted of felonies and most grave crimes, carriers of DRD4 long alleles are found more frequently, similarly to the cohort of MMA fighters (lacking criminal record in both paternal lines). The 9/9 DAT genotype carriers are more frequently encountered among the habitual offenders. A frequency of the combination of the DRD4 genotype 4/7 and DAT genotype 10/10 is clearly higher among the convicts of violent crimes and the MMA fighters. One can speculate the presence of a 'controlled aggression' without a predisposition to pathological violence in the MMA fighters. Our study supports the hypothesis of genetic predisposition to different variants of extreme behaviour mediated by genetic determinants involved in the functioning of neuromediator systems including those controlling dopamine pathways.

  11. DRD4 dopamine receptor genotype and CSF monoamine metabolites in Finnish alcoholics and controls

    Energy Technology Data Exchange (ETDEWEB)

    Adamson, M.D.; Dean, M.; Goldman, D. [National Institute on Alcohol Abuse and Alcoholism, Rockville, MD (United States)] [and others

    1995-06-19

    The DRD4 dopamine receptor is thus far unique among neurotransmitter receptors in having a highly polymorphic gene structure that has been reported to produce altered receptor functioning. These allelic variations are caused by a 48-bp segment in exon III of the coding region which may be repeated from 2-10 times. Varying the numbers of repeated segments changes the length, structure, and, possibly, the functional efficiency of the receptor, which makes this gene an intriguing candidate for variations in dopamine-related behaviors, such as alcoholism and drug abuse. Thus far, these DRD4 alleles have been investigated for association with schizophrenia, bipolar disorder, Parkinson`s disease, and chronic alcoholism, and all have been largely negative for a direct association. We evaluated the DRD4 genotype in 226 Finish adult males, 113 of whom were alcoholics, many of the early onset type with features of impulsivity and antisocial traits. Genotype frequencies were compared to 113 Finnish controls who were free of alcohol abuse, substance abuse, and major mental illness. In 70 alcoholics and 20 controls, we measured CSF homovanillic acid (HVA), the major metabolite of dopamine, and 5-hydroxyindoleacetic acid (5-HIAA). No association was found between a particular DRD4 dopamine receptor allele and alcoholism. CSF concentrations of the monoamine metabolites showed no significant difference among the DRD4 genotypes. This study of the DRD4 dopamine receptor in alcoholics is the first to be conducted in a clinically and ethnically homogeneous population and to relate the DRD4 genotype to CSF monoamine concentrations. The results indicate that there is no association of the DRD4 receptor with alcoholism. 52 refs., 3 figs., 1 tab.

  12. Dopamine Genes (DRD2/ANKK1-TaqA1 and DRD4-7R) and Executive Function: Their Interaction with Obesity

    Science.gov (United States)

    Ariza, Mar; Garolera, Maite; Jurado, Maria Angeles; Garcia-Garcia, Isabel; Hernan, Imma; Sánchez-Garre, Consuelo; Vernet-Vernet, Maria; Sender-Palacios, Maria Jose; Marques-Iturria, Idoia; Pueyo, Roser; Segura, Barbara; Narberhaus, Ana

    2012-01-01

    Obesity is a multifactorial disease caused by the interaction between genotype and environment, and it is considered to be a type of addictive alteration. The A1 allele of the DRD2/ANKK1-TaqIA gene has been associated with addictive disorders, with obesity and with the performance in executive functions. The 7 repeat allele of the DRD4 gene has likewise been associated with the performance in executive functions, as well as with addictive behaviors and impulsivity. Participants were included in the obesity group (N = 42) if their body mass index (BMI) was equal to or above 30, and in the lean group (N = 42) if their BMI was below 25. The DRD2/ANKK1-TaqIA and DRD4 VNTR polymorphisms were obtained. All subjects underwent neuropsychological assessment. Eating behavior traits were evaluated. The ‘DRD2/ANKK1-TaqIA A1-allele status’ had a significant effect on almost all the executive variables, but no significant ‘DRD4 7R-allele status’ effects were observed for any of the executive variables analyzed. There was a significant ‘group’ x ‘DRD2/ANKK1-TaqIA A1-allele status’ interaction effect on LN and ‘group’ x ‘DRD4 7R-allele status’ interaction effect on TMT B-A score. Being obese and a carrier of the A1 allele of DRD2/ANKK1-TaqIA or the 7R allele of DRD4 VNTR polymorphisms could confer a weakness as regards the performance of executive functions. PMID:22848508

  13. Dopamine genes (DRD2/ANKK1-TaqA1 and DRD4-7R and executive function: their interaction with obesity.

    Directory of Open Access Journals (Sweden)

    Mar Ariza

    Full Text Available Obesity is a multifactorial disease caused by the interaction between genotype and environment, and it is considered to be a type of addictive alteration. The A1 allele of the DRD2/ANKK1-TaqIA gene has been associated with addictive disorders, with obesity and with the performance in executive functions. The 7 repeat allele of the DRD4 gene has likewise been associated with the performance in executive functions, as well as with addictive behaviors and impulsivity. Participants were included in the obesity group (N = 42 if their body mass index (BMI was equal to or above 30, and in the lean group (N = 42 if their BMI was below 25. The DRD2/ANKK1-TaqIA and DRD4 VNTR polymorphisms were obtained. All subjects underwent neuropsychological assessment. Eating behavior traits were evaluated. The 'DRD2/ANKK1-TaqIA A1-allele status' had a significant effect on almost all the executive variables, but no significant 'DRD4 7R-allele status' effects were observed for any of the executive variables analyzed. There was a significant 'group' x 'DRD2/ANKK1-TaqIA A1-allele status' interaction effect on LN and 'group' x 'DRD4 7R-allele status' interaction effect on TMT B-A score. Being obese and a carrier of the A1 allele of DRD2/ANKK1-TaqIA or the 7R allele of DRD4 VNTR polymorphisms could confer a weakness as regards the performance of executive functions.

  14. The DRD4 Gene and Severity of Tics and Comorbid Symptoms : Main Effects and Interactions with Delivery Complications

    NARCIS (Netherlands)

    Bos-Veneman, Netty G. P.; Minderaa, Ruud B.; Hoekstra, Pieter J.

    2010-01-01

    In this study, we investigated the role of the dopamine receptor D4 (DRD4) 48-base pairs (bp) variable number of tandem repeats (VNTR) and perinatal adversities regarding severity of tics and comorbid symptoms in children with tic disorders. We genotyped 110 children with tics with regard to the

  15. The DRD4 Gene and Severity of Tics and Comorbid Symptoms : Main Effects and Interactions with Delivery Complications

    NARCIS (Netherlands)

    Bos-Veneman, Netty G. P.; Minderaa, Ruud B.; Hoekstra, Pieter J.

    2010-01-01

    In this study, we investigated the role of the dopamine receptor D4 (DRD4) 48-base pairs (bp) variable number of tandem repeats (VNTR) and perinatal adversities regarding severity of tics and comorbid symptoms in children with tic disorders. We genotyped 110 children with tics with regard to the 48-

  16. Smoking-specific parenting and smoking onset in adolescence: the role of genes from the dopaminergic system (DRD2, DRD4, DAT1 genotypes.

    Directory of Open Access Journals (Sweden)

    Marieke Hiemstra

    Full Text Available Although only few studies have shown direct links between dopaminergic system genes and smoking onset, this does not rule out the effect of a gene-environment interaction on smoking onset. Therefore, the aim of this study was to examine the associations between smoking-specific parenting (i.e., frequency and quality of communication and house rules and smoking onset while considering the potential moderating role of dopaminergic system genes (i.e., DRD2, DRD4, and DAT1 genotypes. Data from five annual waves of the 'Family and Health' project were used. At time 1, the sample comprised 365 non-smoking adolescents (200 younger adolescents, mean age = 13.31, SD = .48; 165 older adolescents, mean age = 15.19, SD = .57. Advanced longitudinal analyses were used (i.e., logistic regression analyses, (dual latent growth curves, and cross-lagged path models. The results showed a direct effect of quality of communication on smoking onset. No direct effects were found for frequency of communication and house rules. Furthermore, no direct and moderating effects of the DRD2, DRD4, or DAT1 genotypes were found. In conclusion, the findings indicated that the effects of smoking-specific parenting on smoking are similar for adolescent carriers and non-carriers of the dopaminergic system genes.

  17. Smoking-specific parenting and smoking onset in adolescence: the role of genes from the dopaminergic system (DRD2, DRD4, DAT1 genotypes).

    Science.gov (United States)

    Hiemstra, Marieke; Engels, Rutger C M E; Barker, Edward D; van Schayck, Onno C P; Otten, Roy

    2013-01-01

    Although only few studies have shown direct links between dopaminergic system genes and smoking onset, this does not rule out the effect of a gene-environment interaction on smoking onset. Therefore, the aim of this study was to examine the associations between smoking-specific parenting (i.e., frequency and quality of communication and house rules) and smoking onset while considering the potential moderating role of dopaminergic system genes (i.e., DRD2, DRD4, and DAT1 genotypes). Data from five annual waves of the 'Family and Health' project were used. At time 1, the sample comprised 365 non-smoking adolescents (200 younger adolescents, mean age = 13.31, SD = .48; 165 older adolescents, mean age = 15.19, SD = .57). Advanced longitudinal analyses were used (i.e., logistic regression analyses, (dual) latent growth curves, and cross-lagged path models). The results showed a direct effect of quality of communication on smoking onset. No direct effects were found for frequency of communication and house rules. Furthermore, no direct and moderating effects of the DRD2, DRD4, or DAT1 genotypes were found. In conclusion, the findings indicated that the effects of smoking-specific parenting on smoking are similar for adolescent carriers and non-carriers of the dopaminergic system genes.

  18. [The influence of parents personality and DRD4 and 5HTT genes polymorphisms on predisposition to alcohol dependence in their sons].

    Science.gov (United States)

    Samochowiec, Agnieszka; Horodnicki, Jan M; Samochowiec, Jerzy

    2011-01-01

    The aim of this work was to investigate differences in parents' personality and dopaminergic and serotoninergic gene polymorphisms which may affect certain predispositions to alcohol dependence as described in the typology developed by R. Cloninger and O.M. Lesch. Also the possibility of recognising their genotypes DRD4 (Gene ID: 1815A ) and 5HTT (Gene ID: 6532) could be helpful in predicting predisposition to addiction. A total number of 213 individuals (71 Polish trios), Caucasian families were investigated. Fathers' mean age was: 61.7 +/- 10.8 and mothers were 59 +/- 10 years old. None of the parents fulfilled the criteria of alcohol dependence. The alcohol dependent probands were male, with confirmed biological descent, mean age: 35.2 +/- 9.7 years. In all the participants TCI was performed. Characterisation of alcohol dependence and the course of withdrawal were obtained by SSAGA. Specially designed questionnaires based on Cloninger and Lesch typologies were used. The essential data on both parents was collected and AUDIT was performed. DRD4 and 5HTT gene polymorphisms were determined by PCR and TDT test was calculated. TDT analysis showed no differences in the transmission of alleles of 5HTT and DRD4 genes in the investigated families. The analysis of TCI personality profiles confirmed no statistically significant relations between Cloninger 1 and 2 subtypes of alcoholics. A statistically significant difference was recorded between the scores for groups I and II classified according to Lesch's typology in dimensions NS, NS2 and NS4. Fathers of probands characterised as type I according to Cloninger had statistically lower scores in dimension C and C5 in comparison to type II fathers. Fathers of type II alcoholics according to Lesch's typology had higher NS2. Mothers of type I alcoholics according to Cloninger had statistically lower scores in dimension HA2 in comparison with type II mothers. On the basis of the above presented findings it can be stated that

  19. No evidence for the association of DRD4 with ADHD in a Taiwanese population within-family study

    Directory of Open Access Journals (Sweden)

    Huang Yu-Shu

    2005-09-01

    Full Text Available Abstract Background Attention Deficit Hyperactivity Disorder (ADHD is a prevalent and highly heritable childhood disorder. The dopamine D4 receptor (DRD4 gene has shown a genetic association with ADHD in Caucasian populations with meta-analysis indicating a small but significant effect across datasets. It remains uncertain whether this association can be generalised to non-Caucasian ethnic groups. Here we investigate two markers within the DRD4 gene in a Taiwanese population, the exon 3 variable number tandem repeat (VNTR and a 5' 120 base-pair duplication. Methods Within-family transmission disequilibrium tests of association of the 5' 120 base-pair duplication, and exon 3 VNTR in a Taiwanese population. Results No evidence of association of ADHD with either polymorphism in this population was observed. Conclusion The DRD4 gene markers investigated were not found to be associated with ADHD in this Taiwanese sample. Further work in Taiwanese and other Asian populations will therefore be required to establish whether the reports of association of DRD4 genetic variants in Caucasian samples can be generalised to Asian populations.

  20. Dopamine Receptor Gene DRD4 7-Repeat Allele X Maternal Sensitivity Interaction on Child Externalizing Behavior Problems: Independent Replication of Effects at 18 Months.

    Science.gov (United States)

    King, Anthony P; Muzik, Maria; Hamilton, Lindsay; Taylor, Alexander B; Rosenblum, Katherine L; Liberzon, Israel

    2016-01-01

    The DRD4 VNTR has been associated with child behavior problems in interaction with maternal insensitivity in European and American cohorts of preschoolers, with the 7-repeat (7R) allele associated with greater problems. We sought to replicate and expand these findings by examining effects on reports of child behavior problems at 18 months. A 63 family sample with data for observed maternal sensitivity ratings, DRD4 VNTR genotype, and maternal report of child behavior problems at 18-months was used in this preliminary analysis. Maternal sensitivity was measured at 6-months of age using laboratory observational measures (free-play and a teaching task). Maternal report of toddler behavior was obtained at 18-months via the standard Child Behavior Checklist, and infant genotype on the DRD4 VNTR was obtained using PCR. Infants carrying the DRD4 7R allele showed greater effects of maternal insensitivity than non-carriers for behavioral problems at 18-months. We replicated previous findings of association of infant DRD4 x maternal sensitivity interactions with child Externalizing problems in the European-ancestry sample (N = 42) in a median split of maternal sensitivity (p = .00011, eta2 = .329) and in regression analyses controlling for maternal age, maternal depression, and child gender in European ancestry (B = -3.4, SE 1.33, p = .01) and the total sample (B = -2.2, SE 1.02, p = .02). Exploratory analyses also found evidence of DRD4 x maternal sensitivity interaction with the CBCL ADHD scale. These findings replicate in an independent cohort DRD4 x maternal insensitivity interaction effect on child externalizing behavior problems at 18 months, further supporting the role of the DRD4 genotype in differential sensitivity to parenting.

  1. Genetic studies of DRD4 and clinical response to neuroleptic medications

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, J.L.; Petronis, A.; Gao, J. [Univ. of Toronto, Ontario (Canada)] [and others

    1994-09-01

    Clozapine is an atypical antipsychotic drug that, like most other medications, is effective for some people and not for others. This variable response across individuals is likely significantly determined by genetic factors. An important candidate gene to investigate in clozapine response is the dopamine D4 receptor gene (DRD4). The D4 receptor has a higher affinity for clozapine than any of the other dopamine receptors. Furthermore, recent work by our consortium has shown a remarkable level of variability in the part of the gene coding for the third cytoplasmic loop. We have also identified polymorphisms in the upstream 5{prime} putative regulatory region and at two other sites. These polymorphisms were typed in a group of treatment-resistant schizophrenia subjects who were subsequently placed on clozapine (n = 60). In a logistic regression analysis, we compared genotype at the DRD4 polymorphism to response versus non-response to clozapine. Neither the exon-III nor any of the 5{prime} polymorphisms alone significantly predicted response; however, when the information from these polymorphisms was combined, more predictive power was obtained. In a correspondence analysis of the four DRD4 polymorphisms vs. response, we were able to predict 76% of the variance in response. Refinement of the analyses will include assessment of subfactors involved in clinical response phenotype and incorporation of the debrisoquine metabolizing locus (CYP2D6) into the prediction algorithm.

  2. Analysis of clozapine response and polymorphisms of the dopamine D4 receptor gene (DRD4) in schizophrenic patients

    Energy Technology Data Exchange (ETDEWEB)

    Shaikh, S.; Collier, D.A.; Sham, P. [Institute of Psychiatry, De Crespigny, London (United Kingdom)] [and others

    1995-12-18

    We have examined the hypothesis that a variable number of tandem repeats in the third cytoplasmic loop of the dopamine D4 receptor influences clinical response to clozapine using a sample of 189 schizophrenic patients. Alleles of the 48-bp repeat, which range from two to ten copies in the normal human population, were analysed by the polymerase chain reaction using genomic DNA as template. Association between these alleles and response to clozapine was tested using the difference in pre- and post-treatment GAS scores as a measure of response. We found no statistically significant variation between genotypic groups and response by analysis of variance. We conclude that the variation of the number of 48-bp repeats alone does not determine response to clozapine. Larger studies are underway to determine if there is a more subtle relationship with sequence variation within the repeats or at other polymorphic sites within the gene that may provide evidence for a component of clozapine`s action being at D4 receptors. 28 refs., 1 fig., 3 tabs.

  3. The interplay of birth weight, dopamine receptor D4 gene (DRD4), and early maternal care in the prediction of disorganized attachment at 36 months of age.

    Science.gov (United States)

    Wazana, Ashley; Moss, Ellen; Jolicoeur-Martineau, Alexis; Graffi, Justin; Tsabari, Gal; Lecompte, Vanessa; Pascuzzo, Katherine; Babineau, Vanessa; Gordon-Green, Cathryn; Mileva, Viara; Atkinson, Leslie; Minde, Klaus; Bouvette-Turcot, André Anne; Sassi, Roberto; St-André, Martin; Carrey, Normand; Matthews, Stephen; Sokolowski, Marla; Lydon, John; Gaudreau, Helene; Steiner, Meir; Kennedy, James L; Fleming, Alison; Levitan, Robert; Meaney, Michael J

    2015-11-01

    Disorganized attachment is an important early risk factor for socioemotional problems throughout childhood and into adulthood. Prevailing models of the etiology of disorganized attachment emphasize the role of highly dysfunctional parenting, to the exclusion of complex models examining the interplay of child and parental factors. Decades of research have established that extreme child birth weight may have long-term effects on developmental processes. These effects are typically negative, but this is not always the case. Recent studies have also identified the dopamine D4 receptor (DRD4) as a moderator of childrearing effects on the development of disorganized attachment. However, there are inconsistent findings concerning which variant of the polymorphism (seven-repeat long-form allele or non-seven-repeat short-form allele) is most likely to interact with caregiving in predicting disorganized versus organized attachment. In this study, we examined possible two- and three-way interactions and child DRD4 polymorphisms and birth weight and maternal caregiving at age 6 months in longitudinally predicting attachment disorganization at 36 months. Our sample is from the Maternal Adversity, Vulnerability and Neurodevelopment project, a sample of 650 mother-child dyads. Birth weight was cross-referenced with normative data to calculate birth weight percentile. Infant DRD4 was obtained with buccal swabs and categorized according to the presence of the putative allele seven repeat. Macroanalytic and microanalytic measures of maternal behavior were extracted from a videotaped session of 20 min of nonfeeding interaction followed by a 10-min divided attention maternal task at 6 months. Attachment was assessed at 36 months using the Strange Situation procedure, and categorized into disorganized attachment and others. The results indicated that a main effect for DRD4 and a two-way interaction of birth weight and 6-month maternal attention (frequency of maternal looking away

  4. Links between DRD4, Executive Attention, and Alphabetic Skills in a Nonclinical Sample

    Science.gov (United States)

    Kegel, Cornelia A. T.; Bus, Adriana G.

    2013-01-01

    Background: The dopamine D4 receptor gene (DRD4) has been linked to attention deficit hyperactivity disorder (ADHD) and reading disorders. In this study, we examined whether diminished anticipatory dopamine cell firing--typical of the long variant of the DRD4 allele--is related to emergent and advanced alphabetic skills, and whether executive…

  5. Polymorphisms in HTR2A and DRD4 Predispose to Smoking and Smoking Quantity

    Science.gov (United States)

    Pérez-Rubio, Gloria; Ramírez-Venegas, Alejandra; Noé Díaz, Valeri; García Gómez, Leonor; Elvira Fabián, Karina; García Carmona, Salvador; López-Flores, Luis A.; Ambrocio-Ortiz, Enrique; Contreras Romero, Rocío; Alcantar-Ayala, Noé; Sansores, Raúl H.

    2017-01-01

    Background Genes encoding the receptors involved in the dopaminergic and serotonergic pathways are potential candidates in the mechanisms of nicotine addiction. Aims To identify genetic variants in the promoter regions and exons of the DRD4 and HTR2A genes associated with tobacco smoking and the degree of nicotine addiction in Mexican mestizos. Methods The study included 438 non-smokers (NS) and 1,157 current smokers, ranked based on their consumption of cigarettes per day (cpd): 574 heavy smokers (HS, >20 cpd) and 583 light smokers (LS, 1–10 cpd). Genotyping was performed for 4 and 8 single nucleotide polymorphisms (SNPs) in the DRD4 and HTR2A genes, respectively. Results The C allele of rs1800955 in DRD4 was found to be associated with cigarette smoking in the HS vs. NS and LS vs. NS comparisons (p = 2.34E-03 and p = 1.13E-03, respectively); the association was maintained in the homozygous CC genotype (p = 5.00E-04 and p = 2.00E-04, respectively). The T allele of rs6313 in HTR2A was significantly associated with cigarette smoking and a greater degree of nicotine addiction (p = 4.77E-03, OR = 1.55); the association was maintained in the homozygous genotype (TT) (p = 4.90E-03, OR = 1.96). The A allele of rs6313 was associated with cigarette smoking in the HS vs. NS comparison (p = 1.53E-02, OR = 1.36); the risk was nearly doubled in the homozygous AA genotype (p = 1.30E-03, OR = 1.83) compared with the heterozygous GA genotype (OR = 1.38). Conclusions Among Mexican mestizos, the C allele of rs1800955 in the DRD4 gene and the A allele of rs6311 in the HTR2A gene are associated with cigarette smoking, whereas the T allele of rs6313 in HTR2A is associated with cigarette smoking and the degree of nicotine addiction. PMID:28103253

  6. Data describing the effect of DRD4 promoter polymorphisms on promoter activity

    Directory of Open Access Journals (Sweden)

    Shoin Tei

    2016-06-01

    Full Text Available This data article tested whether polymorphisms within the dopamine D4 receptor (DRD4 gene promoter can lead to differences in the promoter activity. The variants, a 120-bp variable number tandem repeat (VNTR, −906 T/C, −809 G/A, −616G/C, and −521C/T, were introduced into the DRD4 promoter and the promoter activity was measured in a neural cell line using the luciferase assay. However, no differences were detected among the haplotypes investigated, and the in vitro data obtained from our protocol could not support the involvement of DRD4 promoter polymorphisms in heritable human traits.

  7. Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

    Science.gov (United States)

    Ebstein, Richard P.; Monakhov, Mikhail V.; Lu, Yunfeng; Jiang, Yushi; Lai, Poh San; Chew, Soo Hong

    2015-01-01

    Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified. PMID:26246555

  8. Data describing the effect of DRD4 promoter polymorphisms on promoter activity

    OpenAIRE

    Shoin Tei; Hiroaki Mitsuhashi; Shoichi Ishiura

    2016-01-01

    This data article tested whether polymorphisms within the dopamine D4 receptor (DRD4) gene promoter can lead to differences in the promoter activity. The variants, a 120-bp variable number tandem repeat (VNTR), −906 T/C, −809 G/A, −616G/C, and −521C/T, were introduced into the DRD4 promoter and the promoter activity was measured in a neural cell line using the luciferase assay. However, no differences were detected among the haplotypes investigated, and the in vitro data obtained from our pro...

  9. Dopamine D4 receptor exon III polymorphism, adverse life events and personality traits in a nonclinical German adult sample.

    Science.gov (United States)

    Reiner, Iris; Spangler, Gottfried

    2011-01-01

    Personality and temperament embrace a wide area of both psychological and behavioral processes which are also based on disposition. A functional polymorphism in exon III of the dopamine D4 receptor gene (DRD4) has been a highly suspect genetic marker for personality in spite of ambiguous results. The present study aimed to further elucidate the relationship between DRD4, negative life events and personality in a representative nonclinical sample. Hundred sixty-seven Germans completed the NEO Five-Factor Inventory, the Tridimensional Personality Questionnaire and the California Adult Q-Sort. A factor analysis revealed 3 factors: emotional stability, social orientation and impulsivity. DNA from buccal cells was genotyped for the DRD4 variable-number tandem-repeat exon III polymorphism with respect to presence versus absence of the DRD4 7-repeat allele. Adverse life events were assessed by means of the Adverse Life Events Scale. Men carrying the DRD4 7-repeat allele were more impulsive than those without. Male 7-repeat carriers were more emotionally instable than others, but only when they experienced a large amount of negative life events. No genotype-personality relationships were found for women. The results indicate gender-specific influences of the DRD4 gene on human behavior and invite researchers to further investigate gene-environment correlations on personality traits.

  10. Exploring DRD4 and its interaction with SLC6A3 as possible risk factors for adult ADHD: a meta-analysis in four European populations.

    Science.gov (United States)

    Sánchez-Mora, Cristina; Ribasés, Marta; Casas, Miquel; Bayés, Mònica; Bosch, Rosa; Fernàndez-Castillo, Noelia; Brunso, Lucas; Jacobsen, Kaya K; Landaas, Elisabeth T; Lundervold, Astri J; Gross-Lesch, Silke; Kreiker, Susanne; Jacob, Christian P; Lesch, Klaus-Peter; Buitelaar, Jan K; Hoogman, Martine; Kiemeney, Lambertus A L M; Kooij, J J Sandra; Mick, Eric; Asherson, Phil; Faraone, Stephen V; Franke, Barbara; Reif, Andreas; Johansson, Stefan; Haavik, Jan; Ramos-Quiroga, Josep Antoni; Cormand, Bru

    2011-07-01

    Attention-deficit hyperactivity disorder (ADHD) is a common behavioral disorder affecting about 4-8% of children. ADHD persists into adulthood in around 65% of cases, either as the full condition or in partial remission with persistence of symptoms. Pharmacological, animal and molecular genetic studies support a role for genes of the dopaminergic system in ADHD due to its essential role in motor control, cognition, emotion, and reward. Based on these data, we analyzed two functional polymorphisms within the DRD4 gene (120 bp duplication in the promoter and 48 bp VNTR in exon 3) in a clinical sample of 1,608 adult ADHD patients and 2,352 controls of Caucasian origin from four European countries that had been recruited in the context of the International Multicentre persistent ADHD CollaboraTion (IMpACT). Single-marker analysis of the two polymorphisms did not reveal association with ADHD. In contrast, multiple-marker meta-analysis showed a nominal association (P = 0.02) of the L-4R haplotype (dup120bp-48bpVNTR) with adulthood ADHD, especially with the combined clinical subtype. Since we previously described association between adulthood ADHD and the dopamine transporter SLC6A3 9R-6R haplotype (3'UTR VNTR-intron 8 VNTR) in the same dataset, we further tested for gene × gene interaction between DRD4 and SLC6A3. However, we detected no epistatic effects but our results rather suggest additive effects of the DRD4 risk haplotype and the SLC6A3 gene. Copyright © 2011 Wiley-Liss, Inc.

  11. Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species

    DEFF Research Database (Denmark)

    Larsen, Svend Arild; Mogensen, Line; Dietz, Rune;

    2005-01-01

    composed of 15- and 12- bp modules. Tandem repeats composed of 18-bp modules were found in sequences from the horse, zebra, onager, and donkey, Asiatic bear, polar bear, common raccoon, dolphin, harbor porpoise, and domestic cat. Several of these sequences have been analyzed previously without a tandem...

  12. Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species

    DEFF Research Database (Denmark)

    Larsen, Svend Arild; Mogensen, Line; Dietz, Rune

    2005-01-01

    tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could...... repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp...

  13. Parenting quality, DRD4, and the prediction of externalizing and internalizing behaviors in early childhood.

    Science.gov (United States)

    Propper, C; Willoughby, M; Halpern, C T; Carbone, M A; Cox, M

    2007-09-01

    Recent research has found that the dopamine D4 receptor (DRD4) gene and maternal insensitivity may interact to predict externalizing behavior in preschoolers. The current study attempted to replicate and extend this finding in a sample of 18-30-month-old children. The current study examined two distinct dimensions of parenting (warm-responsive and negative-intrusive) as predictors of childhood externalizing and internalizing behavior. Further, race was investigated as a moderator of gene-environment relationships. Results revealed that high warm-responsive parenting was associated with decreased externalizing behavior only for African American children possessing the short polymorphism of DRD4. The data indicate that children may be differentially susceptible to different aspects of parenting depending on their genotype, and it is important to consider differences in racial composition when studying these relationships. .

  14. How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes?

    Science.gov (United States)

    Sawada, Ryusuke; Mitaku, Shigeki

    2011-01-01

    The exon-intron structure of eukaryotic genes raises a question about the distribution of transmembrane regions in membrane proteins. Were exons that encode transmembrane regions formed simply by inserting introns into preexisting genes or by some kind of exon shuffling? To answer this question, the exon-per-gene distribution was analyzed for all genes in 40 eukaryotic genomes with a particular focus on exons encoding transmembrane segments. In 21 higher multicellular eukaryotes, the percentage of multi-exon genes (those containing at least one intron) within all genes in a genome was high (>70%) and with a mean of 87%. When genes were grouped by the number of exons per gene in higher eukaryotes, good exponential distributions were obtained not only for all genes but also for the exons encoding transmembrane segments, leading to a constant ratio of membrane proteins independent of the exon-per-gene number. The positional distribution of transmembrane regions in single-pass membrane proteins showed that they are generally located in the amino or carboxyl terminal regions. This nonrandom distribution of transmembrane regions explains the constant ratio of membrane proteins to the exon-per-gene numbers because there are always two terminal (i.e., the amino and carboxyl) regions - independent of the length of sequences.

  15. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation.

    Science.gov (United States)

    Verhulst, Eveline C; Mateman, A Christa; Zwier, Mathijs V; Caro, Samuel P; Verhoeven, Koen J F; van Oers, Kees

    2016-04-01

    Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  16. DRD4 and DAT1 in ADHD: Functional neurobiology to pharmacogenetics

    Directory of Open Access Journals (Sweden)

    Darko Turic

    2010-05-01

    Full Text Available Darko Turic1, James Swanson2, Edmund Sonuga-Barke1,31Institute for Disorders of Impulse and Attention, School of Psychology, University of Southampton, UK; 2Child Development Center, University of California, Irvine, California, US; 3Department of Experimental, Clinical and Health Psychology, Ghent University, BelgiumAbstract: Attention deficit/hyperactivity disorder (ADHD is a common and potentially very impairing neuropsychiatric disorder of childhood. Statistical genetic studies of twins have shown ADHD to be highly heritable, with the combination of genes and gene by environment interactions accounting for around 80% of phenotypic variance. The initial molecular genetic studies where candidates were selected because of the efficacy of dopaminergic compounds in the treatment of ADHD were remarkably successful and provided strong evidence for the role of DRD4 and DAT1 variants in the pathogenesis of ADHD. However, the recent application of noncandidate gene strategies (eg, genome-wide association scans has failed to identify additional genes with substantial genetic main effects, and the effects for DRD4 and DAT1 have not been replicated. This is the usual pattern observed for most other physical and mental disorders evaluated with current state-of-the-art methods. In this paper we discuss future strategies for genetic studies in ADHD, highlighting both the pitfalls and possible solutions relating to candidate gene studies, genome-wide studies, defining the phenotype, and statistical approaches.Keywords: dopamine, ADHD, pharmacogenetics, candidate gene

  17. Are infants differentially sensitive to parenting? Early maternal care, DRD4 genotype and externalizing behavior during adolescence.

    Science.gov (United States)

    Nikitopoulos, Jörg; Zohsel, Katrin; Blomeyer, Dorothea; Buchmann, Arlette F; Schmid, Brigitte; Jennen-Steinmetz, Christine; Becker, Katja; Schmidt, Martin H; Esser, Günter; Brandeis, Daniel; Banaschewski, Tobias; Laucht, Manfred

    2014-12-01

    Insensitive and unresponsive caregiving during infancy has been linked to externalizing behavior problems during childhood and adolescence. The 7-repeat (7r) allele of the dopamine D4 receptor (DRD4) gene has meta-analytically been associated with a heightened susceptibility to adverse as well as supportive environments. In the present study, we examined long-term effects of early maternal care, DRD4 genotype and the interaction thereof on externalizing and internalizing psychopathology during adolescence. As part of an ongoing epidemiological cohort study, early maternal care was assessed at child's age 3 months during a nursing and playing situation. In a sample of 296 offspring, externalizing and internalizing symptoms were assessed using a psychiatric interview conducted at age 15 years. Parents additionally filled out a questionnaire on their children's psychopathic behaviors. Results indicated that adolescents with the DRD4 7r allele who experienced less responsive and stimulating early maternal care exhibited more symptoms of ADHD and CD/ODD as well as higher levels of psychopathic behavior. In accordance with the hypothesis of differential susceptibility, 7r allele carriers showed fewer ADHD symptoms and lower levels of psychopathic behavior when exposed to especially beneficial early caregiving. In contrast, individuals without the DRD4 7r allele proved to be insensitive to the effects of early maternal care. This study replicates earlier findings with regard to an interaction between DRD4 genotype and early caregiving on externalizing behavior problems in preschoolers. It is the first one to imply continuity of this effect until adolescence. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Sequence analysis of Drd2, Drd4, and Dat1 in SHR and WKY rat strains

    Directory of Open Access Journals (Sweden)

    Mill Jonathan

    2005-12-01

    Full Text Available Abstract Background The Spontaneously Hypertensive Rat (SHR shows a number of behaviours that closely parallel those seen in children with attention-deficit hyperactivity disorder. These include motor hyperactivity, excessive responses under a fixed-interval/extinction schedule, difficulty in acquiring operant tasks and increased sensitivity to immediate behavioural reinforcement. As in children with ADHD, the behavioural and cognitive deficits in the SHR are responsive to stimulants, including d-amphetamine and d,l-methylphenidate. The non-hyperactive Wistar Kyoto (WKY rat strain is often used as a control in behavioural studies of the SHR, and WKY itself has been suggested to be a useful animal model of depression. Numerous studies have shown that dopaminergic neurotransmission is altered between the two strains. Human genetic studies have found associations between several dopaminergic genes and both ADHD and depression. Methods We sequenced three candidate dopaminergic genes (Drd2, Drd4, and Dat1 in the SHR and WKY to identify between-strain sequence differences. Results No between-strain sequence differences were found in either Drd2 or Drd4, but several variations were found in the Dat1 gene that encodes the dopamine transporter. Conclusion It is plausible that DNA sequence changes in the Dat1 gene account for some of the behavioural differences observed between the SHR and WKY strains. Future work will focus on elucidating the functional effects of the observed polymorphisms.

  19. DRD4 polymorphism moderates the effect of alcohol consumption on social bonding.

    Directory of Open Access Journals (Sweden)

    Kasey G Creswell

    Full Text Available Development of interpersonal relationships is a fundamental human motivation, and behaviors facilitating social bonding are prized. Some individuals experience enhanced reward from alcohol in social contexts and may be at heightened risk for developing and maintaining problematic drinking. We employed a 3 (group beverage condition ×2 (genotype design (N = 422 to test the moderating influence of the dopamine D4 receptor gene (DRD4 VNTR polymorphism on the effects of alcohol on social bonding. A significant gene x environment interaction showed that carriers of at least one copy of the 7-repeat allele reported higher social bonding in the alcohol, relative to placebo or control conditions, whereas alcohol did not affect ratings of 7-absent allele carriers. Carriers of the 7-repeat allele were especially sensitive to alcohol's effects on social bonding. These data converge with other recent gene-environment interaction findings implicating the DRD4 polymorphism in the development of alcohol use disorders, and results suggest a specific pathway by which social factors may increase risk for problematic drinking among 7-repeat carriers. More generally, our findings highlight the potential utility of employing transdisciplinary methods that integrate genetic methodologies, social psychology, and addiction theory to improve theories of alcohol use and abuse.

  20. DRD4 polymorphism moderates the effect of alcohol consumption on social bonding.

    Science.gov (United States)

    Creswell, Kasey G; Sayette, Michael A; Manuck, Stephen B; Ferrell, Robert E; Hill, Shirley Y; Dimoff, John D

    2012-01-01

    Development of interpersonal relationships is a fundamental human motivation, and behaviors facilitating social bonding are prized. Some individuals experience enhanced reward from alcohol in social contexts and may be at heightened risk for developing and maintaining problematic drinking. We employed a 3 (group beverage condition) ×2 (genotype) design (N = 422) to test the moderating influence of the dopamine D4 receptor gene (DRD4 VNTR) polymorphism on the effects of alcohol on social bonding. A significant gene x environment interaction showed that carriers of at least one copy of the 7-repeat allele reported higher social bonding in the alcohol, relative to placebo or control conditions, whereas alcohol did not affect ratings of 7-absent allele carriers. Carriers of the 7-repeat allele were especially sensitive to alcohol's effects on social bonding. These data converge with other recent gene-environment interaction findings implicating the DRD4 polymorphism in the development of alcohol use disorders, and results suggest a specific pathway by which social factors may increase risk for problematic drinking among 7-repeat carriers. More generally, our findings highlight the potential utility of employing transdisciplinary methods that integrate genetic methodologies, social psychology, and addiction theory to improve theories of alcohol use and abuse.

  1. Association study between the dopamine D4 receptor gene and schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Petronis, A.; Macciardi, F.; Athanassiades, A.; Paterson, A.D. [Clarke Institute of Psychiatry, Toronto (Canada)] [and others

    1995-10-09

    The dopamine D4 receptor is of major interest in schizophrenia research due to its high affinity for the atypical neuroleptic clozapine and a high degree of variability in the receptor gene (DRD4). Although several genetic linkage analyses performed on schizophrenia multiplex families from different regions of the world have either excluded or failed to prove that DRD4 is a major genetic factor for the development of schizophrenia, analyses for moderate predisposing effects are still of significant interest. We performed a study examining differences in allele frequencies of 4 different DRD4 polymorphisms in schizophrenia patients and age, sex, and ethnic origin matched controls. None of these 4 polymorphisms showed evidence for genetic association with schizophrenia, although a trend towards excess of the allele with 7 repeats in the (48){sub n} bp exon III polymorphism was observed. Complexities in the DRD4 genetic investigation and further analytic approaches are discussed. 18 refs., 2 tabs.

  2. Exon Deletions of Parkin Gene in Patients with Parkinson Disease

    Institute of Scientific and Technical Information of China (English)

    王涛; 梁直厚; 孙圣刚; 曹学兵; 彭海; 刘红进; 童萼塘

    2004-01-01

    Summary: Mutations in the parkin gene have recently been identified in familial and isolated patients with early-onset Parkinson disease (PD) and that subregions between exon 2 and 4 of the parkin gene are hot spots of deletive mutations. To study the distribution of deletions in the parkin gene among variant subset patients with PD in China, and to explore the role of parkin gene in the pathogenesis of PD, 63 patients were divided into early onset and later onset groups. Exons 1-12 were amplified by PCR, templated by the genomic DNA of patients, and then the deletion distribution detected by agarose electrophoresis. Four patients were found to be carrier of exon deletions in 63 patients with PD. The location of the deletion was on exon 2 (1 case), exon 3 (2 cases) and exon 4 (1 case). All patients were belong to the group of early onset PD. The results showed that parkin gene deletion on exon 2, exon 3 and exon 4 found in Chinese population contributes partly to early onset PD.

  3. Best friends and alcohol use in adolescence: the role of the dopamine D4 receptor gene.

    Science.gov (United States)

    van der Zwaluw, Carmen S; Larsen, Helle; Engels, Rutger C M E

    2012-11-01

    The influence of friends and peers is theoretically one of the most consistent and important factors explaining adolescent alcohol use. However, not all adolescents are equally likely to be influenced by their friends' drinking behaviors. Genetic factors may underlie these inter-individual differences in susceptibility to the drinking behavior of friends. Because the long allele (≥ 7 repeats) of the dopamine D4 receptor (DRD4) gene has been associated with susceptibility to alcohol and alcohol-related cues, we tested whether associations between best friend's and adolescent's alcohol use differed for DRD4 genotypes. A Dutch nationwide sample of 308 adolescents (age 13 at baseline) participated in a prospective, community-based study with five annual waves. A cross-lagged path analysis was carried out in Mplus to examine bi-directional relations between friends' and adolescents' weekly alcohol use (number of drinks). A multi-group approach was applied to test for moderation effects of a 48-base pair variable number of tandem repeats polymorphism in exon 3 of the DRD4 gene. Additionally, with latent growth curve models, it was examined whether the interaction between friends' drinking and DRD4 genotype predicted the development of adolescents' alcohol use. Results showed that both cross-sectionally and longitudinally higher levels of friends' alcohol use resulted in higher levels of adolescents' alcohol consumption over time (and vice versa). No significant moderation of DRD4 genotype was found: Associations between adolescents' and friends' drinking did not differ for adolescent carriers of the DRD4 long allele, when compared with adolescents without the DRD4 long allele. Because this is the first study to examine DRD4 × friends' drinking effects prospectively, replication is essential. Future longitudinal studies, possibly with observational or diary designs, are needed to increase our understanding of the interplay between genetic and environmental risk factors

  4. The executive function in Han Chinese children with Tourette's syndrome and its association with the polymorphism of DRD4exonIII48bp VNTR%抽动秽语综合征汉族患者的执行功能及与多巴胺D4受体第3外显子48bp可重复序列多态性

    Institute of Scientific and Technical Information of China (English)

    季卫东; 周家秀; 杨闯; 黄晓琪; 姚静; 郭田友; 郭兰婷; 刘协和

    2010-01-01

    目的:了解多巴胺D4受体基因第3外显子48bp可重复序列多态性(DRD4 exonⅢ NTR)与抽动秽语综合征(Gilles de la Tourette syndrome,GTS)患者执行功能缺陷之间的关系.方法:对86例GTS患者进行威斯康星卡片测验(Modified Wisconsin Card sorting test,WCST)、Stroop色词测验(Stroop test)和连线测验,并和51例正常对照组进行比较;利用PCR技术对GTS患者进行了DRD4 exonⅢ 48bpVNTR分析.结果:与正常对照组比较,GTS组在Stroop测验中的C错误数[(44.39±65.3)vs.(20.50±10.85),P<0.01]等(包括C纠错数、C时间、CW正确数、CW错误数、CW纠错数和CW时间)、连线测验A时间[(69.80±25.84)vs.(35.69±8.25),P<0.01](包括连线B时间、错误数、犯规数)、WCST正确数[(44.39±65.37)vs.(27.49±10.85),P<0.01](错误数、持续错误数、非持续错误数和分类数)等测验项目上成绩较差,从共病情况来看,注意缺陷多动综合征共病组在Stroop测验部分项目上比单纯GTS组要差;从GTS组内分析来看,DRD4exonⅢ48bpVNTR和各神经心理学测验成绩没有关联.结论:抽动秽语综合征患者存在执行功能缺陷,DRD4exonⅢ 48bpVNTR和抽动秽语综合征执行功能缺陷之间可能没有关联.

  5. Exon duplications in the ATP7A gene

    DEFF Research Database (Denmark)

    Mogensen, Mie; Skjørringe, Tina; Kodama, Hiroko

    2011-01-01

    BACKGROUND: Menkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene...

  6. Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product.

    Science.gov (United States)

    Datson, N A; van de Vosse, E; Dauwerse, H G; Bout, M; van Ommen, G J; den Dunnen, J T

    1996-03-15

    To facilitate the scanning of large genomic regions for the presence of exonic gene segments we have constructed a cosmid-based exon trap vector. The vector serves a dual purpose since it is also suitable for contig construction and physical mapping. The exon trap cassette of vector sCOGH1 consists of the human growth hormone gene driven by the mouse mettallothionein-1 promoter. Inserts are cloned in the multicloning site located in intron 2 of the hGH gene. The efficiency of the system is demonstrated with cosmids containing multiple exons of the Duchenne Muscular Dystrophy gene. All exons present in the inserts were successfully retrieved and no cryptic products were detected. Up to seven exons were isolated simultaneously in a single spliced product. The system has been extended by a transcription-translation-test protocol to determine the presence of large open reading frames in the trapped products, using a combination of tailed PCR primers directing protein synthesis in three different reading frames, followed by in vitro transcription-translation. Having larger stretches of coding sequence in a single exon trap product rather than small single exons greatly facilitates further analysis of potential genes and offers new possibilities for direct mutation analysis of exon trap material.

  7. Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene

    Directory of Open Access Journals (Sweden)

    Shomron Noam

    2007-11-01

    Full Text Available Abstract Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes. Results Genome-wide analysis of exonization of transposed elements revealed a higher rate of exonization within duplicated genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, underwent a humanoid-specific triplication, all three copies of the gene are active transcriptionally, although only one copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted into the first intron. In one of the non-protein coding copies, this Alu is exonized. We identified a single point mutation leading to exonization in one of the gene duplicates. When this mutation was introduced into the TIF-IA coding copy, exonization was activated and the level of the protein-coding mRNA was reduced substantially. A very low level of exonization was detected in normal human cells. However, this exonization was abundant in most leukemia cell lines evaluated, although the genomic sequence is unchanged in these cancerous cells compared to normal cells. Conclusion The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. These results further our understanding of the delicate interplay between gene duplication and alternative splicing and of the molecular evolutionary mechanisms leading to genetic innovations. This implies the existence of purifying selection against exonization in single copy genes, with duplicate genes free from such constrains.

  8. Intron phase correlations and the evolution of the intron/exon structure of genes.

    Science.gov (United States)

    Long, M; Rosenberg, C; Gilbert, W

    1995-01-01

    Two issues in the evolution of the intron/exon structure of genes are the role of exon shuffling and the origin of introns. Using a large data base of eukaryotic intron-containing genes, we have found that there are correlations between intron phases leading to an excess of symmetric exons and symmetric exon sets. We interpret these excesses as manifestations of exon shuffling and make a conservative estimate that at least 19% of the exons in the data base were involved in exon shuffling, suggesting an important role for exon shuffling in evolution. Furthermore, these excesses of symmetric exons appear also in those regions of eukaryotic genes that are homologous to prokaryotic genes: the ancient conserved regions. This last fact cannot be explained in terms of the insertional theory of introns but rather supports the concept that some of the introns were ancient, the exon theory of genes. PMID:8618928

  9. Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product.

    OpenAIRE

    Datson, N.A.; Vosse, E van de; Dauwerse, H.G.; Bout, M; van Ommen, G J; J T den Dunnen

    1996-01-01

    To facilitate the scanning of large genomic regions for the presence of exonic gene segments we have constructed a cosmid-based exon trap vector. The vector serves a dual purpose since it is also suitable for contig construction and physical mapping. The exon trap cassette of vector sCOGH1 consists of the human growth hormone gene driven by the mouse mettallothionein-1 promoter. Inserts are cloned in the multicloning site located in intron 2 of the hGH gene. The efficiency of the system is de...

  10. Polymorphism of exon 3 of the HLA-G gene

    DEFF Research Database (Denmark)

    Hviid, T V; Meldgaard, Michael; Sørensen, S

    1997-01-01

    populations have only revealed a limited polymorphism. We investigated the polymorphism of the exon 3 of HLA-G by means of Polymerase Chain Reaction (PCR)-Single Strand Conformation Polymorphism (SSCP)- and DNA sequencing analysis in a Danish population. We detected four single-base substitutions in exon 3...... rate of embryos. HLA-G seems to play an important role in the feto-maternal relationship. The polymorphism of the HLA-G locus is not fully clarified. One study has shown extensive nucleotide sequence variation in the exon 3 (alpha-2 domain) in healthy African Americans. A few studies in other...... compared to the sequence of HLA-6.0 (G*01011); one of these has not been reported before. We also found a deletion of the first base of codon 130 or the third of codon 129 in a heterozygous individual. This study, together with previous results, suggests that the polymorphism of exon 3 of the HLA-G gene...

  11. Ondansetron and sertraline may interact with 5-HTTLPR and DRD4 polymorphisms to reduce drinking in non-treatment seeking alcohol-dependent women: exploratory findings.

    Science.gov (United States)

    Kenna, George A; Zywiak, William H; Swift, Robert M; McGeary, John E; Clifford, James S; Shoaff, Jessica R; Fricchione, Samuel; Brickley, Michael; Beaucage, Kayla; Haass-Koffler, Carolina L; Leggio, Lorenzo

    2014-09-01

    The purpose of this exploratory study was to examine the interaction of 5-HTTLPR and DRD4 exon III polymorphisms with gender in non-treatment seeking alcohol-dependent (AD) individuals while alternately taking ondansetron and sertraline. Evidence suggests that alcohol dependence may be influenced by a genetic interaction that may be gender-specific with temporal changes making pharmacological treatment with serotonergic drugs complex. The main trial was a within-subject double-blind placebo-controlled human laboratory study with 77 non-treatment-seeking AD individuals randomized (55 completed, 49 complete data) to receive 200 mg/day of sertraline or 0.5 mg/day of ondansetron for 3 weeks followed by an alcohol self-administration experiment (ASAE), then placebo for 3 weeks followed by a second ASAE, then receive the alternate drug, in a counterbalanced order, for 3 weeks followed by a third ASAE. Results for men were not significant. Women with the LL 5-HTTLPR genotype receiving ondansetron and SS/SL 5-HTTLPR genotype receiving sertraline (matched), drank significantly fewer drinks per drinking day (DDD) during the 7 days prior to the first and third ASAEs than women receiving the mismatched medication (i.e., sertraline to LL and ondansetron to SS/SL). In a 3-way interaction, 5-HTTLPR alleles by DRD4 alleles by medications, women with the LL genotype who received ondansetron and had DRD4≥7 exon III repeats drank significantly fewer DDD as did SS/SL women who received sertraline but conversely had DRD4<7 repeats in the 7-day period leading up to the first and third ASAEs. Consistent with these data was a significant reduction of milliliters consumed ad libitum during these same ASAEs. These exploratory findings add possible support to gender and genetic differences among AD individuals in response to serotonergic pharmacotherapies. Future trials should be powerful enough to take into account that endophenotypes and a targeting of serotonergic interactions may be

  12. Ondansetron and sertraline may interact with 5-HTTLPR and DRD4 polymorphisms to reduce drinking in non-treatment seeking alcohol dependent women: exploratory findings

    Science.gov (United States)

    Kenna, George A.; Zywiak, William H.; Swift, Robert M.; McGeary, John E.; Clifford, James S.; Shoaff, Jessica R.; Fricchione, Samuel; Brickley, Michael; Beaucage, Kayla; Haass-Koffler, Carolina L.; Leggio, Lorenzo

    2014-01-01

    The purpose of this exploratory study was to examine the interaction of 5-HTTLPR and DRD4 exon III polymorphisms with gender in non-treatment seeking alcohol dependent (AD) individuals while alternately taking ondansetron and sertraline. Evidence suggests that alcohol dependence may be influenced by a genetic interaction that may be gender specific with temporal changes making pharmacological treatment with serotonergic drugs complex. The main trial was a within-subject double-blind placebo-controlled human laboratory study with 77 non-treatment-seeking AD individuals randomized (55 completed, 49 complete data) to receive 200mg/day of sertraline or 0.5mg/day of ondansetron for 3-weeks followed by an alcohol self-administration experiment (ASAE), then placebo for three weeks followed by a second ASAE, then receive the alternate drug, in a counterbalanced order, for three weeks followed by a third ASAE. Results for men were not significant. Women with the LL 5-HTTLPR genotype receiving ondansetron and SS/SL 5-HTTLPR genotypes receiving sertraline (matched), drank significantly fewer drinks per drinking day (DDD) during the 7-days prior to the first and third ASAEs than women receiving the mismatched medication (i.e. sertraline to LL and ondansetron to SS/SL). In a three-way interaction, 5-HTTLPR alleles by DRD4 alleles by medications, women with the LL genotype who received ondansetron and had DRD4 ≥7 exon III repeats drank significantly fewer DDD as did SS/SL women who received sertraline but conversely had DRD4 <7-repeats in the 7-day period leading up to the first and third ASAEs. Consistent with these data was a significant reduction of milliliters consumed ad lib during these same ASAEs. These exploratory findings add possible support to gender and genetic differences among AD individuals in response to serotonergic pharmacotherapies. Future trials should be powerful enough to take into account that endophenotypes and a targeting of serotonergic interactions

  13. Prediction of preschool aggression from DRD4 risk, parental ADHD symptoms, and home chaos.

    Science.gov (United States)

    Farbiash, Tali; Berger, Andrea; Atzaba-Poria, Naama; Auerbach, Judith G

    2014-01-01

    This study investigated the influence of a child's DRD4 risk, parental levels of ADHD symptoms, and the interactive influence of these factors on the development of preschool aggression. Additionally, the study investigated the role of home chaos as a mediator between parental ADHD symptoms and child aggression. The sample consisted of 84 4.5-year-old children and their parents. Children were genotyped for the DRD4 polymorphism. ADHD symptoms were self-reported by parents when the child was 2 to 6 months old. Parental reports of home chaos and the child's aggression were collected 4 years later. Child's DRD4 risk and parental ADHD symptoms significantly contributed to the prediction of preschool aggression. However, contrary to our hypotheses, no interactions were found between the child's DRD4 risk and the levels of parental ADHD symptoms. Home chaos played a mediating role in the relation between paternal ADHD symptoms and the child's aggression. The relation between maternal ADHD symptoms and the child's aggression was not significantly mediated through the level of home chaos. The current study emphasizes the importance of longitudinally investigating the contribution of parental ADHD symptoms to child aggression, while also exploring the differential contribution of maternal/paternal inattention and hyperactivity-impulsivity symptoms. Moreover, home chaos was found to be a significant environmental mechanism through which paternal ADHD symptoms affect children's aggression in the preschool years.

  14. ExonMiner: Web service for analysis of GeneChip Exon array data

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    Imoto Seiya

    2008-11-01

    Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

  15. ExonMiner: Web service for analysis of GeneChip Exon array data

    Science.gov (United States)

    Numata, Kazuyuki; Yoshida, Ryo; Nagasaki, Masao; Saito, Ayumu; Imoto, Seiya; Miyano, Satoru

    2008-01-01

    Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1) data normalization, (2) statistical analysis based on two-way ANOVA, (3) finding transcripts with significantly different splice patterns, (4) efficient visualization based on heatmaps and barplots, and (5) meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL . Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers. PMID:19036125

  16. Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

    Directory of Open Access Journals (Sweden)

    Mironov Andrey A

    2009-06-01

    Full Text Available Abstract Background Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons. Results We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs. Conclusion Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.

  17. Targeted exon skipping to correct exon duplications in the dystrophin gene

    National Research Council Canada - National Science Library

    Greer, Kane L; Lochmüller, Hanns; Flanigan, Kevin; Fletcher, Susan; Wilton, Steve D

    2014-01-01

    .... Differences in exon-skipping efficiencies in vitro were observed between oligomer analogues of the same sequence, with the phosphorodiamidate morpholino oligomer coupled to a cell-penetrating peptide...

  18. Antisense oligonucleotide induced exon skipping and the dystrophin gene transcript: cocktails and chemistries

    Directory of Open Access Journals (Sweden)

    Fletcher Sue

    2007-07-01

    Full Text Available Abstract Background Antisense oligonucleotides (AOs can interfere with exon recognition and intron removal during pre-mRNA processing, and induce excision of a targeted exon from the mature gene transcript. AOs have been used in vitro and in vivo to redirect dystrophin pre-mRNA processing in human and animal cells. Targeted exon skipping of selected exons in the dystrophin gene transcript can remove nonsense or frame-shifting mutations that would otherwise have lead to Duchenne Muscular Dystrophy, the most common childhood form of muscle wasting. Results Although many dystrophin exons can be excised using a single AO, several exons require two motifs to be masked for efficient or specific exon skipping. Some AOs were inactive when applied individually, yet pronounced exon excision was induced in transfected cells when the AOs were used in select combinations, clearly indicating synergistic rather than cumulative effects on splicing. The necessity for AO cocktails to induce efficient exon removal was observed with 2 different chemistries, 2'-O-methyl modified bases on a phosphorothioate backbone and phosphorodiamidate morpholino oligomers. Similarly, other trends in exon skipping, as a consequence of 2'-O-methyl AO action, such as removal of additional flanking exons or variations in exon skipping efficiency with overlapping AOs, were also seen when the corresponding sequences were prepared as phosphorodiamidate morpholino oligomers. Conclusion The combination of 2 AOs, directed at appropriate motifs in target exons was found to induce very efficient targeted exon skipping during processing of the dystrophin pre-mRNA. This combinatorial effect is clearly synergistic and is not influenced by the chemistry of the AOs used to induce exon excision. A hierarchy in exon skipping efficiency, observed with overlapping AOs composed of 2'-O-methyl modified bases, was also observed when these same sequences were evaluated as phosphorodiamidate morpholino

  19. Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder

    Directory of Open Access Journals (Sweden)

    Mayor-Olea Alvaro

    2011-05-01

    Dehydrogenase (MTHFD rs2236225 (OR = 3.09; 95%CI 1.27, 7.50; p = 0.016 and allele A of Methionine Synthase Reductase (MTRR rs1801394 (OR = 2.35; 95CI 1.10, 5.00; p = 0.037. An inflammatory oxidative stress enzyme, Gluthatione S-Tranferase Mu-1(GSTM1, null allele (OR = 2.21; 95%CI 1.24, 4.36; p = 0.030 and a neurotransmission receptor, Dopamine Receptor D4 (DRD4, long allele of 48 bp-repeat (OR = 3.62; 95%CI 0.76, 17.26; p = 0.161. Conclusions Some genetic polymorphisms related to folates metabolism, inflammatory oxidative stress, and neurotransmission responses to pain, has been significantly associated to TMD syndrome

  20. The evolutionary fate of alternatively spliced homologous exons after gene duplication.

    Science.gov (United States)

    Abascal, Federico; Tress, Michael L; Valencia, Alfonso

    2015-04-29

    Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Evidence for a novel exon in the coding region of the adenomatous polyposis coli (APC) gene

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Ling; St. Denis, K.A.; Bapat, B. [Univ. of Toronto (Canada)

    1995-08-10

    Germline mutations of the tumor suppressor gene APC cause familial adenomatous polyposis. Somatic APC alterations are involved in several sporadic neoplasma, including colorectal, duodenal, gastric, and esophageal carcinoma. The APC mRNA is encoded by 15 exons. Additional transcripts have been reported, due to alternative splicing of coding as well as noncoding regions. Two mRNA isoforms occur due to a deletion of exon 7 or a partial deletion of exon 9. We have identified a novel exon, flanked by APC exons 10 and 11, which is expressed as an alternatively transcribed product of the gene. Further, we have shown that the novel exon consists of a heptad repeat motif and is conserved across species. 18 refs., 2 figs.

  2. Examining impulsivity as an endophenotype using a behavioral approach: a DRD2 TaqI A and DRD4 48-bp VNTR association study

    Directory of Open Access Journals (Sweden)

    Beauchemin Joshua

    2007-01-01

    Full Text Available Abstract Background Research on the genetic basis for impulsivity has revealed an array of ambiguous findings. This may be a result of limitations to self-report assessments of impulsivity. Behavioral measures that assess more narrowly defined aspects of impulsivity may clarify genetic influences. This study examined the relationship between possession of the DRD2 TaqI A and DRD4 48 bp VNTR genetic polymorphisms and performance on a behavioral measure of impulsivity, the delay discounting task (DDT, and three traditional self-report measures. Methods 195 individuals (42% male were recruited from a university campus and were assessed in small group sessions using personal computers. Genotyping was conducted using previously established protocols. For the DRD2 TaqI A locus, individuals were designated as possessing at least one copy of the A1 allele (A1+ or not (A1-, and for the DRD4 48-bp VNTR locus, individuals were designated as having at least one long allele (7 repeats or longer, L+ or not (L-. Principal analyses used multiple univariate factorial 2 (A1+/A1- × 2 (L+/L- analyses of variance. Results A significant main effect of A1+ status on DDT performance was evident (p = .006 as well as a significant interaction effect (p = .006 between both genes. No other significant effects were evident on the self-report measures, with the exception of a trend toward an interaction effect on the Sensation Seeking Scale. Exploratory analyses suggested that the significant effects were not a function of population stratification or gender. Discussion These data suggest that the DRD2 TaqI A and DRD4 VNTR polymorphisms influence impulsivity as measured with a delay discounting task. Specifically, these findings suggest that an interaction between the functional effects of the two unlinked genotypes results in significant difference in the balance of mesolimbic dopaminergic activation relative to frontal-parietal activation. However, these findings are also

  3. DRD4/DAT1 mRNA expression in attention deficit hyperactivity disorder children before and after methylphenidate treatment%哌醋甲酯治疗注意缺陷多动障碍前后DRD4和DAT1基因mRNA表达的研究

    Institute of Scientific and Technical Information of China (English)

    丁凯景; 康传媛; 刘瑞湘; 张艳; 刘华

    2015-01-01

    目的 探讨注意缺陷多动障碍(attention deficit hyperactivity disorder, ADHD)患儿服用哌醋甲酯前后外周血中多巴胺转运体基因(dopamine transporter gene/solute carrier family 6,member3,DATl/SLC6A3)和多巴胺D4受体基因(dopamine receptor D4,DRD4)的mRNA表达水平的变化,探索其与症状严重程度、药物疗效的关系.方法共纳入符合美国《精神疾病诊断和统计手册》第4版(DSM-Ⅳ) ADHD诊断标准的6~15岁首诊的ADHD患儿45例,进行6周哌醋甲酯药物系统滴定,采用ADHD症状分级父母评定量表(ADHD rating scale-Ⅳ Home Version,ADHD-RS-Ⅳbome version)、威斯康辛卡片分类测试(Wisconsin card sorting test,WCST)、视觉注意力持续操作测验(visual continuous performance task, VCPT)进行临床症状和认知功能评定.采用试剂盒提取样本血总RNA并进行逆转录,采用实时荧光定量聚合酶链反应(quantitative real time polymerase chain reaction,qRT-PCR)法测定两目的基因服药前后的mRNA相对表达量.结果 ADHD患儿DRD4服药后的mRNA相对表达量(0.23±0.23)高于服药前(0.16±0.18) (P=0.041),而DAT1服药前的mRNA相对表达量(0.43±0.40)与服药后(0.39±0.53)差异无统计学意义(P>0.05);治疗有效组和无效组间两目的基因服药前相对表达量差异无统计学意义(均P>0.05),服药前后mRNA表达变化倍数均差异无统计学意义(均P>0.05);基线DRD4基因mRNA相对表达量与CPT错判T分呈正相关(r=0.424, P=0.025),而与ADHD-RS-Ⅳ总分、WCST概念化水平、CPT漏判T分及反应时间T分均无统计学线性相关关系;基线DAT1 mRNA相对表达量与ADHD-RS-Ⅳ总分、WCST概念化水平和CPT成绩均无显著相关性(均P>0.05).结论 本研究初步提示服用哌醋甲酯后ADHD患儿DRD4基因功能可能有提高.同时,该基因表达水平可能与ADHD患儿冲动症状有关,因此,DRD4基因mRNA表达可能可作为ADHD诊断和疗效评价的生物学标记.%Objective To

  4. Epistatic interactions involving DRD2, DRD4, and COMT polymorphisms and risk of substance abuse in women with binge-purge eating disturbances.

    Science.gov (United States)

    Steiger, Howard; Thaler, Lea; Gauvin, Lise; Joober, Ridha; Labbe, Aurelie; Israel, Mimi; Kucer, Audrey

    2016-06-01

    Substance abuse is common in individuals with bulimia-spectrum (binge-purge) eating disturbances, a co-occurrence that has been attributed to shared neurobiological substrates--notably alterations in dopaminergic activity. We examined the implications of variations of selected, dopamine-relevant polymorphisms (DRD2 Taq1A, DRD4 7R, and COMT) for risk of substance abuse in women with binge-purge eating syndromes. We genotyped 183 women (66.1% showing full-threshold BN and 33.9% showing sub-syndromic variants), and assessed lifetime presence of alcohol, cannabis, cocaine, and stimulant abuse or dependence using structured interviews. Tests for main and interaction effects of various allele combinations revealed that individuals who carried high function COMT and low-function DRD4 7R alleles (a combination expected to be associated with higher risk) did indeed show more lifetime substance abuse and, specifically, more cannabis abuse. Our findings suggest that a gene combination that, in theory, codes for low levels of dopaminergic neurotransmission coincides with sensitivity to substance abuse in a sample displaying binge-purge eating-disorder variants.

  5. Dopamine D4 Receptor Gene and Religious Affiliation Correlate with Dictator Game Altruism in Males and not Females: Evidence for Gender-sensitive Gene x Culture Interaction

    Directory of Open Access Journals (Sweden)

    Yushi eJiang

    2015-09-01

    Full Text Available On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion based on self-reports, and genotyped for the dopamine D4 receptor (DRD4 gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R ‘susceptibility’ genotype is more responsive to a positive environment provided by some religions.

  6. Dopamine D4 receptor and serotonin transporter gene effects on the longitudinal development of infant temperament.

    Science.gov (United States)

    Holmboe, K; Nemoda, Z; Fearon, R M P; Sasvari-Szekely, M; Johnson, M H

    2011-07-01

    Existing studies of the effect on infant temperament of the 48 base pair variable number of tandem repeats polymorphism in exon 3 of the dopamine D4 receptor gene, DRD4 VNTR, and the serotonin transporter-linked polymorphic region, 5-HTTLPR, have provided contradictory results, and age seems to be an important factor. The present study investigated the effect of these two polymorphisms on the stability of infant temperament between 4 and 9 months of age. Furthermore, the effect of a recently discovered single nucleotide polymorphism which modulates the 5-HTTLPR (rs25531) was investigated in relation to infant temperament. The study sample consisted of 90 infants, who were assessed by parental report at the two ages under consideration using the Revised Infant Behavior Questionnaire. It was found that infants carrying the 7-repeat allele of the DRD4 VNTR had higher levels of Negative Affect. Furthermore, there was an interaction between DRD4 VNTR and 5-HTTLPR genotype such that infants with the DRD4 VNTR 7-repeat allele and the highest expressing 5-HTTLPR genotype (L(A) L(A) ) had the highest level of Negative Affect. These effects were largely driven by scores on the Falling Reactivity scale. Genetic effects were stable across age. The results emphasize the need for developmental studies of genetic effects on temperament.

  7. A Brassica exon array for whole-transcript gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Christopher G Love

    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

  8. Molecular characterization of exon 3 of caprine myostatin gene in Marwari goat

    Directory of Open Access Journals (Sweden)

    Jai Prakash Khichar

    2016-06-01

    Full Text Available Aim: To estimate genetic variability in exon 3 of caprine myostatin gene in Marwari goats. Materials and Methods: A total of 120 blood samples from unrelated Marwari goats were randomly collected from different villages of Bikaner (Rajasthan, India. Genomic DNA was extracted from whole blood using blood DNA isolation kit (Himedia Ltd. as per manufacturer’s protocol. The quality of extracted genomic DNA was checked on 0.8% agarose gel. Specifically designed a primer set for caprine myostatin (MSTN gene (Genebank accession no. DQ167575 was used to amplify the exon 3 region of MSTN gene in Marwari goat. The genetic variability in exon 3 of MSTN gene in Marwari goat was assessed on 8% polyacrylamide gel electrophoresis to detect single strand conformation polymorphism (SSCP pattern. Results: The exon 3 of MSTN gene in Marwari goat showed two types of conformation patterns on 8% polyacrylamide gel. One of the patterns showed only two bands and was considered as genotype AA, whereas another pattern having an extra band was designated as genotype AB. The frequencies of AA and AB genotype for exon 3 region of MSTN gene were calculated as 0.90 and 0.10, respectively. Conclusion: Low level of polymorphism was observed at exon 3 region of MSTN gene in Marwari goat through SSCP analysis. This information could be utilized in future breeding plan to exploit the unique characteristics of Marwari goat of Rajasthan.

  9. Menzerath-Altmann law in mammalian exons reflects the dynamics of gene structure evolution.

    Science.gov (United States)

    Nikolaou, Christoforos

    2014-12-01

    Genomic sequences exhibit self-organization properties at various hierarchical levels. One such is the gene structure of higher eukaryotes with its complex exon/intron arrangement. Exon sizes and exon numbers in genes have been shown to conform to a law derived from statistical linguistics and formulated by Menzerath and Altmann, according to which the mean size of the constituents of an entity is inversely related to the number of these constituents. We herein perform a detailed analysis of this property in the complete exon set of the mouse genome in correlation to the sequence conservation of each exon and the transcriptional complexity of each gene locus. We show that extensive linear fits, representative of accordance to Menzerath-Altmann law are restricted to a particular subset of genes that are formed by exons under low or intermediate sequence constraints and have a small number of alternative transcripts. Based on this observation we propose a hypothesis for the law of Menzerath-Altmann in mammalian genes being predominantly due to genes that are more versatile in function and thus, more prone to undergo changes in their structure. To this end we demonstrate one test case where gene categories of different functionality also show differences in the extent of conformity to Menzerath-Altmann law. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Mutations of p53 gene exons 4-8 in human esophageal cancer

    Institute of Scientific and Technical Information of China (English)

    Li-Ya Li; Jin-Tian Tang; Li-Qun Jia; Pei-Wen Li

    2005-01-01

    AIM: To characterize the tumor suppressor gene p53 mutations in exon 4, esophageal cancer and adjacent noncancerous tissues.METHODS: We performed p53 (exons 4-8) gene mutation analysis on 24 surgically resected human esophageal cancer specimens by PCR, single-strand conformation polymorphism, and DNA sequencing. RESULTS: p53 gene mutations were detected in 9 of 22 (40.9%) esophageal cancer specimens and 10 of 17 (58.8%) adjacent non-cancerous tissues. Eight of sixteen (50.0%) point mutations detected were G-A transitions and 9 of 18 (50.0%) p53 gene mutations occurred in exon 4 in esophageal cancer specimens. Only 1 of 11 mutations detected was G-A transition and 4 of 11 (36.4%) p53 gene mutations occurred in exon 4 in adjacent non-cancerous tissues.CONCLUSION: Mutation of p53 gene in exon 4 may play an important role in development of esophageal cancer. The observation of p53 gene mutation in adjacent noncancerous tissues suggests that p53 gene mutation may be an early event in esophageal carcinogenesis. Some clinical factors, including age, sex, pre-operation therapy and location of tumors, do not influence p53 gene mutation rates.

  11. Polymorphisms of exon 5, exon 7 and intron 10 of MMP2 gene and their association with wool density in Rex rabbits

    Directory of Open Access Journals (Sweden)

    S.J. Chen

    2017-06-01

    Full Text Available Wool density is an important index that influences Rex rabbit fur quality. In our earlier studies, we found some important differentially expressed genes in different wool density of Rex rabbit by cDNA microarray. Based on the outcome, we conducted an association study to identify single nucleotide polymorphisms (SNPs of exon 1, 5, 7 and 10 of matrix metalloproteinase-2 (MMP2 gene and their ligands associated with wool density. The results showed that exon 1 and exon 10 of MMP2 gene did not occur mutation in 100 Rex rabbits, meanwhile 3 SNPs were identified in exon 5, exon 7 and intron 10 of MMP2 gene sequence respectively, the 3 mutation sites were as follows: MMP2-exon 5-26C/G, MMP2-exon 7-101C/T and MMP2-intron 10-6C/T. The 3 SNPs were all in Hardy-Weinberg equilibrium. Phenotypic correlation analysis results showed the 3 mutations lacked significant associations (P>0.05 with the wool density.

  12. Molecular analysis of contiguous exons of the phenylalanine hydroxylase gene: identification of a new PKU mutation.

    OpenAIRE

    Dianzani, I; Camaschella, C.; Saglio, G; Ferrero, G B; Ramus, S; Ponzone, A; Cotton, R G

    1993-01-01

    A modified application of the chemical cleavage of mismatch (CCM) method has been used to screen three contiguous exons (exons 9, 10, and 11) of the phenylalanine hydroxylase gene in 17 Italian PKU patients. A new nonsense heterozygous C-->G transversion within exon 11 (S359X) was identified in a single patient. Only one of the four mutations previously reported in this DNA region in Caucasians was found. This lesion, IVS X-546, was detected in five of the 34 PKU alleles examined. Our results...

  13. Decoding of exon splicing patterns in the human RUNX1-RUNX1T1 fusion gene.

    Science.gov (United States)

    Grinev, Vasily V; Migas, Alexandr A; Kirsanava, Aksana D; Mishkova, Olga A; Siomava, Natalia; Ramanouskaya, Tatiana V; Vaitsiankova, Alina V; Ilyushonak, Ilia M; Nazarov, Petr V; Vallar, Laurent; Aleinikova, Olga V

    2015-11-01

    The t(8;21) translocation is the most widespread genetic defect found in human acute myeloid leukemia. This translocation results in the RUNX1-RUNX1T1 fusion gene that produces a wide variety of alternative transcripts and influences the course of the disease. The rules of combinatorics and splicing of exons in the RUNX1-RUNX1T1 transcripts are not known. To address this issue, we developed an exon graph model of the fusion gene organization and evaluated its local exon combinatorics by the exon combinatorial index (ECI). Here we show that the local exon combinatorics of the RUNX1-RUNX1T1 gene follows a power-law behavior and (i) the vast majority of exons has a low ECI, (ii) only a small part is represented by "exons-hubs" of splicing with very high ECI values, and (iii) it is scale-free and very sensitive to targeted skipping of "exons-hubs". Stochasticity of the splicing machinery and preferred usage of exons in alternative splicing can explain such behavior of the system. Stochasticity may explain up to 12% of the ECI variance and results in a number of non-coding and unproductive transcripts that can be considered as a noise. Half-life of these transcripts is increased due to the deregulation of some key genes of the nonsense-mediated decay system in leukemia cells. On the other hand, preferred usage of exons may explain up to 75% of the ECI variability. Our analysis revealed a set of splicing-related cis-regulatory motifs that can explain "attractiveness" of exons in alternative splicing but only when they are considered together. Cis-regulatory motifs are guides for splicing trans-factors and we observed a leukemia-specific profile of expression of the splicing genes in t(8;21)-positive blasts. Altogether, our results show that alternative splicing of the RUNX1-RUNX1T1 transcripts follows strict rules and that the power-law component of the fusion gene organization confers a high flexibility to this process.

  14. STUDY OF ECK GENE EXON-3 FROM HUMAN NORMAL TISSUE AND BREAST CANCER CELL LINE

    Institute of Scientific and Technical Information of China (English)

    李瑶琛; 孔令洪; 王一理; 司履生

    2003-01-01

    Objective To establish a method cloning the exon 3 of eck gene from normal tissue and ZR-75-1 cell line (a human breast cancer cell line)and study whether these genes exist mutant. Methods Designed a pair of specific primers and amplified the exon 3 of eck gene fragment from the extracted genomic DNA derived from normal epithelial cells from skin tissue and ZR-75-1 cell line respectively by PCR technique. Transformed the E.coil. JM109 with recombinant plamids constructed by inserting the amplified fragments into medium vector pUCm-T and sequenced these amplified fragments after primary screening of endonuclease restriction digestion and PCR amplification. Results ① Obtained the genomic DNA of human normal epithelial cells and ZR-75-1 cell line respectively. ② Obtained the amplified fragments of human exon 3 of eck gene through PCR technique. ③ Obtained the cloning vectors of exon 3 of eck gene of human normal epithelial cells and ZR-75-1 cell line respectively. ④ ZR-75-1 cell line exists mutation of nucleotides. Conclusion Successfully established the method of cloning the human exon 3 of eck gene and found some mutations in the detected samples. This study lays a foundation for further studying the function of eck gene in tumorgenesis.

  15. The proximal first exon architecture of the murine ghrelin gene is highly similar to its human orthologue

    Directory of Open Access Journals (Sweden)

    Seim Inge

    2009-05-01

    Full Text Available Abstract Background The murine ghrelin gene (Ghrl, originally sequenced from stomach tissue, contains five exons and a single transcription start site in a short, 19 bp first exon (exon 0. We recently isolated several novel first exons of the human ghrelin gene and found evidence of a complex transcriptional repertoire. In this report, we examined the 5' exons of the murine ghrelin orthologue in a range of tissues using 5' RACE. Findings 5' RACE revealed two transcription start sites (TSSs in exon 0 and four TSSs in intron 0, which correspond to 5' extensions of exon 1. Using quantitative, real-time RT-PCR (qRT-PCR, we demonstrated that extended exon 1 containing Ghrl transcripts are largely confined to the spleen, adrenal gland, stomach, and skin. Conclusion We demonstrate that multiple transcription start sites are present in exon 0 and an extended exon 1 of the murine ghrelin gene, similar to the proximal first exon organisation of its human orthologue. The identification of several transcription start sites in intron 0 of mouse ghrelin (resulting in an extension of exon 1 raises the possibility that developmental-, cell- and tissue-specific Ghrl mRNA species are created by employing alternative promoters and further studies of the murine ghrelin gene are warranted.

  16. Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.

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    Mohammad Azhar Aziz

    Full Text Available Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by 'Genomic Identification of Significant Targets In Cancer (GISTIC' analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data--gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA. ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.

  17. Detection of an exon 53 polymorphism in the dystrophin gene.

    Science.gov (United States)

    Prior, T W; Papp, A C; Snyder, P J; Sedra, M S

    1993-10-01

    We utilized a heteroduplex method to screen for small mutations in Duchenne muscular dystrophy patients who did not have deletions or duplications. A dystrophin exon 53 heteroduplex band was identified in 14.4% of the affected patients. Direct sequencing of the amplified product from DNA producing the heteroduplex revealed the presence of a polymorphism in the coding region. The codon for asparagine was converted from AAT to AAC.

  18. MOLECULAR ANALYSIS OF RADIATION-INDUCED MUTATION IN EXON 7/8 OF RAT HPRT GENE

    Institute of Scientific and Technical Information of China (English)

    任晓庆; 黄定九; 黄钢; 王利民

    2003-01-01

    Objective To investigate the relationship between the radiation dose and the HPRT gene locus mutation in rat smooth muscle cells, and provide the molecular basis for prevention of restenosis after percutaneous transluminal coronary angioplasty (PTCA).MethodsThe smooth muscle cells cultured in vitro were irradiated by radionuclide 188Re in different doses. HPRT gene mutation colonies were selected and isolated by 6 thioguanine. Analysis of mutation in exon 7/8 of HPRT gene were accomplished by polymerase chain reaction and single strand conformation polymorphism.ResultsThe HPRT gene mutation frequency of rat smooth muscle cells that were irradiated by radionuclide 188Re ranged from 5.5×10-6 to 13×10-6. Of 91 HPRT gene mutation colonies, 13(14.3%) contained exon 7/8 deletion and 15(16.5%) had point mutation. The exon 7/8 mutation frequency was 30.8%. There were significant relationships between radiation dose and mutation frequency of HPRT gene and exon 7/8.ConclusionThe DNA damage and gene mutation induced by radiation has positive relationship with radiation dose, and is a basis of proliferation inhibition and apoptosis of smooth muscle cells.

  19. Gene correction of a duchenne muscular dystrophy mutation by meganuclease-enhanced exon knock-in.

    Science.gov (United States)

    Popplewell, Linda; Koo, Taeyoung; Leclerc, Xavier; Duclert, Aymeric; Mamchaoui, Kamel; Gouble, Agnés; Mouly, Vincent; Voit, Thomas; Pâques, Frédéric; Cédrone, Frédéric; Isman, Olga; Yáñez-Muñoz, Rafael J; Dickson, George

    2013-07-01

    Duchenne muscular dystrophy (DMD) is a severe inherited, muscle-wasting disorder caused by mutations in the DMD gene. Gene therapy development for DMD has concentrated on vector-based DMD minigene transfer, cell-based gene therapy using genetically modified adult muscle stem cells or healthy wild-type donor cells, and antisense oligonucleotide-induced exon-skipping therapy to restore the reading frame of the mutated DMD gene. This study is an investigation into DMD gene targeting-mediated correction of deletions in human patient myoblasts using a target-specific meganuclease (MN) and a homologous recombination repair matrix. The MN was designed to cleave within DMD intron 44, upstream of a deletion hotspot, and integration-competent lentiviral vectors expressing the nuclease (LVcMN) were generated. MN western blotting and deep gene sequencing for LVcMN-induced non-homologous end-joining InDels (microdeletions or microinsertions) confirmed efficient MN expression and activity in transduced DMD myoblasts. A homologous repair matrix carrying exons 45-52 (RM45-52) was designed and packaged into integration-deficient lentiviral vectors (IDLVs; LVdRM45-52). After cotransduction of DMD myoblasts harboring a deletion of exons 45 to 52 with LVcMN and LVdRM45-52 vectors, targeted knock-in of the RM45-52 region in the correct location in DMD intron 44, and expression of full-length, correctly spliced wild-type dystrophin mRNA containing exons 45-52 were observed. This work demonstrates that genome surgery on human DMD gene mutations can be achieved by MN-induced locus-specific genome cleavage and homologous recombination knock-in of deleted exons. The feasibility of human DMD gene repair in patient myoblasts has exciting therapeutic potential.

  20. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    Energy Technology Data Exchange (ETDEWEB)

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  1. Exon organization of the mouse entactin gene corresponds to the structural domains of the polypeptide and has regional homology to the low-density lipoprotein receptor gene

    DEFF Research Database (Denmark)

    Durkin, M E; Wewer, U M; Chung, A E

    1995-01-01

    Entactin is a widespread basement membrane protein of 150 kDa that binds to type IV collagen and laminin. The complete exon-intron structure of the mouse entactin gene has been determined from lambda genomic DNA clones. The gene spans at least 65 kb and contains 20 exons. The exon organization...... of the mouse entactin gene closely corresponds to the organization of the polypeptide into distinct structural and functional domains. The two amino-terminal globular domains are encoded by three exons each. Single exons encode the two protease-sensitive, O-glycosylated linking regions. The six EGF......-like repeats and the single thyroglobulin-type repeat are each encoded by separate exons. The carboxyl-terminal half of entactin displays sequence homology to the growth factor-like region of the low-density lipoprotein receptor, and in both genes this region is encoded by eight exons. The positions of four...

  2. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

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    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  3. The role of D4 receptor gene exon III polymorphisms in shaping human altruism and prosocial behavior

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    Yushi eJiang

    2013-05-01

    Full Text Available Human beings are an extraordinarily altruistic species often willing to help strangers at a considerable cost (sometimes life itself to themselves. But as Darwin noted …he who was ready to sacrifice his life, as many a savage has been, rather than betray his comrades, would often leave no offspring to inherit his noble nature. Hence, this is the paradox of altruism. Twin studies have shown that altruism and other prosocial behavior show considerable heritability and more recently a number of candidate genes have been identified with this phenotype. Among these first provisional findings are genes encoding elements of dopaminergic transmission. In this article we will review the evidence for the involvement of one of these, the dopamine D4 receptor (DRD4 gene, in shaping human prosocial behavior and consider the methodologies employed in measuring this trait, specific molecular genetic findings and finally, evidence from several Gene x Environment (GxE studies that imply differential susceptibility of this gene to environmental influences.

  4. Differential splicing of exon 5 of the Wilms tumour (WTI) gene.

    Science.gov (United States)

    Renshaw, J; King-Underwood, L; Pritchard-Jones, K

    1997-08-01

    The WTI gene encodes a developmentally regulated transcription factor whose function is altered by alternative splicing at two sites: the 17 amino acids of exon 5, whose functional effects are ill-defined, and the 3 amino acids (KTS) between exons 9 and 10, which determine sequence-specific DNA binding and nuclear localisation. Germline mutations, which prevent normal KTS splicing, can underlie the Denys-Drash syndrome, and disruptions of splicing of exon 5 may occur in Wilms tumours. We analysed by reverse transcriptase polymerase chain reaction (RT-PCR) amplification the relative ratios of the four splice variants of WTI mRNA in normal and tumour tissues and found tissue-specific, developmental stage-specific, and species-specific differences in the splicing of exon 5 but not of KTS. We found no evidence for disrupted splicing in acute leukaemias or gonadal tumours. The significance of these findings is discussed, and the possibility is raised that WTI may orchestrate the appropriate response to growth and differentiation factor signalling, mediated by alterations in the relative levels of exon 5 containing WTI isoforms.

  5. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

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    Aramburu Ander

    2010-11-01

    Full Text Available Abstract Background Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP and sensitivity (ST of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results. Conclusions The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.

  6. Multi-exon deletions of the FBN1 gene in Marfan syndrome

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    Schrijver Iris

    2001-10-01

    Full Text Available Abstract Background Mutations in the fibrillin -1 gene (FBN1 cause Marfan syndrome (MFS, an autosomal dominant multi-system connective tissue disorder. The 200 different mutations reported in the 235 kb, 65 exon-containing gene include only one family with a genomic multi-exon deletion. Methods We used long-range RT-PCR for mutation detection and long-range genomic PCR and DNA sequencing for identification of deletion breakpoints, allele-specific transcript analyses to determine stability of the mutant RNA, and pulse-chase studies to quantitate fibrillin synthesis and extracellular matrix deposition in cultured fibroblasts. Southern blots of genomic DNA were probed with three overlapping fragments covering the FBN1 coding exons Results Two novel multi-exon FBN1 deletions were discovered. Identical nucleotide pentamers were found at or near the intronic breakpoints. In a Case with classic MFS, an in-frame deletion of exons 42 and 43 removed the C-terminal 24 amino acids of the 5th LTBP (8-cysteine domain and the adjacent 25th calcium-binding EGF-like (6-cysteine domain. The mutant mRNA was stable, but fibrillin synthesis and matrix deposition were significantly reduced. A Case with severe childhood-onset MFS has a de novo deletion of exons 44–46 that removed three EGF-like domains. Fibrillin protein synthesis was normal, but matrix deposition was strikingly reduced. No genomic rearrangements were detected by Southern analysis of 18 unrelated MFS samples negative for FBN1 mutation screening. Conclusions Two novel deletion cases expand knowledge of mutational mechanisms and genotype/phenotype correlations of fibrillinopathies. Deletions or mutations affecting an LTBP domain may result in unstable mutant protein cleavage products that interfere with microfibril assembly.

  7. Rapid Characterization of Spider Silk Genes via Exon Capture

    Science.gov (United States)

    2015-03-28

    eco - friendly than manmade fibers such as nylon and Kevlar, which are industrially manufactured using harsh chemicals and solvents. These...is persistent demand for the mass production of silks, which requires knowledge of the underlying silk gene sequences. Spidroins (spider fibroins...persistent demand for the mass production of silks, which requires knowledge of the underlying silk gene sequences. Spidroins (spider fibroins), the most

  8. Characterization of Exon 2 and Intron 2 of Leptin Gene in Native Anatolian Goat Breeds

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    Özge BAKIRCIOĞLU

    2016-07-01

    Full Text Available Studies performed on farm animals like cattle and pig have shown that there has been a relationship between leptin gene (LEP and carcass meat quality, milk production and content, and economic parameters such as reproduction and food consumption. There has been scarce research conducted related to leptin gene of sheep and especially goat. The aim of the study is to reveal the genetic structures of goats living in Turkey through nucleotide sequence analysis in targeted zones of LEP gene Exon 2 and Intron 2 of Anatolian Black, Kilis and Angora goat breeds which are commonly fed in Anatolia. According to the sequence analysis results of each three breeds, Anatolian Black goat breed have the highest haplotype number with nucleotide and haplotype diversity both in exon 2 and intron 2. There was only one haplotype found in both exon 2 and intron 2 in Angora goat breed. There was no nucleotide diversity found in individuals belonging to Angora goat breed. Taking the regions analyzed for LEP gene into consideration, it is seen that Anatolian Black goat breed has the highest genetic diversity among other goat breeds fed in Anatolia. Future studies upon the LEP gene in goats should take into account of increasing the sample size and of base in order to obtain more useful information for better understanding the gene structure.

  9. Gene identification using exon amplification on human chromosome 18q21: implications for bipolar disorder.

    Science.gov (United States)

    Chen, H; Huo, Y; Patel, S; Zhu, X; Swift-Scanlan, T; Reeves, R H; DePaulo, R; Ross, C A; McInnis, M G

    2000-09-01

    We previously reported linkage between bipolar disorder and a region on human chromosome (HC) 18q21. To identify genes in this region, exon trapping was performed on cosmids isolated from an HC18-specific cosmid library (LL18NC02) using 47 sequence tagged site (STS) markers from 18q21 as hybridization probes. A total of 285 unique sequences (exons) were obtained from 850 sequenced clones. Homology searching of the databases using NCBI's BLAST algorithms revealed that 31 exons have identity to known genes and/or ESTs, seven are identical to regions of finished genomic sequences in the 18q21 region, 20 have significant similarity (>30% sequence identity) to genes from human and/or other species, 19 were repetitive sequences, and 208 sequences (72%) are novel. Seventy per cent of the trapped sequences were predicted to be derived from genes using library screening and RT-PCR analyses. This represents an initial stage in characterizing genes in a susceptibility region for further study in bipolar disorder or other diseases that map to this region.

  10. Associations between dopamine D4 receptor gene variation with both infidelity and sexual promiscuity.

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    Justin R Garcia

    Full Text Available BACKGROUND: Human sexual behavior is highly variable both within and between populations. While sex-related characteristics and sexual behavior are central to evolutionary theory (sexual selection, little is known about the genetic bases of individual variation in sexual behavior. The variable number tandem repeats (VNTR polymorphism in exon III of the human dopamine D4 receptor gene (DRD4 has been correlated with an array of behavioral phenotypes and may be predicatively responsible for variation in motivating some sexual behaviors, particularly promiscuity and infidelity. METHODOLOGY/PRINCIPAL FINDINGS: We administered an anonymous survey on personal history of sexual behavior and intimate relationships to 181 young adults. We also collected buccal wash samples and genotyped the DRD4 VNTR. Here we show that individuals with at least one 7-repeat allele (7R+ report a greater categorical rate of promiscuous sexual behavior (i.e., having ever had a "one-night stand" and report a more than 50% increase in instances of sexual infidelity. CONCLUSIONS/SIGNIFICANCE: DRD4 VNTR genotype varies considerably within and among populations and has been subject to relatively recent, local selective pressures. Individual differences in sexual behavior are likely partially mediated by individual genetic variation in genes coding for motivation and reward in the brain. Conceptualizing these findings in terms of r/K selection theory suggests a mechanism for selective pressure for and against the 7R+ genotype that may explain the considerable global allelic variation for this polymorphism.

  11. Exons 16 and 17 of the amyloid precursor protein gene in familial inclusion body myopathy.

    Science.gov (United States)

    Sivakumar, K; Cervenáková, L; Dalakas, M C; Leon-Monzon, M; Isaacson, S H; Nagle, J W; Vasconcelos, O; Goldfarb, L G

    1995-08-01

    Accumulation of beta-amyloid protein (A beta) occurs in some muscle fibers of patients with inclusion body myopathy and resembles the type of amyloid deposits seen in the affected tissues of patients with Alzheimer's disease and cerebrovascular amyloidosis. Because mutations in exons 16 and 17 of the beta-amyloid precursor protein (beta APP) gene on chromosome 21 have been identified in patients with early-onset familial Alzheimer's disease and Dutch-type cerebrovascular amyloidosis, we searched for mutations of the same region in patients with familial inclusion body myopathy. Sequencing of both alleles in 8 patients from four unrelated families did not reveal any mutations in these exons. The amyloid deposition in familial forms of inclusion body myopathy may be either due to errors in other gene loci, or it is secondary reflecting altered beta APP metabolism or myocyte degeneration and cell membrane degradation.

  12. Intron 1 and exon 1 alpha estrogen receptor gene polymorphisms in women with endometriosis.

    Science.gov (United States)

    Sato, Hélio; Nogueira-de-Souza, Naiara C; D'Amora, Paulo; Silva, Ismael D C G; Girão, Manoel J B C; Schor, Eduardo

    2008-12-01

    To evaluate the association of intron 1 and exon 1 polymorphisms in the estrogen receptor alpha gene (ER-alpha) with endometriosis in women. Association study. Endometriosis Unit, Federal University of São Paulo. The control group consisted of volunteers older than 45 years who had no evidence of endometriosis antecedents. Two groups with the disease were evaluated: the first group had stage I or II endometriosis and the second group stage III or IV. Polymerase chain reaction (PCR) followed by digestion with HaeIII and MspI endonucleases (RFLP) were applied to detect intron 1 and exon 1 polymorphisms, respectively, in a total of 125 controls and 105 affected women. Frequency and distribution of HaeIII and MspI polymorphisms in ER-alpha. No significant differences in the frequency of polymorphisms either in intron 1 or exon 1 of ER-alpha were found when endometriosis patients were compared with control subjects. Furthermore, the frequency of ER-alpha polymorphisms within the two different groups of patients with disease was statistically similar. The odds ratio between presence of intron 1 single-nucleotide polymorphisms (SNP) and endometriosis was 0.904, and the odds ratio between exon 1 SNP and endometriosis was 0.976. The evaluated polymorphisms were not associated with endometriosis.

  13. Transcriptional enhancers in protein-coding exons of vertebrate developmental genes.

    Directory of Open Access Journals (Sweden)

    Deborah I Ritter

    Full Text Available Many conserved noncoding sequences function as transcriptional enhancers that regulate gene expression. Here, we report that protein-coding DNA also frequently contains enhancers functioning at the transcriptional level. We tested the enhancer activity of 31 protein-coding exons, which we chose based on strong sequence conservation between zebrafish and human, and occurrence in developmental genes, using a Tol2 transposable GFP reporter assay in zebrafish. For each exon we measured GFP expression in hundreds of embryos in 10 anatomies via a novel system that implements the voice-recognition capabilities of a cellular phone. We find that 24/31 (77% exons drive GFP expression compared to a minimal promoter control, and 14/24 are anatomy-specific (expression in four anatomies or less. GFP expression driven by these coding enhancers frequently overlaps the anatomies where the host gene is expressed (60%, suggesting self-regulation. Highly conserved coding sequences and highly conserved noncoding sequences do not significantly differ in enhancer activity (coding: 24/31 vs. noncoding: 105/147 or tissue-specificity (coding: 14/24 vs. noncoding: 50/105. Furthermore, coding and noncoding enhancers display similar levels of the enhancer-related histone modification H3K4me1 (coding: 9/24 vs noncoding: 34/81. Meanwhile, coding enhancers are over three times as likely to contain an H3K4me1 mark as other exons of the host gene. Our work suggests that developmental transcriptional enhancers do not discriminate between coding and noncoding DNA and reveals widespread dual functions in protein-coding DNA.

  14. Delineation of the Marfan phenotype associated with mutations in exons 23-32 of the FBN1 gene

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, E.A.; Cho, M.; Milewicz, D.M. [Univ. of Texas-Houston Medical School, Houston, TX (United States)] [and others

    1996-03-29

    Marfan syndrome is a dominantly inherited connective tissue disorder with a wide range of phenotypic severity. The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. We screened 8 patients with either neonatal Marfan syndrome or severe cardiovascular complications of Marfan syndrome for mutations in this region of the gene. Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. This analysis documented mutations in exons 25-27 of the FBN1 mutations in 6 of these patients. These results, taken together with previously published FBN1 mutations in this region, further define the phenotype associated with mutations in exons 24-32 of the FBN1 gene, information important for the development of possible diagnostic tests and genetic counseling. 49 refs., 4 figs., 2 tabs.

  15. The role of germline promoters and I exons in cytokine-induced gene-specific class switch recombination.

    Science.gov (United States)

    Dunnick, Wesley A; Shi, Jian; Holden, Victoria; Fontaine, Clinton; Collins, John T

    2011-01-01

    Germline transcription precedes class switch recombination (CSR). The promoter regions and I exons of these germline transcripts include binding sites for activation- and cytokine-induced transcription factors, and the promoter regions/I exons are essential for CSR. Therefore, it is a strong hypothesis that the promoter/I exons regions are responsible for much of cytokine-regulated, gene-specific CSR. We tested this hypothesis by swapping the germline promoter and I exons for the murine γ1 and γ2a H chain genes in a transgene of the entire H chain C-region locus. We found that the promoter/I exon for γ1 germline transcripts can direct robust IL-4-induced recombination to the γ2a gene. In contrast, the promoter/I exon for the γ2a germline transcripts works poorly in the context of the γ1 H chain gene, resulting in expression of γ1 H chains that is type level. Nevertheless, the small amount of recombination to the chimeric γ1 gene is induced by IFN-γ. These results suggest that cytokine regulation of CSR, but not the magnitude of CSR, is regulated by the promoter/I exons.

  16. Detection of c-kit gene mutations in Exon 11 of Leukemias

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    Syed Rizwan Hussain

    2012-03-01

    Full Text Available OBJECTIVE: To identify mutations in c-kit gene in exon 11 in Leukemia cases. METHODS: In order to determine the frequency of mutations of Exon 11 of c-kit gene in 50 Leukemia cases (31 samples Acute Myeloid Leukemia, 5 samples Acute Lymphoblastic Leukemia, 9 samples Chronic Myeloid Leukemia and 5 samples Chronic Lymphocytic Leukemia, we have done PCR-SSCP followed by direct DNA sequencing. RESULTS: Of 50 Leukemia cases, 28 were male and 22 were female with ages ranging from 2 to 65 years. The mean age of cases was 31.88 years. We have detected total twenty mutations in nineteen cases that include Lys550Asn, Tyr568Ser, Ile571Thr, Thr574Pro, Gln575His, Tyr578Pro, Asp579His, His580Gln, Arg586Thr, Asn587Asp and Arg588Met as well as novel point mutations at codons Ile563Lys, Val569Leu, Tyr570Ser, and Pro577Ser. Ile571Leu substitution is found in two independent cases whereas Trp582Ser substitution is found in three individual cases. CONCLUSION: These observations suggest that mutations in exon 11 of the c-kit gene might represent useful molecular genetic markers in Leukemia.

  17. The SNPs Analysis of the Exons of Three Genes of MyoD Gene Family in Seven Swine Breeds (Line)

    Institute of Scientific and Technical Information of China (English)

    LI Jing-fen; LIU Di; YU Hao

    2005-01-01

    The study objects includes seven swine breeds: Minzhu, Sanjiangbaizhu, Yorkshire, Landrace, Junmuyihao, Duroc and Double muscle Yorkshire. According to the sequences of MyoG, MyoD and Myf5 of swine in GenBank, seventeen pairs of primers for MyoG, MyoD and Myf5 were designed. PCR-SSCP technology was applied to detect SNPs of the exons of the three genes. The results showed that no polymorphism was in MyoG and MyoD, and some SNPs were in three exons of Myf5. There was one mutant site in the first exon of Myf5 (G → C), three mutant sites in the second exon of Myf5 (C → A, A → G and G → A); in the third exon of Myf5, there was one base A deficiency at 3 387 bp, three bases T deficiency at 3 417 bp, one mutant site at 3 443 bp (T → C).This study obtained a tendency conclusion that gene frequency of allele M of Myf5 on the one hand is positively correlated with lean meat percentage, on the other hand is correlated with the orientation of selective breeding; it also deduced that allele F is possibly correlated with high lean meat percentage. Through statistical analysis, allele A, B, C of Myf5 have no obvious correlation with lean meat percentage of different swine breeds, In addition, the high polymorphism of Myf5 showed that seven swine breeds are rich in genetic variation, and have high selective competency.

  18. Performance of genotype imputation for rare variants identified in exons and flanking regions of genes.

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    Li Li

    Full Text Available Genotype imputation has the potential to assess human genetic variation at a lower cost than assaying the variants using laboratory techniques. The performance of imputation for rare variants has not been comprehensively studied. We utilized 8865 human samples with high depth resequencing data for the exons and flanking regions of 202 genes and Genome-Wide Association Study (GWAS data to characterize the performance of genotype imputation for rare variants. We evaluated reference sets ranging from 100 to 3713 subjects for imputing into samples typed for the Affymetrix (500K and 6.0 and Illumina 550K GWAS panels. The proportion of variants that could be well imputed (true r(2>0.7 with a reference panel of 3713 individuals was: 31% (Illumina 550K or 25% (Affymetrix 500K with MAF (Minor Allele Frequency less than or equal 0.001, 48% or 35% with 0.0010.05. The performance for common SNPs (MAF>0.05 within exons and flanking regions is comparable to imputation of more uniformly distributed SNPs. The performance for rare SNPs (0.01exon resequencing into additional samples with GWAS data, but imputation of very rare variants (MAF< = 0.005 will require reference panels with thousands of subjects.

  19. Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis

    Directory of Open Access Journals (Sweden)

    Lacombe Didier

    2011-05-01

    Full Text Available Abstract Background Usher syndrome (USH combines sensorineural deafness with blindness. It is inherited in an autosomal recessive mode. Early diagnosis is critical for adapted educational and patient management choices, and for genetic counseling. To date, nine causative genes have been identified for the three clinical subtypes (USH1, USH2 and USH3. Current diagnostic strategies make use of a genotyping microarray that is based on the previously reported mutations. The purpose of this study was to design a more accurate molecular diagnosis tool. Methods We sequenced the 366 coding exons and flanking regions of the nine known USH genes, in 54 USH patients (27 USH1, 21 USH2 and 6 USH3. Results Biallelic mutations were detected in 39 patients (72% and monoallelic mutations in an additional 10 patients (18.5%. In addition to biallelic mutations in one of the USH genes, presumably pathogenic mutations in another USH gene were detected in seven patients (13%, and another patient carried monoallelic mutations in three different USH genes. Notably, none of the USH3 patients carried detectable mutations in the only known USH3 gene, whereas they all carried mutations in USH2 genes. Most importantly, the currently used microarray would have detected only 30 of the 81 different mutations that we found, of which 39 (48% were novel. Conclusions Based on these results, complete exon sequencing of the currently known USH genes stands as a definite improvement for molecular diagnosis of this disease, which is of utmost importance in the perspective of gene therapy.

  20. De novo exonic mutation in MYH7 gene leading to exon skipping in a patient with early onset muscular weakness and fiber-type disproportion.

    Science.gov (United States)

    Pajusalu, Sander; Talvik, Inga; Noormets, Klari; Talvik, Tiina; Põder, Haide; Joost, Kairit; Puusepp, Sanna; Piirsoo, Andres; Stenzel, Werner; Goebel, Hans H; Nikopensius, Tiit; Annilo, Tarmo; Nõukas, Margit; Metspalu, Andres; Õunap, Katrin; Reimand, Tiia

    2016-03-01

    Here we report on a case of MYH7-related myopathy in a boy with early onset of muscular weakness and delayed motor development in infancy. His most affected muscles were neck extensors showing a dropped head sign, proximal muscles of lower limbs with positive Gower's sign, and trunk muscles. Brain and spinal cord MRI scans, echocardiography, and laboratory analyses including creatine kinase and lactate did not reveal any abnormalities. Muscle histopathology showed fiber-type disproportion. Whole exome sequencing of the parents-offspring trio revealed a novel de novo c.5655G>A p.(Ala1885=) synonymous substitution of the last nucleotide in exon 38 of the MYH7 gene. Further RNA investigations proved the skipping of exon 38 (p.1854_1885del). This is a first report of an exon-skipping mutation in the MYH7 gene causing myopathy. This report broadens both the phenotypic and genotypic spectra of MYH7-related myopathies. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Point mutation in exon 4 of presenilin-1 gene and early-onset familial Alzheimer disease

    Institute of Scientific and Technical Information of China (English)

    Yu Liao; Fan Zhao

    2006-01-01

    BACKGROUND:A total of 50 missense mutations of presenilin-1 (PS-1) have been found thus far in early-onset familial Alzheimer disease(EOFAD),PS-1 gene might be a causative gene for Chinese EOFAD.OBJECTIVE:To investigate mutation of PS-1 gene in the blood of Chinese patients with familial Alzheimer disease(FAD).DESIGN:A design with randomized control and repeated sequencing.SETTlNG:Department of Neurology,the Second People's Hospital of Wuxi.PARTICIPANTS:The experiment was carried out in Huaihua Hospital Affiliated to Nanhua University in September 1993.Eight FAD patients were graded as FAD group.There were 6 males and 2 females with the mean age of(36±16)years.The control group was composed of 42 persons,including 8 hospitalized SAD patients diagnosed according to the criteria of Practical Neuralgia and conformed to the revised fourth edition of the Diagnostic and Statistical Manual of Mental Disorders(DCM-Ⅳ-TR),11 dementia patients caused by multipie cerebral infarction,13 normal persons in the FAD family mentioned above family,and 10 normal healthy adults provided by the health examination section of our hospital.METHODS:GeneAmp PCR System 2400 (Applied Biosystems,USA),DNA-Sequencer Model 310(Perkin Elmer,USA),Taq DNA Polymerase(Fermentas,Canada).All reagents used for DNA extraction were prepared with analytical reagents manufactured in China.The samples were stratified carefully,collected the leukocytic cream from the interface,added STMT to each sample and vortexed to suspend evenly.Then the samples were centrifugated.The nuclear pellet was resuspended in digestion solution with proteinase K and incubated under appropriate condition.Genomic DNA was extract with phenol/chloroform,precipitated with dehvdraled ethanol,and washed with 70%sterilized ethanol.Finally,genomic DNA was dissolved in ultra pure water and stored for Iater use.The sequences were 5'-ACT AAC AAT GGA TGA CCT GGT GAA ATC-3'and 3'-ACG GTC TGA CCT AAG TGA ATA GTA GAG-5' to flank the exon 2 of

  2. Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation

    Directory of Open Access Journals (Sweden)

    Coulombe-Huntington Jasmin

    2009-11-01

    Full Text Available Abstract Background The emergence of isoform-sensitive microarrays has helped fuel in-depth studies of the human transcriptome. The Affymetrix GeneChip Human Exon 1.0 ST Array (Exon Array has been previously shown to be effective in profiling gene expression at the isoform level. More recently, the Affymetrix GeneChip Human Gene 1.0 ST Array (Gene Array has been released for measuring gene expression and interestingly contains a large subset of probes from the Exon Array. Here, we explore the potential of using Gene Array probes to assess expression variation at the sub-transcript level. Utilizing datasets of the high quality Microarray Quality Control (MAQC RNA samples previously assayed on the Exon Array and Gene Array, we compare the expression measurements of the two platforms to determine the performance of the Gene Array in detecting isoform variations. Results Overall, we show that the Gene Array is comparable to the Exon Array in making gene expression calls. Moreover, to examine expression of different isoforms, we modify the Gene Array probe set definition file to enable summarization of probe intensity values at the exon level and show that the expression profiles between the two platforms are also highly correlated. Next, expression calls of previously known differentially spliced genes were compared and also show concordant results. Splicing index analysis, representing estimates of exon inclusion levels, shows a lower but good correlation between platforms. As the Gene Array contains a significant subset of probes from the Exon Array, we note that, in comparison, the Gene Array overlaps with fewer but still a high proportion of splicing events annotated in the Known Alt Events UCSC track, with abundant coverage of cassette exons. We discuss the ability of the Gene Array to detect alternative splicing and isoform variation and address its limitations. Conclusion The Gene Array is an effective expression profiling tool at gene and

  3. Acetylcholinesterase (AChE) gene modification in transgenic animals: functional consequences of selected exon and regulatory region deletion.

    Science.gov (United States)

    Camp, Shelley; Zhang, Limin; Marquez, Michael; de la Torre, Brian; Long, Jeffery M; Bucht, Goran; Taylor, Palmer

    2005-12-15

    AChE is an alternatively spliced gene. Exons 2, 3 and 4 are invariantly spliced, and this sequence is responsible for catalytic function. The 3' alternatively spliced exons, 5 and 6, are responsible for AChE disposition in tissue [J. Massoulie, The origin of the molecular diversity and functional anchoring of cholinesterases. Neurosignals 11 (3) (2002) 130-143; Y. Li, S. Camp, P. Taylor, Tissue-specific expression and alternative mRNA processing of the mammalian acetylcholinesterase gene. J. Biol. Chem. 268 (8) (1993) 5790-5797]. The splice to exon 5 produces the GPI anchored form of AChE found in the hematopoietic system, whereas the splice to exon 6 produces a sequence that binds to the structural subunits PRiMA and ColQ, producing AChE expression in brain and muscle. A third alternative RNA species is present that is not spliced at the 3' end; the intron 3' of exon 4 is used as coding sequence and produces the read-through, unanchored form of AChE. In order to further understand the role of alternative splicing in the expression of the AChE gene, we have used homologous recombination in stem cells to produce gene specific deletions in mice. Alternatively and together exon 5 and exon 6 were deleted. A cassette containing the neomycin gene flanked by loxP sites was used to replace the exon(s) of interest. Tissue analysis of mice with exon 5 deleted and the neomycin cassette retained showed very low levels of AChE expression, far less than would have been anticipated. Only the read-through species of the enzyme was produced; clearly the inclusion of the selection cassette disrupted splicing of exon 4 to exon 6. The selection cassette was then deleted in exon 5, exon 6 and exons 5 + 6 deleted mice by breeding to Ella-cre transgenic mice. AChE expression in serum, brain and muscle has been analyzed. Another AChE gene targeted mouse strain involving a region in the first intron, found to be critical for AChE expression in muscle cells [S. Camp, L. Zhang, M. Marquez, B

  4. Sequences and polymorphisms of exons 3 and 4 in porcine UCP2 gene

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Uncoupling proteins are mitochondrial membrane transporters, which regulate metabolic pathways of energy balance, and are associated with biological traits of animal body weight, resting metabolic rates and energy conversion. In this study, a region of the exons 3 and 4 of pig UCP2 gene was cloned and analyzed, and a new single nucleotide polymorphic site was detected by PCR-SSCP in five pig breeds. This newfound polymorphism results from a T to G substitution at the position of nucleotide 272, which is located in intron3.

  5. Deleting exon 55 from the nebulin gene induces severe muscle weakness in a mouse model for nemaline myopathy

    OpenAIRE

    Ottenheijm, Coen A. C.; Buck, Danielle; de Winter, Josine M; Ferrara, Claudia; Piroddi, Nicoletta; Tesi, Chiara; Jasper, Jeffrey R.; Malik, Fady I.; Meng, Hui; Stienen, Ger J. M.; Beggs, Alan H.; Labeit, Siegfried; Poggesi, Corrado; Lawlor, Michael W.; Granzier, Henk

    2013-01-01

    Nebulin—a giant sarcomeric protein—plays a pivotal role in skeletal muscle contractility by specifying thin filament length and function. Although mutations in the gene encoding nebulin (NEB) are a frequent cause of nemaline myopathy, the most common non-dystrophic congenital myopathy, the mechanisms by which mutations in NEB cause muscle weakness remain largely unknown. To better understand these mechanisms, we have generated a mouse model in which Neb exon 55 is deleted (NebΔExon55) to repl...

  6. Accelerated exchange of exon segments in Viperid three-finger toxin genes (Sistrurus catenatus edwardsii; Desert Massasauga

    Directory of Open Access Journals (Sweden)

    Mackessy Stephen P

    2008-07-01

    Full Text Available Abstract Background Snake venoms consist primarily of proteins and peptides showing a myriad of potent biological activities which have been shaped by both adaptive and neutral selective forces. Venom proteins are encoded by multigene families that have evolved through a process of gene duplication followed by accelerated evolution in the protein coding region. Results Here we report five gene structures of three-finger toxins from a viperid snake, Sistrurus catenatus edwardsii. These toxin genes are structured similarly to elapid and hydrophiid three-finger toxin genes, with two introns and three exons. Both introns and exons show distinct patterns of segmentation, and the insertion/deletion of segments may define their evolutionary history. The segments in introns, when present, are highly similar to their corresponding segments in other members of the gene family. In contrast, some segments in the exons show high similarity, while others are often distinctly different among corresponding regions of the isoforms. Conclusion Ordered, conserved exon structure strongly suggests that segments in corresponding regions in exons have been exchanged with distinctly different ones during the evolution of these genes. Such a "switching" of segments in exons may result in drastically altering the molecular surface topology and charge, and hence the molecular targets of these three-finger toxins. Thus the phenomenon of accelerated segment switch in exons to alter targeting (ASSET may play an important role in the evolution of three-finger toxins, resulting in a family of toxins with a highly conserved structural fold but widely varying biological activities.

  7. An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

    Directory of Open Access Journals (Sweden)

    Haddley Kate

    2011-05-01

    Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

  8. DRD2 and DRD4 in relation to regular alcohol and cannabis use among adolescents : Does parenting modify the impact of genetic vulnerability? The TRAILS study

    NARCIS (Netherlands)

    Creemers, H.E.; Harakeh, Z.; Dick, D.M.; Meyers, J.; Vollebergh, W.A.; Ormel, J.; Verhulst, F.C.; Huizink, A.C.

    2011-01-01

    Aims: The aims of the present study were to determine the direct effect of DRD2 and DRD4, as well as their interaction with parenting (i.e. rejection, overprotection and emotional warmth), on the development of regular alcohol and cannabis use in 1192 Dutch adolescents from the general population. M

  9. DRD2 and DRD4 in relation to regular alcohol and cannabis use among adolescents: does parenting modify the impact of genetic vulnerability? The TRAILS study

    NARCIS (Netherlands)

    H.E. Creemers; Z. Harakeh; D.M. Dick; J. Meyers; W.A.M. Vollebergh; J. Ormel; F.C. Verhulst; A.C. Huizink

    2011-01-01

    Aims The aims of the present study were to determine the direct effect of DRD2 and DRD4, as well as their interaction with parenting (i.e. rejection, overprotection and emotional warmth), on the development of regular alcohol and cannabis use in 1192 Dutch adolescents from the general population. Me

  10. DRD2 and DRD4 in relation to regular alcohol and cannabis use among adolescents: Does parenting modify the impact of genetic vulnerability? The TRAILS study

    NARCIS (Netherlands)

    H.E. Creemers (Hanneke); Z. Harakeh (Zeena); D.M. van Dick; J. Meyers; W.A.M. Vollebergh (Wilma); J. Ormel (Johan Hans); F.C. Verhulst (Frank); A.C. Huizink (Anja)

    2010-01-01

    textabstractAims: The aims of the present study were to determine the direct effect of DRD2 and DRD4, as well as their interaction with parenting (i.e. rejection, overprotection and emotional warmth), on the development of regular alcohol and cannabis use in 1192 Dutch adolescents from the general p

  11. Identification of true EST alignments and exon regions of gene sequences

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yanhong; JING Hui; LI Yanen; LIU Huailan

    2004-01-01

    Expressed sequence tags (ESTs), which have piled up considerably so far, provide a valuable resource for finding new genes, disease-relevant genes, and for recognizing alternative splicing variants, SNP sites, etc. The prerequisite for carrying out these researches is to correctly ascertain the gene-sequence-related ESTs. Based on analysis of the alignment results between some known gene sequences and ESTs in public database, several measures including Identity Check, Gap Check, Inclusion Check and Length Check have been introduced to judge whether an EST alignment is related to a gene sequence or not. A computational program EDSAc1.0 has been developed to identify true EST alignments and exon regions of query gene sequences. When tested with human gene sequences in the standard dataset HMR195 and evaluated with the standard measures of gene prediction performance, EDSAc1.0 can identify protein- coding regions with specificity of 0.997 and sensitivity of 0.88 at the nucleotide level, which outperform that of the counterpart TAP. A web server of EDSAc1.0 is available at http://infosci.hust.edu.cn.

  12. Screening the dystrophin gene suggests a high rate of polymorphism in general but no exonic deletions in schizophrenics

    Energy Technology Data Exchange (ETDEWEB)

    Lindor, N.M.; Sobell, J.L.; Thibodeau, S.N. [Mayo Clinic/Foundation, Rochester, MN (United States)] [and others

    1994-03-15

    The dystrophin gene, located at chromosome Xp21, was evaluated as a candidate gene in chronic schizophrenia in response to the report of a large family in which schizophrenia cosegregated with Becker muscular dystrophy. Genomic DNA from 94 men with chronic schizophrenia was evaluated by Southern blot analysis using cDNA probes that span exons 1-59. No exonic deletions were identified. An unexpectedly high rate of polymorphism was calculated in this study and two novel polymorphisms were found, demonstrating the usefulness of the candidate gene approach even when results of the original study are negative. 41 refs., 1 fig., 4 tabs.

  13. Detection of c-kit gene mutations in Exon 11 of Leukemias

    Directory of Open Access Journals (Sweden)

    Syed Rizwan Hussain

    2012-03-01

    Full Text Available METHODS: In order to determine the frequency of mutations of Exon 11 of c-kit gene in 50 Leukemia cases (31 samples Acute Myeloid Leukemia, 5 samples Acute Lymphoblastic Leukemia, 9 samples Chronic Myeloid Leukemia and 5 samples Chronic Lymphocytic Leukemia, we have done PCR-SSCP followed by direct DNA sequencing. RESULTS: Of 50 Leukemia cases, 28 were male and 22 were female with ages ranging from 2 to 65 years. The mean age of cases was 31.88 years. We have detected total twenty mutations in nineteen cases that include Lys550Asn, Tyr568Ser, Ile571Thr, Thr574Pro, Gln575His, Tyr578Pro, Asp579His, His580Gln, Arg586Thr, Asn587Asp and Arg588Met as well as novel point mutations at codons Ile563Lys, Val569Leu, Tyr570Ser, and Pro577Ser. Ile571Leu substitution is found in two independent cases whereas Trp582Ser substitution is found in three individual cases. CONCLUSION: These observations suggest that mutations in exon 11 of the c-kit gene might represent useful molecular genetic markers in Leukemia.

  14. Specific Genes Associated with Adverse Events of Methylphenidate Use in the Pediatric Population

    DEFF Research Database (Denmark)

    Joensen, Beinta; Meyer, Morten; Aagaard, Lise

    2017-01-01

    were significantly associated with the following genes: appetite reduction (CES1*G); buccal-lingual movements (T1065G); diastolic blood pressure (ADRA2A Mspl C/C-GC); emotionality (DAT1*9/9); irritability (SNAP25 T1065G); picking (DRD4*7/DRD4*4); social withdrawal (DRD4*7/DRD4*4); somatic complaints....... They included small patient samples, poorly standardized treatment regimens, and limited outcome assessments. In the future, more pharmacogenomic studies in ADHD are needed, preferably using randomized, controlled study designs and of longer duration (more than 6 months)....

  15. Dietary Methionine Affect Meat Qulity and Myostatin Gene Exon 1 Region Methylation in Skeletal Muscle Tissues of Broilers

    Institute of Scientific and Technical Information of China (English)

    LIU Guo-qing; ZONG Kai; ZHANG Li-li; CAO Shu-qing

    2010-01-01

    Dietary amino acids imbalance will result in stunted broiler performance and deteriorated meat quality,which are involved in various biochemical cycles in vivo.In this study,the effects of dietary methionine on meat quality and methylation of myostatin exon 1 were investigated.Drip loss of the broilers fed with diet of high methionine levels(0.2%)increased from(6.3±0.1)%(control group)to(10.1±1.0)%,and the muscle shearing force increased from(22.8±1.9)N(control group)to(26.3±2.3)N.Moreover,many CpG sites were found at the myostatin exon 1 region(nucleotides 2360-2540 bp).To further understand the regulation of broiler myostatin expression,the methylation status of broiler myostatin exon 1 and its mRNA expression were analyzed.At the myostatin exon 1 region where CG enriches(nucleotides 2360-2540 bp),the percentages of methylation were 46 and 84% in low Met and high Met content groups after 55-d feeding,respectively.In skeletal muscle tissues,the exon 1 hypermethylation status of myostatin gene was found to be negatively correlated with the gene expression.These results suggested that methylation of this gene is a dynamic process,which plays a dominant role in regulating gene expression for development of individuals.

  16. DETECTION OF POINT MUTATIONS IN EXON 2 OF THE G6PD GENE IN CHINESE G6PD VARIANTS

    Institute of Scientific and Technical Information of China (English)

    许卫明; 王菁; 华小云; 杜传书

    1994-01-01

    In the past few years,a total of 6 different mutations of the G6PD gene have been reported in china.One of these,the C6 mutation(A95→G),accounted for about 15.4% of the Chinese G6PD variants.In ordet to develop a strategy for rapid detection of mutation-containing exons of the G6PD gene,we applied the single-strand confor-mation polymorphism(SSCP)technique to the detection of mutations in exon 2 of this gene.We observed four pa-tients with abnormal migration patterns of the exon 2 band among 20 cases of G6PD variants.Direct PCR se-quencing confirmed a Tto C substitution in exon 2 that has previously been reported.This procedure is therefore of particular importance for the rapid detection of mutation-containing exons in the G6PD gene.

  17. An exonic insertion within Tex14 gene causes spermatogenic arrest in pigs

    Directory of Open Access Journals (Sweden)

    Sironen Anu

    2011-12-01

    Full Text Available Abstract Background Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Sperm development is a complex process, where diploid spermatogonia develop into haploid, highly specialized spermatozoa. Correct expression and function of various genes and their protein products are required for production of fertile sperm. We have identified an infertility defect in Finnish Yorkshire boars caused by spermatogenic arrest. The aim of this study was to locate the disease associated region using genome wide screen with the PorcineSNP60 Beadchip and identify the causal mutation by candidate gene approach. Results In the Finnish Yorkshire pig population the spermatogenic arrest (SA defect appears to be of genetic origin and causes severe degeneration of germ cells and total absence of spermatozoa. Genome wide scan with the PorcineSNP60 Beadchip localized the SA defect to porcine chromosome 12 in a 2 Mbp region. Sequencing of a candidate gene Tex14 revealed a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon. The expression of Tex14 was markedly down regulated in the testis of a SA affected boar compared to control boars and no protein product was identified by Western blotting. The SA insertion sequence was also found within intron 27 in all analyzed animals, thus the insertion appears to be a possible duplication event. Conclusion In this study we report the identification of a causal mutation for infertility caused by spermatogenic arrest at an early meiotic phase. Our results highlight the role of TEX14 specifically in spermatogenesis and the importance of specific genomic remodeling events as causes for inherited defects.

  18. NUCLEOTIDE-SEQUENCE OF THE LAST EXON OF THE GENE FOR HUMAN CYTOCHROME-C-OXIDASE SUBUNIT-VIB AND ITS FLANKING REGIONS

    NARCIS (Netherlands)

    TAANMAN, JW; SCHRAGE, C; BOKMA, E; REUVEKAMP, P; AGSTERIBBE, E; DEVRIES, H

    1991-01-01

    A human genomic clone encompassing the last exon of the gene for cytochrome c oxidase subunit VIb and a human genomic clone containing the most distal end of this gene were characterized. The last exon of the gene codes for the 17 C-terminal amino acid residues of the subunit and the 3' noncoding re

  19. POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation.

    Science.gov (United States)

    Johansson, Anna-Mia; Stenberg, Per; Pettersson, Fredrik; Larsson, Jan

    2007-11-01

    Two specific chromosome-targeting and gene regulatory systems are present in Drosophila melanogaster. The male X chromosome is targeted by the male-specific lethal complex believed to mediate the 2-fold up-regulation of the X-linked genes, and the highly heterochromatic fourth chromosome is specifically targeted by the Painting of Fourth (POF) protein, which, together with heterochromatin protein 1 (HP1), modulates the expression level of genes on the fourth chromosome. Here we use chromatin immunoprecipitation and tiling microarray analysis to map POF and HP1 on the fourth chromosome in S2 cells and salivary glands at high resolution. The enrichment profiles were complemented by transcript profiles to examine the link between binding and transcripts. The results show that POF specifically binds to genes, with a strong preference for exons, and the HP1 binding profile is a mirror image of POF, although HP1 displays an additional "peak" in the promoter regions of bound genes. HP1 binding within genes is much higher than the basal HP1 enrichment on Chromosome 4. Our results suggest a balancing mechanism for the regulation of the fourth chromosome where POF and HP1 competitively bind at increasing levels with increased transcriptional activity. In addition, our results contradict transposable elements as a major nucleation site for HP1 on the fourth chromosome.

  20. POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation.

    Directory of Open Access Journals (Sweden)

    Anna-Mia Johansson

    2007-11-01

    Full Text Available Two specific chromosome-targeting and gene regulatory systems are present in Drosophila melanogaster. The male X chromosome is targeted by the male-specific lethal complex believed to mediate the 2-fold up-regulation of the X-linked genes, and the highly heterochromatic fourth chromosome is specifically targeted by the Painting of Fourth (POF protein, which, together with heterochromatin protein 1 (HP1, modulates the expression level of genes on the fourth chromosome. Here we use chromatin immunoprecipitation and tiling microarray analysis to map POF and HP1 on the fourth chromosome in S2 cells and salivary glands at high resolution. The enrichment profiles were complemented by transcript profiles to examine the link between binding and transcripts. The results show that POF specifically binds to genes, with a strong preference for exons, and the HP1 binding profile is a mirror image of POF, although HP1 displays an additional "peak" in the promoter regions of bound genes. HP1 binding within genes is much higher than the basal HP1 enrichment on Chromosome 4. Our results suggest a balancing mechanism for the regulation of the fourth chromosome where POF and HP1 competitively bind at increasing levels with increased transcriptional activity. In addition, our results contradict transposable elements as a major nucleation site for HP1 on the fourth chromosome.

  1. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

    Full Text Available BACKGROUND: Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals. CONCLUSIONS/SIGNIFICANCE: Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

  2. Polymorphysims of Gene in the Exons Were Associated with the Reproductive Endocrine of Japanese Flounder (

    Directory of Open Access Journals (Sweden)

    R. Q. Ma

    2012-06-01

    Full Text Available The cytochrome P450c17-I (CYP17-I is one of the enzymes critical to gonadal development and the synthesis of androgens. Two single nucleotide polymorphisms (SNPs were detected within the coding region of the CYP17-I gene in a population of 75 male Japanese flounder (Paralichthys olivaceus. They were SNP1 (c.C445T located in exon2 and SNP2 (c.T980C (p.Phe307Leu located in exon5. Four physiological indices, which were serum testosterone (T, serum 17β-estradiol (E2, Hepatosomatic index (HSI, and Gonadosomatic index (GSI, were studied to examine the effect of the two SNPs on the reproductive endocrines of Japanese flounder. Multiple comparisons revealed that CT genotype of SNP1 had a much lower T level than CC genotype (p<0.05 and the GSI of individuals with CC genotype of SNP2 was higher than those with TT genotype (p<0.05. Four diplotypes were constructed based on the two SNPs and the diplotype D3 had a significantly lower T level and GSI. In conclusion, the two SNPs were significantly associated with reproductive traits of Japanese flounder.

  3. Characterization of a silencer element in the first exon of the human osteocalcin gene.

    Science.gov (United States)

    Li, Y P; Chen, W; Stashenko, P

    1995-01-01

    Osteocalcin, the major non-collagenous protein in bone, is transcribed in osteoblasts at the onset of extracellular matrix mineralization. In this study it was demonstrated that sequences located in the first exon of the human osteocalcin gene possess a differentiation-related osteocalcin silencer element (OSE). Osteocalcin was rendered transcribable in UMR-106 cells and proliferating normal osteoblasts after deletion of the -3 to +51 region. Site-specific mutagenesis of this region revealed that a 7 bp sequence (TGGCCCT) (+29 to +35) is critical for silencing function. Mobility shift assays demonstrated that a nuclear factor bound to the OSE. The OSE binding protein was present in proliferating normal pre-osteoblasts and in UMR-106 and ROS 17/2.8 osteosarcoma cells, but was absent from post-proliferative normal osteoblasts. The binding protein was inhibited by fragments containing the +29/+35 sequence, but not by other promoter fragments or by the consensus oligomers of unrelated nuclear factors AP-1 and Sp1. DNase 1 footprinting demonstrated that the OSE binding-protein protected the +17 to +36 portion of the first exon, consistent with the results of mapping studies and competitive mobility shift assays. It is hypothesized that this silencer is activated by complexing of the OSE binding protein to the OSE during the osteoblast proliferation stage and that the OSE binding protein is down-regulated at the onset of extracellular matrix mineralization. Images PMID:8559666

  4. Genetic variation in exon 5 of troponin - I gene in hypertrophic cardiomyopathy cases

    Directory of Open Access Journals (Sweden)

    Annapurna S

    2007-01-01

    Full Text Available Background: Cardiomyopathies are a heterogeneous group of heart muscle disorders and are classified as 1 Hypertrophic Cardiomyopathy (HCM 2 Dilated cardiomyopathy (DCM 3 Restrictive cardiomyopathy (RCM and 4 Arrhythmogenic right ventricular dysplasia (ARVD as per WHO classification, of which HCM and DCM are common. HCM is a complex but relatively common form of inherited heart muscle disease with prevalence of 1 in 500 individuals and is commonly associated with sarcomeric gene mutations. Cardiac muscle troponin I (TNNI-3 is one such sarcomeric protein and is a subunit of the thin filament-associated troponin-tropomyosin complex involved in calcium regulation of skeletal and cardiac muscle contraction. Mutations in this gene were found to be associated with a history of sudden cardiac death in HCM patients. Aim: Therefore the present study aims to identify for mutations associated with troponin I gene in a set of HCM patients from Indian population. Materials and Methods: Mutational analyses of 92 HCM cases were carried out following PCR based SSCP analysis. Results: The study revealed band pattern variation in 3 cases from a group of 92 HCM patients. This band pattern variation, on sequencing revealed base changes, one at nt 2560 with G>T transversion in exon-5 region with a wobble and others at nt 2479 and nt 2478 with G>C and C>G transversions in the intronic region upstream of the exon 5 on sequencing. Further analysis showed that one of the probands showed apical form of hypertrophy, two others showing asymmetric septal hypertrophy. Two of these probands showed family history of the condition. Conclusions: Hence, the study supports earlier reports of involvement of TNNI-3 in the causation of apical and asymmetrical forms of hypertrophy.

  5. A novel break point of the BMPR2 gene exonic deletion in a patient with pulmonary arterial hypertension.

    Science.gov (United States)

    Aimi, Yuki; Hirayama, Tomomi; Kataoka, Masaharu; Momose, Yuichi; Nishimaki, Saiko; Matsushita, Kenichi; Yoshino, Hideaki; Satoh, Toru; Gamou, Shinobu

    2013-12-01

    The presence of genetic rearrangements of bone morphogenetic protein type 2 receptor (BMPR2) was identified in pulmonary arterial hypertension (PAH) patients as the deletion or duplication of one or more exons of the gene. We recently investigated the deletion break points in exonic deletions of BMPR2 in two Japanese familial cases with PAH, and found that these were Alu-mediated via either non-allelic homologous recombination or non-homologous recombination. We herein report the third case of exonic deletion, which was in a 25-year-old female PAH patient with a deletion of BMPR2 exon 3. The break point in this case was not located in an Alu sequence. The 5'- and 3'-break point maps between the inverted Alu sequences in intron 2 and in exon 3, respectively, resulted in a 759-bp deletion. This novel exonic deletion in this PAH case may be a unique and non-recurrent rearrangement, and appears to be of a different size from that in other patients.

  6. Positive Darwinian selection in Vipera palaestinae phospholipase A2 genes is unexpectedly limited to the third exon.

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    Kordis, D; Bdolah, A; Gubensek, F

    1998-10-20

    The venom of Vipera palaestinae contains a two-component toxin, consisting of an acidic phospholipase A2 (PLA2) and a basic protein. Here we report the cloning and sequence analysis of the complete V. palaestinae PLA2 genes. Since in all Viperidae PLA2 multigene families the 5' and 3' flanking regions are highly conserved, we designed oligonucleotide primers that allow amplification of the whole PLA2 multigene family in a single step. The structural organization of both genes is the same as in the Vipera ammodytes PLA2 multigene family, there being five exons separated by four introns. Comparison of V. palaestinae PLA2 genes with other Viperidae PLA2 genes has shown that the structural organization of the genes and the nucleotide sequence of all introns and flanking regions are highly conserved, whereas the third exon clearly shows a higher number of amino acid replacements, an indication of positive Darwinian selection. The positive Darwinian selection is surprisingly limited to the third exon, in contrast to other Viperidae PLA2 genes, where it is present in all mature protein coding exons. Copyright 1998 Academic Press.

  7. Three types of polymorphisms in exon 14 in porcine Mx1 gene.

    Science.gov (United States)

    Morozumi, T; Sumantri, C; Nakajima, E; Kobayashi, E; Asano, A; Oishi, T; Mitsuhashi, T; Watanabe, T; Hamasima, N

    2001-08-01

    Much is known about the antiviral activity of Mx proteins in species such as mouse and human. In the mouse, loss of resistability to influenza virus has been shown to be due to specific polymorphisms in the Mx gene. This gene is therefore an interesting candidate gene for disease resistance in farm animals. The porcine Mx1 gene has already been identified and characterized based on its homology with mouse Mx1; however, until now no evidence of polymorphisms in the porcine gene has been reported. In this study, we have found two new polymorphisms in exon 14 of porcine Mx1 by DNA sequencing and confirmed their presence in different breeds, using polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) with NarI and NaeI restriction enzymes. On the basis of the deduced amino acid sequence, one allele contains a deletion that may result in a frameshift to yield several amino acid substitutions and extension of the carboxyl terminal region of Mx1 protein. The deletion allele, Mx1c, was found to be segregating in Landrace, Berkshire, Duroc, Hampshire, and Yucatan miniature pig. A second point mutation, Mx1b, was detected in Meishan and two Vietnamese native pig breeds. All other breeds tested were fixed for the Mx1a allele that is identical to the sequence reported previously. It will be interesting to determine if the Mx1c deletion is associated with variation in resistance to the myxovirus family in the pig.

  8. Polymorphism in exon2 of BMP15 gene in Iranian sangsari sheep

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    zana pirkhezranian

    2015-04-01

    Full Text Available Fertility rate is an economically important trait in sheep, which is influenced by genetic and environment. So far, three genes have been identified that affects this trait, one of them would be the BMP family, the most famous one is BMP15. Different mutations in the BMP15 gene, increases reproductive performance and growth rate in sheep. The aim of this study was to investigate the genetic and phylogenetic of BMP15 gene sequence in Iranian Sangsari sheep. For this purpose, the blood samples from 20 animal of Damghan station were collected. After DNA extracting, a segment of 222 bp of exon 2 of BMP15 gene was amplified using polymerase chain reaction. Then, all of the PCR products were sequenced. The results showed existence of four haplotypes and three significant mutations of the gene that which one of them was seen for first. In order to determine the genetic distance of Sansari sheep with other animals especially sheep breeds about 103 sequences were taken from Genebank, Then, phylogenetic trees were drawn. Genetic distances and nucleotide differences were calculated. The results showed that goat, cattle and buffalo have minimum genetic distance and monkey, human and mouse have maximum distance with Sangsari sheep and native Hindi and Kashmiri sheep have not any differences with Iranian Sangsari sheep.

  9. The interplay of birthweight, DRD4 and early maternal care in the prediction of disorganized attachment at 36 months of age

    Science.gov (United States)

    Wazana, Ashley; Moss, Ellen; Jolicoeur-Martineau, Alexis; Graffi, Justin; Tsabari, Gal; Lecompte, Vanessa; Pascuzzo, Katherine; Babineau, Vanessa; Gordon-Green, Cathryn; Mileva, Viara; Atkinson, Leslie; Minde, Klaus; Bouvette-Turcot, Andrée-Anne; Sassi, Roberto; St-André, Martin; Carrey, Normand; Matthews, Stephen; Sokolowski, Marla; Lydon, John; Gaudreau, Helene; Steiner, Meir; Kennedy, James L.; Fleming, Alison; Levitan, Robert; Meaney, Michael J

    2017-01-01

    Background Disorganized attachment is an important early risk factor for socio-emotional problems throughout childhood and into adulthood. Prevailing models of the etiology of disorganized attachment emphasize the role of highly dysfunctional parenting, to the exclusion of complex models examining the interplay of child and parental factors. Decades of research have established that extreme child birth weight may have long-term effects on developmental processes. These effects are typically negative, but this is not always the case. Recent studies have also identified the dopamine D4 receptor (DRD4) as a moderator of childrearing effects on the development of disorganized attachment. However, there are inconsistent findings concerning which variant of the polymorphism (7-repeat long-form allele or non 7-repeat short form) is most likely to interact with caregiving in predicting disorganized versus organized attachment. In this study we examined possible 2- and 3-way interactions between child DRD4 polymorphisms and birth weight and maternal caregiving at age 6 months in longitudinally predicting attachment disorganization at 36 months. Method Our sample is from the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) project, a sample of 650 mother-child dyads. Birth weight was cross-referenced with normative data to calculate birth weight percentile. Infant DRD4 was obtained with buccal swabs and categorized according to the presence of the putative allele 7-Repeat. Macro-analytic and a micro-analytic measures of maternal behavior were extracted from a videotaped session of 20-minutes of non-feeding interaction followed by a 10-minute divided attention maternal task at 6 months. Attachment was assessed at 36 months using the Strange Situation Procedure, and categorized into disorganized attachment and others. Results Results indicated that a main effect for DRD4 and a two-way interaction of birth weight and 6 month maternal attention (frequency of

  10. Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts

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    Herington Adrian C

    2007-08-01

    Full Text Available Abstract Background Ghrelin is a multifunctional peptide hormone expressed in a range of normal tissues and pathologies. It has been reported that the human ghrelin gene consists of five exons which span 5 kb of genomic DNA on chromosome 3 and includes a 20 bp non-coding first exon (20 bp exon 0. The availability of bioinformatic tools enabling comparative analysis and the finalisation of the human genome prompted us to re-examine the genomic structure of the ghrelin locus. Results We have demonstrated the presence of an additional novel exon (exon -1 and 5' extensions to exon 0 and 1 using comparative in silico analysis and have demonstrated their existence experimentally using RT-PCR and 5' RACE. A revised exon-intron structure demonstrates that the human ghrelin gene spans 7.2 kb and consists of six rather than five exons. Several ghrelin gene-derived splice forms were detected in a range of human tissues and cell lines. We have demonstrated ghrelin gene-derived mRNA transcripts that do not code for ghrelin, but instead may encode the C-terminal region of full-length preproghrelin (C-ghrelin, which contains the coding region for obestatin and a transcript encoding obestatin-only. Splice variants that differed in their 5' untranslated regions were also found, suggesting a role of these regions in the post-transcriptional regulation of preproghrelin translation. Finally, several natural antisense transcripts, termed ghrelinOS (ghrelin opposite strand transcripts, were demonstrated via orientation-specific RT-PCR, 5' RACE and in silico analysis of ESTs and cloned amplicons. Conclusion The sense and antisense alternative transcripts demonstrated in this study may function as non-coding regulatory RNA, or code for novel protein isoforms. This is the first demonstration of putative obestatin and C-ghrelin specific transcripts and these findings suggest that these ghrelin gene-derived peptides may also be produced independently of preproghrelin

  11. Single nucleotide polymorphism mining and nucleotide sequence analysis of Mx1 gene in exonic regions of Japanese quail

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    Diwesh Kumar Niraj

    2015-12-01

    Full Text Available Aim: An attempt has been made to study the Myxovirus resistant (Mx1 gene polymorphism in Japanese quail. Materials and Methods: In the present, investigation four fragments viz. Fragment I of 185 bp (Exon 3 region, Fragment II of 148 bp (Exon 5 region, Fragment III of 161 bp (Exon 7 region, and Fragment IV of 176 bp (Exon 13 region of Mx1 gene were amplified and screened for polymorphism by polymerase chain reaction-single-strand conformation polymorphism technique in 170 Japanese quail birds. Results: Out of the four fragments, one fragment (Fragment II was found to be polymorphic. Remaining three fragments (Fragment I, III, and IV were found to be monomorphic which was confirmed by custom sequencing. Overall nucleotide sequence analysis of Mx1 gene of Japanese quail showed 100% homology with common quail and more than 80% homology with reported sequence of chicken breeds. Conclusion: The Mx1 gene is mostly conserved in Japanese quail. There is an urgent need of comprehensive analysis of other regions of Mx1 gene along with its possible association with the traits of economic importance in Japanese quail.

  12. Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients.

    Science.gov (United States)

    Miyagawa, Maiko; Naito, Takehiko; Nishio, Shin-ya; Kamatani, Naoyuki; Usami, Shin-ichi

    2013-01-01

    Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30-40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss.

  13. Sequence polymorphism of PrP exon 3 gene in Istrian and crossbred sheep

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    Ino Curik

    2010-01-01

    Full Text Available Polymorphisms in sheep PrP (prion protein gene are known for scrapie susceptibility. We sequenced part of PrP exon 3 gene in 92 autochthonous Istrian (IS and 38 crossbred sheep (CBS. ARQ, ARR and AHQ alleles were predominant with frequency of 0.674 (0.526, 0.228 (0.132 and 0.082 (0.263 in IS (CBS, respectively, while VRQ (0.011 in IS and ARH (0.005 in IS and 0.079 in CBS alleles were rare. We also found non-synonymous mutations at codons 112 (M→T, 127 (G→S and 143 (H→R, and synonymous mutations at codons 231 (R and 237 (L. Additional mutations were associated only with AHQ, ARH and ARQ alleles. The polymorphism of PrP gene in IS was not critical with respect to scrapie susceptibility and with some efforts number of “favourable” genotypes can be increased.

  14. Deleting exon 55 from the nebulin gene induces severe muscle weakness in a mouse model for nemaline myopathy.

    Science.gov (United States)

    Ottenheijm, Coen A C; Buck, Danielle; de Winter, Josine M; Ferrara, Claudia; Piroddi, Nicoletta; Tesi, Chiara; Jasper, Jeffrey R; Malik, Fady I; Meng, Hui; Stienen, Ger J M; Beggs, Alan H; Labeit, Siegfried; Poggesi, Corrado; Lawlor, Michael W; Granzier, Henk

    2013-06-01

    Nebulin--a giant sarcomeric protein--plays a pivotal role in skeletal muscle contractility by specifying thin filament length and function. Although mutations in the gene encoding nebulin (NEB) are a frequent cause of nemaline myopathy, the most common non-dystrophic congenital myopathy, the mechanisms by which mutations in NEB cause muscle weakness remain largely unknown. To better understand these mechanisms, we have generated a mouse model in which Neb exon 55 is deleted (Neb(ΔExon55)) to replicate a founder mutation seen frequently in patients with nemaline myopathy with Ashkenazi Jewish heritage. Neb(ΔExon55) mice are born close to Mendelian ratios, but show growth retardation after birth. Electron microscopy studies show nemaline bodies--a hallmark feature of nemaline myopathy--in muscle fibres from Neb(ΔExon55) mice. Western blotting studies with nebulin-specific antibodies reveal reduced nebulin levels in muscle from Neb(ΔExon55) mice, and immunofluorescence confocal microscopy studies with tropomodulin antibodies and phalloidin reveal that thin filament length is significantly reduced. In line with reduced thin filament length, the maximal force generating capacity of permeabilized muscle fibres and single myofibrils is reduced in Neb(ΔExon55) mice with a more pronounced reduction at longer sarcomere lengths. Finally, in Neb(ΔExon55) mice the regulation of contraction is impaired, as evidenced by marked changes in crossbridge cycling kinetics and by a reduction of the calcium sensitivity of force generation. A novel drug that facilitates calcium binding to the thin filament significantly augmented the calcium sensitivity of submaximal force to levels that exceed those observed in untreated control muscle. In conclusion, we have characterized the first nebulin-based nemaline myopathy model, which recapitulates important features of the phenotype observed in patients harbouring this particular mutation, and which has severe muscle weakness caused by

  15. Deletion of twenty seven nucleotides within exon 11 of the band 3 gene identified in ovalocytosis in Lombok Island, Indonesia.

    Science.gov (United States)

    Alimsardjono, H; Mukono, I S; Dachlan, Y P; Matsuo, M

    1997-03-01

    This study reports the molecular characterization of ovalocytosis in Lombok Island, Indonesia. The analysis of genomic DNA by polymerase chain reaction shows that all 21 ovalocytotic individuals have two amplified products of different size from a region encompassing exon 11 of the band 3 gene. The sequence of the larger product matched perfectly with that of normal individuals. In the sequence of the smaller product, 27 nucleotides within exon 11 were deleted. The heterozygous presence of the deletion identified in other parts of Southeast Asia was confirmed in patients with ovalocytosis in an isolated island of eastern Indonesia.

  16. The multifunctional peptidylglycine alpha-amidating monooxygenase gene: exon/intron organization of catalytic, processing, and routing domains.

    Science.gov (United States)

    Ouafik, L H; Stoffers, D A; Campbell, T A; Johnson, R C; Bloomquist, B T; Mains, R E; Eipper, B A

    1992-10-01

    Peptidylglycine alpha-amidating monooxygenase (PAM; EC 1.14.17.3) is a multifunctional protein containing two enzymes that act sequentially to catalyze the alpha-amidation of neuroendocrine peptides. Peptidylglycine alpha-hydroxylating monooxygenase (PHM) catalyzes the first step of the reaction and is dependent on copper, ascorbate, and molecular oxygen. Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) catalyzes the second step of the reaction. Previous studies demonstrated that alternative splicing results in the production of bifunctional PAM proteins that are integral membrane or soluble proteins as well as soluble monofunctional PHM proteins. Rat PAM is encoded by a complex single copy gene that consists of 27 exons and encompasses more than 160 kilobases (kb) of genomic DNA. The 12 exons comprising PHM are distributed over at least 76 kb genomic DNA and range in size from 49-185 base pairs; four of the introns within the PHM domain are over 10 kb in length. Alternative splicing in the PHM region can result in a truncated, inactive PHM protein (rPAM-5), or a soluble, monofunctional PHM protein (rPAM-4) instead of a bifunctional protein. The eight exons comprising PAL are distributed over at least 19 kb genomic DNA. The exons encoding PAL range in size from 54-209 base pairs and have not been found to undergo alternative splicing. The PHM and PAL domains are separated by a single alternatively spliced exon surrounded by lengthy introns; inclusion of this exon results in the production of a form of PAM (rPAM-1) in which endoproteolytic cleavage at a paired basic site can separate the two catalytic domains. The exon following the PAL domain encodes the trans-membrane domain of PAM; alternative splicing at this site produces integral membrane or soluble PAM proteins. The COOH-terminal domain of PAM is comprised of a short exon subject to alternative splicing and a long exon encoding the final 68 amino acids present in all bifunctional PAM proteins along

  17. Single exon mutation in arylsulfatase A gene has two effects: loss of enzyme activity and aberrant splicing.

    Science.gov (United States)

    Hasegawa, Y; Kawame, H; Ida, H; Ohashi, T; Eto, Y

    1994-04-01

    The arylsulfatase A gene of a Japanese patient who has the juvenile form of metachromatic leukodystrophy, and who has been previously reported as a heterozygote of the 1070A mutation, was investigated. Nucleotide sequence analysis revealed the presence of a previously unreported C-to-T substitution (designated 2330T), 22 nucleotides downstream from the exon 8 splice acceptor site. Although the 2330T mutation itself results in a single amino acid substitution of Thr409 by Ile, the analysis of the patient's cDNA fragments amplified by the reverse transcription-polymerase chain reaction revealed that transcripts of the 2330T allele were spliced both normally and aberrantly. The aberrant splicing produced a 27-nucleotide deletion from the usual exon 8 splice acceptor site. These results indicate that the new mutation is a rare case of an exon mutation affecting splice site selection. The mechanism of this aberrant pre-mRNA splicing is discussed.

  18. The relationship between gene isoform multiplicity, number of exons and protein divergence.

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    Jordi Morata

    Full Text Available At present we know that phenotypic differences between organisms arise from a variety of sources, like protein sequence divergence, regulatory sequence divergence, alternative splicing, etc. However, we do not have yet a complete view of how these sources are related. Here we address this problem, studying the relationship between protein divergence and the ability of genes to express multiple isoforms. We used three genome-wide datasets of human-mouse orthologs to study the relationship between isoform multiplicity co-occurrence between orthologs (the fact that two orthologs have more than one isoform and protein divergence. In all cases our results showed that there was a monotonic dependence between these two properties. We could explain this relationship in terms of a more fundamental one, between exon number of the largest isoform and protein divergence. We found that this last relationship was present, although with variations, in other species (chimpanzee, cow, rat, chicken, zebrafish and fruit fly. In summary, we have identified a relationship between protein divergence and isoform multiplicity co-occurrence and explained its origin in terms of a simple gene-level property. Finally, we discuss the biological implications of these findings for our understanding of inter-species phenotypic differences.

  19. Random Splicing of Several Exons Caused by a Single Base Change in the Target Exon of CRISPR/Cas9 Mediated Gene Knockout

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    Marcel Kapahnke

    2016-12-01

    Full Text Available The clustered regularly interspaced short palindromic repeats (CRISPR-associated sequence 9 (CRISPR/Cas9 system is widely used for genome editing purposes as it facilitates an efficient knockout of a specific gene in, e.g. cultured cells. Targeted double-strand breaks are introduced to the target sequence of the guide RNAs, which activates the cellular DNA repair mechanism for non-homologous-end-joining, resulting in unprecise repair and introduction of small deletions or insertions. Due to this, sequence alterations in the coding region of the target gene frequently cause frame-shift mutations, facilitating degradation of the mRNA. We here show that such CRISPR/Cas9-mediated alterations in the target exon may also result in altered splicing of the respective pre-mRNA, most likely due to mutations of splice-regulatory sequences. Using the human FLOT-1 gene as an example, we demonstrate that such altered splicing products also give rise to aberrant protein products. These may potentially function as dominant-negative proteins and thus interfere with the interpretation of the data generated with these cell lines. Since most researchers only control the consequences of CRISPR knockout at genomic and protein level, our data should encourage to also check the alterations at the mRNA level.

  20. Identification of two point mutations and a one base deletion in exon 19 of the dystrophin gene by heteroduplex formation.

    Science.gov (United States)

    Prior, T W; Papp, A C; Snyder, P J; Burghes, A H; Sedra, M S; Western, L M; Bartello, C; Mendell, J R

    1993-03-01

    Two thirds of the Duchenne muscular dystrophy population have either gene deletions or duplications. The nondeletion/duplication cases are most likely the result of point mutations or small deletions and duplications that cannot be easily identified by current strategies. The major obstacle in identifying small mutations is due to the large size of the dystrophin gene. We selectively screened 5 DMD exons containing CpG dinucleotides in 110 DMD patients without detectable deletions or duplications. Nonsenses mutations are frequently due to a C- to -T transition within a CG dinucleotide pair. To screen for the nonsense mutations, we used the heteroduplex method. Utilizing this approach, we identified 2 different nonsense mutations and a single base deletion all occurring in exon 19. This is the first report of a clustering of small mutations in the dystrophin gene.

  1. Polymorphism analysis of IGFBP-5 gene exon 1 in Tibet Mini-pig and Junmu No. 1 White pig.

    Science.gov (United States)

    Chen, A; Hao, L L; Fang, X B; Lu, K; Liu, S C; Zhang, Y L

    2014-03-12

    The genetic resources and the mechanism of miniaturization in the Tibet Mini-pig have not been comprehensively studied. Polymorphisms in genes related to the insulin-like growth factor (IGF) axis have been investigated for years, but few on the polymorphism of IGF-binding protein-5 (IGFBP-5) in the Tibetan pig. In this study, allele-specific polymerase chain reaction (AS-PCR) was used to analyze polymorphisms in exon 1 of the IGFBP-5 gene in two pig breeds, Tibet Mini-pigs and Junmu No. 1 White pigs. A BLAST analysis of the expressed sequence tags in the porcine IGFBP-5 gene revealed that exon 1 of this gene has two single nucleotide polymorphisms (SNPs), G188T and G503A. The AS-PCR results demonstrated that in both pig breeds examined, the TT, GT, and GG genotypes existed at the G188T locus, with GT as the most common genotype. At the G503A locus, GG, GA, and AA genotypes existed in Junmu No. 1 White pigs, with the GA genotype as the most frequently occurring. By contrast, at this locus, only the GA and AA genotypes were observed in the Tibetan pigs, and AA was more common than GA. There was a significant difference (P Tibet Mini-pigs than in Junmu No. 1 White pigs. The present study revealed SNPs in exon 1 of IGFBP-5 gene in the Tibet Mini-pig, possibly providing more understanding of the mechanism of miniaturization.

  2. Haplotype determination of the upstream regulatory region and the second exon of the BoLA-DRB3 gene in Holstein cattle.

    Science.gov (United States)

    Goszczynski, D E; Ripoli, M V; Takeshima, S-N; Baltian, L; Aida, Y; Giovambattista, G

    2014-03-01

    Polymorphisms of the BoLA-DRB3 gene are located primarily in the second exon [antigen binding site (ABS)] and, to a lesser extent, in the upstream regulatory region (URR). It can be hypothesised that exon 2 and the URR are under different types of natural selection. The aim of this work was to determine the URR-exon 2 haplotypes; 34 Holstein samples were genotyped by direct sequencing. A total of 7 URR alleles and 23 exon 2 alleles were detected, and 3 of the URR alleles were novel. Our results may suggest that no relationship exists between the URR and exon 2 of the BoLA-DRB3 gene (linkage disequilibrium P value > 0.05), most likely due to recombination over time. Our results also suggest that both regions of class II genes may be included in the development of new genotyping methods based on next-generation DNA sequencing technologies.

  3. Functional analysis of splicing mutations in exon 7 of NF1 gene

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    Calvieri Stefano

    2007-02-01

    Full Text Available Abstract Background Neurofibromatosis type 1 is one of the most common autosomal dominant disorders, affecting about 1:3,500 individuals. NF1 exon 7 displays weakly defined exon-intron boundaries, and is particularly prone to missplicing. Methods In this study we investigated the expression of exon 7 transcripts using bioinformatic identification of splicing regulatory sequences, and functional minigene analysis of four sequence changes [c.910C>T (R304X, c.945G>A/c.946C>A (Q315Q/L316M, c.1005T>C (N335N] identified in exon 7 of three different NF1 patients. Results Our results detected the presence of three exonic splicing enhancers (ESEs and one putative exonic splicing silencer (ESS element. The wild type minigene assay resulted in three alternative isoforms, including a transcript lacking NF1 exon 7 (NF1ΔE7. Both the wild type and the mutated constructs shared NF1ΔE7 in addition to the complete messenger, but displayed a different ratio between the two transcripts. In the presence of R304X and Q315Q/L316M mutations, the relative proportion between the different isoforms is shifted toward the expression of NF1ΔE7, while in the presence of N335N variant, the NF1ΔE7 expression is abolished. Conclusion In conclusion, it appears mandatory to investigate the role of each nucleotide change within the NF1 coding sequence, since a significant proportion of NF1 exon 7 mutations affects pre-mRNA splicing, by disrupting exonic splicing motifs and modifying the delicate balance between aberrantly and correctly spliced transcripts.

  4. Assembly of splicing complexes on exon 11 of the human insulin receptor gene does not correlate with splicing efficiency in-vitro

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    Caples Matt

    2004-07-01

    Full Text Available Abstract Background Incorporation of exon 11 of the insulin receptor gene is both developmentally and hormonally-regulated. Previously, we have shown the presence of enhancer and silencer elements that modulate the incorporation of the small 36-nucleotide exon. In this study, we investigated the role of inherent splice site strength in the alternative splicing decision and whether recognition of the splice sites is the major determinant of exon incorporation. Results We found that mutation of the flanking sub-optimal splice sites to consensus sequences caused the exon to be constitutively spliced in-vivo. These findings are consistent with the exon-definition model for splicing. In-vitro splicing of RNA templates containing exon 11 and portions of the upstream intron recapitulated the regulation seen in-vivo. Unexpectedly, we found that the splice sites are occupied and spliceosomal complex A was assembled on all templates in-vitro irrespective of splicing efficiency. Conclusion These findings demonstrate that the exon-definition model explains alternative splicing of exon 11 in the IR gene in-vivo but not in-vitro. The in-vitro results suggest that the regulation occurs at a later step in spliceosome assembly on this exon.

  5. Shared gene structures and clusters of mutually exclusive spliced exons within the metazoan muscle myosin heavy chain genes.

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    Martin Kollmar

    Full Text Available Multicellular animals possess two to three different types of muscle tissues. Striated muscles have considerable ultrastructural similarity and contain a core set of proteins including the muscle myosin heavy chain (Mhc protein. The ATPase activity of this myosin motor protein largely dictates muscle performance at the molecular level. Two different solutions to adjusting myosin properties to different muscle subtypes have been identified so far: Vertebrates and nematodes contain many independent differentially expressed Mhc genes while arthropods have single Mhc genes with clusters of mutually exclusive spliced exons (MXEs. The availability of hundreds of metazoan genomes now allowed us to study whether the ancient bilateria already contained MXEs, how MXE complexity subsequently evolved, and whether additional scenarios to control contractile properties in different muscles could be proposed, By reconstructing the Mhc genes from 116 metazoans we showed that all intron positions within the motor domain coding regions are conserved in all bilateria analysed. The last common ancestor of the bilateria already contained a cluster of MXEs coding for part of the loop-2 actin-binding sequence. Subsequently the protostomes and later the arthropods gained many further clusters while MXEs got completely lost independently in several branches (vertebrates and nematodes and species (for example the annelid Helobdella robusta and the salmon louse Lepeophtheirus salmonis. Several bilateria have been found to encode multiple Mhc genes that might all or in part contain clusters of MXEs. Notable examples are a cluster of six tandemly arrayed Mhc genes, of which two contain MXEs, in the owl limpet Lottia gigantea and four Mhc genes with three encoding MXEs in the predatory mite Metaseiulus occidentalis. Our analysis showed that similar solutions to provide different myosin isoforms (multiple genes or clusters of MXEs or both have independently been developed

  6. Dietary selenomethionine increases exon-specific DNA methylation of the p53 gene in rat liver and colon mucosa.

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    Zeng, Huawei; Yan, Lin; Cheng, Wen-Hsing; Uthus, Eric O

    2011-08-01

    The regulation of site-specific DNA methylation of tumor suppressor genes has been considered as a leading mechanism by which certain nutrients exert their anticancer property. This study was to investigate whether selenium (Se) affects the methylation of globe genomic DNA and the exon-specific p53 gene. Three groups of rats (n = 6-7/group) were fed the AIN-93G basal diet supplemented with 0 [Se deficient (D)], 0.15 [Se adequate (A)], or 4 mg [Se supranutritional (S)] (Se as l-selenomethionine)/kg diet for 104 d, respectively. Rats fed the A or S diet had greater plasma and liver glutathione peroxidase activity, liver thioredoxin reductase activity, and plasma homocysteine concentration than those fed the D diet. However, compared with the A diet, rats fed the S diet did not further increase these Se-dependent enzyme activities or homocysteine concentration. In contrast, Se concentrations in kidney, liver, gastrocnemius muscle, and plasma were increased in a Se-dose-dependent manner. Interestingly, rats fed the S diet had significantly less global liver genomic DNA methylation than those fed the D diet. However, the S diet significantly increased the methylation of the p53 gene (exons 5-8) but not the β-actin gene (exons 2-3) DNA in liver and colon mucosa compared with those fed the D diet. Taken together, long-term Se consumption not only affects selenoprotein enzyme activities, homocysteine, tissue Se concentrations, and global genomic DNA methylation but also increases exon-specific DNA methylation of the p53 gene in a Se-dose-dependent manner in rat liver and colon mucosa.

  7. Exons I and VII of the gene (Ker10) encoding human keratin 10 undergo structural rearrangements within repeats.

    Science.gov (United States)

    Tkachenko, A V; Buchman, V L; Bliskovsky, V V; Shvets YuP; Kisselev, L L

    1992-07-15

    A genomic fragment containing the K51 gene previously isolated from a rat genomic library by hybridization with the v-mos probe in nonstringent conditions [Chumakov et al., Dokl. Akad. Nauk SSSR 290 (1986) 1252-1254], resembles a human keratin type-I-encoding gene [Shvets et al., Mol. Biol. 24 (1990) 663-677]. This genomic clone, K51, has been used as a probe to search for related human genes. A recombinant clone, HK51, with a 1.5-kb insert, was isolated from a human embryonic skin cDNA library, and its nucleotide (nt) sequence was determined. Analysis has shown that the cloned cDNA encodes human keratin 10 (Ker10). All presently known nt sequences of the human Ker10-encoding gene (Ker10) are not identical. Differences are concentrated in the 5'-end of the first exon and in the middle of the seventh exon within repeats. In spite of structural rearrangements in two of eight exons, the reading frame and position of the stop codon are preserved. The genetic rearrangements cause changes in hydrophobicity profiles of the N and C termini of Ker10. It was also noticed that insertion of one nt leads to the formation of an unusual 3'-end of the transcript.

  8. Deletion of exon 8 from the EXT1 gene causes multiple osteochondromas (MO) in a family with three affected members.

    Science.gov (United States)

    Zhuang, Lei; Gerber, Simon D; Kuchen, Stefan; Villiger, Peter M; Trueb, Beat

    2016-01-01

    Multiple osteochondromas (also called hereditary multiple exostoses) is an autosomal dominant disorder characterized by multiple cartilaginous tumors, which are caused by mutations in the genes for exostosin-1 (EXT1) and exostosin-2 (EXT2). The goal of this study was to elucidate the genetic alterations in a family with three affected members. Isolation of RNA from the patients' blood followed by reverse transcription and PCR amplification of selected fragments showed that the three patients lack a specific region of 90 bp from their EXT1 mRNA. This region corresponds to the sequence of exon 8 from the EXT1 gene. No splice site mutation was found around exon 8. However, long-range PCR amplification of the region from intron 7 to intron 8 indicated that the three patients contain a deletion of 4318 bp, which includes exon 8 and part of the flanking introns. There is evidence that the deletion was caused by non-homologous end joining because the breakpoints are not located within a repetitive element, but contain multiple copies of the deletion hotspot sequence TGRRKM. Exon 8 encodes part of the active site of the EXT1 enzyme, including the DXD signature of all UDP-sugar glycosyltransferases. It is conceivable that the mutant protein exerts a dominant negative effect on the activity of the EXT glycosyltransferase since it might interact with normal copies of the enzyme to form an inactive hetero-oligomeric complex. We suggest that sequencing of RNA might be superior to exome sequencing to detect short deletions of a single exon.

  9. Mutations in exons of the CYP17-II gene affect sex steroid concentration in male Japanese flounder ( Paralichthys olivaceus)

    Science.gov (United States)

    Ma, Ruiqin; He, Feng; Wen, Haishen; Li, Jifang; Shi, Bao; Shi, Dan; Liu, Miao; Mu, Weijie; Zhang, Yuanqing; Hu, Jian; Han, Weiguo; Zhang, Jianan; Wang, Qingqing; Yuan, Yuren; Liu, Qun

    2012-03-01

    As a specific gene of fish, cytochrome P450c17-II ( CYP17-II) gene plays a key role in the growth, development an reproduction level of fish. In this study, the single-stranded conformational polymorphism (SSCP) technique was used to characterize polymorphisms within the coding region of CYP17-II gene in a population of 75 male Japanese flounder ( Paralichthys olivaceus). Three single nucleotide polymorphisms (SNPs) were identified in CYP17-II gene of Japanese flounder. They were c.G594A (p.G188R), c.G939A and c.G1502A (p.G490D). SNP1 (c.G594A), located in exon 4 of CYP17-II gene, was significantly associated with gonadosomatic index (GSI). Individuals with genotype GG of SNP1 had significantly lower GSI ( P < 0.05) than those with genotype AA or AG. SNP2 (c.G939A) located at the CpG island of CYP17-II gene. The mutation changed the methylation of exon 6. Individuals with genotype AA of SNP2 had significantly lower serum testosterone (T) level and hepatosomatic index (HSI) compared to those with genotype GG. The results suggested that SNP2 could influence the reproductive endocrine of male Japanese flounder. However, the SNP3 (c.G1502A) located in exon 9 did not affect the four measured reproductive traits. This study showed that CYP17-II gene could be a potentially useful candidate gene for the research of genetic breeding and physiological aspects of Japanese flounder.

  10. Mutations in Exons of the CYP17- Ⅱ Gene Affect Sex Steroid Concentration in Male Japanese Flounder (Paralichthys olivaceus)

    Institute of Scientific and Technical Information of China (English)

    MA Ruiqin; HU Jian; HAN Weiguo; ZHANG Jianan; WANG Qingqing; YUAN Yuren; LIU Qun; HE Feng; WEN Haishen; LI Jifang; SHI Bao; SHI Dan; LIU Miao; MU Weijie; ZHANG Yuanqing

    2012-01-01

    As a specific gene of fish,cytochrome P450c 17-Ⅱ (CYP17-Ⅱ) gene plays a key role in the growth,development and reproduction level of fish.In this study,the single-stranded conformational polymorphism (SSCP) technique was used to characterize polymorphisms within the coding region of CYP17- Ⅱ gene in a population of 75 male Japanese flounder (Paralichthys olivaceus).Three single nucleotide polymorphisms (SNPs) were identified in CYP17-Ⅱ gene of Japanese flounder.They were c.G594A (p.G188R),c.G939A and c.G1502A (p.G490D).SNP1 (c.G594A),located in exon 4 of CYP17-Ⅱ gene,was significantly associated with gonadosomatic index (GSI).Individuals with genotype GG of SNP1 had significantly lower GSI (P<0.05) than those with genotype AA or AG.SNP2 (c.G939A) located at the CpG island of CYP17-Ⅱ gene.The mutation changed the methylation of exon 6.Individuals with genotype AA of SNP2 had significantly lower serum testosterone (T) level and hepatosomatic index (HSI) compared to those with genotype GG.The results suggested that SNP2 could influence the reproductive endocrine of male Japanese flounder.However,the SNP3 (c.G 1502A) located in exon 9 did not affect the four measured reproductive traits.This study showed that CYP17-Ⅱgene could be a potentially useful candidate gene for the research of genetic breeding and physiological aspects of Japanese flounder.

  11. Polymorphisms of Exon 17 of Insulin-Receptor Gene in Pathogenesis of Human Disorders With Insulin Resistance

    Institute of Scientific and Technical Information of China (English)

    LU WANG; JIE MI; XIAO-YUAN ZHAO; JIAN-XIN WU; HONG CHENG; ZHI-KUN ZHANG; XIU-YUAN DING; DONG-QING HOU; HUILI

    2004-01-01

    To investigate the relationship between polymorphisms of insulin-receptor (INSR) gene and insulin resistance in a population-based study in China. Methods Polymerase Chain Reaction (PCR) was used to the amplify Exon 17 of INSR gene and all amplified products were analyzed by direct sequencing. Results Six single-nucleotide polymorphisms (SNPs) were found at the following loci: T to TC at the locus of 10699 (Tyr984), G to GC at the locus of 10731 (Glu994), Deletion G at the locus of 10798 (Asp1017), C to T/TC at the locus of 10923 (His1058), C to CA at the locus of 10954 (Leu1069), and T to TA at the locus of 10961 (Phe1071), which might not change the amino acid sequence. The data were in agreement with the test of Hardy-Weinberg balance (P>0.05). Among the 345 cases, all clinical indices were higher in males than in females except for HDL cholesterol (P0.05). After sex stratification in analysis,all allele frequencies on the six loci of SNPs of Exon 17 had different distributions between the insulin resistant group and the control group, but P>0.05. Conclusion SNPs of Exon 17 of INSR gene are unlikely to play a direct role in the pathogenesis of human disorders with insulin resistance.

  12. Parental smoke exposure and the development of nicotine craving in adolescent novice smokers: the roles of DRD2, DRD4, and OPRM1 genotypes

    OpenAIRE

    2015-01-01

    Background Among adolescent novice smokers, craving is often the first, and is the most reported, symptom of nicotine dependence. Until now, little has been known about the development of craving symptoms in novice smokers. The aim of this study was to identify specific genetic (i.e., DRD2 Taq1A, DRD4 48 bp VNTR, and OPRM1 A118G polymorphisms) and environmental mechanisms that underlie the emergence of both cue-induced and cognitive craving among adolescent novice smokers. Method A five-wave ...

  13. Mechanistic Evaluation for Mixed-field Agglutination in the K562 Cell Study Model with Exon 3 Deletion of A1 Gene.

    Science.gov (United States)

    Chen, Ding-Ping; Tseng, Ching-Ping; Lin, Chi-Jui; Wang, Wei-Ting; Sun, Chien-Feng

    2015-01-01

    In the case of blood type B3 with typical mixed-field agglutination of RBCs in the presence of anti-B or anti-AB antibody, a number of genetic alternations have been reported. It is well known that the IVS3+5G→A mutation in the B gene destroys the consensus of the splice donor site leading to exon 3 skipping during mRNA splicing. The lack of exon 3 likely causes a short stem region, producing an unstable B3 protein, and is concomitant with a decrease in B3 protein expression. Whether the phenomenon also appears in the type A blood group is of question. In this study, we evaluate whether exon 3 deletion in the blood type A gene also results in mixed-field phenotype. Site-directed mutagenesis was used to generate cDNA encoding A1 gene with exon 3 deletion. The cDNA was stably expressed in K562 cells. The expression of A antigen was compared with expression in parental K562 cells that did not express A antigen and in the stable K562 cell line expressing A(1) cDNA by flow cytometry analyses. The expression of A antigen in A1 stable cells and parental K562 cells was set as 100% and 0%, respectively. The mean relative percentage of A antigen expression for the cells of A1 with exon 3 deletion was 59.9% of A1 stable cells. Consistent with the observations of B3, which is B gene with exon 3 deletion, mixed field agglutination was observed for the cells expressing A1 with exon 3 deletion. Exon 3 deletion results in mixed field phenotype in both type A and B RBCs. However, the degree of antigen expression change for exon 3 deletion in A gene was less severe when compared with the deletion occurred in B gene.

  14. The association between creativity and 7R polymorphism in the dopamine receptor D4 gene (DRD4)

    OpenAIRE

    2013-01-01

    Creativity can be defined as the ability to produce responses that are both novel and appropriate. One way to assess creativity is to measure divergent thinking (DT) abilities that involve generating multiple novel and meaningful responses to open-ended questions. DT abilities have been shown to be associated with dopaminergic activity, and impaired DT has been reported in populations with dopaminergic dysfunctions. Given the strong association between DT and the dopaminergic system, the curr...

  15. The association between creativity and 7R polymorphism in the dopamine receptor D4 gene (DRD4)

    OpenAIRE

    2013-01-01

    Creativity can be defined as the ability to produce responses that are both novel and appropriate. One way to assess creativity is to measure divergent thinking (DT) abilities that involve generating multiple novel and meaningful responses to open-ended questions. DT abilities have been shown to be associated with dopaminergic (DA) activity, and impaired DT has been reported in populations with DA dysfunctions. Given the strong association between DT and the DA system, the current study exami...

  16. Family-based association study of DRD4 gene in methylphenidate-responded Attention Deficit/Hyperactivity Disorder

    National Research Council Canada - National Science Library

    Patrick Wing-leung Leung; Janice Ka Yan Chan; Lu Hua Chen; Chi Chiu Lee; Se Fong Hung; Ting Pong Ho; Chun Pan Tang; Robert K Moyzis; James M Swanson

    2017-01-01

    ...) is implicated in the etiology of attention-deficit/ hyperactivity disorder (ADHD). In particular, ADHD in European-ancestry population is associated with an increased prevalence of the 7-repeat (7R...

  17. Differential Susceptibility in Early Literacy Instruction through Computer Games: The Role of the Dopamine D4 Receptor Gene (DRD4)

    Science.gov (United States)

    Kegel, Cornelia A. T.; Bus, Adriana G.; van IJzendoorn, Marinus H.

    2011-01-01

    Not every child seems equally susceptible to the same parental, educational, or environmental influences even if cognitive level is similar. This study is the first randomized controlled trial to apply the differential susceptibility paradigm to education in relation to children's genotype and early literacy skills. A randomized pretest-posttest…

  18. Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Shou-Tao Chen

    2007-07-01

    Full Text Available We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of approximately 300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than approximately 13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3' side by the transposon DINE-1 (Drosophila interspersed element-1. We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (approximately >20-fold between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent

  19. Dopamine receptor genes and evolutionary differentiation in the domestication of fighting cocks and long-crowing chickens

    KAUST Repository

    Komiyama, Tomoyoshi

    2014-07-31

    The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo) and the long-crowing chicken (Naganakidori), have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (NST) newly devised in this study, we found that the NST value of DRD4 for Shamo (0.072) was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time. © 2014 Komiyama et al.

  20. Dopamine receptor genes and evolutionary differentiation in the domestication of fighting cocks and long-crowing chickens.

    Science.gov (United States)

    Komiyama, Tomoyoshi; Iwama, Hisakazu; Osada, Naoki; Nakamura, Yoji; Kobayashi, Hiroyuki; Tateno, Yoshio; Gojobori, Takashi

    2014-01-01

    The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo) and the long-crowing chicken (Naganakidori), have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (NST) newly devised in this study, we found that the NST value of DRD4 for Shamo (0.072) was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time.

  1. Dopamine receptor genes and evolutionary differentiation in the domestication of fighting cocks and long-crowing chickens.

    Directory of Open Access Journals (Sweden)

    Tomoyoshi Komiyama

    Full Text Available The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo and the long-crowing chicken (Naganakidori, have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (NST newly devised in this study, we found that the NST value of DRD4 for Shamo (0.072 was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time.

  2. Comparative sequence analysis in the exon 5 of growth hormone gene in the various livestock species of India.

    Science.gov (United States)

    Singh, Lakshya Veer; Sharma, Anurodh; Kumari, Namita; Kaur, Navneet; Jayakumar, S; Dixit, S P; Gupta, Neelam; Gupta, S C

    2014-01-01

    The aim of the study was to identify genetic polymorphism in growth hormone (GH) gene locus of six different livestock species using PCR-Direct DNA sequencing method. In exon 5 of GH gene, 10 SNPs variants were identified in all livestock species studied, namely Bubalus bubalis, Bos indicus, Bos frontalis, Bos grunniens, Ovis aries, and Capra hircus. Four SNPs were observed in Bubalus bubalis, two SNPs in Bos indicus, one SNP in Ovis aries, and three SNPs in Capra hircus. No changes were observed in Bos grunniens and Bos frontalis when compared with the template sequence and the SNPs observed in the present investigation may be useful in the marker assisted selection.

  3. A nonsense mutation in the 4-hydroxyphenylpyruvic acid dioxygenase gene (Hpd) causes skipping of the constitutive exon and hypertyrosinemia in mouse strain III

    Energy Technology Data Exchange (ETDEWEB)

    Endo, Fumio; Awata, Hisataka; Matsuda, Ichiro [Kumamoto Univ. (Japan)

    1995-01-01

    4-Hydroxyphenylpyruvic acid dioxygenase (HPD; EC 1.13.11.27) is an important enzyme in tyrosine catabolism in most organisms. Decreased activity of 4-hydroxyphenylpyruvic acid dioxygenase in the liver of mouse strain III is associated with tyrosinemia. We report a nucleotide substitution that generates a termination codon in exon 7 of the 4-hydroxyphenylpyruvic acid dioxygenase gene in III mice. This mutation is associated with partial exon skipping, and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Mouse strain III is a model for human tyrosinemia type 3 (McKusick 276710), and this train together with recently established models for tyrosinemia type 1 will facilitate studies of hereditary tyrosinemias.

  4. A nonsense mutation in the 4-hydroxyphenylpyruvic acid dioxygenase gene (Hpd) causes skipping of the constitutive exon and hypertyrosinemia in mouse strain III.

    Science.gov (United States)

    Endo, F; Awata, H; Katoh, H; Matsuda, I

    1995-01-01

    4-Hydroxyphenylpyruvic acid dioxygenase (HPD; EC 1.13.11.27) is an important enzyme in tyrosine catabolism in most organisms. Decreased activity of 4-hydroxyphenylpyruvic acid dioxygenase in the liver of mouse strain III is associated with tyrosinemia. We report a nucleotide substitution that generates a termination codon in exon 7 of the 4-hydroxyphenylpyruvic acid dioxygenase gene in III mice. This mutation is associated with partial exon skipping, and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Mouse strain III is a model for human tyrosinemia type 3 (McKusick 276710), and this strain together with recently established models for tyrosinemia type 1 will facilitate studies of hereditary tyrosinemias.

  5. Mutation analysis in exons 22 and 24 of SCN4A gene in Iranian patients with non-dystrophic myotonia

    Directory of Open Access Journals (Sweden)

    Mohammad Mehdi Heidari

    2015-10-01

    Full Text Available Background: Non-dystrophic myotonias are a heterogeneous set of skeletal, muscular channelopathies, which have been associated with point mutations within sodium channel α-subunit (SCN4A gene. Because exons 22 and 24 of SCN4A gene are recognized as hot spots for this disease, the purpose of the study is to identify mutation in exons 22 and 24 of SCN4A gene in Iranian non-dystrophic myotonias patients.Methods: In this study, 28 Iranian patients with non-dystrophic myotonia analyzed for the mutation scanning in exons 22 and 24 of SCN4A gene by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP and sequencing.Results: We found 29073G>C substitution in SCN4A gene in one case and 31506A>G substitution in seven cases. The 29073G>C substitution causes a missense mutation G1306A, located in the conserved cytoplasmic loop connecting repeat III and IV of the SCN4A channel but, 31506A>G substitution do not alter amino acid in SCN4A protein.Conclusion: G1306A residue is located in functionally important protein region. In “hinged-lid model” for Na+ channel inactivation in which glycines1306 act as the hinge of the lid occluding the channel pore. Mutation in this region slowed fast inactivation. Therefore, it might be a pathogenic mutation. The causal relationship of this mutation with the disease is an object for further discussion.

  6. Structure of the human zinc finger protein HIVEP3: molecular cloning, expression, exon-intron structure, and comparison with paralogous genes HIVEP1 and HIVEP2.

    Science.gov (United States)

    Hicar, M D; Liu, Y; Allen, C E; Wu, L C

    2001-01-01

    Here we report the cloning and characterization of HIVEP3, the newest member in the human immunodeficiency virus type 1 enhancer-binding protein family that encodes large zinc finger proteins and regulates transcription via the kappaB enhancer motif. The largest open reading frame of HIVEP3 contains 2406 aa. and is approximately 80% identical to the mouse counterpart. The HIVEP3 gene is located in the chromosomal region 1p34 and is at least 300 kb with 10 exons. RNA studies show that multiple HIVEP3 transcripts are differentially expressed and regulated. Additionally, transcription termination occurs in the ultimate exon, exon 10, or in exon 6. Therefore, HIVEP3 may produce protein isoforms that contain or exclude the carboxyl DNA binding domain and the leucine zipper by alternative RNA splicing and differential polyadenylation. Sequence homologous to HIVEP3 exon 6 is not found in mouse nor are the paralogous genes HIVEP1 and HIVEP2. Zoo-blot analysis suggests that sequences homologous to the human exon 6 are present only in primates and cow. Therefore, a foreign DNA harboring a termination exon likely was inserted into the HIVEP3 locus relatively recently in evolution, resulting in the acquisition of novel gene regulatory mechanisms as well as the generation of structural and functional diversity. Copyright 2001 Academic Press.

  7. Identification of Exonic Nucleotide Variants of the Gene Associated with Carcass Traits and Fatty Acid Composition in Korean Cattle

    Directory of Open Access Journals (Sweden)

    Dong-yep Oh

    2014-10-01

    Full Text Available The thyroid hormone responsive protein (THRSP gene is a functional gene that can be used to indicate the fatty acid compositions. This study investigates the relationships of exonic single nucleotide polymorphisms (SNPs in the THRSP gene and fatty acid composition of muscle fat and marbling score in the 612 Korean cattle. The relationships between fatty acid composition and eight SNPs in the THRSP gene (g.78 G>A, g.173 C>T, g.184 C>T, g.190 C>A, g.194 C>T, g.277 C>G, g.283 T>G and g.290 T>G were investigated, and according to the results, two SNPs (g.78 G>A and g.184 C>T in exon 1 were associated with fatty acid composition. The GG and CC genotypes of g.78 G>A and g.184 C>T had higher unsaturated fatty acid (UFA and monounsaturated fatty acid (MUFA content (pA and g.184 C>T had significantly relationships with UFAs and MUFAs. Two SNPs in the THRSP gene affected fatty acid composition, suggesting that GG and CC genotypes and the ht1*ht1 group (Val/Ala haplotype can be markers to genetically improve the quality and flavor of beef.

  8. Association of G>A transition in exon-1 of alpha crystallin gene in age-related cataracts

    Directory of Open Access Journals (Sweden)

    S G Bhagyalaxmi

    2010-01-01

    Full Text Available Aim : To identify the presence of a known or novel mutation/SNP in Exon-1 (ex-1 of alpha crystallin (CRYAA gene in different types of age-related cataract (ARC patients. Materials and Methods : Single strand Conformation Polymorphism (SSCP analysis was carried for the detection of single nucleotide polymorphism (SNP in ex-1 of alpha crystallin (CRYAA gene which was confirmed by sequencing. Results : The SSCP analysis of ex-1 of CRYAA gene revealed mobility shift in patients and controls, which was due to G>A transition at 6 th position in exon-1 of CRYAA gene. All the three genotypes, GG, AA and GA, were detected in patients and controls indicating that G>A substitution is polymorphic. The analysis showed significant risk for heterozygotes (GA as compared to pooled frequencies of homozygotes (GG+AA, which was 1.81 times for all the types of cataracts in general and 2.5 times for Nuclear Cataract and twice for Cortical Cataract. Conclusion : The GA heterozygotes were at higher risk for developing NC and CC types of cataracts, where as the GG homozygotes for MT and AA homozygotes for PSC types were at risk. To our knowledge, an association of G>A transition found in ex-1 of CRYAA gene with ARC, with differential risk of genotypes for individual type of cataracts has not been reported previously.

  9. Association of Single Nucleotide Polymorphisms in Exon 3 of Porcine LMCD1 Gene with Meat Quality and Carcass Traits

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; DENG Chang-yan; XIONG Yuan-zhu; ZUO Bo; LI Feng-e; LEI Ming-gang; ZHENG Rong; LI Jia-lian; JIANG Si-wen

    2008-01-01

    LIM domain proteins are found to be important regulators in cell growth,cell fate determination,cell differentiation,and remodelling of the cell cytoskeleton by their interaction with some structural proteins,kinases,transcriptional regulators,etc.The presence of LIM domains in LMCDI gene implies it may be involved in skeletal muscle protein-protein interactions.This study was to investigate polymorphisms of LIM and cysteine-rich domain 1(LMCD1)gene and its effect on meat quality and carcass traits in pig.The polymorphism(G294A)in exon 3 region of porcine LMCD1 gene,which is synonymous mutation,was genotyped in the population of 178 F2 pigs of a Large White×Meishan resource family.Statistical results indicated the distribution of allele G(with a A→G mutation)and A(without mutation).Analysis of variante showed that the polymorphism of LMCD1 gene was associated with variation in several carcass traits of interest for pig breeding.Some carcass traits and meat quality traits are close to significance by association.An analysis of more animals is necessary to analyze the polymorphisms in exon 3 of porcine LMCD1 gene if it was selected as a marker for the pig carcass traits.

  10. Alternative splicing of exon 17 and a missense mutation in exon 20 of the insulin receptor gene in two brothers with a novel syndrome of insulin resistance (congenital fiber-type disproportion myopathy)

    DEFF Research Database (Denmark)

    Vorwerk, P; Christoffersen, C T; Müller, J

    1999-01-01

    domain. In the correct spliced variant, the point mutation is silent and results in a normally translated IR. The paternal allele carries a missense mutation in the tyrosine kinase domain. All three cDNA variants were present in the lymphocytes of the patients. Purified IR from 293 cells overexpressing...... to be compound heterozygotes for mutations in the IR gene. The maternal allele was alternatively spliced in exon 17 due to a point mutation in the -1 donor splice site of the exon. The abnormal skipping of exon 17 shifts the amino acid reading frame and leads to a truncated IR, missing the entire tyrosine kinase...... either of the two mutated receptors lacked basal or stimulated IR beta-subunit autophosphorylation. A third brother who inherited both normal alleles has an normal muscle phenotype and insulin sensitivity, suggesting a direct linkage of these IR mutations with the CFTDM phenotype....

  11. Wilson's disease caused by alternative splicing and Alu exonization due to a homozygous 3039-bp deletion spanning from intron 1 to exon 2 of the ATP7B gene.

    Science.gov (United States)

    Mameli, Eva; Lepori, Maria Barbara; Chiappe, Francesca; Ranucci, Giusy; Di Dato, Fabiola; Iorio, Raffaele; Loudianos, Georgios

    2015-09-15

    We describe a case of Wilson's disease (WD) diagnosed at 5 years after routine biochemical test showed increased aminotransferases. Mutation analysis of the ATP7B gene revealed a 3039-bp deletion in the homozygous state spanning from the terminal part of intron 1 to nt position 368 of exon 2. This deletion results in the activation of 3 cryptic splice sites: an AG acceptor splice site in nt positions 578-579 producing a different breakpoint and removing the first 577 nts of exon 2, an acceptor and a donor splice site in nt positions 20363-4 and 20456-7, respectively, in intron 1, resulting in the activation of a 94-bp cryptic Alu exon being incorporated into the mature transcript. The resulting alternative transcript contains a TAG stop codon in the first amino acid position of the cryptic exon, likely producing a truncated, non-functional protein. This study shows that intron exonization can also occur in humans through naturally occurring gross deletions. The results suggest that the combination of DNA and RNA analyses can be used for molecular characterization of gross ATP7B deletions, thus improving genetic counseling and diagnosis of WD. Moreover these studies help to better establish new molecular mechanisms producing Wilson's disease.

  12. Cell line OCI/AML3 bears exon-12 NPM gene mutation-A and cytoplasmic expression of nucleophosmin.

    Science.gov (United States)

    Quentmeier, H; Martelli, M P; Dirks, W G; Bolli, N; Liso, A; Macleod, R A F; Nicoletti, I; Mannucci, R; Pucciarini, A; Bigerna, B; Martelli, M F; Mecucci, C; Drexler, H G; Falini, B

    2005-10-01

    We recently identified a new acute myeloid leukemia (AML) subtype characterized by mutations at exon-12 of the nucleophosmin (NPM) gene and aberrant cytoplasmic expression of NPM protein (NPMc+). NPMc+ AML accounts for about 35% of adult AML and it is associated with normal karyotype, wide morphological spectrum, CD34-negativity, high frequency of FLT3-ITD mutations and good response to induction therapy. In an attempt to identify a human cell line to serve as a model for the in vitro study of NPMc+ AML, we screened 79 myeloid cell lines for mutations at exon-12 of NPM. One of these cell lines, OCI/AML3, showed a TCTG duplication at exon-12 of NPM. This mutation corresponds to the type A, the NPM mutation most frequently observed in primary NPMc+ AML. OCI/AML3 cells also displayed typical phenotypic features of NPMc+ AML, that is, expression of macrophage markers and lack of CD34, and the immunocytochemical hallmark of this leukemia subtype, that is, the aberrant cytoplasmic expression of NPM. The OCI/AML3 cell line easily engrafts in NOD/SCID mice and maintains in the animals the typical features of NPMc+ AML, such as the NPM cytoplasmic expression. For all these reasons, the OCI/AML3 cell line represents a remarkable tool for biomolecular studies of NPMc+ AML.

  13. De novo disruption of promoter and exon 1 of STAR gene reveals essential role for gonadal development

    Directory of Open Access Journals (Sweden)

    Anil Piya

    2017-03-01

    Full Text Available Cholesterol transport into the mitochondria is required for synthesis of the first steroid, pregnenolone. Cholesterol is transported by the steroidogenic acute regulatory protein (STAR, which acts at the outer mitochondrial membrane prior to its import. Mutations in the STAR protein result in lipoid congenital adrenal hyperplasia (CAH. Although the STAR protein consists of seven exons, biochemical analysis in nonsteroidogenic COS-1 cells showed that the first two were not essential for pregnenolone synthesis. Here, we present a patient with ambiguous genitalia, salt-lossing crisis within two weeks after birth and low cortisol levels. Sequence analysis of the STAR, including the exon–intron boundaries, showed the complete deletion of exon 1 as well as more than 50 nucleotides upstream of STAR promoter. Mitochondrial protein import with the translated protein through synthesis cassette of the mutant STAR lacking exon 1 showed protein translation, but it is less likely to have synthesized without a promoter in our patient. Thus, a full-length STAR gene is necessary for physiological mitochondrial cholesterol transport in vivo.

  14. A case of Becker muscular dystrophy resulting from the skipping of four contiguous exons (71-74) of the dystrophin gene during mRNA maturation.

    Science.gov (United States)

    Patria, S Y; Alimsardjono, H; Nishio, H; Takeshima, Y; Nakamura, H; Matsuo, M

    1996-07-01

    The mutations in one-third of both Duchenne and Becker muscular dystrophy patients remain unknown because they do not involve gross rearrangements of the dystrophin gene. Here we report the first example of multiple exon skipping during the splicing of dystrophin mRNA precursor encoded by an apparently normal dystrophin gene. A 9-year-old Japanese boy exhibiting excessive fatigue and high serum creatine kinase activity was examined for dystrophinopathy. An immunohistochemical study of muscle tissue biopsy disclosed faint and discontinuous staining of the N-terminal and rod domains of dystrophin but no staining at all of the C-terminal domain of dystrophin. The dystrophin transcript from muscle tissue was analyzed by the reverse transcriptase polymerase chain reaction. An amplified product encompassing exons 67-79 of dystrophin cDNA was found to be smaller than that of the wild-type product. Sequence analysis of this fragment showed that the 3' end of exon 70 was directly connected to the 5' end of exon 75 and, thus, that exons 71-74 were completely absent. As a result, a truncated dystrophin protein lacking 110 amino acids from the C-terminal domain should result from translation of this truncated mRNA, and the patient was diagnosed as having Becker muscular dystrophy at the molecular level. Genomic DNA was analyzed to identify the cause of the disappearance of these exons. Every exon-encompassing region could be amplified from genomic DNA, indicating that the dystrophin gene is intact. Furthermore, sequencing of these amplified products did not disclose any particular nucleotide change that could be responsible for the multiple exon skipping observed. Considering that exons 71-74 are spliced out alternatively in some tissue-specific isoforms, to suppose that the alternative splicing machinery is present in the muscle tissue of the index case and that it is activated by an undetermined mechanism is reasonable. These results illustrate a novel genetic anomaly that

  15. Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene

    Science.gov (United States)

    Malla, Spundana; Kadimisetty, Karteek; Fu, You-Jun; Choudhary, Dharamainder; Schenkman, John B.; Rusling, James F.

    2017-01-01

    Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites. This method allows direct kinetic measurements by LC-MS/MS sequencing for oligonucleotides longer than 20 base pairs (bp). We used MeC and non-MeC (C) versions of a 32 bp exon 7 fragment of the p53 gene. Methylation of 19 cytosines increased the rate constant 3-fold for adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment. Rate constants for non-CpG codons 244 and 243 were not influenced significantly by MeC. Conformational and hydrophobicity changes in the MeC-p53 exon 7 fragment revealed by CD spectra and molecular modeling increase the BPDE binding constant to G in codon 248 consistent with a pathway in which preceding reactant binding greatly facilitates the rate of covalent SN2 coupling.

  16. Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene

    Science.gov (United States)

    Malla, Spundana; Kadimisetty, Karteek; Fu, You-Jun; Choudhary, Dharamainder; Schenkman, John B.; Rusling, James F.

    2017-01-01

    Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites. This method allows direct kinetic measurements by LC-MS/MS sequencing for oligonucleotides longer than 20 base pairs (bp). We used MeC and non-MeC (C) versions of a 32 bp exon 7 fragment of the p53 gene. Methylation of 19 cytosines increased the rate constant 3-fold for adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment. Rate constants for non-CpG codons 244 and 243 were not influenced significantly by MeC. Conformational and hydrophobicity changes in the MeC-p53 exon 7 fragment revealed by CD spectra and molecular modeling increase the BPDE binding constant to G in codon 248 consistent with a pathway in which preceding reactant binding greatly facilitates the rate of covalent SN2 coupling. PMID:28102315

  17. Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The exon 2 of chalcone synthase (CHS) gene is relatively conserved during evolution.In this study,three exon 2 fragments from two species in gymnosperm (Cycas panzhihuaensis,Ginkgo biloba) and seven from four species in angiosperm (Magnolia denudata,Salix babylonica,Nymphaea tetragona,Camellia japonica) have been amplified by PCR from genomic DNA and sequenced.Together with other 73 sequences of CHS collected from EMBL database and literature,these sequences,which embrace 19 families of gymnosperm and angiosperm,have been analyzed for their phylogenetic relations by parsimony method.The result indicated that sequences from the same systematic family usually grouped together except those from Theaceae,Magnoliaceae and Nymphaeaceae.The relative rate test revealed the rate heterogeneity of CHS genes among the families.For the nucleotide substitution the sequences from Asteraceae and Solanaceae evolve faster than those from the other families analyzed while the sequences from Poaceae,Asteraceae and Solanaceae evolve faster for the nonsynonymous substitution.These results suggest that the duplication and extinction events of CHS genes are different among systematic families,therefore it seems impractical to look for orthologous sequences from CHS genes to study plant phylogeny at the family level and/or above.However,it is possible to do so below the family level.

  18. Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals

    Directory of Open Access Journals (Sweden)

    Diana Chernikova

    2016-07-01

    Full Text Available The abundance of mammalian long intergenic non-coding RNA (lincRNA genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important.

  19. Mutation analysis of exon1 of bone morphogenetic protein-15 gene in Iranian patients with polycystic ovarian syndrome

    Directory of Open Access Journals (Sweden)

    Anahita Mehdizadeh

    2016-08-01

    Full Text Available Background: With the prevalence of 6-10%, polycystic ovarian syndrome (PCOS is considered the most common endocrinological disorder affecting women in their reproductive age. It has been suggested that genetic factors participate in the development of PCOS. Follicular development has been considered as one of the impaired processes in PCOS. Bone morphogenetic protein-15 (BMP-15 gene is a candidate gene in follicular development and its variants may play role in pathogenesis of PCOS. Objective: To investigate whether BMP-15 gene mutations are present in Iranian women with PCOS. Materials and Methods: In this cross-sectional study 5 ml venous blood samples was taken from 70 PCOS women referring to Afzalipour Hospital, Kerman University of Medical Sciences, Kerman, Iran, between January to December 2014. Genomic DNA was extracted from the blood sample by salting out method. Then a set of PCR reactions for exon1 of BMP-15 gene was performed using specific primers followed by genotyping with direct sequencing. Results: Two different polymorphisms were found in the gene under study. In total 20 patients (28.6% were heterozygote (C/G, and 2 patients (2.86% were homozygous (G/G for c.-9C>G in 5´UTR promoter region of BMP-15 gene (rs3810682. In addition, in the coding region of exon1, three patients (4.3% were heterozygote (G/A for c.A308G (rs41308602. Two PCOS patients (2.86% appeared to have both c.-9C>G (C/G and c.A308G (G/A variants simultaneously. Conclusion: Our research detected two polymorphisms of BMP-15 gene among PCOS patients, indicating that even though it cannot be concluded that variants of BMP-15 gene are the principal cause of polycystic ovarian syndrome; they could be involved in pathogenic process in development of PCOS.

  20. Mutation analysis of exon1 of bone morphogenetic protein-15 gene in Iranian patients with polycystic ovarian syndrome

    Science.gov (United States)

    Mehdizadeh, Anahita; Sheikhha, Mohammad Hasan; Kalantar, Seyed Mehdi; Aali, Bibi Shahnaz; Ghanei, Azam

    2016-01-01

    Background: With the prevalence of 6-10%, polycystic ovarian syndrome (PCOS) is considered the most common endocrinological disorder affecting women in their reproductive age. It has been suggested that genetic factors participate in the development of PCOS. Follicular development has been considered as one of the impaired processes in PCOS. Bone morphogenetic protein-15 (BMP-15) gene is a candidate gene in follicular development and its variants may play role in pathogenesis of PCOS. Objective: To investigate whether BMP-15 gene mutations are present in Iranian women with PCOS. Materials and Methods: In this cross-sectional study 5 ml venous blood samples was taken from 70 PCOS women referring to Afzalipour Hospital, Kerman University of Medical Sciences, Kerman, Iran, between January to December 2014. Genomic DNA was extracted from the blood sample by salting out method. Then a set of PCR reactions for exon1 of BMP-15 gene was performed using specific primers followed by genotyping with direct sequencing. Results: Two different polymorphisms were found in the gene under study. In total 20 patients (28.6%) were heterozygote (C/G), and 2 patients (2.86%) were homozygous (G/G) for c.-9C>G in 5´UTR promoter region of BMP-15 gene (rs3810682). In addition, in the coding region of exon1, three patients (4.3%) were heterozygote (G/A) for c.A308G (rs41308602). Two PCOS patients (2.86%) appeared to have both c.-9C>G (C/G) and c.A308G (G/A) variants simultaneously. Conclusion: Our research detected two polymorphisms of BMP-15 gene among PCOS patients, indicating that even though it cannot be concluded that variants of BMP-15 gene are the principal cause of polycystic ovarian syndrome; they could be involved in pathogenic process in development of PCOS. PMID:27679828

  1. Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants.

    Science.gov (United States)

    Ghoraba, Dina A; Mohammed, Magdy M; Zaki, Osama K

    2015-02-01

    Methylmalonic aciduria (MMA) is an autosomal recessive disorder of methylmalonate and cobalamin (cbl; vitamin B12) metabolism. It is an inborn error of organic acid metabolism which commonly results from a defect in the gene encoding the methylmalonyl-CoA mutase (MCM) apoenzyme. Here we report the results of mutation study of exon 2 of the methylmalonyl CoA mutase (MUT) gene, coding MCM residues from 1 to 128, in ten unrelated Egyptian families affected with methylmalonic aciduria. Patients were presented with a wide-anion gap metabolic acidosis. The diagnosis has established by the measurement of C3 (propionylcarnitine) and C3:C2 (propionylcarnitine/acetylcarnitine) in blood by using liquid chromatography-tandem mass spectrometry (LC/MS-MS) and was confirmed by the detection of an abnormally elevated level of methylmalonic acid in urine by using gas chromatography-mass spectrometry (GC/MS) and isocratic cation exchange high-performance liquid-chromatography (HPLC). Direct sequencing of gDNA of the MUT gene exon 2 has revealed a total of 26 allelic variants: ten of which were intronic, eight were located upstream to the exon 2 coding region, four were novel modifications predicted to affect the splicing region, three were novel mutations within the coding region: c.15G > A (p.K5K), c.165C > A (p.N55K) and c.7del (p.R3EfsX14), as well as the previously reported mutation c.323G > A (p.R108H).

  2. Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants

    Directory of Open Access Journals (Sweden)

    Dina A. Ghoraba

    2015-02-01

    Full Text Available Methylmalonic aciduria (MMA is an autosomal recessive disorder of methylmalonate and cobalamin (cbl; vitamin B12 metabolism. It is an inborn error of organic acid metabolism which commonly results from a defect in the gene encoding the methylmalonyl-CoA mutase (MCM apoenzyme. Here we report the results of mutation study of exon 2 of the methylmalonyl CoA mutase (MUT gene, coding MCM residues from 1 to 128, in ten unrelated Egyptian families affected with methylmalonic aciduria. Patients were presented with a wide-anion gap metabolic acidosis. The diagnosis has established by the measurement of C3 (propionylcarnitine and C3:C2 (propionylcarnitine/acetylcarnitine in blood by using liquid chromatography–tandem mass spectrometry (LC/MS–MS and was confirmed by the detection of an abnormally elevated level of methylmalonic acid in urine by using gas chromatography–mass spectrometry (GC/MS and isocratic cation exchange high-performance liquid-chromatography (HPLC. Direct sequencing of gDNA of the MUT gene exon 2 has revealed a total of 26 allelic variants: ten of which were intronic, eight were located upstream to the exon 2 coding region, four were novel modifications predicted to affect the splicing region, three were novel mutations within the coding region: c.15G>A (p.K5K, c.165C>A (p.N55K and c.7del (p.R3EfsX14, as well as the previously reported mutation c.323G>A (p.R108H.

  3. The relationship between MHC-DRB1 gene second exon polymorphism and hydatidosis resistance of Chinese merino (Sinkiang Junken type), Kazakh and Duolang sheep

    OpenAIRE

    Li R.Y.; Hui W.Q.; Jia B; Shi G.Q.; Zhao Z.S.; Shen H.; Peng Q; Lv L.M.; Zhou Q.W.; Li H.T.

    2011-01-01

    The present study aimed at detecting the association of ovine major histocompatibility complex class II (Ovar II) DRB1 gene second exon and susceptibility or resistance to hydatidosis in three sheep breeds of Sinkiang. The MHC-DRB1 second exon was amplified by polymerase chain reaction (PCR) from DNA samples of healthy sheep and sheep with hydatidosis. PCR products were characterized by the restriction fragment length polymorphism (RFLP) technique. Five restriction enzymes, MvaI, HaeIII, SacI...

  4. Single Nucleotide Polymorphisms (SNPs in Exon 6 of Lecithin Cholesterol Acyltransferase (LCAT Gene in Indonesian Local Sheep

    Directory of Open Access Journals (Sweden)

    Hidayati

    2014-08-01

    Full Text Available Lecithin cholesterol acyltransferase (LCAT is a soluble enzyme that converts cholesterol and lecithin to cholesteryl esters and lysolecithins on the surface of high density lipoprotein and plays an important role in lipoprotein metabolism. The research was aimed to explore single nucleotide polymorphisms of LCAT gene in Indonesian local sheep. A total of 118 genomic DNA of Indonesian local sheep were used in this research, consisted of Sumatera Thin Tail (43 heads, Garut (19 heads, Javanese Thin Tail (17 heads, Javanese Fat Tail (6 heads, Rote Island (7 heads, Kissar (7 heads, Sumbawa (10 heads, and Lembah Palu (9 heads. Polymerase chain reaction was used to amplify genomic DNA for exon 6 (250 bp and direct sequencing method was used to identify polymorphism sequences. The sequences were analyzed with BioEdit and MEGA 5.2 software. The BLAST sequence was obtained from Gene Bank GQ 150556.1. The results showed three novel SNPs, i.e. c.742C>T, c.770 T>A and c.882C>T. Substitution of cytosine to thymine c.742 is a synonymous mutation; thymine to adenine c.770 and cytosine to thymine c.882 are non-synonymous mutations. Polymorphisms of LCAT gene exon 6 was found in Sumatera Thin Tail, Javanese Thin Tail, Javanese Fat Tail, Garut, Lembah Palu, and Rote Island.

  5. Becker Muscular Dystrophy (BMD) caused by duplication of exons 3-6 of the dystrophin gene presenting as dilated cardiomyopathy

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, A.C.; Allingham-Hawkins, D.J.; Becker, L. [Univ. of Toronto, Ontario (Canada)] [and others

    1994-09-01

    X-linked dilated cardiomyopathy (XLCM) is a progressive myocardial disease presenting with congestive heart failure in teenage males without clinical signs of skeletal myopathy. Tight linkage of XLCM to the DMD locus has been demonstrated; it has been suggested that, at least in some families, XLCM is a {open_quotes}dystrophinopathy.{close_quotes} We report a 14-year-old boy who presented with acute heart failure due to dilated cardiomyopathy. He had no history of muscle weakness, but physical examination revealed pseudohypertrophy of the calf muscles. He subsequently received a heart transplantation. Family history was negative. Serum CK level at the time of diagnosis was 10,416. Myocardial biopsy showed no evidence of carditis. Dystrophin staining of cardiac and skeletal muscle with anti-sera to COOH and NH{sub 2}termini showed a patchy distribution of positivity suggestive of Becker muscular dystrophy. Analysis of 18 of the 79 dystrophin exons detected a duplication that included exons 3-6. The proband`s mother has an elevated serum CK and was confirmed to be a carrier of the same duplication. A mutation in the muscle promotor region of the dystrophin gene has been implicated in the etiology of SLCM. However, Towbin et al. (1991) argued that other 5{prime} mutations in the dystrophin gene could cause selective cardiomyopathy. The findings in our patient support the latter hypothesis. This suggests that there are multiple regions in the dystrophin gene which, when disrupted, can cause isolated dilated cardiomyopathy.

  6. Identification of polymorphism in exons 7 and 12 of lactoferrin gene and its association with incidence of clinical mastitis in Murrah buffalo.

    Science.gov (United States)

    Dinesh, Krishanender; Verma, Archana; Das Gupta, Ishwar; Thakur, Yash Pal; Verma, Nishant; Arya, Ashwani

    2015-04-01

    Lactoferrin gene is one of the important candidate genes for mastitis resistance. The gene is located on chromosome BTA 22 and consists of 17 exons spanning over 34.5 kb of genomic DNA. The present study was undertaken with the objectives to identify allelic variants in exons 7 and 12 of lactoferrin gene and to analyze association between its genetic variants and incidence of clinical mastitis in Murrah buffalo. The amplification of exons 7 and 12 of lactoferrin gene yielded amplicons of 232- and 461-bp sizes. PCR-restriction fragment length polymorphism (RFLP) analysis of 232-bp amplicon using BccI restriction enzyme revealed three genotypes (AA, AB, and BB) with frequencies of 0.62, 0.22, and 0.16, respectively. The frequencies of two alleles, A and B, were estimated as 0.73 and 0.27. Hpy188I-RFLP for 461-bp amplicon revealed polymorphism with three genotypes, CC, CD, and DD, with respective frequencies of 0.06, 0.39, and 0.56, whereas frequencies for C and D alleles were 0.25 and 0.75. The chi-square (χ(2)) analysis revealed a significant association between incidence of clinical mastitis and genetic variants of exon 7, and animals of AA genotype of exon 7 were found to be least susceptible to mastitis. The findings indicate potential scope for incorporation of lactoferrin gene in selection and breeding of Murrah buffaloes for improved genetic resistance to mastitis.

  7. Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter

    Energy Technology Data Exchange (ETDEWEB)

    Yanagawa, H.; Nishio, H.; Takeshima, Y. [Kobe Univ. School of Medicine (Japan)] [and others

    1994-09-01

    The dystrophin gene, which is muted in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously-unidentified alternative promoter. The case study presented is that of patient with Duchenne muscular dystrophy who had a deletion extending from 5{prime} end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5{prime} part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5{prime} end of the new transcript indicated that the 5{prime} end of exon 3 was extended by 9 codons, only the last (most 3{prime}) of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5{prime} of the previously-identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.

  8. Novel exons in the tbx5 gene locus generate protein isoforms with distinct expression domains and function.

    Science.gov (United States)

    Yamak, Abir; Georges, Romain O; Sheikh-Hassani, Massomeh; Morin, Martin; Komati, Hiba; Nemer, Mona

    2015-03-13

    TBX5 is the gene mutated in Holt-Oram syndrome, an autosomal dominant disorder with complex heart and limb deformities. Its protein product is a member of the T-box family of transcription factors and an evolutionarily conserved dosage-sensitive regulator of heart and limb development. Understanding TBX5 regulation is therefore of paramount importance. Here we uncover the existence of novel exons and provide evidence that TBX5 activity may be extensively regulated through alternative splicing to produce protein isoforms with differing N- and C-terminal domains. These isoforms are also present in human heart, indicative of an evolutionarily conserved regulatory mechanism. The newly identified isoforms have different transcriptional properties and can antagonize TBX5a target gene activation. Droplet Digital PCR as well as immunohistochemistry with isoform-specific antibodies reveal differential as well as overlapping expression domains. In particular, we find that the predominant isoform in skeletal myoblasts is Tbx5c, and we show that it is dramatically up-regulated in differentiating myotubes and is essential for myotube formation. Mechanistically, TBX5c antagonizes TBX5a activation of pro-proliferative signals such as IGF-1, FGF-10, and BMP4. The results provide new insight into Tbx5 regulation and function that will further our understanding of its role in health and disease. The finding of new exons in the Tbx5 locus may also be relevant to mutational screening especially in the 30% of Holt-Oram syndrome patients with no mutations in the known TBX5a exons.

  9. Polymorphisms in exons 1B and 1C of the type I interleukin-1 receptor gene in patients with endometriosis.

    Science.gov (United States)

    D'Amora, Paulo; Sato, Hélio; Girão, Manoel J B C; Silva, Ismael D C G; Schor, Eduardo

    2006-09-01

    To study possible correlation between the prevalence of polymorphisms in the type I interleukin-1 receptor gene and pelvic endometriosis. Genotypes of 223 women were analyzed: 109 women with surgically and histologically confirmed endometriosis and 114 healthy women. Distributions of two single-base polymorphisms of the human interleukin-1 receptor type I (IL-1RI) gene were evaluated: PstI, due to a C-->T transition in exon 1B and BsrBI a C-->A transition at position 52 in exon 1C. Polymorphisms were detected by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis (RFLP) resolved on 3% agarose gels stained with ethidium bromide. Genotypes for PstI polymorphisms did not differ significantly among control and endometriosis (P = 0.058). However, in relation to BsrBI polymorphism, protective risk was observed for the development of endometriosis [OR 0.39-IC 95% (0.2-0.9)]. BsrBI heterozygote genotype (C/A) showed protective effect against endometriosis development.

  10. Detection of mutations within exons 4 to 8 of the p53 tumor suppressor gene in canine mammary glands

    Directory of Open Access Journals (Sweden)

    D.M.B. Souza

    2012-04-01

    Full Text Available Fifteen female canines with mammary tumors and 6 normal females were used to study mutations in exons 4 to 8 of the p53 gene. DNA samples from the tumors, respective adjacent normal mammary tissue and mammary glands from healthy animals were sequenced and analyzed for the presence of mutations. Mutations were found in 71.8% of the samples and the most frequent were missense mutations. The most attacked exons in the mammary tumor were 5, 7 and 8, with 23.4, 31.6 and 23.4% mutations, respectively. Canine mammary tumors are related to mutations in gene p53 and mutations mostly occur in the region of the protein that is linked to the DNA in the cell nucleus, which can change the functionality of the cell and propitiate tumor growth. Despite being macroscopically normal, the mammary tissue adjacent to the tumors has mutations that can lead to recurrence if not removed together with the tumor.

  11. Identification of coding exon 3 duplication in the BMPR1A gene in a patient with juvenile polyposis syndrome.

    Science.gov (United States)

    Yamaguchi, Junya; Nagayama, Satoshi; Chino, Akiko; Sakata, Ai; Yamamoto, Noriko; Sato, Yuri; Ashihara, Yuumi; Kita, Mizuho; Nomura, Sachio; Ishikawa, Yuichi; Igarashi, Masahiro; Ueno, Masashi; Arai, Masami

    2014-10-01

    Juvenile polyposis syndrome is an autosomal dominant inherited disorder characterized by multiple juvenile polyps arising in the gastrointestinal tract and an increased risk of gastrointestinal cancers, specifically colon cancer. BMPR1A and SMAD4 germline mutations have been found in patients with juvenile polyposis syndrome. We identified a BMPR1A mutation, which involves a duplication of coding exon 3 (c.230+452_333+441dup1995), on multiple ligation dependent probe amplification in a patient with juvenile polyposis syndrome. The mutation causes a frameshift, producing a truncated protein (p.D112NfsX2). Therefore, the mutation is believed to be pathogenic. We also identified a duplication breakpoint in which Alu sequences are located. These results suggest that the duplication event resulted from recombination between Alu sequences. To our knowledge, partial duplication in the BMPR1A gene has not been reported previously. This is the first case report to document coding exon 3 duplication in the BMPR1A gene in a patient with juvenile polyposis syndrome.

  12. X-linked familial exudative vitreoretinopathy caused by an arginine to leucine substitution in exon 3 of the Norrie gene

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, K.; Perry, Y.M.; Ferrell, R.E. [Univ. of Pittsburg, PA (United States)] [and others

    1994-09-01

    Familial exudative vitreoretinopathy (FEVR) is a disorder characterized by abnormal vascularization of the peripheral retina affecting both the retina and the vitreous body. This is a bilateral disorder and leads to a clinical phenotype resembling retinopathy of prematurity, but affected individuals experience a normal gestational period, and they do not have a history of oxygen therapy. Manifestations of the disorder may include retinal folds, retinal traction, sub- or intraretinal exudates, and in severe cases enophthalmos or phthisis ultimately leading to blindness. Autosomal dominant and X-linked patterns of segregation have been reported. We studied a large three-generation family in which FEVR segregated as an X-linked recessive trait. The Norrie gene was examined because of a prior report of mutation in this gene in a small X-linked FEVR family. Exons 1-3 of the Norrie gene were amplified and screened for mutations by single stranded conformational analysis. A variant conformer of exon 3 was observed in an affected male and in combination with the normal conformer in an obligate carrier female. Sequence analysis revealed a G{r_arrow}T transversion destroying an MspI restriction site. The mutation was present in all affected males, and all obligate carrier females were heterozygous for the mutation. The mutation was not present in unaffected males or in 108 randomly selected normal females. The G{r_arrow}T mutation leads to the substitution of a hydrophobic leucine residue for the positively charged arginine normally present at position 121 of the Norrie gene product. This study confirms that mutation in the Norrie gene can lead to the FEVR phenotype and the existence of allelic heterogeneity.

  13. The point mutation of p53 gene exon7 in hepatocellular carcinoma from Anhui Province, a non HCC prevalent area in China

    Institute of Scientific and Technical Information of China (English)

    Hu Liu; Yuan Wang; Qing Zhou; Shu-Yu Gui; Xu Li

    2002-01-01

    AIM: In hepatocellular carcinoma (HCC) prevalent areas ofChina, the point mutation of p53 exon7 is highly correlatedwith Hepatitis B virus(HBV) infection and aflatoxin B intake.While in non-HCC-prevalent areas of China, these factorsare not so important in the etiology of HCC. Therefore, thepoint mutation of p.53 exon7 may also be different than thatin HCC-prevalent areas of China. The aim of this study is toinvestigate the status and carcinogenic role of the pointmutation of p53 gene exon7 in hepatocellular carcinoma fromAnhui Province, a non-HCC-prevalent area in China.METHODS: PCR,PCR-SSCP and PCR-RFLP were applied toanalyze the homozygous deletion and point mutation of p53exon7 in HCC samples from Anhui, which were confirmedby DNA sequencing and Genbank comparison.RESULTS: In the 38 samples of hepatocellular carcinoma, nohomozygous deletion of p53 exon7 was detected and pointmutations of p53 exon7 were found in 4 cases, which werefound to be heterozygous mutation of codon 249 With amutation rate of 10.53 %(4/38). The third base mutstion(G→T) of p53 codon 249 was found by DNA sequencing andGenbank comparison.CONCLUSION: The incidence of point mutation of p53 codon249 is lower in hepatocellular carcinoma and theheterozygous mutation of p53 exon7 found in these patientsonly indicate that they have genetic susceptibility to HCC.p53 codon 249 is a hotspot of p53 exon7 point mutation,suggesting that the point mutation of p53 exon 7 may notplay a major role in the carcinogenesis of HCC in AnhuiProvince, a non-HCC-prsvalent area in China.

  14. No role for estrogen receptor 1 gene intron 1 Pvu II and exon 4 C325G polymorphisms in migraine susceptibility

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    Quinlan Sharon

    2006-02-01

    Full Text Available Abstract Background We have previously reported an association between the estrogen receptor 1 (ESR1 gene exon 8 G594A polymorphism and migraine susceptibility in two independent Australian cohorts. In this paper we report results of analysis of two further single nucleotide polymorphisms (SNPs in the ESR1 gene in the same study group, the T/C Pvu II SNP in intron 1 and the C325G SNP in exon 4, as well as results of linkage disequilibrium (LD analysis on these markers. Methods We investigated these variants by case-control association analysis in a cohort of 240 migraineurs and 240 matched controls. The SNPs were genotyped using specific restriction enzyme assays. Results were analysed using contingency table methods incorporating the chi-squared statistic. LD results are presented as D' statistics with associated P values. Results We found no evidence for association of the Pvu II T/C polymorphism and the C325G polymorphism and migraine susceptibility and no evidence for LD between these two SNPs and the previously implicated exon 8 G594A marker. Conclusion We have found no role for the polymorphisms in intron 1 and exon 4 with migraine susceptibility. To further investigate our previously implicated exon 8 marker, we suggest the need for studies with a high density of polymorphisms be undertaken, with particular focus on markers in LD with the exon 8 marker.

  15. The influence of dopaminergic gene variants on decision making in the ultimatum game

    Directory of Open Access Journals (Sweden)

    Martin eReuter

    2013-06-01

    Full Text Available One of the most prominent paradigms in neuroeconomics is the Ultimatum Game (UG that provides a framework for the study of pro-social behavior in two players interacting anonymously with each other: Player 1 has to split an endowment with player 2. Player 2 can either accept or reject the offer from player 1. If player 2 accepts the offer then the money is split as proposed by player 1. In case of rejection both players get nothing. Until now only one twin study investigated the heritability of the behavior in the UG. Results indicated a strong heritability for the decision behavior of player 2 whereas no genetic influence on player 1 behavior could be detected. Further studies are mandatory to validate these heritability estimates. However, a first candidate polymorphism, the DRD4 exon III, constituting the biological basis of the heritability in the responder behavior has already been identified in a Chinese sample (Zhong et al., 2010. Until now genetic studies in Caucasians on the UG are lacking. The present study wants to fill this gap by investigating the UG in a healthy German sample. Moreover, we intend to find candidate genes that are associated with the first-mover-behavior. In a sample of N=130 healthy participants an online version of the UG was conducted and polymorphisms of the dopamine D2 receptor gene (DRD2 and the DRD4 exon III VNTR were genotyped. We could confirm the DRD4 exon III effect on the responder behavior and the absence of an effect on the proposer behavior reported before. In line with Zhong et al. (2010 carriers of the 4/4 genotype showed a significant higher minimal acceptable offer (p=0.023 than subjects with any other genotype. Furthermore, a DRD2-haplotype-block containing the single nucleotide polymorphisms rs1800497 and rs2283265 was significantly associated with the amount player1 offered (p=.005 but not with the decision of player 2. Results support the importance of the dopaminergic system for pro

  16. The influence of dopaminergic gene variants on decision making in the ultimatum game.

    Science.gov (United States)

    Reuter, Martin; Felten, Andrea; Penz, Sabrina; Mainzer, Anna; Markett, Sebastian; Montag, Christian

    2013-01-01

    One of the most prominent paradigms in neuroeconomics is the ultimatum game (UG) that provides a framework for the study of pro-social behavior in two players interacting anonymously with each other: Player 1 has to split an endowment with player 2. Player 2 can either accept or reject the offer from player 1. If player 2 accepts the offer then the money is split as proposed by player 1. In case of rejection both players get nothing. Until now only one twin study investigated the heritability of the behavior in the UG. Results indicated a strong heritability for the decision behavior of player 2 whereas no genetic influence on player 1 behavior could be detected. Further studies are mandatory to validate these heritability estimates. However, a first candidate polymorphism, the DRD4 exon III, constituting the biological basis of the heritability in the responder behavior has already been identified in a Chinese sample (Zhong et al., 2010). Until now genetic studies in Caucasians on the UG are lacking. The present study wants to fill this gap by investigating the UG in a healthy German sample. Moreover, we intend to find candidate genes that are associated with the first-mover-behavior. In a sample of N = 130 healthy participants an online version of the UG was conducted and polymorphisms of the dopamine D2 receptor gene (DRD2) and the DRD4 exon III VNTR were genotyped. We could confirm the DRD4 exon III effect on the responder behavior and the absence of an effect on the proposer behavior reported before. In line with Zhong et al. (2010) carriers of the 4/4 genotype showed a significant higher minimal acceptable offer (p = 0.023) than subjects with any other genotype. Furthermore, a DRD2-haplotype-block containing the single nucleotide polymorphisms rs1800497 and rs2283265 was significantly associated with the amount player1 offered (p = 0.005) but not with the decision of player 2. Results support the importance of the dopaminergic system for pro-social behavior.

  17. Novel deletion encompassing exons 5-12 of the UBE3A gene in a girl with Angelman syndrome.

    Science.gov (United States)

    Beleza-Meireles, Ana; Cerqueira, Rita; Sousa, Sérgio B; Palmeiro, Aida; Ramos, Lina

    2011-01-01

    Angelman syndrome (AS) is characterised by severe developmental delay, severe speech impairment, gait ataxia and/or limb tremor and a unique behavioural phenotype. The diagnosis of AS is based on a combination of clinical features and molecular genetic testing. Currently, molecular genetic testing (methylation analysis and UBE3A sequence analysis) identifies anomalies in about 90% of individuals. The aetiology of the remaining 10% is still unknown. We report a novel deletion encompassing the exons 5-12 of the UBE3A gene in a girl with AS, identified by MLPA (Multiplex Ligation-dependent Probe Amplification), which was not detected by the conventional diagnostic protocol. We propose that copy number analysis of the UBE3A gene should be considered in individuals whose clinical examination is strongly suggestive of AS, after more common mechanisms have been excluded. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  18. Molecular genetic analysis of cereal β-amylase genes using exon-primed intron-crossing (EPIC PCR

    Directory of Open Access Journals (Sweden)

    Stratula Olga

    2014-01-01

    Full Text Available The proteins encoded by cereal β-amylase genes Bamy1 and Bamy2 genes play an important role in seedling germination and in the brewing process. Here, we use exon-primed intron-crossing (EPIC to analyse Bamy1 and Bamy2 genetic diversity among 38 accessions belonging to six Poaceae tribes. DNA sequence alignment of multiple Poaceae species β-amylase sequences allowed design of EPIC primers that simultaneously amplify Bamy1 and Bamy2 in all the cereal species investigated. The genetic variation observed in the samples investigated is analysed and discussed, and illustrates the effectiveness of this approach for intra- and interspecific analysis in plant species.

  19. Mutations in the unc-52 gene responsible for body wall muscle defects in adult Caenorhabditis elegans are located in alternatively spliced exons

    Energy Technology Data Exchange (ETDEWEB)

    Rogalski, T.M.; Gilchrist, E.J.; Mullen, G.P. [Univ. of British, Columbia, Vancouver (Canada)] [and others

    1995-01-01

    The unc-52 gene in Caenorhabditis elegans produces several large proteins that function in the basement membrane underlying muscle cells. Mutations in this gene result in defects in myofilament assembly and in the attachment of the myofilament lattice to the muscle cell membrane. The st549 and ut111 alleles of unc-52 produce a lethal (Pat) terminal phenotype whereas the e444, e669, e998, e1012 and e1421 mutations result in viable, paralyzed animals. We have identified the sequence alterations responsible for these mutant phenotypes. The st549 allele has a premature stop codon in exon 7 that should result in the complete elimination of unc-52 gene function, and the ut111 allele has a Tc1 transposon inserted into the second exon of the gene. The five remaining mutations are clustered in a small interval containing three adjacent, alternatively spliced exons (16, 17 and 18). These mutations affect some, but not all of the unc-52-encoded proteins. Thirteen intragenic revertants of the e669, e998, e1012 and e1421 alleles have also been sequenced. The majority of these carry the original mutation plus a G to A transition in the conserved splice acceptor site of the affected exon. This result suggests that reversion of the mutant phenotype in these strains may be the result of exon-skipping. 38 refs., 6 figs., 2 tabs.

  20. A novel point mutation within the EDA gene causes an exon dropping in mature RNA in Holstein Friesian cattle breed affected by X-linked anhidrotic ectodermal dysplasia

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    Pariset Lorraine

    2011-07-01

    Full Text Available Abstract Background X-linked anhidrotic ectodermal dysplasia is a disorder characterized by abnormal development of tissues and organs of ectodermal origin caused by mutations in the EDA gene. The bovine EDA gene encodes the ectodysplasin A, a membrane protein expressed in keratinocytes, hair follicles and sweat glands, which is involved in the interactions between cell and cell and/or cell and matrix. Four mutations causing ectodermal dysplasia in cattle have been described so far. Results We identified a new single nucleotide polymorphism (SNP at the 9th base of exon 8 in the EDA gene in two calves of Holstein Friesian cattle breed affected by ectodermal dysplasia. This SNP is located in the exonic splicing enhancer (ESEs recognized by SRp40 protein. As a consequence, the spliceosome machinery is no longer able to recognize the sequence as exonic and causes exon skipping. The mutation determines the deletion of the entire exon (131 bp in the RNA processing, causing a severe alteration of the protein structure and thus the disease. Conclusion We identified a mutation, never described before, that changes the regulation of alternative splicing in the EDA gene and causes ectodermal dysplasia in cattle. The analysis of the SNP allows the identification of carriers that can transmit the disease to the offspring. This mutation can thus be exploited for a rational and efficient selection of unequivocally healthy cows for breeding.

  1. Germ line transcription in mice bearing neor gene downstream of Igamma3 exon in the Ig heavy chain locus.

    Science.gov (United States)

    Samara, Maha; Oruc, Zeliha; Dougier, Hei-Lanne; Essawi, Tamer; Cogné, Michel; Khamlichi, Ahmed Amine

    2006-04-01

    Class switch recombination (CSR) is preceded by germ line transcription that initiates from promoters upstream of switch (S) sequences and terminates downstream of associated constant genes. Previous work showed that germ line transcripts and their processing are required for CSR and that germ line transcription is regulated in a major part by a regulatory region located downstream of the Ig heavy chain locus. This long-range, polarized effect can be disturbed by inserting an expressed neomycine resistance (neo(r)) gene. To contribute to a better understanding of the mechanism of such a long-distance regulation, we generated knock-in mice in which a neo(r) gene was inserted downstream of Igamma3 exon leaving intact all the necessary elements for germ line transcription and splicing. We show that the expressed neo(r) gene interferes with transcription initiation from Igamma3, and that it impairs but does not block S recombination to Cgamma3. Moreover, we show for the first time that the neo(r) gene provides through chimeric neo(r)-Cgamma3 transcripts the necessary elements for splicing of germ line transcripts by activating two novel cryptic splice sites, one in the coding region of the intronless neo(r) gene and the other in the Igamma3-Cgamma3 intron.

  2. Silent exonic mutations in the low-density lipoprotein receptor gene that cause familial hypercholesterolemia by affecting mRNA splicing.

    Science.gov (United States)

    Defesche, J C; Schuurman, E J M; Klaaijsen, L N; Khoo, K L; Wiegman, A; Stalenhoef, A F H

    2008-06-01

    In a large group of patients with the clinical phenotype of familial hypercholesterolemia, such as elevated low-density lipoprotein (LDL) cholesterol and premature atherosclerosis, but without functional mutations in the genes coding for the LDL receptor and apolipoprotein B, we examined the effect of 128 seemingly neutral exonic and intronic DNA variants, discovered by routine sequencing of these genes. Two variants, G186G and R385R, were found to be associated with altered splicing. The nucleotide change leading to G186G resulted in the generation of new 3'-splice donor site in exon 4 and R385R was associated with a new 5'-splice acceptor site in exon 9 of the LDL receptor gene. Splicing of these alternate splice sites leads to an in-frame 75-base pair deletion in a stable mRNA of exon 4 in case of G186G and R385R resulted in a 31-base pair frame-shift deletion in exon 9 and non-sense-mediated mRNA decay.

  3. Complete androgen insensitivity syndrome is frequently due to premature stop codons in exon 1 of the androgen receptor gene: an international collaborative report of 13 new mutations.

    Science.gov (United States)

    Philibert, Pascal; Audran, Françoise; Pienkowski, Catherine; Morange, Isabelle; Kohler, Birgit; Flori, Elisabeth; Heinrich, Claudine; Dacou-Voutetakis, Catherine; Joseph, Marie-Geneviève; Guedj, Anne-Marie; Journel, Hubert; Hecart-Bruna, Annie-Claude; Khotchali, Ines; Ten, Svetlana; Bouchard, Philippe; Paris, Françoise; Sultan, Charles

    2010-07-01

    To confirm the clinical diagnosis of complete androgen insensitivity syndrome (CAIS) by molecular genetic analysis and to determine the prevalence of exon 1 mutations in the androgen receptor (AR) transactivation defects of a large series of CAIS patients. International retrospective study. University Hospital of Montpellier, Department of Hormonology. 105 patients with normal female external genitalia, bilateral intra-abdominal or inguinal testis, normal breast development, absent or sparse pubic hair, normal or high endogenous testosterone production, hypoplastic or absent wolffian structures, and 46,XY karyotype. Sequencing of the AR gene. Prevalence of AR exon 1 mutations. Over a 10-year period (1997 to 2007), we identified 78 AR gene mutations in 105 patients with CAIS; 21 of them were located in exon 1, and 13 of these were new mutations. We report 13 new mutations in the AR gene. All but one were stop codons, and the last was a splicing abnormality. The finding that 27% of the mutations in our cohort were localized in exon 1 versus 15% in previous works justifies the sequencing of this exon in patients with CAIS. Copyright 2010. Published by Elsevier Inc.

  4. Clinical implications of cytosine deletion of exon 5 of P53 gene in non small cell lung cancer patients

    Directory of Open Access Journals (Sweden)

    Rashid Mir

    2016-01-01

    Full Text Available Aim: Lung cancer is considered to be the most common cancer in the world. In humans, about 50% or more cancers have a mutated tumor suppressor p53 gene thereby resulting in accumulation of p53 protein and losing its function to activate the target genes that regulate the cell cycle and apoptosis. Extensive research conducted in murine cancer models with activated p53, loss of p53, or p53 missense mutations have facilitated researchers to understand the role of this key protein. Our study was aimed to evaluate the frequency of cytosine deletion in nonsmall cell lung cancer (NSCLC patients. Methods: One hundred NSCLC patients were genotyped for P53 (exon5, codon168 cytosine deletion leading to loss of its function and activate the target genes by allele-specific polymerase chain reaction. The P53 cytosine deletion was correlated with all the clinicopathological parameters of the patients. Results and Analysis: 59% cases were carrying P53 cytosine deletion. Similarly, the significantly higher incidence of cytosine deletion was reported in current smokers (75% in comparison to exsmoker and nonsmoker. Significantly higher frequency of cytosine deletion was reported in adenocarcinoma (68.08% than squamous cell carcinoma (52.83%. Also, a significant difference was reported between p53 cytosine deletion and metastasis (64.28%. Further, the majority of the cases assessed for response carrying P53 cytosine deletion were found to show faster disease progression. Conclusion: The data suggests that there is a significant association of the P53 exon 5 deletion of cytosine in codon 168 with metastasis and staging of the disease.

  5. Exonic rearrangements in the known Parkinson's disease-causing genes are a rare cause of the disease in South African patients.

    Science.gov (United States)

    van der Merwe, Celia; Carr, Jonathan; Glanzmann, Brigitte; Bardien, Soraya

    2016-04-21

    Parkinson's disease (PD) is a neurodegenerative movement disorder characterized by the loss of dopaminergic neurons in the substantia nigra of the midbrain. To date, a number of PD-causing genes have been found, including SNCA, LRRK2, VPS35, PARK2, PINK1, DJ-1, ATP13A2, and most recently CHCHD2. Mutations in these genes range from point mutations to larger exonic rearrangements including deletions and duplications. This study aimed to detect possible copy number variation (CNV) in the known PD-causing genes in a cohort of South African patients with PD. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis was performed on a total of 210 South African PD patients, and possible CNVs were verified using quantitative real time PCR. No homozygous or compound heterozygous exon rearrangements in the genes analysed were found in the patient group. A heterozygous PARK2 exon 4 deletion was found in a sporadic patient with an age at onset of 51 years. Sanger sequencing did not reveal any additional mutations in PARK2 in this patient. Combining our results with that of previous studies in a South African cohort, the frequency of exonic rearrangements in the known PD-causing genes is only 1.8% (8/439 patients). In conclusion, CNV in the known PD-causing genes are a rare cause of PD in a South African cohort, and there may be as yet unknown genetic causes of PD that are specific to patients of African ethnicity.

  6. CELF family RNA-binding protein UNC-75 regulates two sets of mutually exclusive exons of the unc-32 gene in neuron-specific manners in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Hidehito Kuroyanagi

    Full Text Available An enormous number of alternative pre-mRNA splicing patterns in multicellular organisms are coordinately defined by a limited number of regulatory proteins and cis elements. Mutually exclusive alternative splicing should be strictly regulated and is a challenging model for elucidating regulation mechanisms. Here we provide models of the regulation of two sets of mutually exclusive exons, 4a-4c and 7a-7b, of the Caenorhabditis elegans uncoordinated (unc-32 gene, encoding the a subunit of V0 complex of vacuolar-type H(+-ATPases. We visualize selection patterns of exon 4 and exon 7 in vivo by utilizing a trio and a pair of symmetric fluorescence splicing reporter minigenes, respectively, to demonstrate that they are regulated in tissue-specific manners. Genetic analyses reveal that RBFOX family RNA-binding proteins ASD-1 and FOX-1 and a UGCAUG stretch in intron 7b are involved in the neuron-specific selection of exon 7a. Through further forward genetic screening, we identify UNC-75, a neuron-specific CELF family RNA-binding protein of unknown function, as an essential regulator for the exon 7a selection. Electrophoretic mobility shift assays specify a short fragment in intron 7a as the recognition site for UNC-75 and demonstrate that UNC-75 specifically binds via its three RNA recognition motifs to the element including a UUGUUGUGUUGU stretch. The UUGUUGUGUUGU stretch in the reporter minigenes is actually required for the selection of exon 7a in the nervous system. We compare the amounts of partially spliced RNAs in the wild-type and unc-75 mutant backgrounds and raise a model for the mutually exclusive selection of unc-32 exon 7 by the RBFOX family and UNC-75. The neuron-specific selection of unc-32 exon 4b is also regulated by UNC-75 and the unc-75 mutation suppresses the Unc phenotype of the exon-4b-specific allele of unc-32 mutants. Taken together, UNC-75 is the neuron-specific splicing factor and regulates both sets of the mutually exclusive

  7. A duchenne muscular dystrophy gene hot spot mutation in dystrophin-deficient cavalier king charles spaniels is amenable to exon 51 skipping.

    Directory of Open Access Journals (Sweden)

    Gemma L Walmsley

    Full Text Available BACKGROUND: Duchenne muscular dystrophy (DMD, which afflicts 1 in 3500 boys, is one of the most common genetic disorders of children. This fatal degenerative condition is caused by an absence or deficiency of dystrophin in striated muscle. Most affected patients have inherited or spontaneous deletions in the dystrophin gene that disrupt the reading frame resulting in unstable truncated products. For these patients, restoration of the reading frame via antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach. The major DMD deletion "hot spot" is found between exons 45 and 53, and skipping exon 51 in particular is predicted to ameliorate the dystrophic phenotype in the greatest number of patients. Currently the mdx mouse is the most widely used animal model of DMD, although its mild phenotype limits its suitability in clinical trials. The Golden Retriever muscular dystrophy (GRMD model has a severe phenotype, but due to its large size, is expensive to use. Both these models have mutations in regions of the dystrophin gene distant from the commonly mutated DMD "hot spot". METHODOLOGY/PRINCIPAL FINDINGS: Here we describe the severe phenotype, histopathological findings, and molecular analysis of Cavalier King Charles Spaniels with dystrophin-deficient muscular dystrophy (CKCS-MD. The dogs harbour a missense mutation in the 5' donor splice site of exon 50 that results in deletion of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein. Antisense oligonucleotide-mediated skipping of exon 51 in cultured myoblasts from an affected dog restored the reading frame and protein expression. CONCLUSIONS/SIGNIFICANCE: Given the small size of the breed, the amiable temperament and the nature of the mutation, we propose that CKCS-MD is a valuable new model for clinical trials of antisense oligonucleotide-induced exon skipping and other therapeutic approaches for DMD.

  8. Alternative splicing of exon 17 and a missense mutation in exon 20 of the insulin receptor gene in two brothers with a novel syndrome of insulin resistance (congenital fiber-type disproportion myopathy).

    Science.gov (United States)

    Vorwerk, P; Christoffersen, C T; Müller, J; Vestergaard, H; Pedersen, O; De Meyts, P

    1999-01-01

    The insulin receptor (IR) in two brothers with a rare syndrome of congenital muscle fiber type disproportion myopathy (CFTDM) associated with diabetes and severe insulin resistance was studied. By direct sequencing of Epstein-Barr virus-transformed lymphocytes both patients were found to be compound heterozygotes for mutations in the IR gene. The maternal allele was alternatively spliced in exon 17 due to a point mutation in the -1 donor splice site of the exon. The abnormal skipping of exon 17 shifts the amino acid reading frame and leads to a truncated IR, missing the entire tyrosine kinase domain. In the correct spliced variant, the point mutation is silent and results in a normally translated IR. The paternal allele carries a missense mutation in the tyrosine kinase domain. All three cDNA variants were present in the lymphocytes of the patients. Purified IR from 293 cells overexpressing either of the two mutated receptors lacked basal or stimulated IR beta-subunit autophosphorylation. A third brother who inherited both normal alleles has an normal muscle phenotype and insulin sensitivity, suggesting a direct linkage of these IR mutations with the CFTDM phenotype.

  9. EasyExonPrimer: automated primer design for exon sequences.

    Science.gov (United States)

    Wu, Xiaolin; Munroe, David J

    2006-01-01

    EasyExonPrimer is a web-based software that automates the design of PCR primers to amplify exon sequences from genomic DNA. EasyExonPrimer is written in Perl and uses Primer3 to design PCR primers based on the genome builds and annotation databases available at the University of California, Santa Cruz (UCSC) Genome Browser database (http://genome.ucsc.edu/). It masks repeats and known single nucleotide polymorphism (SNP) sites in the genome and designs standardised primers using optimised conditions. Users can input genes by RefSeq mRNA ID, gene name or keyword. The primer design is optimised for large-scale resequencing of exons. For exons larger than 1 kb, the user has the option of breaking the exon sequence down into overlapping smaller fragments. All primer pairs are then verified using the In-Silico PCR software to test for uniqueness in the genome. We have designed >1000 pairs of primers for 90 genes; 95% of the primer pairs successfully amplified exon sequences under standard PCR conditions without requiring further optimisation. EasyExonPrimer is available from http://129.43.22.27/~primer/. The source code is also available upon request. Xiaolin Wu (forestwu@mail.nih.gov).

  10. A nonsense mutation (Arg-196-Term) in exon 6 of the human TP53 gene identified in small cell lung carcinoma

    NARCIS (Netherlands)

    Hayes, VM; Oosthuizen, CJJ; Kotze, MJ; Marx, MP; Buys, CHCM

    1996-01-01

    In a search for mutations of the TP53 tumour suppressor gene in lung cancer samples from gold miners from the Witwatersrand, South Africa, using heteroduplex and single strand conformation polymorphism (SSCP) analysis, a nonsense mutation was found in exon 6, consisting of a C to T transition and re

  11. A novel missense mutation (402C-->T) in exon 1 in the EDA gene in a family with X-linked hypohidrotic ectodermal dysplasia

    DEFF Research Database (Denmark)

    Hertz, Jens Michael; Nørgaard Hansen, K; Juncker, I

    1998-01-01

    families with hypohidrotic ectodermal dysplasia for mutation in exon 1 of the EDA-gene by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). In one large kindred we identified a novel missense mutation (402C-->T), which changes a histidine to tyrosine at position 54...

  12. Complete androgen insensitivity syndrome due to a new frameshift deletion in exon 4 of the androgen receptor gene: Functional analysis of the mutant receptor

    NARCIS (Netherlands)

    J.M. Lobaccaro; S. Lumbroso; N. Poujol (Nicolas); V. Georget; A.O. Brinkmann (Albert); G. Malpuech (Georges); C. Sultan

    1995-01-01

    textabstractWe studied the androgen receptor gene in a large kindred with complete androgen insensitivity syndrome and negative receptor-binding activity, single-strand conformation polymorphism (SSCP) analysis and sequencing identified a 13 base pair deletion within exon 4. This was responsible for

  13. Functional Characterization of Exonic Variants of the PPARGC1B Gene in Coregulation of Estrogen Receptor Alpha.

    Science.gov (United States)

    Chang, Hun Soo; Lee, Shin-Hwa; Lee, Jong-Uk; Park, Jong Sook; Chung, Il Yup; Park, Choon-Sik

    2016-07-01

    Peroxisome proliferator-activated receptor gamma coactivator 1 beta (PPARGC1B) is a coactivator of estrogen receptor (ER)α and ERβ. We previously demonstrated a significant association between a variant of exon 5 of the PPARGC1B gene (+102525 G>A, R265Q) and airway hyperreactivity (AHR). The aims of the study were to evaluate the genetic effects of variants of the PPARGC1B gene on the function of ERs. PPARGC1B +102525G and A gene constructs were generated using PCR and cloned into a pCMV4 promoter vector. A luciferase reporter assay was undertaken in 293T cells cotransfected with one of the PPARGC1B +102525G>A constructs, ERα, and an estrogen response element (ERE) containing a luciferase construct after treatment with 17β-estradiol. According to the luciferase reporter assay, the +102525A allele showed higher ERα activity than the +102525G allele in response to stimulation with 17β-estradiol. In addition, the interaction between ERα and PPARGC1B was evaluated by coprecipitation assay. Human influenza hemagglutinin-tagged PPARGC1B coprecipitated more intensely with ERα in the +102525A than the +102525G construct after 17β estradiol treatment. The variant +102525A allele enhances the activity of ERα to a greater degree than the +102525G allele of PPARGC1B.

  14. Pseudohypoparathyroidism type Ib is not caused by mutations in the coding exons of the human parathyroid hormone (PTH)/PTH-related peptide receptor gene

    Energy Technology Data Exchange (ETDEWEB)

    Schipani, E.; Bergwitz, C.; Iida-Klein, A. [Massachusetts General Hospital, Boston, MA (United States)] [and others

    1995-05-01

    Pseudohypoparathyroidism type Ib (PHP-Ib) is thought to be from caused by a PTH/PTH-related peptide (PTHrP) receptor defect. To search for receptor mutations in genomic DNA from 17 PHP-Ib patients, three recently isolated human genomic DNA clones were further characterized by restriction enzyme mapping and nucleotide sequencing across intron/exon borders. Regions including all 14 coding exons and their splice junctions were amplified by polymerase chain reaction, and the products were analyzed by either temperature gradient gel electrophoresis or direct nucleotide sequencing. Silent polymorphisms were identified in exons G (1 of 17), M4 (1 of 17), and M7 (15 of 17). Two base changes were found in introns, 1 at the splice-donor site of the intron between exons E2 and E3 (1 of 17) and the other between exons G and M1 (2 of 17). Total ribonucleic acid from COS-7 cells expressing minigenes with or without the base change between exons E2 and E3 showed no difference by either Northern blot analysis or reverse transcriptase-polymerase chain reaction. Radioligand binding was indistinguishable for both transiently expressed constructs. A missense mutation (E546 to K546) in the receptor`s cytoplamic tail (3 of 17) was also found in 1 of 60 healthy individuals, and PTH/PTHrP receptors with this mutation were functionally indistinguishable from wild-type receptors. PHP-Ib thus appears to be rarely, if ever, caused by mutations in the coding exons of the PTH/PTHrP receptor gene. 58 refs., 4 figs., 4 tabs.

  15. Association between the SMN2 gene copy number and clinical characteristics of patients with spinal muscular atrophy with homozygous deletion of exon 7 of the SMN1 gene

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    Žarkov Marija

    2015-01-01

    Full Text Available Background/Aim. Spinal muscular atrophy (SMA is an autosomal recessive disease characterized by degeneration of alpha motor neurons in the spinal cord and the medulla oblongata, causing progressive muscle weakness and atrophy. The aim of this study was to determine association between the SMN2 gene copy number and disease phenotype in Serbian patients with SMA with homozygous deletion of exon 7 of the SMN1 gene. Methods. The patients were identified using regional Serbian hospital databases. Investigated clinical characteristics of the disease were: patients’ gender, age at disease onset, achieved and current developmental milestones, disease duration, current age, and the presence of the spinal deformities and joint contractures. The number of SMN1 and SMN2 gene copies was determined using real-time polymerase chain reaction (PCR. Results. Among 43 identified patients, 37 (86.0% showed homozygous deletion of SMN1 exon 7. One (2.7% of 37 patients had SMA type I with 3 SMN2 copies, 11 (29.7% patients had SMA type II with 3.1 ± 0.7 copies, 17 (45.9% patients had SMA type III with 3.7 ± 0.9 copies, while 8 (21.6% patients had SMA type IV with 4.2 ± 0.9 copies. There was a progressive increase in the SMN2 gene copy number from type II towards type IV (p < 0.05. A higher SMN2 gene copy number was associated with better current motor performance (p < 0.05. Conclusion. In the Serbian patients with SMA, a higher SMN2 gene copy number correlated with less severe disease phenotype. A possible effect of other phenotype modifiers should not be neglected.

  16. R25G mutation in exon 1 of LMNA gene is associated with dilated cardiomyopathy and limb-girdle muscular dystrophy 1B

    Institute of Scientific and Technical Information of China (English)

    YUAN Wo-liang; HUANG Wei-jun; HUANG Chun-yan; WANG Jing-feng; XIE Shuang-lun; NIE Ru-qiong; LIU Ying-mei; LIU Pin-ming; ZHOU Shu-xian; CHEN Su-qin

    2009-01-01

    Background Mutations of the LMNA gene encoding lamin A and C are associated with dilated cardiomyopathy (DCM), conduction system defects and skeletal muscle dystrophy. Here we report a family with a mutation of the LMNA gene to identify the relationship between genotype and phenotype.Methods All 30 members of the family underwent clinical and genetic evaluation. A mutation analysis of the LMNA gene was performed. All of the 12 exons of LMNA gene were extended with polymerase chain reaction (PCR) and the PCR products were screened for gene mutation by direct sequencing.Results Ten members of the family had limb-girdle muscular dystrophy (LGMD) and 6 are still alive. Two patients suffered from DCM. Cardiac arrhythmias included atrioventricular block and atrial fibrillation; sudden death occurred in 2 patients. The pattern of inheritance was autosomal dominant. Mutation c.73C>G (R25G) in exon 1 encoding the globular domains was confirmed in all of the affected members, resulting in the conversion of arginine (Arg) to glycine (Gly). Conclusions The mutation R25G in exon 1 of LMNA gene we reported here in a Chinese family had a phenotype of malignant arrhythmia and mild LGMD, suggesting that patients with familial DCM, conduction system defects and skeletal muscle dystrophy should be screened by genetic testing for the LMNA gene.

  17. Polymorphism of the promoter region and exon 1 of the CTLA4 gene in endemic pemphigus foliaceus (fogo selvagem

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    D.P. Pavoni

    2006-09-01

    Full Text Available Endemic pemphigus foliaceus (EPF is an autoimmune bullous skin disease characterized by acantholysis and antibodies against a desmosomal protein, desmoglein 1. Genetic and environmental factors contribute to development of this multifactorial disease. HLA class II and some cytokine gene polymorphisms are the only genetic markers thus far known to be associated with susceptibility to or protection from EPF. The cytotoxic T-lymphocyte antigen-4 gene (CTLA4 encodes a key immunoreceptor molecule that regulates and inhibits T-cell proliferation. It participates in the regulatory process controlling autoreactivity and therefore has been considered a strong candidate gene in autoimmune diseases. In the search for genes that might influence EPF pathogenesis, we analyzed variants of the CTLA4 gene in a sample of 118 patients and 291 controls from a Brazilian population. This is the first study investigating the possible role of polymorphisms of the 2q33 chromosomal region in differential susceptibility to pemphigus foliaceus. Promoter region and exon 1 single nucleotide polymorphisms -318 (C,T and 49 (A,G were genotyped using sequence-specific oligonucleotide probes after amplification by the polymerase chain reaction. The allelic and genotypic frequencies did not differ significantly between the patient and the control groups (-318T: 9.8 and 10.9%, 49G: 33.0 and 35.2% were the allelic frequencies in patients and controls, respectively. In addition, no significant difference was found when the patient and control population samples were stratified by the presence of HLA-DRB1 alleles. We conclude that the CTLA4 -318 (C,T and 49 (A,G polymorphisms do not play a major role in EPF development.

  18. One Novel Frameshift Mutation on Exon 64 of COL7A1 Gene in an Iranian Individual Suffering Recessive Dystrophic Epidermolysis Bullosa.

    Science.gov (United States)

    Khaniani, Mahmoud Shekari; Sohrabi, Nasrin; Derakhshan, Neda Mansoori; Derakhshan, Sima Mansoori

    2015-01-01

    Recessive dystrophic epidermolysis bullosa (RDEB) is an extremely rare subtype of bullous dermatosis caused by the COL7A1 gene mutation. After genomic DNA extraction from the peripheral blood sample of all subjects (3 pedigree members and 3 unrelated control individuals), COL7A1 gene screening was performed by PCR amplification and direct DNA sequencing of all of the coding exons and flanking intronic regions. Genetic analysis of the COL7A1 gene in an affected individual revealed a novel mutation: c.5493delG (p.K1831Nfs*10) in exon 64 of the COL7A1 gene in homozygous state. This mutation was not discovered in 3 unrelated Iranian control individuals. These data suggest that c.5493delG may influence the phenotype of RDEB. The result of this case report contributes to the expanding database on COL7A1 mutations.

  19. A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP).

    Science.gov (United States)

    Garcia-Rubio, Rocio; Gil, Horacio; Monteiro, Maria Candida; Pelaez, Teresa; Mellado, Emilia

    2016-01-01

    Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson's index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks.

  20. A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

    Science.gov (United States)

    Garcia-Rubio, Rocio; Gil, Horacio; Monteiro, Maria Candida; Pelaez, Teresa; Mellado, Emilia

    2016-01-01

    Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks. PMID:27701437

  1. [Analysis of polymorphisms in exon 14 in porcine Mx1 gene and identification of new mutation points].

    Science.gov (United States)

    Wu, Sheng-Long; Bao, Wen-Bin; Ju, Hui-Ping; Chen, Guo-Hong; Li, Bi-Chun; Cheng, Jin-Hua; Zhu, Guo-Qiang

    2007-06-01

    By the PCR-RFLP method, the polymorphisms of exon 14 of Mx1 gene were detected in 7 native and foreign pig breeds. Taken together with the analysis of restriction enzyme Hin6 I digestion, there were 6 genotypes and 3 alleles. And, all individuals of Duroc exhibited the AA genotype but the Sutai pigs exhibited all three kinds of genotypes. The BB genotype was detected only in Meishan pigs and their derivate Sutai pigs. Among all pig breeds, the allele B only appeared in Chinese indigenous pig breeds and developed pig breed in this study, and the allele A was dominant allele in all pig breeds except for Songliao black pig. The results of Chi Square test showed that there were abundant polymorphisms in all pig breeds. The gene frequency of Meishan pig and Songliao black pig showed greatly significant difference to other pig breeds (P0.05). Three new mutation points in three genotypes were identified by sequencing comparison analysis of PCR products, two of which resulted in Thr-->Ala and Glu-->Arg respectively, the last one was a silence mutation, the Glu-->Arg mutation point and this silence mutation point only appeared in the individuals with the BB genotype.

  2. Combined detection of gene mutation with PCR-SSCP and PCR sequencing on exon 7 of neurofibromatosis 2 gene in patients with sporadic Schwannoma%联合应用PCR-SSCP和PCR产物测序检测神经鞘瘤患者NF2基因Exon7突变及其意义

    Institute of Scientific and Technical Information of China (English)

    薛跃华; 林亦海; 李招云; 张黎明; 应炎斌

    2011-01-01

    目的 研究散发神经鞘瘤患者中Ⅱ型多发神经纤维瘤病基因(neurofibromatosis2,NF2)外显子7(Exon7)的突变及意义.方法 采用聚合酶链反应单链构象多态性技术和DNA测序技术检测25例神经鞘瘤中NF2基因Exon7突变.结果 25例神经鞘瘤患者中共发现3例NF2基因Exon7突变,均发生于脊神经鞘瘤,其中剪切受体位点突变1例、移码突变2例.结论 NF2基因Exon7突变可能是脊神经鞘瘤发生的关键因素.%Objective To detect gene mutation on exon 7 of neurofbromatos is 2 (NF2) in patients with sporadic Schwannoma.Methods Gene mutations on exon 7 of NF 2 gene in 25 cases of Schwannoma were detected by PCR- SSCP and DNA sequence.Results Three mutations were found in 25 cases of Schwannoma, including one splice donor mutation and two frameshift mutations in spinal tumors.Conclusion Mutations on exon7 of NF2 gene might be one of the critical factors in tumorogenesis of spinal Schwannoma.

  3. Single base mutation in the pro. alpha. 2(I) collagen gene that causes efficient splicing of RNA from exon 27 to exon 29 and synthesis of a shortened but in-frame pro. alpha. 2(I) chain

    Energy Technology Data Exchange (ETDEWEB)

    Tromp, G.; Prockop, D.J. (Thomas Jefferson Univ., Philadelphia, PA (USA))

    1988-07-01

    Previous observations demonstrated that a lethal variant of osteogenesis imperfecta had two altered alleles for pro{alpha}2(I) chains of type I procollagen. One mutation produced a nonfunctioning allele in that there was synthesis of mRNA but no detectable synthesis of pro{alpha}2(I) chains from the allele. The mutation in the other allele caused synthesis of shortened pro{alpha}2(I) chains that lacked most or all of the 18 amino acids encoded by exon 28. Subclones of the pro{alpha}2(I) gene were prepared from the proband's DNA and the DNA sequence was determined for a 582-base-pair (bp) region that extended from the last 30 bp of intervening sequence 26 to the first 26 bp of intervening sequence 29. Data from six independent subclones demonstrated that all had the same sequence as a previously isolated normal clone for the pro{alpha}2(I) gene except that four subclones had a single base mutation at the 3{prime} end of intervening sequence 27. The mutation was a substitution of guanine for adenine that changed the universal consensus sequence for the 3{prime} splicing site of RNA from -AG- to -GG-. S1 nuclease experiments demonstrated that about half the pro{alpha}2(I) mRNA in the proband's fibroblasts was abnormally spliced and that the major species of abnormal pro{alpha}2(I) mRNA was completely spliced from the last codon of exon 27 to the first codon of exon 29. The mutation is apparently unique among RNA splicing mutations of mammalian systems in producing a shortened polypeptide chain that is in-frame in terms of coding sequences, that is used in the subunit assembly of a protein, and that contributes to a lethal phenotype.

  4. Mutations in exon 6 and 7 of the phenylalanine hydroxylase(PAH) gene in chinese patients with phenylketonuria%苯丙酮尿症患儿苯丙氨酸羟化酶exon6基因、exon7基因突变的研究

    Institute of Scientific and Technical Information of China (English)

    周永安; 郁梁; 李素云; 张改秀; 张全斌; 刘建平; 杨建萍; 王钰; 马云霞; 张晓刚

    2011-01-01

    目的 探讨山西省苯丙酮尿症(PKU)患儿的苯丙氨酸羟化酶(PAH)exon6 基因、exon7 基因的突变特征.方法 通过测序及序列比对的方法对56 例PKU 患儿和112 例健康儿童的336 个PAH exon6 基因、exon7 基因进行序列分析,以确定其突变位点、性质和频率.结果 通过序列分析,发现在PKU 患儿和健康儿童中均高频率的出现Q232Q(CAA→CAG)、V245V(GTG→GTA)两种同义突变,其中cDNA 696 位点的频率高达96.2%,cDNA 735 位点的频率高达76.1%.健康儿童的其他序列与Genbank 完全相同.而PKU 患儿的基因序列中还发现了9 种共计37 个突变基因,占全部PAH 突变基因的33.04%.exon 6 仅发现一种突变基因Y204C,突变频率达9.8%;exon 7 中R243Q 的突变率最高,占10.7%,其次为Ivs7 +2 T >A,占5.4%,其余的G247V、R252Q、L255S、R261Q、T278I 和E280K 分别占0.9%、0.9%、0.9%、0.9%、2.7%和0.9%.9 种突变都在之前文献中有过报道,其中有7 种错义突变和2 种剪接位点突变.结论 明确了PAH exon6 基因、exon7 基因的突变种类和分布等特征,表明exon6 基因、exon7 基因中Y204C 和R243Q属于山西人群中PAH 基因突变的热点.%Objective To study mutation in exon 6 and 7 of the gene for the phenylalanine hydroxylase ( PAH) . Methods The mutations in exon 6 and 7 and flanking sequence of PAH gene were detected by DNA sequencing , involved in 56 patients with phenylketonura and112 healthy kids. Results Two synonymous mutations-Q232Q ( CAA→CAG) and V245V ( GTG→GTA) were also detected ,which the frequency of cDNA 696 mutation G type and cDNA735-A point mutation was respectively up tO 96. 2% and 76. 1%,we concluded that the 696 735 wild-type site may be G,A in Shanxi Ptovince. Besides , thirty-seven different mutations account for 33. 04% of mutant alleles,Y204C was found in exon6 ; In exon 7,R243Q was the highest incidence ,accounting for 10. 7%,followed by Ivs7 + 2 T> A,5. 4% ,G247V , R252Q , L255S

  5. Variable number of tandem repeat polymorphisms of DRD4: re-evaluation of selection hypothesis and analysis of association with schizophrenia

    Science.gov (United States)

    Hattori, Eiji; Nakajima, Mizuho; Yamada, Kazuo; Iwayama, Yoshimi; Toyota, Tomoko; Saitou, Naruya; Yoshikawa, Takeo

    2009-01-01

    Associations have been reported between the variable number of tandem repeat (VNTR) polymorphisms in the exon 3 of dopamine D4 receptor gene gene and multiple psychiatric illnesses/traits. We examined the distribution of VNTR alleles of different length in a Japanese cohort and found that, as reported earlier, the size of allele ‘7R' was much rarer (0.5%) in Japanese than in Caucasian populations (∼20%). This presents a challenge to an earlier proposed hypothesis that positive selection favoring the allele 7R has contributed to its high frequency. To further address the issue of selection, we carried out sequencing of the VNTR region not only from human but also from chimpanzee samples, and made inference on the ancestral repeat motif and haplotype by use of a phylogenetic analysis program. The most common 4R variant was considered to be the ancestral haplotype as earlier proposed. However, in a gene tree of VNTR constructed on the basis of this inferred ancestral haplotype, the allele 7R had five descendent haplotypes in relatively long lineage, where genetic drift can have major influence. We also tested this length polymorphism for association with schizophrenia, studying two Japanese sample sets (one with 570 cases and 570 controls, and the other with 124 pedigrees). No evidence of association between the allele 7R and schizophrenia was found in any of the two data sets. Collectively, this study suggests that the VNTR variation does not have an effect large enough to cause either selection or a detectable association with schizophrenia in a study of samples of moderate size. PMID:19092778

  6. ATRX binds to atypical chromatin domains at the 3' exons of zinc finger genes to preserve H3K9me3 enrichment.

    Science.gov (United States)

    Valle-García, David; Qadeer, Zulekha A; McHugh, Domhnall S; Ghiraldini, Flávia G; Chowdhury, Asif H; Hasson, Dan; Dyer, Michael A; Recillas-Targa, Félix; Bernstein, Emily

    2016-06-02

    ATRX is a SWI/SNF chromatin remodeler proposed to govern genomic stability through the regulation of repetitive sequences, such as rDNA, retrotransposons, and pericentromeric and telomeric repeats. However, few direct ATRX target genes have been identified and high-throughput genomic approaches are currently lacking for ATRX. Here we present a comprehensive ChIP-sequencing study of ATRX in multiple human cell lines, in which we identify the 3' exons of zinc finger genes (ZNFs) as a new class of ATRX targets. These 3' exonic regions encode the zinc finger motifs, which can range from 1-40 copies per ZNF gene and share large stretches of sequence similarity. These regions often contain an atypical chromatin signature: they are transcriptionally active, contain high levels of H3K36me3, and are paradoxically enriched in H3K9me3. We find that these ZNF 3' exons are co-occupied by SETDB1, TRIM28, and ZNF274, which form a complex with ATRX. CRISPR/Cas9-mediated loss-of-function studies demonstrate (i) a reduction of H3K9me3 at the ZNF 3' exons in the absence of ATRX and ZNF274 and, (ii) H3K9me3 levels at atypical chromatin regions are particularly sensitive to ATRX loss compared to other H3K9me3-occupied regions. As a consequence of ATRX or ZNF274 depletion, cells with reduced levels of H3K9me3 show increased levels of DNA damage, suggesting that ATRX binds to the 3' exons of ZNFs to maintain their genomic stability through preservation of H3K9me3.

  7. The detection of a novel insertion mutation in exon 2 of the MEFV gene associated with familial mediterranean fever in a moroccan family.

    Science.gov (United States)

    Mejtoute, Touhami; Sayel, Hanane; El-Akhal, Jamila; Moufid, Fatima Z; Bouguenouch, Laila; El Bouchikhi, Ihssane; Hida, Mustapha; Couissi, Driss; Ouldim, Karim

    2017-01-01

    Familial Mediterranean fever (FMF) is a hereditary autoinflammatory disease that is inherited in an autosomal recessive manner and is caused by mutations in the MEFV gene. As the name indicates, FMF occurs within families and is more common in individuals of Mediterranean descent than in persons of any other ethnicity. To date, 314 mutations have been reported. We studied a Moroccan family with a total of five members, including a mother who was presenting with symptoms of FMF, while her four children remained asymptomatic. The five patients were screened by DNA sequencing of exon 2 and exon 10 of the MEFV gene. Then, complete exome sequencing analysis of the MEFV gene was done for the patients in whom a novel mutation was detected. This analysis identified a novel single base Cytosine (C) insertion mutation in the coding region of the MEFV gene, named c.441dupC (p. Glu148Argfs*5 or E148RfsX5), which resulted in a mutated Pyrin/Marenostrin protein. This is the first report of a new mutation in exon 2 of the MEFV gene in a Moroccan family. This novel insertion mutation may provide important information for further studies of FMF pathogenesis.

  8. Common exon 3 polymorphism of the GH receptor (GHR) gene and effect of GH therapy on growth in Korean children with idiopathic short stature (ISS).

    Science.gov (United States)

    Ko, Jung Min; Park, Jung Young; Yoo, Han-Wook

    2009-01-01

    A human GH receptor (GHR) gene exon 3 polymorphism (d3-GHR) has been reported to be associated with responsiveness to GH therapy. We assessed the frequencies of this polymorphism in Korean control and idiopathic short stature (ISS) populations, and analysed short-term growth response to GH therapy according to GHR-exon 3 genotypes in Korean children with ISS. This was a retrospective study in 158 ISS children. Auxological and endocrine parameters were measured, and the GHR-exon 3 genotype was analysed. Allelic frequencies of GHR-exon 3 genotype were compared between the ISS group and a control group. GH had been administered for 62 patients, 52 of whom remained prepubertal after the first follow-up year. Changes in height velocity (HV) and IGF-1 and IGFBP-3 concentrations following GH therapy were compared in patients with these genotypes. There was no difference in GHR-exon 3 genotype frequency between ISS and control groups of Koreans. However, the fl/fl genotype was more frequent in Koreans than in Caucasians. ISS children with d3-GHR showed a significantly higher increment in HV (P = 0.002) and a marginally significant increment in IGF-1 concentration (P = 0.064) at the first year of GH therapy. fl-GHR was more frequently detected in a Korean population than in Caucasians. The growth promotion efficacy of GH therapy differed significantly between ISS patients with and without the d3-GHR allele. These findings indicate that the GHR-exon 3 polymorphism can affect the growth promoting efficacy of short-term GH therapy in Korean children with ISS.

  9. The Polymorphism of Exon 2 of GOLA-DRB3 Gene in Nadushan Goat Using PCR-RFLP

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    E Abbaszadeh

    2012-02-01

    Full Text Available This study was conducted to determine polymorphism of GOLA-DRB3 in Nadushan goat using PCR-RFLP. Blood samples were randomly taken from 100 goats. DNA was extracted from the blood samples using DIAtom DNA prep Kit. Spectrophotometer and 1% agarose gel were used for determining its quantities and qualities. Exon 2 of DRB 3.2 gene encompassing 285 bp was amplified with heminested-PCR method in two rounds and PCR products were digested with TaqI. Digested PCR products were electrophoresed in 10% Acryl Amide gel or 2% Agarose gel and gels stained with ethidium bromide. Digested PCR products with TaqI included 2 fragments at 122bp and 163bp (T restriction pattern or undigested fragment at 285bp (t restriction pattern. Population was in Hardy-Weinberg equilibrium (p>0.05. Shanon index, Nei index, observed and expected heterozygosity were 0.68, 0.49, 0.55 and 0.49, respectively. With regard to results of this study, GOLA-DRB3 marker has good efficiency for genetic diversity determining. Using results of this study and former studies and records and quantitative information of locus in this population, we can perform determining and identifying QTL

  10. Polymorphisms of exon 5, exon 7 and intron 10 of MMP2 gene and their association with wool density in Rex rabbits

    National Research Council Canada - National Science Library

    S.J. Chen; Y.J. Liu; T. Liu; B.J. Chen; Z.L. Gu

    2017-01-01

    Wool density is an important index that influences Rex rabbit fur quality. In our earlier studies, we found some important differentially expressed genes in different wool density of Rex rabbit by cDNA microarray...

  11. Polymorphism in Exon 2 of CD1 Genes in Southwest of Iran

    Directory of Open Access Journals (Sweden)

    Hossein Golmoghaddam

    2013-07-01

    Full Text Available Background: The CD1 family is less variable transmembrane antigen presenting molecules related to the MHC molecules. CD1a and CD1e genes are the most polymorphic ones associated with autoimmune diseases. The aim was to better clarify the map of CD1 genes in Southwest Iranian normal population for implications in vaccine design.Methods: In this study we investigated the polymorphism of CD1a, CD1d and CD1e in 311 healthy individuals from Fars Province in Southwest of Iran by PCR-SSP method.Results: Six of individuals had homozygote CD1a 01/01 genotype and 248 had homozygote CD1a 02/02 genotype. CD1d was found to be monomorphic with all tested individuals showing CD1d 01/01 genotype. Hundred and eleven individuals had homozygote CD1e 01/01 genotype and 48 had homozygote CD1e 02/02 genotype. The frequencies of CD1a 01 and CD1a 02 alleles were 11% and 89% while the frequencies of CD1e 01 and CD1e 02 alleles were 60.1% and 39.9%, respectively. Consistent with previous reports on other genes, a high degree of similarity in CD1a and CD1e allelic distribution was observed between Southwest Iranians and other Indo-European populations. However, the allelic frequency of the CD1a and CD1e alleles showed a significant difference from those of Chinese Han and She populations.Conclusion: These data are notable in the light of relatively recent genetic admixture along the Silk Road. Considering the significance of CD1 alleles in some autoimmune and infectious diseases and with the admixed nature of Iranian population, mapping the distribution of CD1e alleles in different regions of Iran can be useful in future designing of preventive and therapeutic vaccines.

  12. No evidence for mutations in exons 1, 8 and 18 of the patched gene in sporadic skin lesions of Brazilian patients

    Directory of Open Access Journals (Sweden)

    Granja F.

    2003-01-01

    Full Text Available There is strong evidence that the patched (PTCH gene is a gene for susceptibility to the nevoid basal cell carcinoma syndrome. PTCH has also been shown to mutate in both familial and sporadic basal cell carcinomas. However, mutations of the gene seem to be rare in squamous cell carcinomas. In order to characterize the role of the gene in the broader spectrum of sporadic skin malignant and pre-malignant lesions, we performed a polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP analysis of genomic DNA extracted from 105 adult patients (46 females and 59 males. There were 66 patients with basal cell carcinomas, 30 with squamous cell carcinomas, 2 with malignant melanomas and 7 patients with precancerous lesions. Two tissue samples were collected from each patient, one from the central portion of the tumor and another from normal skin. Using primers that encompass the entire exon 1, exon 8 and exon 18, where most of the mutations have been detected, we were unable to demonstrate any band shift. Three samples suspected to present aberrant migrating bands were excised from the gel and sequenced directly. In addition, we sequenced 12 other cases, including tumors and corresponding normal samples. A wild-type sequence was found in all 15 cases. Although our results do not exclude the presence of clonal alterations of the PTCH gene in skin cancers or mutations in other exons that were not screened, the present data do not support the presence of frequent mutations reported for non-melanoma skin cancer of other populations.

  13. Genetic polymorphisms within exon 3 of heat shock protein 90AA1 gene and its association with heat tolerance traits in Sahiwal cows

    Science.gov (United States)

    Kumar, Rakesh; Gupta, I. D.; Verma, Archana; Verma, Nishant; Vineeth, M. R.

    2015-01-01

    Aim: The present study was undertaken to identify novel single nucleotide polymorphism (SNP) in Exon 3 of HSP90AA1 gene and to analyze their association with respiration rate (RR) and rectal temperature (RT) in Sahiwal cows. Materials and Methods: The present study was carried out in Sahiwal cows (n=100) with the objectives to identify novel SNP in exon 3 of HSP90AA1 gene and to explore the association with heat tolerance traits. CLUSTAL-W multiple sequence analysis was used to identify novel SNPs in exon 3 of HSP90AA1 gene in Sahiwal cows. Gene and genotype frequencies of different genotypes were estimated by standard procedure POPGENE version 1.32 (University of Alberta, Canada). The significant effect of SNP variants on physiological parameters, e.g. RR and RT were analyzed using the General Linear model procedure of SAS Version 9.2. Results: The polymerase chain reaction product with the amplicon size of 450 bp was successfully amplified, covering exon 3 region of HSP90AA1 gene in Sahiwal cows. On the basis of comparative sequence analysis of Sahiwal samples (n=100), transitional mutations were detected at locus A1209G as compared to Bos taurus (NCBI GenBank AC_000178.1). After chromatogram analysis, three genotypes AA, AG, and GG with respective frequencies of 0.23, 0.50, and 0.27 ascertained. RR and RT were recorded once during probable extreme hours in winter, spring, and summer seasons. It was revealed that significant difference (pcows. PMID:27047179

  14. The 3'-terminal exon of the family of steroid and phenol sulfotransferase genes is spliced at the N-terminal glycine of the universally conserved GXXGXXK motif that forms the sulfonate donor binding site.

    OpenAIRE

    Chiba, H; Komatsu, K.; Lee, Y.C.; Tomizuka, T; Strott, C A

    1995-01-01

    The guinea pig estrogen sulfotransferase gene has been cloned and compared to three other cloned steroid and phenol sulfotransferase genes (human estrogen sulfotransferase, human phenol sulfotransferase, and guinea pig 3 alpha-hydroxysteroid sulfotransferase). The four sulfotransferase genes demonstrate a common outstanding feature: the splice sites for their 3'-terminal exons are identically located. That is, the 3'-terminal exon splice sites involve a glycine that constitutes the N-terminal...

  15. Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size.

    Science.gov (United States)

    Hou, J X; An, X P; Han, P; Peng, J Y; Cao, B Y

    2015-02-01

    Guanzhong (n = 321) and Boer (n = 191) goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the coding regions of the prolactin receptor (PRLR) gene by DNA sequencing and PCR-RFLP. Two SNPs (c.1457G>A and c.1645G>A) were identified that caused amino acid variations p.Ser485Asn and p.Val548Met respectively. Statistical results indicated that the c.1457G>A and c.1645G>A SNPs were significantly associated with litter size in Boer and Guanzhong goat breeds. Further analysis revealed that combined genotype C4 (GGGG) and haplotype G-G were better than the others for litter size in both goat breeds. These results might contribute to goat genetic resources and breeding. © 2014 Stichting International Foundation for Animal Genetics.

  16. Identification of endotrypanum species from a sloth, a squirrel and Lutzomyia sandflies in ecuador by PCR amplification and sequencing of the mini-exon gene.

    Science.gov (United States)

    Katakura, Ken; Mimori, Tatsuyuki; Furuya, Masato; Uezato, Hiroshi; Nonaka, Shigeo; Okamoto, Munehiro; Gomez L, Eduardo A; Hashiguchi, Yoshihisa

    2003-05-01

    PCR amplification and nucleotide sequencing of the mini-exon gene revealed that four strains isolated from a sloth (Choloepus hoffmanni), a squirrel (Sciurus granatensis) and two sandflies (Lutzomyia hartmanni) in Ecuador were indistinguishable from Endotrypanum monterogeii. Another strain isolated from Lu. hartmanni showed the high sequence similarity to E. schaudinni. Since three of these strains have been previously identified as Leishmania (Viannia) equatorensis, the results demonstrate that L. (V.) equatorensis is genetically closely related to the genus Endotrypanum. The present study also indicates that Endotrypanum species are distributed in arboreal animals and sandflies in Ecuador, and that mini-exon gene amplification is useful for epidemiological studies of Leishmania and Endotrypanum in the New World.

  17. hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene.

    Directory of Open Access Journals (Sweden)

    Indrani Talukdar

    Full Text Available Exon 11 of the insulin receptor gene (INSR is alternatively spliced in a developmentally and tissue-specific manner. Linker scanning mutations in a 5' GA-rich enhancer in intron 10 identified AGGGA sequences that are important for enhancer function. Using RNA-affinity purification and mass spectrometry, we identified hnRNP F and hnRNP A1 binding to these AGGGA sites and also to similar motifs at the 3' end of the intron. The hnRNPs have opposite functional effects with hnRNP F promoting and hnRNP A1 inhibiting exon 11 inclusion, and deletion of the GA-rich elements eliminates both effects. We also observed specific binding of hnRNP A1 to the 5' splice site of intron 11. The SR protein SRSF1 (SF2/ASF co-purified on the GA-rich enhancer and, interestingly, also competes with hnRNP A1 for binding to the splice site. A point mutation -3U→C decreases hnRNP A1 binding, increases SRSF1 binding and renders the exon constitutive. Lastly, our data point to a functional interaction between hnRNP F and SRSF1 as a mutant that eliminates SRSF1 binding to exon 11, or a SRSF1 knockdown, which prevents the stimulatory effect of hnRNP F over expression.

  18. Complete androgen insensitivity syndrome due to a new frameshift deletion in exon 4 of the androgen receptor gene: Functional analysis of the mutant receptor

    OpenAIRE

    Lobaccaro, J.M.; Lumbroso, S.; Poujol, Nicolas; Georget, V.; Brinkmann, Albert; Malpuech, Georges; Sultan, C.

    1995-01-01

    textabstractWe studied the androgen receptor gene in a large kindred with complete androgen insensitivity syndrome and negative receptor-binding activity, single-strand conformation polymorphism (SSCP) analysis and sequencing identified a 13 base pair deletion within exon 4. This was responsible for a predictive frameshift in the open reading frame and introduction of a premature stop codon at position 783 instead of 919. The deletion was reproduced in androgen receptor wildtype cDNA and tran...

  19. Identification of a new complex deleterious mutation in exon 18 of the BRCA2 gene in a hereditary male/female breast cancer family.

    Science.gov (United States)

    Diez, Orland; Gutiérrez-Enríquez, Sara; Masas, Miriam; Tenés, Anna; Yagüe, Carme; Arcusa, Angels; Llort, Gemma

    2010-09-01

    We report a novel complex mutation that consists of a deletion of 12 bp and an insertion of 2 bp (c.8402_8413del12ins2bp) in the exon 18 of the BRCA2 gene. This is a frameshift mutation that causes a disruption of the translational reading frame resulting in a stop codon downstream in the 2729 position of the BRCA2 protein. The mutation was present in a Spanish hereditary male/female breast cancer family.

  20. Proteins, exons and molecular evolution.

    Science.gov (United States)

    Holland, S K; Blake, C C

    1987-01-01

    The discovery of the eukaryotic gene structure has prompted research into the potential relationship between protein structure and function and the corresponding exon/intron patterns. The exon shuffling hypothesis put forward by Gilbert and Blake suggests the encodement of structural and functional protein elements by exons which can recombine to create novel proteins. This provides an explanation for the relatively rapid evolution of proteins from a few primordial molecules. As the number of gene and protein structures increases, evidence of exon shuffling is becoming more apparent and examples are presented both from modern multi-domain proteins and ancient proteins. Recent work into the chemical properties and catalytic functions of RNA have led to hypotheses based upon the early existence of RNA. These theories suggest that the split gene structure originated in the primordial soup as a result of random RNA synthesis. Stable regions of RNA, or exons, were utilised as primitive enzymes. In response to selective pressures for information storage, the activity was directly transferred from the RNA enzymes or ribozymes, to proteins. These short polypeptides fused together to create larger proteins with a wide range of functions. Recent research into RNA processing and exon size, discussed in this review, provides a clearer insight into the evolutionary development of the gene and protein structure.

  1. A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells

    Directory of Open Access Journals (Sweden)

    Kloster Maria

    2012-11-01

    Full Text Available Abstract Background Malignant cells in tumours of B-cell origin account for 0.1% to 98% of the total cell content, depending on disease entity. Recently, gene expression profiles (GEPs of B-cell lymphomas based on microarray technologies have contributed significantly to improved sub-classification and diagnostics. However, the varying degrees of malignant B-cell frequencies in analysed samples influence the interpretation of the GEPs. Based on emerging next-generation sequencing technologies (NGS like tag sequencing (tag-seq for GEP, it is expected that the detection of mRNA transcripts from malignant B-cells can be supplemented. This study provides a quantitative assessment and comparison of the ability of microarrays and tag-seq to detect mRNA transcripts from malignant B-cells. A model system was established by eight serial dilutions of the malignant B-cell lymphoma cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, prior to parallel analysis by exon microarrays and tag-seq. Results We identified 123 and 117 differentially expressed genes between pure OCI-Ly8 and HEK293 cells by exon microarray and tag-seq, respectively. There were thirty genes in common, and of those, most were B-cell specific. Hierarchical clustering from all dilutions based on the differentially expressed genes showed that neither technology could distinguish between samples with less than 1% malignant B-cells from non-B-cells. A novel statistical concept was developed to assess the ability to detect single genes for both technologies, and used to demonstrate an inverse proportional relationship with the sample purity. Of the 30 common genes, the detection capability of a representative set of three B-cell specific genes - CD74, HLA-DRA, and BCL6 - was analysed. It was noticed that at least 5%, 13% and 22% sample purity respectively was required for detection of the three genes by exon microarray whereas at least 2%, 4% and 51% percent sample purity of

  2. Androgen receptor gene methylation and exon one CAG repeat length in ovarian cancer: differences from breast cancer.

    Science.gov (United States)

    Kassim, Samar; Zoheiry, Nivan M; Hamed, Wael M; Going, James J; Craft, John A

    2004-07-01

    More than one neoplastic founder clone can exist in benign epithelial tumours. Although theories of clonal selection make pluriclonality appear unlikely in carcinomas, published data do not exclude this possibility. This study looked for evidence of multiclonal X inactivation in ovarian carcinoma using AR methylation as a marker. Fifteen unifocal ovarian carcinomas and 14 multifocal carcinomas all in Scottish patients were studied. One representative formalin-fixed paraffin-embedded tumour block was chosen for each of the former and two for the latter. From each of these 43 tumour blocks three samples each of approximately 10(4) carcinoma cells were obtained by microdissection (129 in all). DNA released by proteinase K digestion was subjected to PCR amplification of the androgen receptor gene AR exon I CAG repeat polymorphism with and without prior digestion with methylation-sensitive restriction enzymes HpaII and HhaI. Complex amplification patterns were consistent with mosaic X inactivation in some ovarian carcinomas but acquired anomalies of AR methylation cannot be excluded. Parallel analysis of other X-linked polymorphic loci would strengthen the inference of clonality status from DNA methylation data in tumour X studies. Strikingly, the number of CAG repeats in the 29 ovarian tumour patients (median 16, range 11 - 20) was substantially fewer than in 34 previously studied breast cancer patients from the same scottish population (median 21, range 14 - 26; P CAG repeat were over-represented in the ovarian cancer patients but not in the breast cancer series. These findings reinforce recent suggestions that AR may have a role in ovarian carcinogenesis.

  3. Polymorphisms in the Dopamine D4 and D2 Receptor Genes and Reproductive and Sexual Behaviors

    Directory of Open Access Journals (Sweden)

    Dan T.A. Eisenberg

    2007-10-01

    Full Text Available Human reproductive and sexual behaviors are heritable and may represent integral life history traits that are likely partially subserved by the dopamine system. Two dopamine receptor polymorphisms, DRD4 48bp VNTR and DRD2 TaqI A, were examined in relation to the Sexual-Orientation Inventory (SOI, age at first sexual intercourse, desired age of marriage, and desired age to have children in 195 (45% male individuals from a general student population. As DRD4 7R alleles have been associated with migratory behavior, we also examined whether those with more 7R alleles had a greater frequency of multi-racial ancestries. Minor alleles of both polymorphisms (7R and A1 respectively are believed to decrease the function of their respective receptors. Individuals with DRD4 7R alleles were more likely to have had sexual intercourse and to desire children earlier in life. In addition, DRD4 7R+ individuals were more likely to report multi-racial ancestries. Individuals with DRD2 A1 alleles were more likely to not want children and not want to marry. These results suggest that polymorphisms in the DRD4 and DRD2 genes are meaningfully associated with variation in reproductive and sexual behaviors. These results are provisionally interpreted as consistent with other findings suggesting that DRD4 7R and DRD2 A1 alleles are adaptive for lower offspring investment strategies in dynamic social environments.

  4. Identification of protein features encoded by alternative exons using Exon Ontology.

    Science.gov (United States)

    Tranchevent, Léon-Charles; Aubé, Fabien; Dulaurier, Louis; Benoit-Pilven, Clara; Rey, Amandine; Poret, Arnaud; Chautard, Emilie; Mortada, Hussein; Desmet, François-Olivier; Chakrama, Fatima Zahra; Moreno-Garcia, Maira Alejandra; Goillot, Evelyne; Janczarski, Stéphane; Mortreux, Franck; Bourgeois, Cyril F; Auboeuf, Didier

    2017-06-01

    Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Screening Duchenne and Becker muscular dystrophy patients for deletions in 30 exons of the dystrophin gene by three-multiplex PCR

    Energy Technology Data Exchange (ETDEWEB)

    Risch, N. (Yale Univ., New Haven, CT (United States))

    1992-09-01

    Deletion mutations of the dystrophin gene may cause either the severe Duchenne muscular dystrophy (DMD) or the milder, allelic Becker muscular dystrophy (BMD) and are clustered in two high-frequency-deletion regions (HFDRs) located, respectively, 500 kb and 1,200 kb downstream from the 5[prime] end of the gene. Three PCR reactions described allowed the analysis of a total of 30 exons and led, to the identification of three additional deletions involving the following exons: (a) 42 only, (b) 28-42, and (c) 16 only, none of which were detected with the two original multiplex reactions. Therefore, the three modified multiplexes detected 95 of the 96 deletions identified among the 152 patients studied so far by using Southern analysis and cDNA probes. The only deletion that remained undetected with this system involves exons 22-25 and generates the junction fragment described elsewhere. The percentage of deletion mutations among DMS/BMD patients amounts to 63%, which is in agreement with similar estimates from other laboratories. When field-inversion gel electrophoresis is coupled to Southern analysis, the detection rate of deletion and duplication mutations reaches 65%.

  6. Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes.

    Science.gov (United States)

    Koonin, Eugene V; Csuros, Miklos; Rogozin, Igor B

    2013-01-01

    In eukaryotes, protein-coding sequences are interrupted by non-coding sequences known as introns. During mRNA maturation, introns are excised by the spliceosome and the coding regions, exons, are spliced to form the mature coding region. The intron densities widely differ between eukaryotic lineages, from 6 to 7 introns per kb of coding sequence in vertebrates, some invertebrates and green plants, to only a few introns across the entire genome in many unicellular eukaryotes. Evolutionary reconstructions using maximum likelihood methods suggest intron-rich ancestors for each major group of eukaryotes. For the last common ancestor of animals, the highest intron density of all extant and extinct eukaryotes was inferred, at 120-130% of the human intron density. Furthermore, an intron density within 53-74% of the human values was inferred for the last eukaryotic common ancestor. Accordingly, evolution of eukaryotic genes in all lines of descent involved primarily intron loss, with substantial gain only at the bases of several branches including plants and animals. These conclusions have substantial biological implications indicating that the common ancestor of all modern eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins. Copyright © 2012 John Wiley & Sons, Ltd.

  7. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution.

    Science.gov (United States)

    Yu, Xianxian; Duan, Xiaoshan; Zhang, Rui; Fu, Xuehao; Ye, Lingling; Kong, Hongzhi; Xu, Guixia; Shan, Hongyan

    2016-01-01

    AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.

  8. Disease-causing mutations in exon 11 of the medium-chain acyl-CoA dehydrogenase gene

    DEFF Research Database (Denmark)

    Andresen, B S; Jensen, T G; Bross, P

    1994-01-01

    spot. Here we describe the results from sequence analysis of exon 11 and part of the flanking introns from 36 compound heterozygous patients with MCAD deficiency. We have identified four previously unknown disease-causing mutations (M301T, S311R, R324X, and E359X) and two silent mutations in exon 11......Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most commonly recognized defect of the mitochondrial beta-oxidation in humans. It is a potentially fatal, autosomal recessive inherited defect. Most patients with MCAD deficiency are homozygous for a single disease-causing mutation (G985......), causing a change from lysine to glutamate at position 304 (K304E) in the mature MCAD. Only seven non-G985 mutations, all of which are rare, have been reported. Because the G985 mutation and three of the non-G985 mutations are located in exon 11, it has been suggested that this exon may be a mutational hot...

  9. Two novel mutations on exon 8 and intron 65 of COL7A1 gene in two Chinese brothers result in recessive dystrophic epidermolysis bullosa.

    Directory of Open Access Journals (Sweden)

    Ying Lin

    Full Text Available Dystrophic epidermolysis bullosa is an inherited bullous dermatosis caused by the COL7A1 gene mutation in autosomal dominant or recessive mode. COL7A1 gene encodes type VII collagen - the main component of the anchoring fibrils at the dermal-epidermal junction. Besides the 730 mutations reported, we identified two novel COL7A1 gene mutations in a Chinese family, which caused recessive dystrophic epidermolysis bullosa (RDEB. The diagnosis was established histopathologically and ultrastructurally. After genomic DNA extraction from the peripheral blood sample of all subjects (5 pedigree members and 136 unrelated control individuals, COL7A1 gene screening was performed by polymerase chain reaction amplification and direct DNA sequencing of the whole coding exons and flanking intronic regions. Genetic analysis of the COL7A1 gene in affected individuals revealed compound heterozygotes with identical novel mutations. The maternal mutation is a 2-bp deletion at exon 8 (c.1006_1007delCA, leading to a subsequent reading frame-shift and producing a premature termination codon located 48 amino acids downstream in exon 9 (p.Q336EfsX48, consequently resulting in the truncation of 2561 amino acids downstream. This was only present in two affected brothers, but not in the other unaffected family members. The paternal mutation is a 1-bp deletion occurring at the first base of intron 65 (c.IVS5568+1delG that deductively changes the strongly conserved GT dinucleotide at the 5' donor splice site, results in subsequent reading-through into intron 65, and creates a stop codon immediately following the amino acids encoded by exon 65 (GTAA→TAA. This is predicted to produce a truncated protein lacking of 1089 C-terminal amino acids downstream. The latter mutation was found in all family members except one of the two unaffected sisters. Both mutations were observed concurrently only in the two affected brothers. Neither mutation was discovered in 136 unrelated Chinese

  10. Deletion of exon 20 of the Familial Dysautonomia gene Ikbkap in mice causes developmental delay, cardiovascular defects, and early embryonic lethality.

    Directory of Open Access Journals (Sweden)

    Paula Dietrich

    Full Text Available Familial Dysautonomia (FD is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population, and leads to death before the age of 40. The disease is characterized by abnormal development and progressive degeneration of the sensory and autonomic nervous system. A single base pair substitution in intron 20 of the Ikbkap gene accounts for 98% of FD cases, and results in the expression of low levels of the full-length mRNA with simultaneous expression of an aberrantly spliced mRNA in which exon 20 is missing. To date, there is no animal model for the disease, and the essential cellular functions of IKAP--the protein encoded by Ikbkap--remain unknown. To better understand the normal function of IKAP and in an effort to generate a mouse model for FD, we have targeted the mouse Ikbkap gene by homologous recombination. We created two distinct alleles that result in either loss of Ikbkap expression, or expression of an mRNA lacking only exon 20. Homozygosity for either mutation leads to developmental delay, cardiovascular and brain malformations, accompanied with early embryonic lethality. Our analyses indicate that IKAP is essential for expression of specific genes involved in cardiac morphogenesis, and that cardiac failure is the likely cause of abnormal vascular development and embryonic lethality. Our results also indicate that deletion of exon 20 abolishes gene function. This implies that the truncated IKAP protein expressed in FD patients does not retain any significant biological function.

  11. Genetic and physical mapping of 2q35 in the region of NRAMP and IL8R genes: Identification of a polymorphic repeat in exon 2 of NRAMP

    Energy Technology Data Exchange (ETDEWEB)

    White, J.K.; Shaw, M.A.; Barton, C.H. [Addenbrooke`s Hospital, Cambridge (United Kingdom)] [and others

    1994-11-15

    Recent interest has focused on the region of conserved synteny between mouse chromosome 1 and human 2q33-q37, particularly over the region encoding the murine macrophage resistance gene Ity/Lsh/Bcg (candidate Nramp) and members of the Il8r interleukin-8 (IL8) receptor gene cluster. In this paper, identification of a restriction fragment length polymorphism in the Il8RB gene in 35 pedigrees previously typed for markers in the 2q33-37 interval provided evidence (lod scores > 3) for linkage between Il8RB and the 2q34-135 markers FN1, TNP1, VIL1, and DES. Physical mapping, using yeast artificial chromosomes isolated with VIL1, confirmed that IL8RA, IL8RB and the IL8RB pseudogene map within the NRAMP-VIL1 interval, with the physical distance (155 kb) from 5{prime} LSH to 3{prime} VIL1 representing {approx}3-fold that observed in the mouse. Partial sequencing of NRAMP confirmed the presence of the N-terminal proline/serine-rich putative SH3 binding domain in exon 2 of the human gene. Further analysis of Brazilian leprosy and visceral leishmaniasis pedigrees identified a rare second allele varying in a 9-nucleotide repeat motif of the exon 2 sequence but segregating independently of the disease phenotype. 38 refs., 4 figs., 3 tabs.

  12. Complex phenotype linked to a mutation in exon 11 of the lamin A/C gene: Hypertrophic cardiomyopathy, atrioventricular block, severe dyslipidemia and diabetes.

    Science.gov (United States)

    Francisco, Ana Rita G; Santos Gonçalves, Inês; Veiga, Fátima; Mendes Pedro, Mónica; Pinto, Fausto J; Brito, Dulce

    2017-09-01

    The lamin A/C (LMNA) gene encodes lamins A and C, which have an important role in nuclear cohesion and chromatin organization. Mutations in this gene usually lead to the so-called laminopathies, the primary cardiac manifestations of which are dilated cardiomyopathy and intracardiac conduction defects. Some mutations, associated with lipodystrophy but not cardiomyopathy, have been linked to metabolic abnormalities such as diabetes and severe dyslipidemia. Herein we describe a new phenotype associated with a mutation in exon 11 of the LMNA gene: hypertrophic cardiomyopathy, atrioventricular block, severe dyslipidemia and diabetes. A 64-year-old woman with hypertrophic cardiomyopathy and a point mutation in exon 11 of the LMNA gene (c.1718C>T, Ser573Leu) presented with severe symptomatic ventricular hypertrophy and left ventricular outflow tract obstruction. She underwent septal alcohol ablation, followed by Morrow myectomy. The patient was also diagnosed with severe dyslipidemia, diabetes and obesity, and fulfilled diagnostic criteria for metabolic syndrome. No other characteristics of LMNA mutation-related phenotypes were identified. The development of type III atrioventricular block with no apparent cause, and mildly depressed systolic function, prompted referral for cardiac resynchronization therapy. In conclusion, the association between LMNA mutations and different phenotypes is complex and not fully understood, and can present with a broad spectrum of severity. Copyright © 2017 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

  13. Alternative-splicing in the exon-10 region of GABA(A receptor beta(2 subunit gene: relationships between novel isoforms and psychotic disorders.

    Directory of Open Access Journals (Sweden)

    Cunyou Zhao

    Full Text Available BACKGROUND: Non-coding single nucleotide polymorphisms (SNPs in GABRB2, the gene for beta(2-subunit of gamma-aminobutyric acid type A (GABA(A receptor, have been associated with schizophrenia (SCZ and quantitatively correlated to mRNA expression and alternative splicing. METHODS AND FINDINGS: Expression of the Exon 10 region of GABRB2 from minigene constructs revealed this region to be an "alternative splicing hotspot" that readily gave rise to differently spliced isoforms depending on intron sequences. This led to a search in human brain cDNA libraries, and the discovery of two novel isoforms, beta(2S1 and beta(2S2, bearing variations in the neighborhood of Exon-10. Quantitative real-time PCR analysis of postmortem brain samples showed increased beta(2S1 expression and decreased beta(2S2 expression in both SCZ and bipolar disorder (BPD compared to controls. Disease-control differences were significantly correlated with SNP rs187269 in BPD males for both beta(2S1 and beta(2S2 expressions, and significantly correlated with SNPs rs2546620 and rs187269 in SCZ males for beta(2S2 expression. Moreover, site-directed mutagenesis indicated that Thr(365, a potential phosphorylation site in Exon-10, played a key role in determining the time profile of the ATP-dependent electrophysiological current run-down. CONCLUSION: This study therefore provided experimental evidence for the importance of non-coding sequences in the Exon-10 region in GABRB2 with respect to beta(2-subunit splicing diversity and the etiologies of SCZ and BPD.

  14. Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant.

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    Siva Arumugam Saravanaperumal

    Full Text Available Stem cell factor (SCF is a growth factor, essential for haemopoiesis, mast cell development and melanogenesis. In the hematopoietic microenvironment (HM, SCF is produced either as a membrane-bound (- or soluble (+ forms. Skin expression of SCF stimulates melanocyte migration, proliferation, differentiation, and survival. We report for the first time, a novel mRNA splice variant of SCF from the skin of white merino sheep via cloning and sequencing. Reverse transcriptase (RT-PCR and molecular prediction revealed two different cDNA products of SCF. Full-length cDNA libraries were enriched by the method of rapid amplification of cDNA ends (RACE-PCR. Nucleotide sequencing and molecular prediction revealed that the primary 1519 base pair (bp cDNA encodes a precursor protein of 274 amino acids (aa, commonly known as 'soluble' isoform. In contrast, the shorter (835 and/or 725 bp cDNA was found to be a 'novel' mRNA splice variant. It contains an open reading frame (ORF corresponding to a truncated protein of 181 aa (vs 245 aa with an unique C-terminus lacking the primary proteolytic segment (28 aa right after the D(175G site which is necessary to produce 'soluble' form of SCF. This alternative splice (AS variant was explained by the complete nucleotide sequencing of splice junction covering exon 5-intron (5-exon 6 (948 bp with a premature termination codon (PTC whereby exons 6 to 9/10 are skipped (Cassette Exon, CE 6-9/10. We also demonstrated that the Northern blot analysis at transcript level is mediated via an intron-5 splicing event. Our data refine the structure of SCF gene; clarify the presence (+ and/or absence (- of primary proteolytic-cleavage site specific SCF splice variants. This work provides a basis for understanding the functional role and regulation of SCF in hair follicle melanogenesis in sheep beyond what was known in mice, humans and other mammals.

  15. The nucleotide sequence of a CpG island demonstrates the presence of the first exon of the gene encoding the human lysosomal membrane protein lamp2 and assigns the gene to Xq24.

    Science.gov (United States)

    Manoni, M; Tribioli, C; Lazzari, B; DeBellis, G; Patrosso, C; Pergolizzi, R; Pellegrini, M; Maestrini, E; Rivella, S; Vezzoni, P

    1991-03-01

    An EagI-EcoRI clone of human genomic DNA, p2-7, mapped to Xq24 has been sequenced. This analysis has confirmed the presence of a CpG island and has identified the first exon of the human LAMP2 gene, encoding a glycoprotein of the lysosomal membrane. Since the p2-7 clone corresponds to single-copy DNA, we can assign the human LAMP2 gene to Xq24.

  16. A one base pair deletion in the canine ATP13A2 gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier.

    Directory of Open Access Journals (Sweden)

    Anne Wöhlke

    2011-10-01

    Full Text Available Neuronal ceroid lipofuscinosis (NCL is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells. Tibetan terriers show a late-onset lethal form of NCL manifesting first visible signs at 5-7 years of age. Genome-wide association analyses for 12 Tibetan-terrier-NCL-cases and 7 Tibetan-terrier controls using the 127K canine Affymetrix SNP chip and mixed model analysis mapped NCL to dog chromosome (CFA 2 at 83.71-84.72 Mb. Multipoint linkage and association analyses in 376 Tibetan terriers confirmed this genomic region on CFA2. A mutation analysis for 14 positional candidate genes in two NCL-cases and one control revealed a strongly associated single nucleotide polymorphism (SNP in the MAPK PM20/PM21 gene and a perfectly with NCL associated single base pair deletion (c.1620delG within exon 16 of the ATP13A2 gene. The c.1620delG mutation in ATP13A2 causes skipping of exon 16 presumably due to a broken exonic splicing enhancer motif. As a result of this mutation, ATP13A2 lacks 69 amino acids. All known 24 NCL cases were homozygous for this deletion and all obligate 35 NCL-carriers were heterozygous. In a sample of 144 dogs from eleven other breeds, the c.1620delG mutation could not be found. Knowledge of the causative mutation for late-onset NCL in Tibetan terrier allows genetic testing of these dogs to avoid matings of carrier animals. ATP13A2 mutations have been described in familial Parkinson syndrome (PARK9. Tibetan terriers with these mutations provide a valuable model for a PARK9-linked disease and possibly for manganese toxicity in synucleinopathies.

  17. X-linked Alport syndrome: an SSCP-based mutation survey over all 51 exons of the COL4A5 gene.

    Science.gov (United States)

    Renieri, A.; Bruttini, M.; Galli, L.; Zanelli, P.; Neri, T.; Rossetti, S.; Turco, A.; Heiskari, N.; Zhou, J.; Gusmano, R.; Massella, L.; Banfi, G.; Scolari, F.; Sessa, A.; Rizzoni, G.; Tryggvason, K.; Pignatti, P. F.; Savi, M.; Ballabio, A.; De Marchi, M.

    1996-01-01

    The COL4A5 gene encodes the alpha5 (type IV) collagen chain and is defective in X-linked Alport syndrome (AS). Here, we report the first systematic analysis of all 51 exons of COL4A5 gene in a series of 201 Italian AS patients. We have previously reported nine major rearrangements, as well as 18 small mutations identified in the same patient series by SSCP analysis of several exons. After systematic analysis of all 51 exons of COL4A5, we have now identified 30 different mutations: 10 glycine substitutions in the triple helical domain of the protein, 9 frameshift mutations, 4 in-frame deletions, 1 start codon, 1 nonsense, and 5 splice-site mutations. These mutations were either unique or found in two unrelated families, thus excluding the presence of a common mutation in the coding part of the gene. Overall, mutations were detected in only 45% of individuals with a certain or likely diagnosis of X-linked AS. This finding suggests that mutations in noncoding segments of COL4A5 account for a high number of X-linked AS cases. An alternative hypothesis is the presence of locus heterogeneity, even within the X-linked form of the disease. A genotype/phenotype comparison enabled us to better substantiate a significant correlation between the degree of predicted disruption of the alpha5 chain and the severity of phenotype in affected male individuals. Our study has significant implications in the diagnosis and follow-up of AS patients. PMID:8651296

  18. SOD1 Gene +35A/C (exon3/intron3) Polymorphism in Type 2 Diabetes Mellitus among South Indian Population

    OpenAIRE

    Nithya, K.; Angeline, T.; Isabel, W.; A J Asirvatham

    2016-01-01

    Superoxide dismutase is an antioxidant enzyme that is involved in defence mechanisms against oxidative stress. Cu/Zn SOD is a variant that is located in exon3/intron3 boundary. The aim of the present study was to investigate whether the Cu/Zn SOD (+35A/C) gene polymorphism is associated with the susceptibility to type 2 diabetes mellitus among south Indian population. The study included patients with type 2 diabetes mellitus (n = 100) and healthy controls (n = 75). DNA was isolated from the b...

  19. Hb Filottrano [codon 120 (-A)]: a novel frameshift mutation in exon 3 of the β-globin gene causing dominantly inherited β-thalassemia intermedia.

    Science.gov (United States)

    Amato, Antonio; Cappabianca, Maria Pia; Perri, Maria; Zaghis, Ivo; Mastropietro, Fabrizio; Ponzini, Donatella; Di Biagio, Paola; Piscitelli, Roberta

    2012-01-01

    We report a novel frameshift mutation in exon 3 of the β-globin gene, that, in the heterozygous state, leads to a β-thalassemia intermedia (β-TI) phenotype (marked anemia, splenomegaly, hyperbilirubinemia, jaundice, unbalanced synthesis of α/non-α chains in a 34-year-old Italian woman. This frameshift mutation, due to the deletion of the first nucleotide (-A) at codon 120, results in a β-globin chain that is elongated to 156 amino acid residues. These highly unstable abnormal chains precipitate in the erythroblasts as inclusion bodies, thus causing inefficient erythropoiesis and ultimately resulting in the observed dominant clinical phenotype.

  20. Myopia and Late-Onset Progressive Cone Dystrophy Associate to LVAVA/MVAVA Exon 3 Interchange Haplotypes of Opsin Genes on Chromosome X.

    Science.gov (United States)

    Orosz, Orsolya; Rajta, István; Vajas, Attila; Takács, Lili; Csutak, Adrienne; Fodor, Mariann; Kolozsvári, Bence; Resch, Miklós; Sényi, Katalin; Lesch, Balázs; Szabó, Viktória; Berta, András; Balogh, István; Losonczy, Gergely

    2017-03-01

    Rare interchange haplotypes in exon 3 of the OPN1LW and OPN1MW opsin genes cause X-linked myopia, color vision defect, and cone dysfunction. The severity of the disease varies on a broad scale from nonsyndromic high myopia to blue cone monochromatism. Here, we describe a new genotype-phenotype correlation attributed to rare exon 3 interchange haplotypes simultaneously present in the long- and middle-wavelength sensitive opsin genes (L- and M-opsin genes). A multigenerational family with X-linked high myopia and cone dystrophy was investigated. Affected male patients had infantile onset myopia with normal visual acuity and color vision until their forties. Visual acuity decreased thereafter, along with the development of severe protan and deutan color vision defects. A mild decrease in electroretinography response of cone photoreceptors was detected in childhood, which further deteriorated in middle-aged patients. Rods were also affected, however, to a lesser extent than cones. Clinical exome sequencing identified the LVAVA and MVAVA toxic haplotypes in the OPN1LW and OPN1MW opsin genes, respectively. Here, we show that LVAVA haplotype of the OPN1LW gene and MVAVA haplotype of the OPN1MW gene cause apparently nonsyndromic high myopia in young patients but lead to progressive cone-rod dystrophy with deuteranopia and protanopia in middle-aged patients corresponding to a previously unknown disease course. To the best of our knowledge, this is the first report on the joint effect of these toxic haplotypes in the two opsin genes on chromosome X.

  1. Simultaneous detection of the exon 10 polymorphism and a novel intronic single base insertion polymorphism in the XPD gene using single strand conformation polymorphism.

    Science.gov (United States)

    Kumar, Rajiv; Angelini, Sabrina; Hemminki, Kari

    2003-03-01

    We developed a new method based on the single strand conformation polymorphism (SSCP) technique for the detection of a G23591A (Asp312Asn) polymorphism in exon 10 of the XPD gene. In the process we also identified a novel polymorphism 23623C-ins (IVS10+17C-ins) in intron 10 of the same gene. With this newly developed SSCP-based method of genotyping we could detect both polymorphisms in the same assay and thus consequently determine the haplotype. In order to determine the population frequency of the novel polymorphism and the haplotype frequency, 302 healthy individuals were genotyped. The allelic frequency of the 23623C-ins intronic polymorphism was 0.16, whereas the frequency of the variant allele for the G23591A polymorphism was 0.39. Forty-three individuals (14%) were heterozygous for both polymorphisms but none carried polymorphic variants for both G23591A and 23623C-ins on the same allele. The effect of the novel intronic insertion polymorphism, which is located 16 nt downstream of the 3'-end of exon 10 of the XPD gene and involves a mononucleotide C repeat sequence, on expression remains to be determined.

  2. Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

    Directory of Open Access Journals (Sweden)

    Hammesfahr Björn

    2011-06-01

    Full Text Available Abstract Background Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. Results We have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algorithm, mutually exclusive exons in several example genes, a dynein heavy chain, a muscle myosin heavy chain, and Dscam were correctly identified. In addition, the algorithm was applied to the whole Drosophila melanogaster X chromosome and the results were compared to the Flybase annotation and an ab initio prediction. Clusters of mutually exclusive exons might be subsequent to each other and might encode dozens of exons. Conclusions This is the first implementation of an automatic search for mutually exclusive exons in eukaryotes. Exons are predicted and reconstructed in the same run providing the complete gene structure for the protein query of interest. WebScipio offers high quality gene structure figures with the clusters of mutually exclusive exons colour-coded, and several analysis tools for further manual inspection. The genome scale analysis of all genes of the Drosophila melanogaster X chromosome showed that WebScipio is able to find all but two of the 28

  3. Association of an Exon SNP of SLC2A9 Gene with Hyperuricemia Complicated with Type 2 Diabetes Mellitus in the Chinese Male Han Population.

    Science.gov (United States)

    Xing, Shi-Chao; Wang, Xu-Fu; Miao, Zhi-Min; Zhang, Xue-Zhi; Zheng, Jun; Yuan, Ying

    2015-04-01

    Several recent genome-wide association studies and following studies have identified that genetic variants of SLC2A9 are associated with hyperuricemia (HUA) and diabetes mellitus (DM). Here, we set to investigate whether the exon 9 of SLC2A9 gene variations is associated with HUA complicated with Type 2 DM (T2DM) in the Chinese male Han population. The present study was designed to study rs2280205 polymorphism in exon 9 of SLC2A9 in 232 Chinese male subjects. Rs2280205 locus was genotyped in 52 T2DM subjects, 65 HUA subjects, 55 subjects with HUA complicated with T2DM, as well as 60 control subjects in this study. DNA from peripheral blood was purified and amplified by polymerase chain reaction (PCR). The PCR products were then digested by restriction enzyme MSPI, and part of PCR products was sequenced and analyzed. There was no significant difference in the levels of cholesterol, creatinine, and urea nitrogen between the Control Group and the HUA group. There was also no significant difference in levels of cholesterol between the DM group and Control Group. No significant difference in cholesterol and uric acid was observed between the HUA group and the HUA accompanied with DM group (P > 0.05). However, there was no statistical significance in the genotype frequency in these groups (P > 0.01). Results of the present study suggest that the exon 9 of SLC2A9 gene 109C/T polymorphism is not associated with HUA and diabetes in population living in the coastal area of Shandong province, China.

  4. Polymorphism Analysis of the Thirteenth Exon of Equine MxA Gene%马MxA基因第13外显子的多态性研究

    Institute of Scientific and Technical Information of China (English)

    萨仁高娃; 菊林花

    2008-01-01

    [Objective] To investigate the polymorphism of the thirteenth exon of MxA gene in 4 species of horse. [Method] The thirteenth exon of MxA gene fragments were amplified from genomic DNA of Sanhe horse, Xinihe horse, Wushen horse and Baerhu horse with the primers designed according to the MxA sequence announced in GenBank; the polymorphism of MxA gene was detected by PCR-SSCP and the products were sequenced. [Result] The polymorphism of the thirteenth exon of MxA gene appeared only in Wushen horse, the 2 081 nt of which mutated from guanine (G) to adenine (A) and the corresponding amino acid of which changed from glutamate (Glu) to alanine (Ala). [Conclusion] The study provided a basis for exploring the antiviral effect of MxA protein.

  5. Apparent Homozygosity of p.Phe508del in CFTR due to a Large Gene Deletion of Exons 4–11

    Directory of Open Access Journals (Sweden)

    Vassos Neocleous

    2014-01-01

    Full Text Available We report a classic cystic fibrosis (CF boy with a large deletion of exons 4–11 in the cystic fibrosis transmembrane conductance regulator (CFTR gene on one allele and p.Phe508del in exon 10 on the second allele. Both parents of Georgian and Ukrainian background had no personal or family history of the disease. The initial molecular diagnostic investigation identified the patient as homozygous for the p.Phe508del and not compatible with his parent’s genetic status. The possibility of nonpaternity or uniparental disomy (UPD7 was investigated and excluded using microsatellite analysis of highly polymorphic markers on chromosome 7. Array-CGH was also performed on the patient and revealed a male profile with a subtle deletion within the CFTR gene on the long arm (q-arm of chromosome 7 (7q31.2. The deletion was confirmed by MLPA extending from probe L02380 to probe L14978 (28.7 kb and that was inherited from his father, while p.PheF508del was inherited from his mother. These data highlight the need for additional testing for large deletions in patients with apparent homozygosity for a mutated CFTR allele that do not match the carrier status of the parents. Not testing can lead to misdiagnosis and misinterpretation of mutation carrier status and the expected penetrance of the disorder.

  6. The relationship between MHC-DRB1 gene second exon polymorphism and hydatidosis resistance of Chinese Merino (Sinkiang Junken type), Kazakh and Duolang sheep.

    Science.gov (United States)

    Li, R Y; Hui, W Q; Jia, B; Shi, G Q; Zhao, Z S; Shen, H; Peng, Q; Lv, L M; Zhou, Q W; Li, H T

    2011-05-01

    The present study aimed at detecting the association of ovine major histocompatibility complex class II (Ovar II) DRB1 gene second exon and susceptibility or resistance to hydatidosis in three sheep breeds of Sinkiang. The MHC-DRB1 second exon was amplified by polymerase chain reaction (PCR) from DNA samples of healthy sheep and sheep with hydatidosis. PCR products were characterized by the restriction fragment length polymorphism (RFLP) technique. Five restriction enzymes, Mval, Haelll, Sacl, Sacll, Hin1l, were used, yielding 14 alleles and 31 restriction patterns. Frequencies of patterns Mvalbc, Hin1lab, Sacllab, Haelllde, Haellldf, Haellldd (P Sinkiang Junken type) sheep, were significantly higher in healthy sheep compared with infected sheep. These results indicated a strong association between these patterns and hydatidosis resistance. In contrast, the frequencies of Mvalbb, Saclaa, Hinl lbb, Haelllef (P Sinkiang Junken type) were significantly lower in healthy sheep compared with infected sheep. This indicated a strong association between these patterns and hydatidosis susceptibility. In addition, sheep with the pattern of Haelllef demonstrated a high hydatidosis susceptibility (P Sinkiang Junken type). These results suggest that the Ovar-DRB1 gene plays a role in resistance to hydatidosis infection in the three sheep breeds.

  7. A Novel Deletion Mutation of Exon 2 of the C19orf12 Gene in an Omani Family with Mitochondrial Membrane Protein-Associated Neurodegeneration (MPAN)

    Science.gov (United States)

    Al Macki, Nabil; Al Rashdi, Ismail

    2017-01-01

    Mutations in the C19orf12 gene are known to cause mitochondrial membrane protein-associated neurodegeneration (MPAN), which is a neurodegeneration with brain iron accumulation (NBIA) type 4 disorder. To the best of our knowledge, this is the first report of a genetically confirmed case of MPAN from Oman. A novel homozygous deletion of exon 2 of the C19orf12 gene was confirmed on the proband, a seven-year-old girl, who presented with gait instability. Brain magnetic resonance imaging showed iron deposition on the basal ganglia. This report highlights the importance of genetic testing of such a clinically and genetically heterogeneous condition among a population with a high consanguinity rate. To overcome the diagnostic difficulty, implementation of a cost-effective approach to perform cascade screening of carriers at risk is needed as well as programs to address risky consanguineous marriages. PMID:28042406

  8. A novel mutation (4040-4045 nt. delA in exon 14 of the factor VIII gene causing severe hemophilia A

    Directory of Open Access Journals (Sweden)

    Habib Onsori

    2011-01-01

    Full Text Available Hemophilia A is an X-linked congenital bleeding disorder caused by Factor VIII deficiency. Different mutations including point mutations, deletions, insertions and inversions have been reported in the FVIII gene, which cause hemophilia A. In the current study, with the use of conformational sensitive gel electrophoresis (CSGE analysis, we report a novel 1-nt deletion in the A6 sequence at codons 1328-1330 (4040-4045 nt delA occurring in exon 14 of the FVIII gene in a seven-year-old Iranian boy with severe hemophilia A. This mutation that causes frameshift and premature stop-codon at 1331 has not previously been reported in the F8 Hemophilia A Mutation, Structure, Test and Resource Site (HAMSTeRS database.

  9. Sequence of the intron/exon junctions of the coding region of the human androgen receptor gene and identification of a point mutation in a family with complete androgen insensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Lubahn, D.B.; Simental, J.A.; Higgs, H.N.; Wilson, E.M.; French, F.S. (Univ. of North Carolina, Chapel Hill (USA)); Brown, T.R.; Migeon, C.J. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (USA))

    1989-12-01

    Androgens act through a receptor protein (AR) to mediate sex differentiation and development of the male phenotype. The authors have isolated the eight exons in the amino acid coding region of the AR gene from a human X chromosome library. Nucleotide sequences of the AR gene intron/exon boundaries were determined for use in designing synthetic oligonucleotide primers to bracket coding exons for amplification by the polymerase chain reaction. Genomic DNA was amplified from 46, XY phenotypic female siblings with complete androgen insensitivity syndrome. AR binding affinity for dihydrotestosterone in the affected siblings was lower than in normal males, but the binding capacity was normal. Sequence analysis of amplified exons demonstrated within the AR steroid-binding domain (exon G) a single guanine to adenine mutation, resulting in replacement of valine with methionine at amino acid residue 866. As expected, the carrier mother had both normal and mutant AR genes. Thus, a single point mutation in the steroid-binding domain of the AR gene correlated with the expression of an AR protein ineffective in stimulating male sexual development.

  10. Relationship of myocardial damage of chronic and latent Keshan disease with desmin gene exon6 A360P missense mutation%desmin基因exon6 A360P错义突变与慢型及潜在型克山病心肌损伤的关系

    Institute of Scientific and Technical Information of China (English)

    张洁; 刘作功; 郭雄

    2010-01-01

    目的 探讨desmin基因exon6 A360P错义突变与克山病心肌损伤的关系及exon6 A360P错义突变是否是慢型及潜在型克山病损伤的易感基因.方法 在陕西省克山病病区黄陵县店头镇和非病区西安市长安区,采用单纯随机抽样的方法,抽取年龄相匹配的慢型和潜在型克山病患者(病例组)30例及病区(内对照组)和非病区对照(外对照组)各30例.采集外周血5 ml,乙二胺四乙酸(EDTA)抗凝,盐析法制备基因组DNA.采用PCR方法,用特异性的Bsp1286 Ⅰ内切酶对可能发生突变的exon6位点进行酶切.设内对照,在desmin基因exon4位点进行酶切,判定标准为在122 bp和60 bp处各出现1个条带.琼脂糖凝胶电泳分析desmin基因exon6 A360P错义突变位点,判定标准为desmin基因exon6位点酶切后在184 bp和66 bp处各出现1个条带.结果 琼脂糖凝胶电泳结果显示,内对照desmin基因exon4在Bsp1286 Ⅰ酶切前,在182 bp处仅出现1条条带;在酶切后,被切成2个片段,在122 bp和60 bp处各出现1个条带.慢型及潜在型克山病患者desmin基因exon6在Bsp1286 Ⅰ酶切前和酶切后,均在250 bp处出现了1个条带;病区和非病区对照组desmin基因酶切后,也是在250 bp处出现了1个条带.3组结果相同,desmin基因exon6没有被Bsp1286 Ⅰ酶切开,A360P没有发生错义突变.结论 慢型和潜在型克山病患者未检出desmin基因exon6 A360P错义突变位点,desmin基因exon6 A360P错义突变不是克山病心肌损伤的易感基因.%Objective To survey the relationship between myocardial damage of chronic and latent Keshan disease with A360P missense mutation in desmin gene exon6. Methods By clinical epidemiology method,30 cases had been collected randomly among chronic Keshan disease patients and 30 cases equally among healthy adults (inner control groups) in Diantou town,Huangling county,Shaanxi province,a Keshan disease area,and 30 cases among health adults(outer control group) in Chang

  11. Domain mapping of the retinal cyclic GMP phosphodiesterase gamma-subunit. Function of the domains encoded by the three exons of the gamma-subunit gene.

    Science.gov (United States)

    Takemoto, D J; Hurt, D; Oppert, B; Cunnick, J

    1992-02-01

    Retinal rod-outer-segment phosphodiesterase (PDE) is a heterotetramer consisting of two similar, but not identical, catalytic subunits (alpha and beta) and two identical inhibitory subunits (gamma 2). Previously, we have reported that the site of PDE alpha/beta interaction with PDE gamma is located within residues 54-87 [Cunnick, Hurt, Oppert, Sakamoto & Takemoto (1990) Biochem. J. 271, 721-727]. The site for PDE gamma interaction with transducin alpha (T alpha) was found to encompass residues 24-45 of PDE gamma [Morrison, Cunnick, Oppert & Takemoto (1989) J. Biol. Chem. 264, 11671-11681]. In order to identify binding sites and other functional domains of PDE gamma, the three peptides which are encoded by the three exons of the PDE gamma gene were synthesized chemically. These exons encode for residues 1-49, 50-62 and 63-87 of bovine PDE gamma [Piriev, Purishko, Khramtsov & Lipkin (1990) Dokl. Akad. Nauk. SSSR 315, 229-230]. The peptide encompassing residues 63-87 was inhibitory in a PDE assay, whereas peptides 1-49 and 50-62 had no effect. However, both peptides 1-49 and 63-87 bound to PDE alpha/beta in a solid-phase binding assay. Only peptide 1-49 bound to T alpha.GTP[S] (GTP[S] is guanosine 5'-[gamma-thio]triphosphate). These data confirm that the inhibitory region of PDE gamma is encoded by exon 3 (residues 63-87), whereas a separate binding site for PDE alpha/beta and for T alpha.GTP[S] is encoded by exon 1 (residues 1-49). To study further the structure-function relationship of PDE gamma, this entire protein and two mutants were chemically synthesized. One mutant (-CT) lacked residues 78-87, whereas another replaced tyrosine-84 with glycine (TYR-84). Whereas the synthetic PDE gamma inhibited PDE alpha/beta catalytic activity, the -CT and TVR-84 mutants did not. All three synthetic proteins bound to both PDE alpha/beta and and T alpha.GTP[S]. These data confirm the presence of an alternative binding site on PDE gamma and demonstrate the importance of tyrosine

  12. Single-Nucleotide Polymorphism on Exon 17 of Insulin Receptor Gene Influences Insulin Resistance in PCOS: A Pilot Study on North Indian Women.

    Science.gov (United States)

    Gangopadhyay, Sukanya; Agrawal, Nitin; Batra, Aruna; Kabi, Bhaskar Charan; Gupta, Akash

    2016-04-01

    Polycystic ovarian syndrome (PCOS), a major cause of infertility, is also strongly associated with insulin resistance. Defects in insulin receptor signaling are considered as one of the major molecular pathogeneses for insulin resistance. To investigate the possible mechanism of this signaling defect at genetic level, single-nucleotide polymorphism (SNP) [His 1085 C/T] at the exon 17 of insulin receptor gene (INSR) was studied in this pilot study. Polymerase chain reaction was performed on leucocytic DNA of women diagnosed with PCOS, selected from the outpatient department of Safdarjung Hospital, New Delhi, using suitable primer to amplify a region on INSR. An equal number of age-matched healthy women were selected as controls. SNP analysis was performed with restriction enzyme length polymorphism technique using Pm II enzyme. Serum insulin level was measured by ELISA kit and HOMA-IR was calculated mathematically. A higher frequency of the CC genotype was observed in PCOS women than in controls. Also, HOMA-IR, a tool for estimating insulin resistance, was significantly high in PCOS women with the CC genotype. C1008T SNP at exon 17 of INSR is associated with insulin resistance in Indian women with PCOS. Presence of CC genotype (C1085T) could be developed as a marker for insulin resistance and metabolic complications in PCOS women.

  13. Mutations in the exon 7 of Trp53 gene and the level of p53 protein in double transgenic mouse model of Alzheimer's disease.

    Science.gov (United States)

    Dorszewska, Jolanta; Oczkowska, Anna; Suwalska, Monika; Rozycka, Agata; Florczak-Wyspianska, Jolanta; Dezor, Mateusz; Lianeri, Margarita; Jagodzinski, Paweł P; Kowalczyk, Michal J; Prendecki, Michal; Kozubski, Wojciech

    2014-01-01

    Alzheimer's disease (AD) leads to generation of β-amyloid (Aβ) in the brain. Alzheimer's disease model PS/APP mice show a markedly accelerated accumulation of Aβ, which may lead to apoptosis induction e.g. in cells expressing wild-type p53. The TP53 gene is found to be the most frequently mutated gene in human tumour cells. There is accumulating evidence pointing out to the contribution of oxidative stress and chronic inflammation in both AD and cancer. The purpose of this study was to analyze exon 7 mutations of the murine Trp53 gene and Aβ/A4 and p53 protein levels in PS/APP and control mice. The studies were performed on female double transgenic PS/APP mice and young adults (8-12 weeks old) and age-matched control mice. The Trp53 mutation analysis was carried out with the use of PCR and DNA sequencing. The Aβ/A4 and p53 levels were analyzed by Western blotting. The frequency of mutations was almost quadrupled in PS/APP mice (44%), compared to controls (14%). PS/APP mice with the A929T and A857G mutations had a similar p53 level. In cerebral gray matter of PS/APP mice the level of p53 positive correlated with the level of Aβ protein (RS = +0.700, p p53 down-regulation, while in aging ones, G859A substitution was most likely associated with over-expression of p53. In silico protein analysis revealed a possibly substantial impact of all four mutations on p53 activity. Three mutations were in close proximity to zinc-coordinating cysteine residues. It seems that in PS/APP mice missense Trp53 exon 7 mutations may be associated with the degenerative process by changes of p53 protein function.

  14. Deletion of exon 26 of the dystrophin gene is associated with a mild Becker muscular dystrophy phenotype

    DEFF Research Database (Denmark)

    Witting, Nanna; Duno, Morten; Vissing, John

    2011-01-01

    calf hypertrophy was noted. Creatine kinase was normal or raised maximally to 500 U/l. The muscle biopsy was myopathic with increased fiber size variation and many internal nuclei, but no dystrophy. No comorbidity was found. In both cases, western blot showed a reduced dystrophin band. Genetic...... associated with an exon 26 deletion. The proband, a 23-year-old man, had slightly delayed motor milestones, walking 1 1/2 years old. He had no complaints of muscle weakness, but had muscle pain. Clinical examination revealed no muscle wasting or loss of power, but his CK was 1500-7000 U/l. Muscle biopsy...... showed dystrophic changes. He had comorbidity with dystonia, slight mental retardation, low stature and neuropathy. The brother of the proband's mother came to medical attention when he was 43 years old. He complained about muscle pain. On examination, a MRC grade 4+ hip extention palsy and a discrete...

  15. Deletion of exon 26 of the dystrophin gene is associated with a mild Becker muscular dystrophy phenotype

    DEFF Research Database (Denmark)

    Witting, Nanna; Duno, Morten; Vissing, John

    2011-01-01

    calf hypertrophy was noted. Creatine kinase was normal or raised maximally to 500 U/l. The muscle biopsy was myopathic with increased fiber size variation and many internal nuclei, but no dystrophy. No comorbidity was found. In both cases, western blot showed a reduced dystrophin band. Genetic...... associated with an exon 26 deletion. The proband, a 23-year-old man, had slightly delayed motor milestones, walking 1 1/2 years old. He had no complaints of muscle weakness, but had muscle pain. Clinical examination revealed no muscle wasting or loss of power, but his CK was 1500-7000 U/l. Muscle biopsy...... showed dystrophic changes. He had comorbidity with dystonia, slight mental retardation, low stature and neuropathy. The brother of the proband's mother came to medical attention when he was 43 years old. He complained about muscle pain. On examination, a MRC grade 4+ hip extention palsy and a discrete...

  16. The N-terminally truncated µ3 and µ3-like opioid receptors are transcribed from a novel promoter upstream of exon 2 in the human OPRM1 gene.

    Directory of Open Access Journals (Sweden)

    Sonja Andersen

    Full Text Available The human µ opioid receptor gene, OPRM1, produces a multitude of alternatively spliced transcripts encoding full-length or truncated receptor variants with distinct pharmacological properties. The majority of these transcripts are transcribed from the main promoter upstream of exon 1, or from alternate promoters associated with exons 11 and 13. Two distinct transcripts encoding six transmembrane domain (6TM hMOR receptors, µ3 and µ3-like, have been reported, both starting with the first nucleotide in exon 2. However, no mechanism explaining their initiation at exon 2 has been presented. Here we have used RT-PCR with RNA from human brain tissues to demonstrate that the µ3 and µ3-like transcripts contain nucleotide sequences from the intron 1-exon 2 boundary and are transcribed from a novel promoter located upstream of exon 2. Reporter gene assays confirmed the ability of the novel promoter to drive transcription in human cells, albeit at low levels. We also report the identification of a "full-length" seven transmembrane domain (7TM version of µ3, hMOR-1A2, which also contains exon 1, and a novel transcript, hMOR-1Y2, with the potential to encode the previously reported hMOR-1Y receptor, but with exon Y spliced to exon 4 instead of exon 5 as in hMOR-1Y. Heterologous expression of GFP-tagged hMOR variants in HEK 293 cells showed that both 6TM receptors were retained in the intracellular compartment and were unresponsive to exogenous opioid exposure as assessed by their ability to redistribute or affect cellular cAMP production, or to promote intracellular Ca(2+ release. Co-staining with an antibody specific for endoplasmic reticulum (ER indicated that the µ3-like receptor was retained at the ER after synthesis. 7TM receptors hMOR-1A2 and hMOR-1Y2 resided in the plasma membrane, and were responsive to opioids. Notably, hMOR-1A2 exhibits novel functional properties in that it did not internalize in response to the opioid peptide [D-Ala2, N

  17. Single strand confirmation polymorphism (SSCP detection in exon I of the a-lactalbumin gene of Indian Jamunapari milk goats (Capra hircus

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    Dinesh Kumar

    2006-01-01

    Full Text Available The genetic diversity of Jamunapari goats (Capra hircus was investigated using an optimized non-radioactive polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP method to detect a-lactalbumin polymorphism in a sample of 50 goats. Our data show that PCR-SSCP is an appropriate tool for evaluating genetic variability in Jamunapari goats. Polymorphism was detected in the sample, indicating that Jamunapari goats have high genetic variability at loci, exon I of the a-lactalbumin gene. This result opens interesting prospects for future selection programs and conservation strategies. These a-lactalbumin variants can be sequenced and screened in the population to develop single nucleotide polymorphism (SNP markers for association studies and marker assisted selection.

  18. Cutis laxa: reduced elastin gene expression in skin fibroblast cultures as determined by hybridizations with a homologous cDNA and an exon 1-specific oligonucleotide

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, D.R.; Fazio, M.J.; Shamban, A.T.; Rosenbloom, J.; Uitto, J.

    1988-05-15

    Fibroblast cultures were established from six patients with cutis laxa, and elastin gene expression was analyzed by RNA hybridizations with a 2.5-kilobase human elastin cDNA or an exon 1-specific 35-base oligomer. Northern analyses using either probe detected mRNA transcripts of approx. 3.5 kilobases, and no qualitative difference between the control and cutis laxa mRNAs was detected. However, quantitation of the elastin mRNA abundance by slot blot hybridizations revealed markedly reduced levels in all cutis laxa cell strains. Assuming equal translational activity of the control and cutix laxa mRNAs, the reduced mRNA levels could result in diminished elastin production, providing an explanation for the paucity of elastic fibers in the skin and other tissues in cutis laxa.

  19. Polymorphism of exon 2 of BoLA-DRB3 gene and its relationship with somatic cell score in Beijing Holstein cows.

    Science.gov (United States)

    Chu, M X; Ye, S C; Qiao, L; Wang, J X; Feng, T; Huang, D W; Cao, G L; Di, R; Fang, L; Chen, G H

    2012-03-01

    In the present study, the exon 2 and 3' end sequence of intron 1 of BoLA-DRB3 gene of 211 Beijing Holstein cows was amplified and a uniform fragment of 284 bp was obtained. The genetic polymorphism was investigated by PCR-RFLP using two restriction endonucleases HaeIII and BstYI. Seven genotypes were detected by digesting the PCR products with HaeIII. The frequency of AA, AB, AC, AD, BB, BC and BF genotypes was 0.4638, 0.0193, 0.0193, 0.3478, 0.0290, 0.0386 and 0.0822, respectively. Three genotypes were found by digesting the PCR products with BstYI. The frequency of AA, AB and BB genotypes was 0.0569, 0.2844 and 0.6587, respectively. The relationship between the polymorphisms in exon 2 of BoLA-DRB3 gene and somatic cell score (SCS) in Beijing Holstein cows was analyzed by least squares linear model. No significant difference was detected among least squares means of SCS for seven HaeIII-RFLP genotypes (P > 0.05). As for BstYI-RFLP analysis, least squares mean of SCS for AA was significantly lower than that for AB (P 0.05). BstYI AA was the most favorable genotype and BstYI BB was the most unfavorable genotype for mastitis resistance. The information found in the present study is very important for improving mastitis resistance in dairy cattle by marker assisted selection.

  20. Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

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    Gröne Jörn

    2010-11-01

    Full Text Available Abstract Background Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance in cancer. Results In this study, a genome-wide analysis of the alteration of splicing patterns between lung cancer and normal lung tissue was performed. We generated an exon array data set derived from matched pairs of lung cancer and normal lung tissue including both the adenocarcinoma and the squamous cell carcinoma subtypes. An enhanced workflow was developed to reliably detect differential splicing in an exon array data set. In total, 330 genes were found to be differentially spliced in non-small cell lung cancer compared to normal lung tissue. Microarray findings were validated with independent laboratory methods for CLSTN1, FN1, KIAA1217, MYO18A, NCOR2, NUMB, SLK, SYNE2, TPM1, (in total, 10 events and ADD3, which was analysed in depth. We achieved a high validation rate of 69%. Evidence was found that the activity of FOX2, the splicing factor shown to cause cancer-specific splicing patterns in breast and ovarian cancer, is not altered at the transcript level in several cancer types including lung cancer. Conclusions This study demonstrates how alternatively spliced genes can reliably be identified in a cancer data set. Our findings underline that key processes of cancer progression in NSCLC are affected by alternative splicing, which can be exploited in the search for novel targeted therapies.

  1. Detection of a novel mutation Y468X in exon 10 of the low-density lipoprotein receptor gene causing heterozygous familial hypercholesterolemia among French Canadians

    Energy Technology Data Exchange (ETDEWEB)

    Couture, P.; Simard, J.; Moorjani, S. [Laval Univ., Quebec (Canada)

    1994-09-01

    Familial hypercholesterolemia (FH) is caused by mutations in the low-density lipoprotein (LDL) receptor gene and characterized by raised plasma LDL-cholesterol (C) and premature coronary heart disease. FH has higher frequency among French Canadians (FC) in northeastern Quebec than in most other populations, 1:154 vs. 1:500. In FC, five mutations account for all the mutant alleles in homozygous FH and 81% in heterozygous FH; thus 19% are uncharacterized at the molecular level. We investigated the possibility of additional mutations(s), and direct sequencing of asymmetric PCR fragments showed a novel mutation (468 stop-codon) in the heterozygous form in exon 10 of the LDL receptor gene. This mutation results from cytosine to guanine transversion, converting codon 468 (TAC) encoding tyrosine into TAG stop-codon (Y468X). This nonsense mutation will result in a truncated protein shortened by 371 amino acids which will be rapidly degraded. However, we did not ascertain the functional aspects. We rather assessed its effects on the extent of elevation of LDL-C in heterozygous FH children. The Y468X mutation resulted in raised LDL-C levels which were comparable to subjects with a non-functional `null` allele due to deletion of the promoter region and exon 1 (237{plus_minus}49 vs. 248 {plus_minus}41 mg/dl; mean{plus_minus}SD, p<0.05). The relative frequency of the Y468X mutation in a cohort of 343 children suspected for FH is 4.1% and it ranks number 4 in term of its prevalence. High frequency of FH among FC is attributed to a founder effect due to a high prevalence of one mutation; it is suggested that this novel mutation with low prevalence may be of later entry in this population.

  2. Polymorphism in the exon 4 of β-lactoglobulin variant B precursor gene and its association with milk traits and protein structure in Chinese Holstein.

    Science.gov (United States)

    Yang, Fan; Li, Lian; Liu, Huiling; Cai, Yafei; Wang, Genlin

    2012-04-01

    β-lactoglobulin (β-LG) is the major whey protein in the milk. In order to investigate the polymorphism of β-LG variant B precursor (β-LG B*: GenBank accession no. DQ489319) gene and its effects on the milk traits, the single-strand conformation polymorphism method (PCR-SSCP) were adopted to analyze polymorphism between 5229th and 5476th bp in the β-LG B* gene in Chinese Holstein. Four genotypes were found (AA, AB, AC and ABC) and 3 single nucleotide polymorphisms (SNPs) were detected (g.5239C>A, g.5240A>C, g.5305C>T and mix type g.5305C/T) in the exon 4 of β-LG B* gene. It was also found that the protein contents of AB, AC and ABC dairy cows were higher than AA (P A, g.5240A>C and g.5305C>T) might affect the milk trait and all of them were high polymorphism (0.5 Glu, Thr>Pro and Ala>Val) respectively, and the spatial secondary and tertiary structure forecasting result also showed that single amino acid change influence protein spatial structure change in Chinese Holstein. Taken together, it is suggested that these SNPs change β-LG B* gene structure and expression. The polymorphism possibly holds the secret of milk protein and fat contents in the milk of Chinese Holstein.

  3. DMD基因外显子缺失导致进行性肌营养不良%Deletion of exons of DMD gene lead to progressive muscular dystrophy

    Institute of Scientific and Technical Information of China (English)

    王银龙; 潘秀兰; 王友明; 闫纪琳; 魏东敏; 耿建芳; 单铁英

    2013-01-01

    Objective To specific diagnose DMD patient by using gene analysis,further more for carrier and pregnant diagnosis.Methods Multi-PCR method was conducted to analyze DMD gene mutation in DMD/BMD patients.Results Five of eleven patients were found deletion of exons of DMD gene.The deletions are exon 45,48,51 and two exon 4.Conclusion Deletion of exons of DMD gene lead to progressive muscular dystrophy.%目的 通过基因分析对DMD患者做出准确诊断,以便检出携带者和进行产前诊断.方法 运用多重PCR技术对来该院就诊临床上诊断为DMD/BMD患者进行DMD基因突变分析.结果 11例诊断为DMD/BMD患者中发现5例有DMD基因外显子缺失,分别是外显子45、48、51各1例,外显子4有2例.结论 DMD基因外显子缺失导致进行性肌营养不良.

  4. SOD1 Gene +35A/C (exon3/intron3 Polymorphism in Type 2 Diabetes Mellitus among South Indian Population

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    K. Nithya

    2016-01-01

    Full Text Available Superoxide dismutase is an antioxidant enzyme that is involved in defence mechanisms against oxidative stress. Cu/Zn SOD is a variant that is located in exon3/intron3 boundary. The aim of the present study was to investigate whether the Cu/Zn SOD (+35A/C gene polymorphism is associated with the susceptibility to type 2 diabetes mellitus among south Indian population. The study included patients with type 2 diabetes mellitus (n=100 and healthy controls (n=75. DNA was isolated from the blood and genotyping of Cu/Zn SOD gene polymorphism was done by polymerase chain reaction based restriction fragment length polymorphism method. Occurrence of different genotypes and normal (A and mutant (C allele frequencies were determined. The frequency of the three genotypes of the total subjects was as follows: homozygous wild-type A/A (95%, heterozygous genotype A/C (3%, and homozygous mutant C/C (2%. The mutant (C allele and the mutant genotypes (AC/CC were found to be completely absent among the patients with type 2 diabetes mellitus. Absence of mutant genotype (CC shows that the Cu/Zn SOD gene polymorphism may not be associated with the susceptibility to type 2 diabetes mellitus among south Indian population.

  5. SOD1 Gene +35A/C (exon3/intron3) Polymorphism in Type 2 Diabetes Mellitus among South Indian Population.

    Science.gov (United States)

    Nithya, K; Angeline, T; Isabel, W; Asirvatham, A J

    2016-01-01

    Superoxide dismutase is an antioxidant enzyme that is involved in defence mechanisms against oxidative stress. Cu/Zn SOD is a variant that is located in exon3/intron3 boundary. The aim of the present study was to investigate whether the Cu/Zn SOD (+35A/C) gene polymorphism is associated with the susceptibility to type 2 diabetes mellitus among south Indian population. The study included patients with type 2 diabetes mellitus (n = 100) and healthy controls (n = 75). DNA was isolated from the blood and genotyping of Cu/Zn SOD gene polymorphism was done by polymerase chain reaction based restriction fragment length polymorphism method. Occurrence of different genotypes and normal (A) and mutant (C) allele frequencies were determined. The frequency of the three genotypes of the total subjects was as follows: homozygous wild-type A/A (95%), heterozygous genotype A/C (3%), and homozygous mutant C/C (2%). The mutant (C) allele and the mutant genotypes (AC/CC) were found to be completely absent among the patients with type 2 diabetes mellitus. Absence of mutant genotype (CC) shows that the Cu/Zn SOD gene polymorphism may not be associated with the susceptibility to type 2 diabetes mellitus among south Indian population.

  6. Broad spectrum analgesic efficacy of IBNtxA is mediated by exon 11-associated splice variants of the mu-opioid receptor gene

    Science.gov (United States)

    Wieskopf, Jeffrey S.; Pan, Ying-Xian; Marcovitz, Jaclyn; Tuttle, Alexander H.; Majumdar, Susruta; Pidakala, John

    2014-01-01

    Mu-opioids remain vastly important for the treatment of pain, and would represent ideal analgesics if their analgesic effects could be separated from their many side effects. A recently synthesized compound, iodobenzoylnaltrexamide (IBNtxA), acting at 6-transmembrane (6-TM) splice variants of the mu-opioid receptor gene, was shown to have potent analgesic actions against acute, thermal pain accompanied by a vastly improved side-effect profile compared to 7-TM-acting drugs such as morphine. Whether such analgesia can be seen in longer-lasting and non-thermal algesiometric assays is not known. The current study demonstrates potent and efficacious IBNtxA inhibition of a wide variety of assays, including inflammatory and neuropathic hypersensitivity and spontaneous pain. We further demonstrate the dependence of such analgesia on 6-TM mu-opioid receptor variants using isobolographic analysis and the testing of Oprm1 (the mu-opioid receptor gene) exon 11 null mutant mice. Finally, the effect of nerve damage (spared nerve injury) and inflammatory injury (complete Freund’s adjuvant) on expression of mu-opioid receptor variant genes in pain-relevant central nervous system loci was examined, revealing a downregulation of the mMOR-1D splice variant in the dorsal root ganglion after spared nerve injury. These findings are supportive of the potential value of 6-TM-acting drugs as novel analgesics. PMID:25093831

  7. Identification and characterization of polymorphisms within the 5' flanking region, first exon and part of first intron of bovine GH gene.

    Science.gov (United States)

    Ferraz, A L J; Bortolossi, J C; Curi, R A; Ferro, M I T; Ferro, J A; Furlan, L R

    2006-06-01

    The aim of the present study was to identify and characterize polymorphisms within the 5' flanking region, first exon and part of first intron of the bovine growth hormone gene among different beef cattle breeds: Nelore (n = 25), Simmental (n = 39), Simbrasil (n = 24), Simmental x Nelore (n = 30), Canchim x Nelore (n = 30) and Angus x Nelore (n = 30). Two DNA fragments (GH1, 464 bp and GH2, 453 bp) were amplified by polymerase chain reaction and then used for polymorphism identification by SSCP. Within the GH1 fragment, five polymorphisms were identified, corresponding to three different alleles: GH1.1, GH1.2 and GH1.3 (GenBank: AY662648, AY662649 and AY662650, respectively). These allele sequences were aligned and compared with bovine GH gene nucleotide sequence (GenBank: M57764 and AF118837), resulting in the identification of five insertion/deletions (INDELs) and five single nucleotide polymorphisms (SNPs). In the GH2 fragment two alleles were identified, GH2.1 and GH2.2 (GenBank: AY662651 and AY662652, respectively). The allele sequences were compared with GenBank sequences (M57764, AF007750 and AH009106) and three INDELs and four SNPs were identified. In conclusion, we were able to identify six new polymorphisms of the bovine GH gene (one INDEL and five SNPs), which can be used as molecular markers in genetic studies.

  8. 17β-Estradiol Increases Non-CpG Methylation in Exon 1 of the Rainbow Trout (Oncorhynchus mykiss) MyoD Gene.

    Science.gov (United States)

    Koganti, Prasanthi P; Wang, Jian; Cleveland, Beth; Yao, Jianbo

    2017-08-01

    MyoD is an important myogenic transcription factor necessary for the differentiation of myogenic precursor cells (MPC) to form mature myotubes, a process essential for muscle growth. Epigenetic markers such as CpH methylation are known gene regulators that are important for the differentiation process. In this study, we investigated whether DNA methylation is a potential mechanism associated with the ability of 17β-estradiol (E2) to reduce MyoD gene expression and muscle growth in rainbow trout. Rainbow trout received a single intraperitoneal injection of E2 or the injection vehicle (control). Skeletal muscle was collected 24 h post injection and analyzed for DNA methylation within the MyoD gene and the expression of DNA methyltransferases. CpG islands of the MyoD gene were predicted using MethPrimer software, and these regions were PCR amplified and analyzed using bisulfite sequencing. The percent methylation of the targeted CpG did not differ between control and E2-treated fish. However, percent CpH methylation in the MyoD exon 1 region was elevated with E2 treatment. Two of the methylated CpH sites were located in conserved transcription factor binding motifs, estrogen response element (ERE), and Myc binding site. Quantitative real-time PCR analysis revealed a significant increase in expression of DNA methyltransferases, Dnmt3a and Dnmt3b, in E2-treated muscle, suggesting an increased genome methylation. Differential CpH methylation in MyoD gene of control and E2-treated fish suggests an epigenetic mechanism through which E2 decreases MyoD gene expression and contributes to reduced muscle growth.

  9. A deletion in exon 9 of the LIPH gene is responsible for the rex hair coat phenotype in rabbits (Oryctolagus cuniculus.

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    Mathieu Diribarne

    Full Text Available The fur of common rabbits is constituted of 3 types of hair differing in length and diameter while that of rex animals is essentially made up of amazingly soft down-hair. Rex short hair coat phenotypes in rabbits were shown to be controlled by three distinct loci. We focused on the "r1" mutation which segregates at a simple autosomal-recessive locus in our rabbit strains. A positional candidate gene approach was used to identify the rex gene and the corresponding mutation. The gene was primo-localized within a 40 cM region on rabbit chromosome 14 by genome scanning families of 187 rabbits in an experimental mating scheme. Then, fine mapping refined the region to 0.5 cM (Z = 78 by genotyping an additional 359 offspring for 94 microsatellites present or newly generated within the first defined interval. Comparative mapping pointed out a candidate gene in this 700 kb region, namely LIPH (Lipase Member H. In humans, several mutations in this major gene cause alopecia, hair loss phenotypes. The rabbit gene structure was established and a deletion of a single nucleotide was found in LIPH exon 9 of rex rabbits (1362delA. This mutation results in a frameshift and introduces a premature stop codon potentially shortening the protein by 19 amino acids. The association between this deletion and the rex phenotype was complete, as determined by its presence in our rabbit families and among a panel of 60 rex and its absence in all 60 non-rex rabbits. This strongly suggests that this deletion, in a homozygous state, is responsible for the rex phenotype in rabbits.

  10. A deletion in exon 9 of the LIPH gene is responsible for the rex hair coat phenotype in rabbits (Oryctolagus cuniculus).

    Science.gov (United States)

    Diribarne, Mathieu; Mata, Xavier; Chantry-Darmon, Céline; Vaiman, Anne; Auvinet, Gérard; Bouet, Stéphan; Deretz, Séverine; Cribiu, Edmond-Paul; de Rochambeau, Hubert; Allain, Daniel; Guérin, Gérard

    2011-04-28

    The fur of common rabbits is constituted of 3 types of hair differing in length and diameter while that of rex animals is essentially made up of amazingly soft down-hair. Rex short hair coat phenotypes in rabbits were shown to be controlled by three distinct loci. We focused on the "r1" mutation which segregates at a simple autosomal-recessive locus in our rabbit strains. A positional candidate gene approach was used to identify the rex gene and the corresponding mutation. The gene was primo-localized within a 40 cM region on rabbit chromosome 14 by genome scanning families of 187 rabbits in an experimental mating scheme. Then, fine mapping refined the region to 0.5 cM (Z = 78) by genotyping an additional 359 offspring for 94 microsatellites present or newly generated within the first defined interval. Comparative mapping pointed out a candidate gene in this 700 kb region, namely LIPH (Lipase Member H). In humans, several mutations in this major gene cause alopecia, hair loss phenotypes. The rabbit gene structure was established and a deletion of a single nucleotide was found in LIPH exon 9 of rex rabbits (1362delA). This mutation results in a frameshift and introduces a premature stop codon potentially shortening the protein by 19 amino acids. The association between this deletion and the rex phenotype was complete, as determined by its presence in our rabbit families and among a panel of 60 rex and its absence in all 60 non-rex rabbits. This strongly suggests that this deletion, in a homozygous state, is responsible for the rex phenotype in rabbits.

  11. Whole-Transcriptome RNA-seq, Gene Set Enrichment Pathway Analysis, and Exon Coverage Analysis of Two Plastid RNA Editing Mutants.

    Science.gov (United States)

    Hackett, Justin B; Lu, Yan

    2017-04-07

    In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed two plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the beta subunit of cytochrome b559, an essential component of PSII. The accD gene encodes the beta subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly up-regulated in both orrm6 mutants. The up-regulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.

  12. Polymorphic analysis of Mhc-DPB1 gene exon 2 in Tibetan macaques (Macaca thibetana)%藏酋猴 Mhc-DPB1基因 exon2的多态性

    Institute of Scientific and Technical Information of China (English)

    李佳薏; 姚永芳; 周亮; 徐怀亮

    2012-01-01

    主要组织相容性复合体(Major histocompatibility complex,MHC)对许多疾病的易感性和抵抗力起着 重要的作用.为了解藏酋猴(Macaca thibetana)的 MHC 基因遗传背景,以促进藏酋猴遗传资源的保护及其在生 物医学研究中的应用,文章采用 PCR 扩增和克隆测序等方法对来自四川地区的 70 个藏酋猴样品的 Mhc-DPB1 基因 exon 2 进行了检测和分析.首次在藏酋猴中获得了 18 个 DPB1 等位基因(Math-DPB1),其中 1 个为假基因(Math- DPB1*01:06N).18 个等位基因中,Math-DPB1*06:01:01 (67.14%) 的阳性检出率最高,其次为 Math-DPB1*01:03:01 (37.14%)、Math-DPB1*09:02(25.71%)和 Math-DPB1*22:01(15.71%).氨基酸序列比对发现,藏酋猴 Math-DPB1 等位基因编码的氨基酸序列中,有 5 个氨基酸残基变异位点表现出物种特异性.不同物种来源的 DPB1 等位基 因系统发生树表明,藏酋猴、猕猴(Macaca mulatta)和食蟹猴(Macaca fascicularis)的 DPB1 等位基因不是以物种 特异性方式聚类,而是种间混聚在一起,并显示出明显的跨物种多态性(Trans-species polymorphism).选择性检 验表明,平衡选择(Balancing selection)在维持 Math-DPB1 基因的多态性中起着重要的作用.%Major histocompatibility complex (MHC) molecules play an important role in the susceptibility and/or resistance to many diseases. To gain an insight into the MHC background of the Tibetan macaques (Macaca thibetana), and thereby facilitate their protection and application in biomedical research, the second exon of the Mhc-DPBl genes from 70 Tibetan macaques in Sichuan Province were characterized by PCR, cloning, sequencing, and statistical analysis. A total of 18 Mhc-DPB1 alleles were identified from Tibetan macaques, of which one (Math-DPB1* 01:06N) was a pseudogene. Math-DPB1*06:01:01 (67.14%) was the most frequent allele in all the 18 alleles detected, followed by Math-DPBl* 01:03:01 (37.14%), Math-DPB 1*09:02 (25.71%), and Math-DPB 1

  13. Mutations in exon3 and exon4 of SIP1 gene in children with isolated Hirschsprung's disease%先天性巨结肠症SIP1基因外显子3和外显子4的突变分析

    Institute of Scientific and Technical Information of China (English)

    高红; 伍美; 张娟; 张志波; 黄英; 王大佳; 王维林

    2010-01-01

    目的 探讨SIP1基因外显子3和外显子4与散发性先天性巨结肠(Hirschsprung disease,HD)的关联性.方法 检测150例HD患儿SIP1基因突变.采用PCR-变性梯度凝胶电泳(PCR-degenerating gel gradient electrophoresis,PCR-DGGE)与DNA测序法检测患儿SIP1基因exon3 and exon4的突变.另选取150例正常人(排除家族性顽同便秘及其他先天性消化道畸形史健康儿童)外周血DNA作为对照组.结果 在HD组exon3 PCR-DGGE发现83例异常电泳条带,测序证实67/83例SIP1发生在突变集中区域,为错义突变(ACC→ATC,苏氨酸→异亮氨酸).在HD组exon4发现101例异常电泳条带,测序证实68/101例SIP1发生在突变集中区域,有4种突变(CAC→TAC,组氨酸→酪氨酸;GAG→GAT,谷氨酸→天门冬氨酸;GCC→GTC,丙氨酸→缬氨酸;TGT→TTT,胱氨酸→苯丙氨酸).DGGE检测正常对照组中未发现异常电泳条带,测序未发现突变.结论 SIP1基因为HD的致病基因,突变类型多样,已发现热点突变;提示SIP1基因与HD发病存在一定程度的关联.%Objective To screen the mutations of SIP1 gene in children with isolated Hirschsprung disease (HD).Methods Polymerase chain reaction (PCR)and degenerating gel gradient electrophoresis (DGGE)was employed to amplify and separate the target gene.The mutations in exon3 and exon4 of SIP1 gene of 150 HD patients were explored by direct nucleotide sequencing analysis.The peripheral blood of 150 health individuals who had no congenital gastrointestinal malformations and family history of constipation were taken as normal controls.Results Eighty three abnormal electrophoresis bands of exon3 PCR products were found in HD patients.DNA sequencing showed that mutations were found in 67 of the 83 abnormal bands,which was (ACC→ATC).One hundred and one abnormal electrophoresis bands of exon4 PCR products were found in HD patients.Mutations in exon4 of SIP1gene,which were (CAC→TAC;GAG→GAT;GCC→GTC;TGT→TTT),were found in 68

  14. Symptoms of attention-deficit/hyperactivity disorder in Down syndrome: effects of the dopamine receptor D4 gene.

    Science.gov (United States)

    Mason, Gina Marie; Spanó, Goffredina; Edgin, Jamie

    2015-01-01

    This study examined individual differences in ADHD symptoms and executive function (EF) in children with Down syndrome (DS) in relation to the dopamine receptor D4 (DRD4) gene, a gene often linked to ADHD in people without DS. Participants included 68 individuals with DS (7-21 years), assessed through laboratory tasks, caregiver reports, and experimenter ratings. Saliva samples were collected from the DS group and 66 children without DS to compare DRD4 allele distribution, showing no difference between the groups. When the sample with DS was stratified for ethnicity (n  =  32), the DRD4 7-repeat allele significantly related to parent and experimenter ratings, but not to laboratory assessments. These results suggest that nontrisomy genetic factors may contribute to individual differences in ADHD symptoms in persons with DS.

  15. Variable expression of cerebral cavernous malformations in carriers of a premature termination codon in exon 17 of the Krit1 gene

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    Gamero Miguel A

    2003-07-01

    Full Text Available Abstract Background Cerebral cavernous malformations (CCM present as either sporadic or autosomal dominant conditions with incomplete penetrance of symptoms. Differences in genetic and environmental factors might be minimized among first-degree relatives. We therefore studied clinical expression in a family with several affected members. Methods We studied a three-generation family with the onset of CCM as a cerebral haemorrhage in the younger (four-year-old sibling. Identification and enumeration of CCMs were performed in T2-weighted or gradient-echo MRIs of the whole brains. Genetic analysis comprised SCCP, sequencing and restriction polymorphism of the Krit1 gene in the proband and at risk relatives. Results The phenotypes of cerebral cavernous malformations (CCMs in carriers of Krit1 mutations were very variable. We identified a novel frameshift mutation caused by a 1902A insertion in exon 17 of the Krit1 gene, which leads to a premature TAA triplet and predicts the truncating phenotype Y634X. A very striking finding was the absence of both clinical symptoms and CCMs in the eldest sibling harbouring the 1902insA. Conclusions Patients in this family, harbouring the same mutation, illustrate the very variable clinical and radiological expression of a Krit1 mutation. The early and critical onset in the proband contrasts with minor clinical findings in affected relatives. This consideration is important in genetic counselling.

  16. Exon level transcriptomic profiling of HIV-1-infected CD4(+ T cells reveals virus-induced genes and host environment favorable for viral replication.

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    Michaël Imbeault

    Full Text Available HIV-1 is extremely specialized since, even amongst CD4(+ T lymphocytes (its major natural reservoir in peripheral blood, the virus productively infects only a small proportion of cells under an activated state. As the percentage of HIV-1-infected cells is very low, most studies have so far failed to capture the precise transcriptomic profile at the whole-genome scale of cells highly susceptible to virus infection. Using Affymetrix Exon array technology and a reporter virus allowing the magnetic isolation of HIV-1-infected cells, we describe the host cell factors most favorable for virus establishment and replication along with an overview of virus-induced changes in host gene expression occurring exclusively in target cells productively infected with HIV-1. We also establish that within a population of activated CD4(+ T cells, HIV-1 has no detectable effect on the transcriptome of uninfected bystander cells at early time points following infection. The data gathered in this study provides unique insights into the biology of HIV-1-infected CD4(+ T cells and identifies genes thought to play a determinant role in the interplay between the virus and its host. Furthermore, it provides the first catalogue of alternative splicing events found in primary human CD4(+ T cells productively infected with HIV-1.

  17. Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons

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    Zhenxun Wang; Deblina Chatterjee; Hyun Yong Jeon; Martin Akerman; Matthew G. Vander Heiden; Lewis C. Cantley; Adrian R. Krainer

    2012-01-01

    Alternative splicing of the pyruvate kinase M gene (PK-M) can generate the M2 isoform and promote aerobic glycolysis and tumor growth.However,the cancer-specific alternative splicing regulation of PK-M is not completely understood.Here,we demonstrate that PK-M is regulated by reciprocal affects on the mutually exclusive exons 9 and 10,such that exon 9 is repressed and exon 10 is activated in cancer cells.Strikingly,exonic,rather than intronic,cis-elements are key determinants ef PK-M splicing isoform ratios.Using a systematic sub-exonic duplication approach,we identify a potent exonlc splicing enhancer in exon 10,which differs from its homologous counterpart in exon 9 by only two nucleotides.We identify SRSF3 as one of the cognate factors,and show that this serine/arginine-rich protein activates exon 10 and mediates changes in glucose metabolism.These findings provide mechanistic insights into the complex regulation of alternative splicing of a key regulator of the Warburg effect,and also have implications for other genes with a similar pattern of alternative splicing.

  18. The relationship between MHC-DRB1 gene second exon polymorphism and hydatidosis resistance of Chinese merino (Sinkiang Junken type, Kazakh and Duolang sheep

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    Li R.Y.

    2011-05-01

    Full Text Available The present study aimed at detecting the association of ovine major histocompatibility complex class II (Ovar II DRB1 gene second exon and susceptibility or resistance to hydatidosis in three sheep breeds of Sinkiang. The MHC-DRB1 second exon was amplified by polymerase chain reaction (PCR from DNA samples of healthy sheep and sheep with hydatidosis. PCR products were characterized by the restriction fragment length polymorphism (RFLP technique. Five restriction enzymes, MvaI, HaeIII, SacI, SacII, Hin1I, were used, yielding 14 alleles and 31 restriction patterns. Frequencies of patterns MvaIbc, Hin1Iab, SacIIab, HaeIIIde, HaeIIIdf, HaeIIIdd (P < 0.01 in Kazakh sheep, SacIab (P < 0.05 in Duolang sheep, and HaeIIIab, HaeIIIce, HaeIIIde, HaeIIIee (P < 0.01 in Chinese Merino (Sinkiang Junken type sheep, were significantly higher in healthy sheep compared with infected sheep. These results indicated a strong association between these patterns and hydatidosis resistance. In contrast, the frequencies of MvaIbb, SacIIaa, Hin1Ibb, HaeIIIef (P < 0.01 and HaeIIIab (P < 0.05 in Kazakh sheep, SacIbb, HaeIIIae, Hin1Iab (P < 0.05, HaeIIIaa, HaeIIIbe, HaeIIIef (P < 0.01 in Duolang sheep, SacIIaa (P < 0.05 and HaeIIIbd, Hin1Ibb, HaeIIIcf, HaeIIIef (P < 0.01 in Chinese Merino sheep (Sinkiang Junken type were significantly lower in healthy sheep compared with infected sheep. This indicated a strong association between these patterns and hydatidosis susceptibility. In addition, sheep with the pattern of HaeIIIef demonstrated a high hydatidosis susceptibility (P < 0.01 in all three breeds, while sheep with the pattern HaeIIIde demonstrated significant hydatidosis resistance (P < 0.01 in Kazakh and Chinese Merino sheep (Sinkiang Junken type. These results suggest that the Ovar-DRB1 gene plays a role in resistance to hydatidosis infection in the three sheep breeds.

  19. PCR-RFLP to Detect Codon 248 Mutation in Exon 7 of "p53" Tumor Suppressor Gene

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    Ouyang, Liming; Ge, Chongtao; Wu, Haizhen; Li, Suxia; Zhang, Huizhan

    2009-01-01

    Individual genome DNA was extracted fast from oral swab and followed up with PCR specific for codon 248 of "p53" tumor suppressor gene. "Msp"I restriction mapping showed the G-C mutation in codon 248, which closely relates to cancer susceptibility. Students learn the concepts, detection techniques, and research significance of point mutations or…

  20. PCR-RFLP to Detect Codon 248 Mutation in Exon 7 of "p53" Tumor Suppressor Gene

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    Ouyang, Liming; Ge, Chongtao; Wu, Haizhen; Li, Suxia; Zhang, Huizhan

    2009-01-01

    Individual genome DNA was extracted fast from oral swab and followed up with PCR specific for codon 248 of "p53" tumor suppressor gene. "Msp"I restriction mapping showed the G-C mutation in codon 248, which closely relates to cancer susceptibility. Students learn the concepts, detection techniques, and research significance of point mutations or…

  1. Novel insertion in exon 5 of the TCOF1 gene in twin sisters with Treacher Collins syndrome.

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    Marszałek-Kruk, Bożena Anna; Wójcicki, Piotr; Smigiel, Robert; Trzeciak, Wiesław H

    2012-08-01

    Treacher Collins syndrome (TCS) is associated with an abnormal differentiation of the first and second pharyngeal arches during fetal development. This causes mostly craniofacial deformities, which require numerous corrective surgeries. TCS is an autosomal dominant disorder and it occurs in the general population at a frequency of 1 in 50,000 live births. The syndrome is caused by mutations in the TCOF1 gene, which encodes the serine/alanine-rich protein named Treacle. Over 120 mutations of the TCOF1 gene responsible for TCS have been described. About 70% of recognized mutations are deletions, which lead to a frame shift, formation of a termination codon, and shortening of the protein product of the gene. Herewith, a new heterozygotic insertion, c.484_668ins185bp, was described in two monozygotic twin sisters suffering from TCS. This mutation was absent in their father, brother, and uncle, indicating a de novo origin. The insertion causes a shift in the reading frame and premature termination of translation at 167 aa. The novel insertion is the longest ever found in the TCOF1 gene and the only one found among monozygotic twin sisters.

  2. Molecular analysis of exons 6 and 7 of phenylalanine hydroxylase gene mutations in Phenylketonuria patients in Western Iran

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    Keyvan Moradi

    2012-01-01

    Conclusion: The frequency of R261X, the most common mutation in our study, in Iranian population is <5%. Furthermore, there is no report of detection of R176X and R243Q in Isfahan and Azeri Turkish populations. These findings confirm the common Mediterranean mutations in this local population, although with more or lower frequencies than those reported in other related studies in Iran. Therefore, it may be necessary to study the PAH gene mutations in other provinces of Iran separately.

  3. Early-progressive dilated cardiomyopathy in a family with Becker muscular dystrophy related to a novel frameshift mutation in the dystrophin gene exon 27.

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    Tsuda, Takeshi; Fitzgerald, Kristi; Scavena, Mena; Gidding, Samuel; Cox, Mary O; Marks, Harold; Flanigan, Kevin M; Moore, Steven A

    2015-03-01

    We report a family in which two male siblings with Becker muscular dystrophy (BMD) developed severe dilated cardiomyopathy (DCM) and progressive heart failure (HF) at age 11 years; one died at age 14 years while awaiting heart transplant and the other underwent left ventricular assist device implantation at the same age. Genetic analysis of one sibling showed a novel frameshift mutation in exon 27 of Duchenne muscular dystrophy (DMD) gene (c.3779_3785delCTTTGGAinsGG), in which seven base pairs are deleted and two are inserted. Although this predicts an amino-acid substitution and premature termination (p.Thr1260Argfs*8), muscle biopsy dystrophin immunostaining instead indicates that the mutation is more likely to alter splicing. Despite relatively preserved skeletal muscular performance, both the siblings developed progressive HF secondary to early-onset DCM. In addition, their 7-year-old nephew with delayed gross motor development, mild proximal muscle weakness and markedly elevated serum creatine kinase level (>13 000 IU l(-1)) at 16 months was recently demonstrated to have the familial DMD mutation. Here, we report a novel genotype of BMD with early-onset DCM and progressive lethal HF during early adolescence.

  4. Symptoms of Attention-Deficit/Hyperactivity Disorder in Down Syndrome: Effects of the Dopamine Receptor D4 Gene

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    Mason, Gina Marie; Spanó, Goffredina; Edgin, Jamie

    2015-01-01

    This study examined individual differences in ADHD symptoms and executive function (EF) in children with Down syndrome (DS) in relation to the dopamine receptor D4 (DRD4) gene, a gene often linked to ADHD in people without DS. Participants included 68 individuals with DS (7-21 years), assessed through laboratory tasks, caregiver reports, and…

  5. A common variation within the STEAP4 gene exons is associated with obesity in Uygur general population

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    GUO Yan-ying; LI Nan-fang; ZHOU Ling; YAO Xiao-guang; WANG Hong-mei; ZHANG Ju-hong; LUO Wen-li

    2011-01-01

    Background Coordinated regulation of nutrient and inflammatory responses by six transmembrane epithelial antigen of prostate 4 (STEAP4) was essential for metabolic homeostasis. STEAP4 expression in human white adipose tissuewas associated with obesity. This study aimed to evaluate association between STEAP4 genetic polymorphisms and obesity in Uygur Chinese general population.Methods The functional regions of STEAP4 gene were sequenced in 96 Uygur with obesity (body mass index (BMI)>30 kg/m2). Representative variations were selected according to the function and linkage disequilibrium and genotyped in 1507 obesity (BMI ≥25 kg/m2) and 825 non-obesity control (BMI <25 kg/m2), all of whom were selected from epidemiology study of obesity-related diseases during January to February 2007 among Uygur population in Hetian area of Xinjiang Uygur Autonomous Region.Results Fourteen novel and 6 known single nucleotide polymorphism (SNPs), including 2 nonsynonymous SNPs (nsSNPs), in the STEAP4 gene were identified. Of the 3 representative SNPs, the nsSNP rs1981529 (Gly75Asp, 224A/G)was significantly associated with obesity phenotype (additive P/Pc=0.001/0.006, dominant P/Pc=0.003/0.018, odds ratio (OR) and 95% confidence interval (CI) adjusted for age, gender and drinking 0.755 (0.641-0.890) and 0.750(0.621-0.907), respectively). By the multiple linear regression analysis, the quantitative phenotypes of BMI (P/Pc=0.002/0.004) and waist circumference (P/Pc=0.004/0.008) were found to be significantly associated with the genotypes of rs1981529 (Gly75Asp, 224A/G) in Uygur general population, and effect size (beta value) of one allele G of rs1981529 (Gly75Asp, 224A/G) was-0.553 kg/m2 for BMI and -1.311 cm for waist circumference after controlling age,gender and drinking factors.Conclusions The present study shows an association of the common variation rs1981529 (Gly75Asp, 224A/G) in the STEAP4 gene with obesity in Uygur general population. Further studies should replicate the

  6. Allelic polymorphism of Ovar-DRB1 exon2 gene and parasite resistance in two dairy sheep breeds

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    Stavros Spetsarias

    2016-02-01

    Full Text Available The Ovar-DRB1 gene locus is one of the most polymorphic genes of the Major Histocompatibility Complex (Ovar-MHC and holds a functional role to antigen presentation. The aim of this study was: a to describe the Ovar-DRB1 locus variability in two dairy Greek sheep breeds and b to investigate associations between this variability with resistance to gastrointestinal parasitosis. Blood and faecal samples were collected from 231 and 201 animals of Arta and Kalarrytiko breeds, respectively. The identification of alleles was performed using the sequence–base method. Faecal egg counting (FEC of the gastrointestinal parasites and measures of blood plasma pepsinogen levels were performed in order to evaluate parasitological parameters. From this study in the overall examined animals, thirty-nine Ovar-DRB1 alleles were identified, among them, ten new alleles, reported for the first time in the literature. In Arta breed a total of twenty-four alleles were found. Among the detected alleles, ten were breed specific and five were new. Regarding the Kalarrytiko breed, twenty-nine alleles were found, fifteen of them were unique and nine were new. The studied breeds differed in their allelic profile, with only 12 common from the total of 134 different recorded genotypes. A higher number of animals with high parasitic load and high plasma pepsinogen values were found in Kalarrytiko. Associations between Ovar-DRB1 alleles with FEC values were found with certain heterozygous genotypes to present significantly reduced FEC values. The large number of detected alleles with low frequencies and the fact that the majority of animals were heterozygous, make hard to find strong associations

  7. A study on single nucleotide polymorphism of exon 7 T/C (locus 593 of platelet-activating factor acetylhydrolase gene in healthy Han population in the Shanghai region

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    Tian-bao XIA

    2012-08-01

    Full Text Available Objective To investigate the distribution of single nucleotide polymorphism (SNP in platelet-activating factor acetylhydrolase (PAF-AH gene exon 7 T/C (locus 593 in healthy Han population in Shanghai region and the features different from other races. Methods The SNP in PAF-AH gene exon 7 T/C (locus 593 was detected and analyzed by PCR and sequencing in 110 healthy Han people from Shanghai areas. The genotype and allele frequency were then calculated and compared with that in other races in combination with review of relevant literature. Results The amplified product of the SNP in PAF-AH gene exon 7 T/C (locus 593 was 240 bp in 110 healthy Han people, of whom 97 were with TT genotype and 13 with TC genotype, but no CC genotype was found. As to the allele frequency distribution, T type allele took the highest position, and C type followed. The genotype frequency of TT and TC was 88.2% and 11.8%, respectively, and they were markedly different from that in German population (0.95%, while not statistically significant different from that in British population (7.67%. Conclusions There exists SNP in PAF-AH gene exon 7 T/C (position 593 in healthy Han people in Shanghai region, with a higher frequency of T→C mutation. The mutational genotype frequency is found to be located at the locus 593 is 11.81%, and it is markedly different from that in German population, but not significantly different from that in British population.

  8. [The relationships between the single nueleotide polymorphisms of CACNA1S gene 11 exon and thyrotoxic hypokalemic periodic paralysis in the people of Han Nationality in Sichuan Province, China].

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    Xiao, Zhu; Li, Li; Li, Sheyu; Yao, Yu; Liu, Yuping; Tian, Haoming

    2011-06-01

    The present research was aimed to investigate the relationships between the single nueleotide polymorphisms (SNPs) of CACNA1S gene 11 exon and thyrotoxic hypokalemic periodic paralysis (THPP)in the people of Han Nationality in Sichuan China. 100 male subjects were divided into four groups in this study, i.e., 22 patients with THPP, 23 patients with hypokalemic periodic paralysis (HPP), 33 patients with thyrotoxicosis but without hypokalemic periodic paralysis (NTHPP), and 22 healthy (control group) subjects. The sequences of the CACNA1S gene exon 11 polymorphisms, for the four groups respectively, were analysed by the SNPs method with polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA direct sequencing. A meta-analysis of three additional studies was also performed. Three SNPs of exon 11 of the CACNA1S gene (C1491T, T1551C, C1564T) were present in all the four groups. The polymorphisms C1491T and T1551C were present in both homozygotes and heterozygotes, while the C1564T polymorphism was present only in heterozygotes. The genotype frequencies of variants at C1491T and T1551C were not significantly associated with TPP (dominant model: P=0.530 and P=0.568; allele frequency model: P=0.563 and P=0.568). A Meta-analysis yielded combined odds ratio (OR) for TPP of 2. 12 (95% CI: 0.80-5.60) at C1491T, 2.90 (95% CI: 0.71-11.78) at T1551C, and 1.61 (95% CI: 0.36-7.26) at C1564T with the dominant model. These results suggested that three SNPs of CACNA1S gene exon 11 definitely could exist but could not be associated with TPP people of Han Nationality in Sichuan.

  9. Characteristics of transposable element exonization within human and mouse.

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    Noa Sela

    Full Text Available Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.

  10. Study of P53 gene mutations in promoter and exons 2-4 and 9-11 in patient with gastric cancer by PCR-SSCP in Chaharmahal Va Bakhtiari province

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    Javad Saffari Chaleshtary

    2011-11-01

    Full Text Available Background: Gastric cancer is one of the most important diseases and after lung cancer, is the second cause of cancer death worldwide. Genetic factors including oncogenes and tumor suppressor genes are always contributed in progression of this cancer. The P53 tumor suppressor gene has a broad role in genomic stability and DNA repair. The aim of this study was to determine the P53 gene mutations in gastric cancer specimens in Chaharmahal Va Bakhtiari Province. Methods: In this descriptive-lab based study, we investigated the promoter, exons 2-4 and 9-11 of P53 gene mutations in 38 paraffin embedded gastric cancer specimens. DNA was extracted following the standard phenol chloroform protocol. The P53 gene mutations were determined using PCR-SSCP procedure. Results: Our study revealed no P53 gene mutation in promoter and exons 2-4 and 9-11 in the gastric cancer subjects studied. Conclusion: While P53 gene mutations have been reported as the most frequent genetic alterations and are found in about 50% of the human malignancies, no mutation was detected in this study. The reason may be due to small sample size or mutations on other genes or epigenetic factors.

  11. The association of three BACE1 gene polymorphisms (exon5 C/G, intron 5 T/G and 3'UTR T/A) with sporadic Alzheimer's disease susceptibility: a meta-analysis.

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    Yuan, Hai; Ling, Kang; Du, Xunping; Ge, Pingping; Wu, Shaowei; Wang, Xiaotong

    2015-01-01

    Despite biological support for a role of Beta-site APP-cleaving enzyme 1 (BACE1) in sporadic Alzheimer's disease (SAD), studies about the BACE1 genetic polymorphisms in SAD are inconsistent. To explore whether the BACE1 polymorphisms confers susceptibility to SAD, the current meta-analysis was conducted to evaluate the gene-disease association in relevant studies. The serious databases were researched to identify studies. The association between BACE1 (exon5 C/G, intron 5 T/G or 3'UTR T/A) polymorphism and SAD risk was evaluated by odds ratios (ORs) together with their 95% confidence intervals (CIs). The combined results showed no significant difference in all models on the basis of all studies for BACE1 (exon5 C/G, intron 5 T/G or 3'UTR T/A) polymorphisms. When subgroup analysis was performed based on ethnicity and the epsilon 4 allele of apolipoprotein E (APOEε4) carriers status, significant associations were demonstrated (CC versus CG+GG: OR=1.37, 95% CI=1.04-1.82, P=0.03BACE1 (exon5 C/G, intron 5 T/G or 3'UTR T/A) polymorphism could be not a risk factor for SAD. However, individuals with CC genotype have higher risk of SAD with APOEε4 carrier status, and gene-gene interaction might affect on the association. Further studies with large sample size, especially in subgroup analysis, should be done to confirm these findings.

  12. Associations between Dopamine and Serotonin Genes and Job Satisfaction: Preliminary Evidence from the Add Health Study

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    Song, Zhaoli; Li, Wendong; Arvey, Richard D.

    2011-01-01

    Previous behavioral genetic studies have found that job satisfaction is partially heritable. We went a step further to examine particular genetic markers that may be associated with job satisfaction. Using an oversample from the National Adolescent Longitudinal Study (Add Health Study), we found 2 genetic markers, dopamine receptor gene DRD4 VNTR…

  13. Associations between Dopamine and Serotonin Genes and Job Satisfaction: Preliminary Evidence from the Add Health Study

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    Song, Zhaoli; Li, Wendong; Arvey, Richard D.

    2011-01-01

    Previous behavioral genetic studies have found that job satisfaction is partially heritable. We went a step further to examine particular genetic markers that may be associated with job satisfaction. Using an oversample from the National Adolescent Longitudinal Study (Add Health Study), we found 2 genetic markers, dopamine receptor gene DRD4 VNTR…

  14. Species-Specific Exon Loss in Human Transcriptomes

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    Wang, Jinkai; Lu, Zhi-xiang; Tokheim, Collin J.; Miller, Sara E.; Xing, Yi

    2014-01-01

    Changes in exon–intron structures and splicing patterns represent an important mechanism for the evolution of gene functions and species-specific regulatory networks. Although exon creation is widespread during primate and human evolution and has been studied extensively, much less is known about the scope and potential impact of human-specific exon loss events. Historically, transcriptome data and exon annotations are significantly biased toward humans over nonhuman primates. This ascertainm...

  15. Transposable elements in disease-associated cryptic exons.

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    Vorechovsky, Igor

    2010-02-01

    Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.

  16. Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

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    Eyras Eduardo

    2006-06-01

    Full Text Available Abstract Background Alternatively spliced exons play an important role in the diversification of gene function in most metazoans and are highly regulated by conserved motifs in exons and introns. Two contradicting properties have been associated to evolutionary conserved alternative exons: higher sequence conservation and higher rate of non-synonymous substitutions, relative to constitutive exons. In order to clarify this issue, we have performed an analysis of the evolution of alternative and constitutive exons, using a large set of protein coding exons conserved between human and mouse and taking into account the conservation of the transcript exonic structure. Further, we have also defined a measure of the variation of the arrangement of exonic splicing enhancers (ESE-conservation score to study the evolution of splicing regulatory sequences. We have used this measure to correlate the changes in the arrangement of ESEs with the divergence of exon and intron sequences. Results We find evidence for a relation between the lack of conservation of the exonic structure and the weakening of the sequence evolutionary constraints in alternative and constitutive exons. Exons in transcripts with non-conserved exonic structures have higher synonymous (dS and non-synonymous (dN substitution rates than exons in conserved structures. Moreover, alternative exons in transcripts with non-conserved exonic structure are the least constrained in sequence evolution, and at high EST-inclusion levels they are found to be very similar to constitutive exons, whereas alternative exons in transcripts with conserved exonic structure have a dS significantly lower than average at all EST-inclusion levels. We also find higher conservation in the arrangement of ESEs in constitutive exons compared to alternative ones. Additionally, the sequence conservation at flanking introns remains constant for constitutive exons at all ESE-conservation values, but increases for

  17. Increased risk of breast cancer in women bearing a combination of large CAG and GGN repeats in the exon 1 of the androgen receptor gene.

    Science.gov (United States)

    González, Ana; Javier Dorta, F; Rodriguez, Germán; Brito, Buenaventura; Rodríguez, M A Del Cristo; Cabrera, Antonio; Díaz-Chico, Juan C; Reyes, Ricardo; Aguirre-Jaime, Armando; Nicolás Díaz-Chico, B

    2007-11-01

    The exon 1 of the human androgen receptor gene (AR) contains both CAG (polyglutamine) and GGN (polyglycine) repeat length polymorphisms. Large CAG repeats have been related to an increased risk of breast cancer (BC), whereas the influence of the GGN repeats is still unclear. Here, we have studied how the length of CAG and GGN repeats is associated with the risk of BC in a population from Tenerife (Canary Islands, Spain). The study was carried out on 257 woman diagnosed with BC and 393 controls, nesting in the 'CDC of the Canary Islands' cohort study. The AR CAG and GGN genotyping was performed by means of PCR amplification with specific fluorescently labelled primers followed by a capillary electrophoresis. The allelic distribution of CAG and GGN polymorphisms was similar in cases and controls. The mean of short and long CAG and GGN alleles did not show differences between cases and controls and the same was true when the average length of both CAG alleles (CAG(n)) and GGN alleles (GGN(n)) was considered. However, when CAG(n) and GGN(n) were categorised using 22 and 24 repeats as the cut-off point, respectively, significant differences between cases and controls were observed. The CAG(n)>22 repeats were more frequent in cases than in controls, being associated with an increased risk of BC (OR=1.49; CI(95%)=1.06-2.09; p=0.021). No significant differences were found for categorised GGN(n). For CAG(n)/GGN(n) combinations, the highest BC risk was found to be associated with the CAG(n)>22/GGN(n)24 combination (OR=2.47; CI(95%)=1.37-4.46; p=0.003). In conclusion, our results indicate that longer CAG(n)/GGN(n) combinations increase the risk of BC and suggest that CAG and GGN AR polymorphisms should be considered in order to assess the BC risk.

  18. Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

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    Rigau Joan

    2004-07-01

    Full Text Available Abstract Background Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility. Results Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated π was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE. The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion. Conclusion These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using

  19. Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam

    Directory of Open Access Journals (Sweden)

    Takahashi Aya

    2009-08-01

    Full Text Available Abstract Background Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In Drosophila, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon boundary regions where potential exonic splicing enhancers (ESEs reside. In contrast to genomic scale analyses on large datasets, a refined study on a well-controlled set of samples can be effective in demonstrating the effects of particular splice-related factors. Down syndrome cell adhesion molecule (Dscam has the largest number of alternatively spliced exons (ASEs known to date, and the splicing frequency of each ASE is accessible from the relative abundance of the transcript. Thus, these ASEs comprise a unique model system for studying the effect of splicing regulation on synonymous codon usage. Results Codon Bias Indices (CBI in the 3' boundary regions were reduced compared to the rest of the exonic regions among 48 and 33 ASEs of exon 6 and 9 clusters, respectively. These regional differences in CBI were affected by splicing frequency and distance from adjacent exons. Synonymous divergence levels between the 3' boundary region and the remaining exonic region of exon 6 ASEs were similar. Additionally, another sensitive comparison of paralogous exonic regions in recently retrotransposed processed genes and their parental genes revealed that, in the former, the differences in CBI between what were formerly the central regions and the boundary regions gradually became smaller over time. Conclusion Analyses of the multiple ASEs of Dscam allowed direct tests of the effect of splice-related factors on synonymous codon usage and provided clear evidence that synonymous codon usage bias is restricted by exonic splicing signals near the intron-exon boundary. A similar synonymous divergence level between the different exonic

  20. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  1. A novel point mutation (G[sup [minus]1] to T) in a 5[prime] splice donor site of intron 13 of the dystrophin gene results in exon skipping and is responsible for Becker Muscular Dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Hagiwara, Yoko; Nishio, Hisahide; Kitoh, Yoshihiko; Takeshima, Yasuhiro; Narita, Naoko; Wada, Hiroko; Yokoyama, Mitsuhiro; Nakamura, Hajime; Matsuo, Masafumi (Kobe Univ. School of Medicine (Japan))

    1994-01-01

    The mutations in one-third of Duchenne and Becker muscular dystrophy patients remain unknown, as they do not involve gross rearrangements of the dystrophin gene. The authors now report a defect in the splicing of precursor mRNA (pre-mRNA), resulting from a maternally inherited mutation of the dystrophin gene in a patient with Becker muscular dystrophy. This defect results from a G-to-T transversion at the terminal nucleotide of exon 13, within the 5[prime] splice site of intron 13, and causes complete skipping of exon 13 during processing of dystrophin pre-mRNA. The predicted polypeptide encoded by the aberrant mRNA is a truncated dystrophin lacking 40 amino acids from the amino-proximal end of the rod domain. This is the first report of an intraexon point mutation that completely inactivates a 5[prime] splice donor site in dystrophin pre-mRNA. Analysis of the genomic context of the G[sup [minus]1]-to-T mutation at the 5[prime] splice site supports the exon-definition model of pre-mRNA splicing and contributes to the understanding of splice-site selection. 48 refs., 5 figs.

  2. Allele frequency of a 24 bp duplication in exon 10 of the CHIT1 gene in the general Korean population and in Korean patients with Gaucher disease.

    Science.gov (United States)

    Woo, Kyu Ha; Lee, Beom Hee; Heo, Sun Hee; Kim, Jae-Min; Kim, Gu-Hwan; Kim, Yoo-Mi; Kim, Ja Hye; Choi, In-Hee; Yang, Song Hyun; Yoo, Han-Wook

    2014-05-01

    Plasma chitotriosidase activity is used for diagnosis and monitoring of Gaucher disease. However, homozygous duplication of a 24 bp region in exon 10 of the chitotriosidase gene (CHIT1) abolishes enzyme activity, limiting its use as a biomarker in Gaucher disease. This study investigates the allele frequency of the 24 bp duplication, in both the general Korean population and in patients with Gaucher disease. Fifteen Korean patients with Gaucher disease and 231 Korean normal individuals were enrolled. Genotyping was performed to identify the 24 bp duplication in exon 10 of CHIT1 using DNA extracted from peripheral leukocytes or dried blood spots. Two patients with Gaucher disease (13.3%) had normal plasma chitotriosidase activity, and carried a homozygous 24 bp duplication of exon 10 of the CHIT1 gene. Nine patients were heterozygote carriers (60.0%). Of the normal 231 Korean individuals, heterozygous duplication was detected in 109 individuals (47.2%) and homozygous duplication in 75 (32.5%). The allele frequency was 56.1% (95% confidence interval, 49.4-62.7%). The frequency of the 24 bp duplication was remarkably high in both Korean patients with Gaucher disease and in the normal population, limiting the efficacy of chitotriosidase as a biomarker in Gaucher disease in Korea. New biomarkers are required that consider the genetic characteristics of different populations.

  3. Identification of g.170G>A and g.332G>A mutations in exon 3 of leptin gene (Bcnl and Cail) and their association with semen quality and testicular dimensions in Sanjabi rams.

    Science.gov (United States)

    Bakhtiar, Roya; Abdolmohammadi, Alireza; Hajarian, Hadi; Nikousefat, Zahra; Kalantar-Neyestanaki, Davood

    2017-04-01

    The purpose of this study was to investigate leptin gene polymorphisms and their relationships with the characteristics of sperm quality and testicular dimensions. Semen samples were collected from 96 Sanjabi rams during autumn and spring seasons over two years. Simultaneously, the dimensions of length, width and scrotal circumference were measured. Blood samples were taken from the jugular vein to extract DNA. PCR was performed to amplify a 463bp fragment including exon 3 of leptin gene. PCR products were digested by Bcnl and Cail restriction enzymes to identify 170G>A and 332G>A mutations in exon 3, respectively. Leptin gene polymorphism in 170G>A locus had an effect on individual motility trait, water test and scrotal circumference (PA locus had a significant effect on viability trait, water test and scrotal circumference as GA genotypes had the highest amounts for these traits compared with GG genotypes (Pleptin gene polymorphisms with sperm fertility and testicular dimensions in sheep, which suggests leptin gene as a potential gene to be used in breeding programs in order to improve fertility in herds.

  4. The structure of a human neurofilament gene (NF-L): A unique exon-intron organization in the intermediate filament gene family.

    NARCIS (Netherlands)

    J-P. Julien (Jean-Pierre); F.G. Grosveld (Frank); K. Yazdanbakhsh; D. Flavell (David); D.N. Meijer (Dies); W.E. Mushynski

    1987-01-01

    textabstractWe have cloned and determined the nucleotide sequence of the human gene for the neurofilament subunit NF-L. The cloned DNA contains the entire transcriptional unit and generates two mRNAs of approx. 2.6 and 4.3 kb after transfection into mouse L-cells. The NF-L gene has an unexpected

  5. Factor IX[sub Madrid 2]: A deletion/insertion in Facotr IX gene which abolishes the sequence of the donor junction at the exon IV-intron d splice site

    Energy Technology Data Exchange (ETDEWEB)

    Solera, J. (Unidades de Genetica Molecular, Madrid (Spain)); Magallon, M.; Martin-Villar, J. (Hemofilia Hospital, Madrid (Spain)); Coloma, A. (Departamento deBioquimica de la Facultad de Medicina de la Universidad Autonoma, Madrid (Spain))

    1992-02-01

    DNA from a patient with severe hemophilia B was evaluated by RFLP analysis, producing results which suggested the existence of a partial deletion within the factor IX gene. The deletion was further localized and characterized by PCR amplification and sequencing. The altered allele has a 4,442-bp deletion which removes both the donor splice site located at the 5[prime] end of intron d and the two last coding nucleotides located at the 3[prime] end of exon IV in the normal factor IX gene; this fragment has been inserted in inverted orientation. Two homologous sequences have been discovered at the ends of the deleted DNA fragment.

  6. Dopaminergic, Serotonergic, and Oxytonergic Candidate Genes Associated with Infant Attachment Security and Disorganization? In Search of Main and Interaction Effects

    Science.gov (United States)

    Luijk, Maartje P. C. M.; Roisman, Glenn I.; Haltigan, John D.; Tiemeier, Henning; Booth-LaForce, Cathryn; van IJzendoorn, Marinus H.; Belsky, Jay; Uitterlinden, Andre G.; Jaddoe, Vincent W. V.; Hofman, Albert; Verhulst, Frank C.; Tharner, Anne; Bakermans-Kranenburg, Marian J.

    2011-01-01

    Background and methods: In two birth cohort studies with genetic, sensitive parenting, and attachment data of more than 1,000 infants in total, we tested main and interaction effects of candidate genes involved in the dopamine, serotonin, and oxytocin systems ("DRD4", "DRD2", "COMT", "5-HTT", "OXTR") on attachment security and disorganization.…

  7. Underlying Mechanisms of Gene-Environment Interactions in Externalizing Behavior: A Systematic Review and Search for Theoretical Mechanisms

    NARCIS (Netherlands)

    Weeland, J.; Overbeek, G.; Orobio de Castro, B.; Matthys, W.

    2015-01-01

    Over the last decade, several candidate genes (i.e., MAOA, DRD4, DRD2, DAT1, 5-HTTLPR, and COMT) have been extensively studied as potential moderators of the detrimental effects of postnatal family adversity on child externalizing behaviors, such as aggression and conduct disorder. Many studies on s

  8. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD: Findings from a family-based association test (FBAT analysis

    Directory of Open Access Journals (Sweden)

    Gill Michael

    2008-10-01

    Full Text Available Abstract Background Low serotonergic (5-HT activity correlates with increased impulsive-aggressive behavior, while the opposite association may apply to cognitive impulsiveness. Both types of impulsivity are associated with attention-deficit/hyperactivity disorder (ADHD, and genes of functional significance for the 5-HT system are implicated in this disorder. Here we demonstrate the separation of aggressive and cognitive components of impulsivity from symptom ratings and test their association with 5-HT and functionally related genes using a family-based association test (FBAT-PC. Methods Our sample consisted of 1180 offspring from 607 families from the International Multicenter ADHD Genetics (IMAGE study. Impulsive symptoms were assessed using the long forms of the Conners and the Strengths and Difficulties parent and teacher questionnaires. Factor analysis showed that the symptoms aggregated into parent- and teacher-rated behavioral and cognitive impulsivity. We then selected 582 single nucleotide polymorphisms (SNPs from 14 genes directly or indirectly related to 5-HT function. Associations between these SNPs and the behavioral/cognitive groupings of impulsive symptoms were evaluated using the FBAT-PC approach. Results In the FBAT-PC analysis for cognitive impulsivity 2 SNPs from the gene encoding phenylethanolamine N-methyltransferase (PNMT, the rate-limiting enzyme for adrenalin synthesis attained corrected gene-wide significance. Nominal significance was shown for 12 SNPs from BDNF, DRD1, HTR1E, HTR2A, HTR3B, DAT1/SLC6A3, and TPH2 genes replicating reported associations with ADHD. For overt aggressive impulsivity nominal significance was shown for 6 SNPs from BDNF, DRD4, HTR1E, PNMT, and TPH2 genes that have also been reported to be associated with ADHD. Associations for cognitive impulsivity with a SERT/SLC6A4 variant (STin2: 12 repeats and aggressive behavioral impulsivity with a DRD4 variant (exon 3: 3 repeats are also described

  9. A novel donor splice site in intron 11 of the CFTR gene, created by mutation 1811 + 1.6kbA {yields} G, produces a new exon: High frequency in spanish cystic fibrosis chromosomes and association with severe phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Chillon, M.; Casals, T.; Gimenez, J.; Ramos, D.; Nunes, V.; Estivill, X. [Cancer Research Institute, Barcelona (Spain); Doerk, T.; Will, K. [Medizinische Hochschule Hannover (Germany); Fonknechten, N. [Institut Cochin de Genetique Moleculaire, Paris (France)

    1995-03-01

    mRNA analysis of the cystic fibrosis transmembrane regulator (CFTR) gene in tissues of cystic fibrosis (CF) patients has allowed us to detect a cryptic exon. The new exon involves 49 base pairs between exons 11 and 12 and is due to a point mutation (1811+1.6bA{yields}G) that creates a new donor splice site in intron 11. Semiquantitative mRNA analysis showed that 1811+1.6kbA{r_arrow}G-mRNA was 5-10-fold less abundant than {triangle}F508 mRNA. Mutations 1811+1.6kbA{yields}G was found in 21 Spanish and 1 German CF chromosome(s), making it the fourth-most-frequent mutation (2%) in the Spanish population. Individuals with genotype {triangle}F508/1811+1.6kbA{yields}G have only 1%-3% of normal CFTR mRNA. This loss of 97% of normal CFTR mRNA must be responsible for the pancreatic insufficiency and for the severe CF phenotype in these patients. 30 refs., 3 figs., 2 tabs.

  10. The Dopamine Receptor D4 7-Repeat Allele and Prenatal Smoking in ADHD-Affected Children and Their Unaffected Siblings: No Gene-Environment Interaction

    Science.gov (United States)

    Altink, Marieke E.; Arias-Vasquez, Alejandro; Franke, Barbara; Slaats-Willemse, Dorine I. E.; Buschgens, Cathelijne J. M.; Rommelse, Nanda N. J.; Fliers, Ellen A.; Anney, Richard; Brookes, Keeley-Joanne; Chen, Wai; Gill, Michael; Mulligan, Aisling; Sonuga-Barke, Edmund; Thompson, Margaret; Sergeant, Joseph A.; Faraone, Stephen V.; Asherson, Philip; Buitelaar, Jan K.

    2008-01-01

    Background: The dopamine receptor D4 ("DRD4") 7-repeat allele and maternal smoking during pregnancy are both considered as risk factors in the aetiology of attention deficit hyperactivity disorder (ADHD), but few studies have been conducted on their interactive effects in causing ADHD. The purpose of this study is to examine the gene by…

  11. Vanishing white matter disease: an Italian case with A638G mutation in exon 5 of EIF2B2 gene, an unusual early onset and a long course.

    Science.gov (United States)

    Sambati, Luisa; Agati, Raffaele; Bacci, Antonella; Bianchi, Silvia; Capellari, Sabina

    2013-07-01

    We report the clinical description of an Italian patient with c.638A>G mutation in exon 5 of EIF2B2 gene and a very slow progressive Vanishing White Matter disease phenotype. Infact, in relation to her causative mutation, our patient had an unusual early onset and long course. Furthermore, other than standard MRI examination and spectroscopy study, we report DWI and ADC maps and FA maps reconstruction from DTI in order to describe brain tissue degeneration in vanishing white matter disease.

  12. The mutation of exon 2 of neurofbromatosis 2 gene in Schwannoma and its significance%神经鞘瘤中NF2基因外显子2突变及意义

    Institute of Scientific and Technical Information of China (English)

    孙青芳; 卞留贯; 沈建康; 赵卫国; 张天锡

    2001-01-01

    Objective: To study the edffct of mutation of neurofibromatosis 2(NF2) gene (exon 2) in schwannomas. Methods: The NF2 gene (exon2) mutation in 36 schwannomas(16 acoustic neuromas, 20 other schwannomas) were observed by PCR-SSCP and DNA sequence.Results: We found 4 mutations in 36 schwwannomas, all in acoustic neuroma. Of them, two frameshift mutations and two missense mutations. Conclusion: E2 of NF2 gene mutation might be one of the critical factor in the tumorogenesis of acoustic neuromas.%目的:研究神经鞘瘤中Ⅱ型多发神经纤维瘤病基因(NF2)外显子2的突变及其意义。方法:用PCR-SSCP、 DNA测序检测36例神经鞘瘤(听神经瘤16例,其它20例)中NF2基因外显子2的突变。结果:我们共发现4例突变,均为听神经瘤,其中移码突变2例、反义突变2例。结论: NF2基因外显子2的突变可能是听神经瘤发生中的关键因素。

  13. Deletion of the Chd6 exon 12 affects motor coordination.

    Science.gov (United States)

    Lathrop, Melissa J; Chakrabarti, Lisa; Eng, Jeremiah; Rhodes, C Harker; Lutz, Thomas; Nieto, Amelia; Liggitt, H Denny; Warner, Sandra; Fields, Jennifer; Stöger, Reinhard; Fiering, Steven

    2010-04-01

    Members of the CHD protein family play key roles in gene regulation through ATP-dependent chromatin remodeling. This is facilitated by chromodomains that bind histone tails, and by the SWI2/SNF2-like ATPase/helicase domain that remodels chromatin by moving histones. Chd6 is ubiquitously expressed in both mouse and human, with the highest levels of expression in the brain. The Chd6 gene contains 37 exons, of which exons 12-19 encode the highly conserved ATPase domain. To determine the biological role of Chd6, we generated mouse lines with a deletion of exon 12. Chd6 without exon 12 is expressed at normal levels in mice, and Chd6 Exon 12 -/- mice are viable, fertile, and exhibit no obvious morphological or pathological phenotype. Chd6 Exon 12 -/- mice lack coordination as revealed by sensorimotor analysis. Further behavioral testing revealed that the coordination impairment was not due to muscle weakness or bradykinesia. Histological analysis of brain morphology revealed no differences between Chd6 Exon 12 -/- mice and wild-type (WT) controls. The location of CHD6 on human chromosome 20q12 is overlapped by the linkage map regions of several human ataxias, including autosomal recessive infantile cerebellar ataxia (SCAR6), a nonprogressive cerebrospinal ataxia. The genomic location, expression pattern, and ataxic phenotype of Chd6 Exon 12 -/- mice indicate that mutations within CHD6 may be responsible for one of these ataxias.

  14. Endothelial nitric oxide synthase gene polymorphisms (promoter -786T/C, exon 894 G/T and intron G10T) in unexplained female infertility.

    Science.gov (United States)

    Karatas, Ahmet; Eroz, Recep; Bahadır, Anzel; Keskin, Fatih; Ozlu, Tulay; Ozyalvaclı, Mehmet Emin

    2014-01-01

    Recent investigations in both males and females show that there may also be some genetic risk factors associated with infertility, and endothelial nitric oxide synthase (eNOS) has important functions in implantation. We aimed to investigate the association of three different polymorphisms of eNOS (promoter -786T/C, exon 894 G/T and intron G10T) with unexplained female infertility. Two groups of patients were included in the study: (1) women with unexplained infertility and (2) healthy, fertile women with normal menstrual cycles. eNOS polymorphisms were studied in genomic DNA of each patient by polymerase chain reaction-restriction fragment length polymorphism method. Forty-one women with unexplained infertility and 40 fertile women were included. Baseline physical characteristics and hormonal parameters of the two groups were similar. For eNOS exon 894 G/T polymorphism, the GG homozygotes were significantly lower and the heterozygotes GT were significantly higher in the infertile group than in the control group (p 0.05). Altered eNOS protein caused by eNOS exon 894 G/T polymorphism might cause implantation failure, which may be a possible cause of unexplained female infertility. © 2014 S. Karger AG, Basel.

  15. Evolutionary history of exon shuffling.

    Science.gov (United States)

    França, Gustavo S; Cancherini, Douglas V; de Souza, Sandro J

    2012-06-01

    Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.

  16. Exon exchange approach to repair Duchenne dystrophin transcripts.

    Directory of Open Access Journals (Sweden)

    Stéphanie Lorain

    Full Text Available BACKGROUND: Trans-splicing strategies for mRNA repair involve engineered transcripts designed to anneal target mRNAs in order to interfere with their natural splicing, giving rise to mRNA chimeras where endogenous mutated exons have been replaced by exogenous replacement sequences. A number of trans-splicing molecules have already been proposed for replacing either the 5' or the 3' part of transcripts to be repaired. Here, we show the feasibility of RNA surgery by using a double trans-splicing approach allowing the specific substitution of a given mutated exon. METHODOLOGY/PRINCIPAL FINDINGS: As a target we used a minigene encoding a fragment of the mdx dystrophin gene enclosing the mutated exon (exon 23. This minigene was cotransfected with a variety of exon exchange constructions, differing in their annealing domains. We obtained accurate and efficient replacement of exon 23 in the mRNA target. Adding up a downstream intronic splice enhancer DISE in the exon exchange molecule enhanced drastically its efficiency up to 25-45% of repair depending on the construction in use. CONCLUSIONS/SIGNIFICANCE: These results demonstrate the possibility to fix up mutated exons, refurbish deleted exons and introduce protein motifs, while keeping natural untranslated sequences, which are essential for mRNA stability and translation regulation. Conversely to the well-known exon skipping, exon exchange has the advantage to be compatible with almost any type of mutations and more generally to a wide range of genetic conditions. In particular, it allows addressing disorders caused by dominant mutations.

  17. Molecular characterization of HOXC8 gene and methylation status analysis of its exon 1 associated with the length of cashmere fiber in Liaoning cashmere goat.

    Science.gov (United States)

    Bai, Wen L; Wang, Jiao J; Yin, Rong H; Dang, Yun L; Wang, Ze Y; Zhu, Yu B; Cong, Yu Y; Deng, Liang; Guo, Dan; Wang, Shi Q; Yang, Shu H; Xue, Hui L

    2017-02-01

    Homeobox protein Hox-C8 (HOXC8) is a member of Hox family. It is expressed in the dermal papilla of the skin and is thought to be associated with the hair inductive capacity of dermal papilla cells. In the present study, we isolated and characterized a full-length open reading frame of HOXC8 cDNA from the skin tissue of Liaoning cashmere goat, as well as, established a phylogenetic relationship of goat HOXC8 with that of other species. Also, we investigated the effect of methylation status of HOXC8 exon 1 at anagen secondary hair follicle on the cashmere fiber traits in Liaoning cashmere goat. The sequence analysis indicated that the obtained cDNA was 1134-bp in length containing a complete ORF of 729-bp. It encoded a peptide of 242 amino acid residues in length. The structural analysis indicated that goat HOXC8 contained a typical homeobox domain. The phylogenetic analysis revealed that Capra hircus HOXC8 had a closer genetic relationship with that of Ovis aries, followed by Bos Taurus and Bubalus bubalis. The methylation analysis suggested that the methylation degree of HOXC8 exon 1 in anagen secondary hair follicle might be involved in regulating the growth of cashmere fiber in Liaoning cashmere goat. Our results provide new evidence for understanding the molecular structural and evolutionary characteristics of HOXC8 in Liaoning cashmere goat, as well as, for further insight into the role of methylation degree of HOXC8 exon 1 regulates the growth of cashmere fiber in goat.

  18. Identification of HLA-G*01:17, a new allele possibly generated by an interloci gene conversion event involving exon 3 of HLA-B.

    Science.gov (United States)

    Czarnecki, Chris; Van Domselaar, Gary; Embreé, Joanne; Brunham, Robert; Plummer, Francis A; Luo, Ma

    2011-03-01

    HLA-G*01:17 was discovered in a woman of Kenyan descent who was enrolled in a mother-to-child HIV-1 transmission cohort. The new allele was identical to HLA-G*01:06 at exons 2, 3, and 4 with the exception of a base pair substitution at codon 169 (CAC → CGC) resulting in a coding change from histidine to arginine and codon 171 (TAC → CAC), resulting in turn in a coding change from tyrosine to histidine. The World Health Organization (WHO) Nomenclature Committee has named this allele HLA-G*01:17.

  19. 绵羊ras基因第一、二外显子的扩增及序列测定%THE AMPLIFICATION AND SEQUENCING OF THE SHEEP ras GENE FIRST AND SECOND EXON

    Institute of Scientific and Technical Information of China (English)

    刘霄卉; 于立新; 刘畅; 周建华; 马学恩

    2011-01-01

    Objective:To clone and sequenceJSRV infection in sheep and healthy sheep Kras, Nros, Kras gene first and second exon and to study the mutation of the gene. Methods: In this study, the H - ras, N - ras, K-ras gene first and second exon DNA was extracted from healthy sheep and sheep infected with JSRV lung tissue and amplified with PCR. The PCR product was cloned into pMD -18T vector plasmid. Than the recorabinant plasmid was identified and sequenced. Results:Compared with other species, ras gene had little difference among species and highly homology with the cattle ras gene. The U-ras, K-ras gene cloned was identical in the first and second exon region sequence, while the N - ras had a A - V difference in the 81th amino acid. There were no mutation ras gene between the two cases of JSRV infection in sheep and healthy sheep neither in nucleic acid level nor in the amino acid level. Conclusion : The cloning and sequencing of the first and second exon of the sheep ras gene laid a good foundation for further study.%对JSRV感染羊及健康绵羊H-ras、N-ras、K-ras基因第一、二外显子区克隆并测序,研究其变异状况.方法:本研究从JSRV感染羊及健康绵羊肺组织中提取基因组DNA,应用PCR技术扩增Hras、Nras、Kras基因第一、二外显子序列,并通过T-A克隆的方法将其克隆入pMD - 18T载体中,鉴定为阳性的重组质粒进行序列测定分析.结果:与其他物种ras基因相比,所克隆的ras基因与其他物种之间的差异率较小,基本保守,且与牛的ras基因同源性最高.所克隆的H -ras、K-ras基因在第一、二外显子区域序列完全相同;N-ras第81位氨基酸A-V的不同;但试验中检测的2例JSRV感染羊与健康绵羊的ras无论是在核酸水平上,还是在氨基酸水平上均未发现突变.结论:克隆测序了绵羊ras基因第一、二外显子,为下一步实验奠定了基础.

  20. NextSearch: A Search Engine for Mass Spectrometry Data against a Compact Nucleotide Exon Graph.

    Science.gov (United States)

    Kim, Hyunwoo; Park, Heejin; Paek, Eunok

    2015-07-02

    Proteogenomics research has been using six-frame translation of the whole genome or amino acid exon graphs to overcome the limitations of reference protein sequence database; however, six-frame translation is not suitable for annotating genes that span over multiple exons, and amino acid exon graphs are not convenient to represent novel splice variants and exon skipping events between exons of incompatible reading frames. We propose a proteogenomic pipeline NextSearch (Nucleotide EXon-graph Transcriptome Search) that is based on a nucleotide exon graph. This pipeline consists of constructing a compact nucleotide exon graph that systematically incorporates novel splice variations and a search tool that identifies peptides by directly searching the nucleotide exon graph against tandem mass spectra. Because our exon graph stores nucleotide sequences, it can easily represent novel splice variations and exon skipping events between incompatible reading frame exons. Searching for peptide identification is performed against this nucleotide exon graph, without converting it into a protein sequence in FASTA format, achieving an order of magnitude reduction in the size of the sequence database storage. NextSearch outputs the proteome-genome/transcriptome mapping results in a general feature format (GFF) file, which can be visualized by public tools such as the UCSC Genome Browser.

  1. Cytogenetic and molecular analysis of the Y chromosome: absence of a significant relationship between CAG repeat length in exon 1 of the androgen receptor gene and infertility in Indian men.

    Science.gov (United States)

    Dhillon, Varinderpal S; Husain, Syed A

    2003-10-01

    The genetic basis of male infertility remains unclear in the majority of cases. Recent studies have indicated an association between microdeletions of the azoospermia factor a (AZFa)-AZFc regions of Yq and severe oligospermia or azoospermia. Increased (CAG)n repeat lengths in the androgen receptor (AR) gene have also been reported in infertile men. Therefore, in order to assess the prevalence of these genetic defects to male infertility, 183 men with non-obstructive azoospermia (n = 70), obstructive azoospermia (n = 33), severe oligospermia (n = 80) and 59 fertile men were examined cytogenetically and at molecular level for Yq deletions, microdeletions, and AR-CAG repeat lengths along with hormonal profiles [luteinizing hormone (LH), follicle-stimulating hormone (FSH) and testosterone (T)]. We used high resolution cytogenetics to detect chromosome deletions and multiplex polymerase chain reaction (PCR) involving 27 sequence-tagged site (STS) markers on Yq to determine the rate and extent of Yq microdeletions. PCR amplification with primers flanking exon 1 of AR gene was used to determine the AR-(CAG)n repeat lengths. Hormonal profiles (LH, FSH and T levels) were also analysed in infertile and fertile men. Testicular biopsies showed Sertoli cell only (SCO) morphology, maturation arrests (MA) and hypospermatogenesis. No chromosome aberrations were found in infertile men but there was a significant increase (p CAG repeats in AR gene was observed between infertile and fertile men (22.2 +/- 1.5 and 21.5 +/- 1.4 respectively). No significant increase or decrease in levels of LH, FSH and T was observed in infertile and fertile men. In some infertile men, significantly elevated levels of FSH alone or in combination with LH were found to be indicative of failure of spermatogenesis and/or suggestive of testicular failure. Y-chromosome microdeletions contribute to infertility in some patients but no relationship could be established with the (CAG)n repeat lengths in exon 1 of

  2. Correlation between genotype and phenotype in primary open angle glaucoma of Brazilian families with mutations in exon 3 of the TIGR/MYOC gene Correlação entre genótipo-fenótipo em famílias brasileiras com glaucoma primário de ângulo aberto determinada por mutações no exon 3 do gene TIGR/MYOC

    Directory of Open Access Journals (Sweden)

    Cristine Araújo Povoa

    2006-06-01

    Full Text Available PURPOSE: To investigate the phenotype of primary open-angle glaucoma (POAG in Brazilian families with mutation in exon 3 of TIGR/MYOC. METHODS: Seventy-eight POAG patients with a positive family history and eighteen unrelated patients with POAG were screened by automated DNA sequencing for mutations in exon 3 of the TIGR/MYOC gene. The pedigrees of POAG patients with mutations that lead to amino acid change were built. All available relatives of the index cases were also examined and genotyped by sequencing. RESULTS: Four sequence variants were identified in exon 3 of the TIGR/MYOC gene (Tyr347Tyr, Pro370Pro, Lys398Arg and Cys433Arg from the 96 initially screened patients. The Lys398Arg mutation was previously described as a polymorphism and in our study did not segregate with POAG. The most prevalent mutation was Cys433Arg, affecting 3 index cases (3.1% or 3/96. In two different families, 8/56 subjects presented Cys433Arg mutation and had POAG, 5/56 had ocular hypertension and 8/56 had no disease manifestation. POAG patients had a median age at diagnosis of 43.25 yr (17-58 yr and intraocular pressure (IOP with a mean of 36.3 ± 3.8mmHg for the right eye and 37.6 ± 9.75 mmHg for the left eye. The group of patients with Cys433Arg mutation had significantly higher IOP (pOBJETIVO: Identificar nos representantes de famílias com glaucoma primário de ângulo aberto (GPAA mutações no exon 3 do gene TIGR/MYOC e avaliar a expressão fenotípica associada às mutações encontradas em seus respectivos núcleos familiares. MÉTODOS: Setenta e oito pacientes (81,2%, com pelo menos um representante na família com GPAA, e dezoito pacientes (18,7% com glaucoma esporádico tiveram o exon 3, do gene TIGR/MYOC, submetido a seqüenciamento automático para identificação de mutações. Os pacientes, com mutação não silenciosa identificadas nesta triagem inicial, tiveram os heredogramas de suas famílias construídos. Todos os seus familiares dispon

  3. Effects of single nucleotide polymorphisms 869 T/C and 915 G/C in the exon 1 locus of transforming growth factor-β1 gene on chronic obstructive pulmonary disease susceptibility in Chinese

    Institute of Scientific and Technical Information of China (English)

    LIU Dai-shun; LI Xiao-ou; YING Bin-wu; CHEN Lei; WANG Tao; XU Dan; WEN Fu-qiang

    2010-01-01

    Background The main risk factor for chronic obstructive pulmonary disease (COPD) is cigarette smoking. However, only 10%-20% of chronic heavy smokers develop systematic COPD. We hypothesized that the inheritance of gene polymorphisms could influence the development of COPD, which was investigated by studying two single nucleotide polymorphisms (SNP) in exon 1 of the transforming growth factor-β1 (TGF-β1) gene.Methods We enrolled 219 patients with COPD as the research group and 148 healthy people as the control group, all of whom were Chinese Han people. The polymorphisms of the TGF-β1 gene, 869T/C and 915G/C, were analyzed using the method of amplification refractory mutation system-polymerase chain reaction (ARMS-PCR).Results The occurrence of the TGF-β1 gene 869T/C polymorphism in patients with COPD was significantly different from the control group (P 0.05).Conclusions The polymorphism 869T/C in TGF-β1 gene has a significant association with disease occurrence in COPD patients and the C allele might be a risk factor. The homozygous wild-type CC of 869T/C on TGFβ1 could be a predisposing factor in COPD and those who carry the C allele might have particularly susceptibility to developing COPD.

  4. 牛FSHR基因第4外显子多态性检测及序列分析%PCR-SSCP detection and DNA sequence analysis of FSHR gene exon4 in bovine

    Institute of Scientific and Technical Information of China (English)

    许艳丽; 姜昊; 高妍; 熊秋宏; 赵锐锋; 赵志辉; 张嘉保; 于汪洋; 邓琼; 柳思源; 徐靖博; 任久生; 戴立胜; 刘慧玉; 马腾壑

    2011-01-01

    PCR-SSCP was applied to detect single necleotide polymorphism of FSHR gene exon4 for 45 bulls,include Simmental and Charolais bulls. To provide theoretical basis for searching correlation between FSHR gene and reproductive traits of the cattle group, laying foundation for selecting reproductive traits molecular marker. The results showed that polymorphisms were detected by PCR-SSCP in FSHR gene exon4 and found two alleles,A and B,three genotypes AA, AB,and BB. The polymorphism fragments were cloned and sequenced, the sequencing results indicated that there was one single nucleotide mutation:C→G in FSHR gene exon4 located on the 38 th nucleotide. the mutation made a Pro change into Gla in receptor extracellular domain but do not directly effect the binding between FSH and FSHR,or reduce the ability of signal transduction or FSHR. In addition,comparing nucleotide sequences of FSHR gene exon4 for bovine,sheep (Ovisaries L), pig, horse, human and rat,the maximal similarity is 100%,the minimum is 83 %.%以西门塔尔和夏洛莱种公牛为对象,采用PCR-SSCP技术检测了促卵泡素受体(FSHR)基因第4外显子在西门塔尔、夏洛莱种公牛45个个体中的遗传多态性,结果发现多态性,旨在为研究该基因多态性与西门塔尔和夏洛莱种公牛繁殖性状的相关性提供理论依据,为筛选繁殖性状分子标记奠定基础.结果表明,牛FSHR基因第4外显子存在2个等位基因A和B,3种基因型分别为AA型、AB型和BB型.对多态片段的测序分析表明,FSHR基因第4外显子第38位碱基处发生碱基C→G的颠换,使得FSHR基因编码的受体胞外域部分出现一个脯氨酸到丙氨酸的变化,结合FSHR蛋白空间结构分析发现该氨基酸变化不直接影响FSHR与FSH的结合及FSHR转导信号能力.此外,据牛、绵羊、猪、马、人和大鼠FSHR基因第4外显子序列同源性比较表明:牛与绵羊该部分序列的同源最高为100%,与大鼠同源性最低为83%.

  5. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons.

    Science.gov (United States)

    Zhang, Xiang H-F; Chasin, Lawrence A

    2006-09-05

    Orthologous gene structures in eight vertebrate species were compared on a genomic scale to detect the birth and maturation of new internal exons during the course of evolution. We found that 40% of new human exons are alternatively spliced, and most of these are cassette exons (exons that are either included or skipped in their entirety) with low inclusion rates. This proportion decreases steadily as older and older exons are examined, even as splicing efficiency increases. Remarkably, the great majority of new cassette exons are composed of highly repeated sequences, especially Alu. Many new cassette exons are 5' untranslated exons; the proportion that code for protein increases steadily with age. New protein-coding exons evolve at a high rate, as evidenced by the initially high substitution rates (K(s) and K(a)), as well as the SNP density compared with older exons. This dynamic picture suggests that de novo recruitment rather than shuffling is the major route by which exons are added to genes, and that species-specific repeats could play a significant role in recent evolution.

  6. Distribution of Diego blood group alleles and identification of four novel mutations on exon 19 of SLC4A1 gene in the Chinese Han population by polymerase chain reaction sequence-based typing.

    Science.gov (United States)

    Xu, X G; He, J; He, Y M; Tao, S D; Ying, Y L; Zhu, F M; Lv, H J; Yan, L X

    2011-04-01

    The Diego blood group system plays an important role in transfusion medicine. Genotyping of DI1 and DI2 alleles is helpful for the investigation into haemolytic disease of the newborn (HDN) and for the development of rare blood group databases. Here, we set up a polymerase chain reaction sequence-based typing (PCR-SBT) method for genotyping of Diego blood group alleles. Specific primers for exon 19 of the solute carrier family 4, anion exchanger, member1 (SLC4A1) gene were designed, and our PCR-SBT method was established and optimized for Diego genotyping. A total of 1053 samples from the Chinese Han population and the family members of a rare proband with DI1/DI1 genotype were investigated by the PCR-SBT method. An allele-specific primer PCR (PCR-ASP) was used to verify the reliability of the PCR-SBT method. The frequencies of DI1 and DI2 alleles in the Chinese Han population were 0.0247 and 0.9753, respectively. Six new single nucleotide polymorphisms (SNPs) were found in the sequenced regions of the SLC4A1 gene, and four novel SNPs located in the exon 19, in which one SNP could cause an amino acid alteration of Ala858Ser on erythrocyte anion exchanger protein 1. The genotypes for Diego blood group were identical among 41 selected samples with PCR-ASP and PCR-SBT. The PCR-SBT method can be used in Diego genotyping as a substitute of serological technique when the antisera is lacking and was suitable for screening large numbers of donors in rare blood group databases. © 2010 The Author(s). Vox Sanguinis © 2010 International Society of Blood Transfusion.

  7. Lex-SVM: exploring the potential of exon expression profiling for disease classification.

    Science.gov (United States)

    Yuan, Xiongying; Zhao, Yi; Liu, Changning; Bu, Dongbo

    2011-04-01

    Exon expression profiling technologies, including exon arrays and RNA-Seq, measure the abundance of every exon in a gene. Compared with gene expression profiling technologies like 3' array, exon expression profiling technologies could detect alterations in both transcription and alternative splicing, therefore they are expected to be more sensitive in diagnosis. However, exon expression profiling also brings higher dimension, more redundancy, and significant correlation among features. Ignoring the correlation structure among exons of a gene, a popular classification method like L1-SVM selects exons individually from each gene and thus is vulnerable to noise. To overcome this limitation, we present in this paper a new variant of SVM named Lex-SVM to incorporate correlation structure among exons and known splicing patterns to promote classification performance. Specifically, we construct a new norm, ex-norm, including our prior knowledge on exon correlation structure to regularize the coefficients of a linear SVM. Lex-SVM can be solved efficiently using standard linear programming techniques. The advantage of Lex-SVM is that it can select features group-wisely, force features in a subgroup to take equal weihts and exclude the features that contradict the majority in the subgroup. Experimental results suggest that on exon expression profile, Lex-SVM is more accurate than existing methods. Lex-SVM also generates a more compact model and selects genes more consistently in cross-validation. Unlike L1-SVM selecting only one exon in a gene, Lex-SVM assigns equal weights to as many exons in a gene as possible, lending itself easier for further interpretation.

  8. COL5A1: Fine genetic mapping, intron/exon organization, and exclusion as candidate gene in families with tuberous sclerosis complex 1, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II

    Energy Technology Data Exchange (ETDEWEB)

    Greenspan, D.S. [Univ. of Wisconsin, Madison, WI (United States); Papenberg, K.A.; Marchuk, D.A. [Duke Univ., Durham, NC (United States)] [and others

    1994-09-01

    Type V collagen is the only fibrillar collagen which has yet to be implicated in the pathogenesis of genetic diseases in humans or mice. To begin examining the possible role of type V collagen in genetic disease, we have previously mapped COL5A1, the gene for the {alpha}1 chain of type V collagen, to 9q23.2{r_arrow}q34.3 and described two restriction site polymorphisms which allowed us to exclude COL5A1 as candidate gene for nail-patella syndrome. We have now used these polymorphisms to exclude COL5A1 as candidate gene for tuberous sclerosis complex 1 and Ehlers-Danlos syndrome type II. In addition, we describe a CA repeat, with observed heterozygosity of about 0.5, in a COL5A1 intron, which has allowed us to exclude COL5A1 as a candidate gene in hereditary hemorrhagic telangiectasia and to place COL5A1 on the CEPH family genetic map between markers D9S66 and D9S67. We have also determined the entire intron/exon organization of COL5A1, which will facilitate characterization of mutations in genetic diseases with which COL5A1 may be linked in future studies.

  9. 散发性早发帕金森病parkin基因1、2号外显子突变的研究%Mutation Detection on Exon 1 and 2 of Parkin Gene in Sporadic Early-onset Parkinson's Disease

    Institute of Scientific and Technical Information of China (English)

    徐严明; 刘焯霖; 陈彪; 陶恩祥; 陈国俊; 黎锦如

    2001-01-01

    【目的】研究parkin基因1、2号外显子突变与散发性早发帕金森病发病的关系。【方法】应用聚合酶链反应(PCR)、琼脂糖凝胶电泳和单链构象多态性(SSCP)方法检测52例散发性早发帕金森病病人外周血白细胞DNA的parkin基因1、2号外显子突变情况,并对SSCP有异常泳动外显子进行DNA测序。【结果】发现1例病人(1.9%)存在parkin基因2号外显子缺失,2例病人(3.8%)分别存在parkin基因1、2号外显子PCR产物SSCP发生泳动变位,测序发现1号外显子为杂合突变(T103C),2号外显子为纯合突变(G237C)。【结论】 parkin基因1、2号外显子突变可能与部分散发性早发帕金森病发病有关。%【Objective】To study the relationship between mutations on exon 1,2 of parkin gene and sporadic early-onset Parkinson's disease.【Methods】The deletion and single strand mobility shift on exon 1 and 2 of parkin gene in peripheral white blood cell DNA were detected by using PCR,agarose electrophoresis,and SSCP techniques in 52 patients with sporadic early-onset (onset age≤50) Parkinson's disease.The exons with mobility shift on SSCP were sequenced.【Results】One deletion(1.9%) of exon 2,2 cases with single strand mobility shift(3.8%)on exon 1 and exon 2 respectively,one heterozygous mutation (T103C) on exon 1 and one homozygous mutation (G237C) on exon 2 were found by sequencing.【Conclusion】Mutations on exon 1 and 2 of parkin gene are likely to be related to sporadic early-onset Parkinson's disease.

  10. Maternal homozygocity for a 14 basepair insertion in exon 8 of the HLA-G gene and carriage of HLA class II alleles restricting HY immunity predispose to unexplained secondary recurrent miscarriage and low birth weight in children born to these patients

    DEFF Research Database (Denmark)

    Christiansen, Ole B; Kolte, Astrid Marie; Dahl, Mette;

    2012-01-01

    Homozygous carriage of a 14 base pair (bp) insertion in exon 8 of the HLA-G gene may be associated with low levels of soluble HLA-G and recurrent miscarriage (RM). We investigated the G14bp insertion(ins)/deletion(del) polymorphism in 339 women with unexplained RM and 125 control women. In all...

  11. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies.

    Directory of Open Access Journals (Sweden)

    Zhi Yon Charles Toh

    Full Text Available Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.

  12. Antisense-mediated exon skipping to reframe transcripts.

    Science.gov (United States)

    Turczynski, Sandrina; Titeux, Matthias; Pironon, Nathalie; Hovnanian, Alain

    2012-01-01

    Numerous genetic disorders are caused by loss-of-function mutations that disrupt the open reading frame of the gene either by nonsense or by frameshift (insertion, deletion, indel, or splicing) mutations. Most of the time, the result is the absence of functional protein synthesis due to mRNA degradation by nonsense-mediated mRNA decay, or rapid degradation of a truncated protein. Antisense-based splicing modulation is a powerful tool that has the potential to treat genetic disorders by restoring the open reading frame through selective removal of the mutated exon, or by restoring correct splicing.We have developed this approach for a severe genetic skin disorder, recessive dystrophic epidermolysis bullosa, caused by mutations in the COL7A1 gene encoding type VII collagen. This gene is particularly suited for exon-skipping approaches due to its unique genomic structure. It is composed of 118 exons, 83 of which are in frame. Moreover, these exons encode a single repetitive collagenous domain.Using this gene as an example, we describe general methods that demonstrate the feasibility and efficacy of the antisense-mediated exon-skipping strategy to reframe transcripts.

  13. The silent mutation nucleotide 744 G --> A, Lys172Lys, in exon 6 of BRCA2 results in exon skipping

    DEFF Research Database (Denmark)

    Hansen, Thomas V O; Steffensen, Ane Y; Jønson, Lars

    2009-01-01

    Germ-line mutations in BRCA2 predispose to breast and ovarian cancer. Mutations are widespread throughout the gene and include disease-causing mutations as frameshift, nonsense, splicing mutations and large genomic rearrangements. However a large number of mutations, including missense, silent...... and intron variants are of unknown significance. Here, we describe the functional characterization of a silent mutation (nucleotide 744 G --> A/c.516 G --> A, Lys172Lys) in exon 6 of BRCA2 in a Danish family with breast and ovarian cancer. Exon trapping analysis showed that the mutation results in skipping...... of exon 6 and/or both exon 5 and 6, which was verified by RT-PCR analysis on RNA isolated from whole blood of the affected patient. We therefore conclude that the BRCA2 silent mutation Lys172Lys is a disease-causing mutation....

  14. Polymorphism Analysis on Exon 2 of MHC-DQA Gene in 4 Rabbit Breeds%4个家兔品种MHC-DQA基因外显子2Mbo Ⅱ酶切多态性分析

    Institute of Scientific and Technical Information of China (English)

    邝良德; 谢晓红; 黄邓萍; 易军; 雷岷; 任永军; 郭志强; 李丛艳; 郑洁

    2011-01-01

    采用PCR-RFLP方法对4个不同品种家兔MHC-DQA基因外显子2的遗传多态性进行检测,并进行聚类分析.结果表明,在家兔MHC-DQA基因外显子2的第103 bp处表现出多态性;x2适合性检验结果表明,Mbo Ⅱ酶切位点在齐卡大型新西兰白兔和齐卡巨型白兔群体均没有达到Hardy-Weinberg平衡状态(P0.05);聚类分析结果表明,齐卡大型新西兰白兔与齐卡巨型白兔亲缘关系最近.试验结果为进一步利用MHC进行抗病育种提供了分子生物学基础.%Genetic polymorphism on exon 2 of MHC-DQA gene was investigated in 4 rabbits breeds by PCR-RFLP method with Mbo Ⅱ enzyme, and cluster analysis was also performed.The results showed that there was a polymorphism at position 103 bp of exon 2 of MHC-DQA.The x2 tests showed that Mbo Ⅱ restriction enzyme sites were not in Hardy-Weinberg equilibrium among ZIKA large New Zealand white rabbits and ZIKA giant white rabbits(P<0.05), while in Hardy-Weinberg equilibrium among California rabbit and Qixin rabbit(P>0.05), cluster analysis showed that ZIKA large New Zealand white rabbits had the closest genetic relationship with ZIKA giant white rabbits.The results obtained in this study will provide a molecular biological basis for further analysis of relationship of MHC polymorphism and disease resistance in rabbit.

  15. Molecular and Genetic Characterization of HIV-1 Tat Exon-1 Gene from Cameroon Shows Conserved Tat HLA-Binding Epitopes: Functional Implications

    Science.gov (United States)

    Teto, Georges; Fonsah, Julius Y.; Tagny, Claude T.; Mbanya, Dora; Nchindap, Emilienne; Kenmogne, Leopoldine; Fokam, Joseph; Njamnshi, Dora M.; Kouanfack, Charles; Njamnshi, Alfred K.; Kanmogne, Georgette D.

    2016-01-01

    HIV-1 Tat plays a critical role in viral transactivation. Subtype-B Tat has potential use as a therapeutic vaccine. However, viral genetic diversity and population genetics would significantly impact the efficacy of such a vaccine. Over 70% of the 37-million HIV-infected individuals are in sub-Saharan Africa (SSA) and harbor non-subtype-B HIV-1. Using specimens from 100 HIV-infected Cameroonians, we analyzed the sequences of HIV-1 Tat exon-1, its functional domains, post-translational modifications (PTMs), and human leukocyte antigens (HLA)-binding epitopes. Molecular phylogeny revealed a high genetic diversity with nine subtypes, CRF22_01A1/CRF01_AE, and negative selection in all subtypes. Amino acid mutations in Tat functional domains included N24K (44%), N29K (58%), and N40K (30%) in CRF02_AG, and N24K in all G subtypes. Motifs and phosphorylation analyses showed conserved amidation, N-myristoylation, casein kinase-2 (CK2), serine and threonine phosphorylation sites. Analysis of HLA allelic frequencies showed that epitopes for HLAs A*0205, B*5301, Cw*0401, Cw*0602, and Cw*0702 were conserved in 58%–100% of samples, with B*5301 epitopes having binding affinity scores > 100 in all subtypes. This is the first report of N-myristoylation, amidation, and CK2 sites in Tat; these PTMs and mutations could affect Tat function. HLA epitopes identified could be useful for designing Tat-based vaccines for highly diverse HIV-1 populations, as in SSA. PMID:27438849

  16. Cloning of the pig aminopeptidase N gene. Identification of possible regulatory elements and the exon distribution in relation to the membrane-spanning region

    DEFF Research Database (Denmark)

    Sjöström, H; Norén, O; Olsen, Jørgen

    1989-01-01

    We have isolated four lambda-phages covering the complete pig aminopeptidase N/CD13 gene. The sequence of 2.85 kbp encompasses 1.18 kbp of the 5' upstream region and 1.67 kbp of the structural gene. In the promoter region we find a TATA box and potential binding sites for CTF-1/NF-1 and AP-2...

  17. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  18. A novel stop codon mutation in exon 1 (558C>A) of the UGT1A1 gene in a Thai neonate with Crigler-Najjar syndrome type I.

    Science.gov (United States)

    Wanlapakorn, N; Nilyanimit, P; Vorawandthanachai, T; Deesudjit, T; Dumrongpisutikul, N; Poovorawan, Y

    2015-01-23

    Human uridine 5'-diphosphate-glucuronosyltransferases play a critical role in detoxification by conjugating bilirubin with glucoronic acid. Impaired or reduced enzymatic activity causes a spectrum of clinical disorders such as Crigler-Najjar syndrome type I (CN1), Crigler-Najjar syndrome type II, and Gilbert's syndrome. CN1 is a severe form of unconjugated hyperbilirubinemia caused by homozygous or compound heterozygous mutations in the gene for uridine 5'-diphosphate glucuronosyltransferase 1 family, polypeptide A1 (UGT1A1), resulting in complete loss of enzyme function. Here, we report a novel homozygous mutation of UGT1A1 in a female Thai infant who was diagnosed with CN1, and her parents were found to be heterozygous carriers. The patient was homozygous for the c.558C>A mutation, which resulted in a premature stop codon in exon 1. Her asymptomatic parents were carriers of the nonsense c.558C>A mutation. Our result suggests an important role for homozygous c.558C>A mutations in the UGT1A1 gene in the development of severe unconjugated hyperbilirubinemia.

  19. 凹耳蛙MHC Ⅱ类B基因第二外显子多态性分析%Polymorphism of exon 2 of MHC Class Ⅱ B gene in the Chinese concave-eared torrent frog (Odorrana tormota)

    Institute of Scientific and Technical Information of China (English)

    李方; 疏义林; 吴海龙

    2012-01-01

    Currently, amphibians are experiencing global population decline, and it is believed that several amphibian mass extinction events were caused by environmental pathogens (such as chytrid fungus). Major histocompatibility complex (MHC) genes play a critical role in the course of immune response in all jawed vertebrates. MHC gene is considered to be one of the best candidates to analyze animal's adaptive evolution because its polymorphisms are usually associated with resistance or susceptibility to animal diseases. Here, we report our preliminary research on the allelic diversity of MHC class II B gene from the Chinese concave-eared frog (Odorrana tormota), a species endemic to eastern China. We initially amplified a 180-bp fragment of MHC II exon2 gene in O. Tormota using published polymerase chain reaction primers. Based on these results, we successfully obtained sequences of the gene's flanking regions using a ligation-mediated PCR method. After splicing, we obtained a sequence with length of 2,030 bp including whole exon2 and partial sequences of intronl and intron2. Then two exon2-specific primers (IIQ1BU/IIQ1BD) were designed forthe species and were used to investigate the B gene diversity of a wild population (Huangshan Mt., ?=32) using PCR, cloning and sequencing. In total, 34 distinct alleles were obtained and 2 to 5 alleles were found per individual. The proportion of variable sites for nucleotide and amino acid sequences across the 34 alleles was 16.17% (33/204) and 26.87% (18/67), respectively, and the majority of variable amino acids were located in antigen binding sites (ABS). Based on cDNA data and individual allelic diversity, we conclude that O. Tormota possesses at least three class II B loci. These results showed that though the species exhibits a restricted distribution, the Chinese concave-eared frog displays high diversity at the B loci compared to that of other species in Ranidae. Patterns of nucleotide substitution exhibited the signature of

  20. Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus.

    Science.gov (United States)

    Gillingham, Mark A F; Bechet, Arnaud; Geraci, Julia; Wattier, Remi; Dubreuil, Christine; Cezilly, Frank

    2012-08-01

    Body condition is an important determinant of fitness in many natural populations. However, as for many fitness traits, the underlying genes that regulate body condition remain elusive. The dopamine receptor D4 gene (DRD4) is a promising candidate as dopamine is known to play an important role in the regulation of food intake and the metabolism of both glucose and lipids in vertebrates. In this study, we take advantage of a large data set of greater flamingos, Phoenicopterus roseus, to test whether DRD4 polymorphism predicts early body condition (EBC) while controlling for whole-genome effects of inbreeding and outbreeding using microsatellite multilocus heterozygosity (MLH). We typed 670 of these individuals for exon 3 of the homologue of the human DRD4 gene and 10 microsatellite markers. When controlling for the effects of yearly environmental variations and differences between sexes, we found strong evidence of an association between exon 3 DRD4 polymorphisms and EBC, with 2.2-2.3% of the variation being explained by DRD4 polymorphism, whereas there was only weak evidence that MLH predicts EBC. Because EBC is most likely a polygenic trait, this is a considerable amount of variation explained by a single gene. This is to our knowledge, the first study to show an association between exon 3 DRD4 polymorphism and body condition in non-human animals. We anticipate that the DRD4 gene as well as other genes coding for neurotransmitters and their receptors may play an important role in explaining variation in traits that affect fitness.

  1. Multi-exon Skipping Using Cocktail Antisense Oligonucleotides in the Canine X-linked Muscular Dystrophy.

    Science.gov (United States)

    Miskew Nichols, Bailey; Aoki, Yoshitsugu; Kuraoka, Mutsuki; Lee, Joshua J A; Takeda, Shin'ichi; Yokota, Toshifumi

    2016-05-24

    Duchenne muscular dystrophy (DMD) is one of the most common lethal genetic diseases worldwide, caused by mutations in the dystrophin (DMD) gene. Exon skipping employs short DNA/RNA-like molecules called antisense oligonucleotides (AONs) that restore the reading frame and produce shorter but functional proteins. However, exon skipping therapy faces two major hurdles: limited applicability (up to only 13% of patients can be treated with a single AON drug), and uncertain function of truncated proteins. These issues were addressed with a cocktail AON approach. While approximately 70% of DMD patients can be treated by single exon skipping (all exons combined), one could potentially treat more than 90% of DMD patients if multiple exon skipping using cocktail antisense drugs can be realized. The canine X-linked muscular dystrophy (CXMD) dog model, whose phenotype is more similar to human DMD patients, was used to test the systemic efficacy and safety of multi-exon skipping of exons 6 and 8. The CXMD dog model harbors a splice site mutation in intron 6, leading to a lack of exon 7 in dystrophin mRNA. To restore the reading frame in CXMD requires multi-exon skipping of exons 6 and 8; therefore, CXMD is a good middle-sized animal model for testing the efficacy and safety of multi-exon skipping. In the current study, a cocktail of antisense morpholinos targeting exon 6 and exon 8 was designed and it restored dystrophin expression in body-wide skeletal muscles. Methods for transfection/injection of cocktail oligos and evaluation of the efficacy and safety of multi-exon skipping in the CXMD dog model are presented.

  2. 扬子鳄种群MHC Ⅱ类B基因第3外元多态性分析%Polymorphism of Exon 3 of MHC Class Ⅱ B Gene in Chinese Alligator (Alligator sinensis)

    Institute of Scientific and Technical Information of China (English)

    刘辉; 吴孝兵; 晏鹏; 蒋志刚

    2007-01-01

    The polymorphism of MHC class Ⅱ B gene in 14 Chinese alligators was analyzed, which came from three different areas: a wild population from Xuancheng, Anhui, a captive population from Changxing, Zhejiang, and a captive population from Anhui Research Center for Reproduction of Chinese Alligators. The gene fragment was amplified using a pair of specific primers designed from the MHC gene sequence of the spectacled caiman. A total of 34 sequence haplotypes of exon 3 were detected in the sampled Chinese alligators. The numbers of haplotypes of the 3 Chinese alligator populations were 15, 10, and 9, respectively. The overall estimation of the MHC polymorphism in the Chinese alligator population was higher than those in mammals and in cyprinid fish. The rates of nonsynonymous substitutions (dN) occurred at a significantly lower frequency than that of synonymous substitutions (ds), which were not consistent with the common rule. This result might suggest that the polymorphism of exon 3 seemed not to be maintained by the balancing selection. The neutrality test of Tajima excluded the null hypothesis that the polymorphism of exon 3 was generated by a random drift, and the fact that D = -0.401 indicated an excess of rare mutations in the Chinese alligator.The nucleotide diversity of the sequences and the phylogenetic relations were also analyzed, and the results suggested that there was no significant difference in genetic diversity among the 3 populations of Chinese alligator.%分析了取自安徽宣城野生种群、安徽省扬子鳄繁殖研究中心和浙江长兴养殖种群的14条扬子鳄MHCⅡ类B基因第3外元的多态性.在这些扬子鳄样本中共检测到34个单倍型,每个亚种群内检测到的单倍型数量分别为15,9和10个,与其他一些动物如哺乳动物和鲤科鱼类相比,扬子鳄MHC Ⅱ类B基因第3外元多态性较高.另外,非同义替换率显著小于同义替换率,这可能表明扬子鳄种群MHC Ⅱ类B基因第3外元

  3. Molecular cloning, structure and expressional profiles of two novel single-exon genes (PoCCR6A and PoCCR6B) in the Japanese flounder (Paralichthys olivaceus).

    Science.gov (United States)

    Wang, Lei; Zhang, Yong-zhen; Xu, Wen-teng; Jia, Xiao-dong; Chen, Song-lin

    2016-05-01

    CCR6 is an important binding receptor of CCL20 and beta-defensins, and has multiple functions in the innate and acquired immune responses. In this study, we cloned the PoCCR6A and PoCCR6B genes of the Japanese flounder and studied the gene structure and expression patterns of these two genes in bacterial infection. The full-length PoCCR6A cDNA is 1415 bp and the open reading frame (ORF) is 1113 bp, encoding a 370-amino-acid peptide. The full-length PoCCR6B cDNA is 2193 bp and the ORF is 1029 bp, encoding a 363-amino-acid peptide. The structures of PoCCR6A and PoCCR6B indicate that they are single-exon genes. The predicted proteins encoded by PoCCR6A and PoCCR6B have the typical G-protein-coupled receptor (GPCR) family signature of seven transmembrane domains and several conserved structural features. A tissue distribution analysis showed that PoCCR6A is predominately expressed in the intestine, gill, and blood, and PoCCR6B in the gill, spleen, and liver. The expression patterns of the two chemokine receptors were analyzed during bacterial infection. In spleen and kidney, the expression of PoCCR6A was significantly upregulated at 24 h after infection, whereas the expression of PoCCR6B was steady at these time points. While in intestine, both of them were upregulated at 6 h-12 h after infection, and in gill the expression levels of them were upregulated at 24 h. The patterns of expression suggested that PoCCR6A and PoCCR6B play an important role in the immune response of the Japanese flounder, especially in the mucosal tissues.

  4. Multiplex ligation-dependent probe amplification (MLPA) screening for exon copy number variation in the calcium sensing receptor gene: no large rearrangements identified in patients with calcium metabolic disorders

    DEFF Research Database (Denmark)

    Nissen, Peter H; Christensen, Signe E; Wallace, Andrew;

    2010-01-01

    samples were previously found negative for CASR mutations. Multiplex ligation-dependent probe amplification was used to screen the patients for exon copy number variations. Results. All exons were amplified with mean normalised ratios between 0.98 and 1.06. We did not identify any exon copy number......Summary Background. Mutation screening of the CASR by DNA sequencing is commonly used in the diagnosis of disorders of calcium metabolism, such as familial hypocalciuric hypercalcaemia (FHH). Exon copy number variation is not detected by currently used molecular genetic screening methods, and might...... be a genetic cause of inherited forms of hyper- or hypocalcaemia caused by the CASR. Objective. We wanted to further evaluate possible genetic causes for disorders of calcium metabolism, by investigating the prevalence of exon copy number variations, such as large deletions or duplications of the CASR...

  5. Silent exonic mutations in the low-density lipoprotein receptor gene that cause familial hypercholesterolemia by affecting mRNA splicing.

    NARCIS (Netherlands)

    Defesche, J.C.; Schuurman, E.J.M.; Klaaijsen, L.N.; Khoo, K.L.; Wiegman, A.; Stalenhoef, A.F.H.

    2008-01-01

    In a large group of patients with the clinical phenotype of familial hypercholesterolemia, such as elevated low-density lipoprotein (LDL) cholesterol and premature atherosclerosis, but without functional mutations in the genes coding for the LDL receptor and apolipoprotein B, we examined the effect

  6. Analysis of the CAG repeat number in exon 1 of the androgen receptor gene in Slovene men with idiopathic azoospermia and oligoasthenoteratozoospermia

    Institute of Scientific and Technical Information of China (English)

    Borut Peterlin; Branko Zorn; Natasa Teran; Tanja Kunej

    2007-01-01

    @@ Dear Sir, I am Borut Peterlin, from Division of Medical Genetics,Department of Obstetrics and Gynaecology, University Medical Center, Ljubljana, Slovenia. We write to you to discuss if the number of CAG repeats in the androgen receptor (AR) gene is associated with male infertility in a group of 190 Slovene infertile men compared to 137 men with proven fertility.

  7. 联合应用MLPA技术和基因测序技术检测DMD基因单个外显子缺失突变%Use of MLPA and gene sequencing technologies to detect a single exon deletion mutation in DMD gene

    Institute of Scientific and Technical Information of China (English)

    莫桂玲; 胡朝晖; 喻长顺; 詹益鑫; 朱庆义

    2011-01-01

    目的 提高检测DMD基因单个外显子缺突变失的准确率,为DMD家系成员的遗传咨询和产前基因诊断提供准确的依据.方法 收集2009-2010年送本实验室进行DMD基因检测的血样185例,提取外周血DNA,以美国病理学家协会提供的DNA质控品分别为阴性和阳性对照,联合应用MLPA技术、PCR技术和基因测序技术,分析其DMD基因单个外显子的缺失情况.结果 185例样品中,有7例MLPA结果显示为DMD基因单个外显子缺失,经过PCR技术和基因测序技术验证后,其中的6例确实为DMD基因单个外显子的缺失,1例为67号外显子的微小突变.结论 联合应用MLPA技术、PCR技术和基因测序技术,可以提高检测DMD基因单个外显子缺失的准确率,避免将单个外显子的微小突变误判为缺失突变,为DMD家系成员的遗传咨询和产前基因诊断提供准确的依据.%Objective To improve the accuracy of detection of a single exon deletion and provide an accurate basis of genetic counseling and prenatal gene diagnosis of the family members.Methods 185 blood samples were collected and the DMD gene was delected between 2009 to 2010. DNA samples from the College of American Pathologists were used as negative control and positive control. A single exon deletion mutation in DMD gene was detected by MLPA, PCR and gene sequencing technologies..Results In the term of 185 blood samples, the MLPA results showed that there existed single exon deletion mutations in DMD gene of 7 cases. PCR and gene sequencing were used to confirm, and a new mutation (c.9760_9781dup22/p.Pro3261LeufsX5) in DMD gene exon 67 was found just in one blood sample.Conclusion MLPA、PCR and gene sequencing technology are combined to improve the accuracy of detection of a single exon deletion and provide an accurate basis of genetic counseling and diagnosis of prenatal gene in the family members.

  8. Intron Retention and TE Exonization Events in ZRANB2

    Directory of Open Access Journals (Sweden)

    Sang-Je Park

    2012-01-01

    Full Text Available The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2, contains arginine/serine-rich (RS domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3 between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3. Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species. Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3. RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys and were expressed via intron retention (IR. Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.

  9. Human fructose-1,6-bisphosphatase gene (FBP1): Exon-intron organization, localization to chromosome bands 9q22.2-q22.3, and mutation screening in subjects with fructose-1,6-bisphosphatase deficiency

    Energy Technology Data Exchange (ETDEWEB)

    El-Maghrabi, M.R.; Jiang, W. [State Univ. of New York, Stony Brook, NY (United States)] [and others

    1995-06-10

    Fructose-1,6-bisphosphatase (EC 3.1.3.11) is a key regulatory enzyme of gluconeogenesis that catalyzes the hydrolysis of fructose-1,6-bisphosphate to generate fructose-6-phosphate and inorganic phosphate. Deficiency of fructose-1,6-bisphosphatase is associated with fasting hypoglycemia and metabolic acidosis because of impaired gluconeogenesis. We have cloned and characterized the human liver fructose-1,6-bisphosphatase gene (FBP1). FBP1, localized to chromosome bands 9q22.2-q22.3 by fluorescence in situ hybridization, consists of seven exons that span > 31 kb, and the six introns are in the same position as in the rat gene. FBP1 was screened for mutations in two subjects with fructose-1,6-bisphosphatase deficiency. Four nucleotide substitutions were identified, two of which were silent mutations in the codons for Ala-216 (GCT {yields} GCC) and Gly-319 (GGG {yields} GGA). The other substitutions were in intron 3, a C {yields} T substitution 7 nucleotides downstream from the splice donor site, and in the promoter region, an A {yields} T substitution 188 nucleotides upstream from the start of transcription. These nucleotide substitutions were also found in normal unaffected subjects and thus are not the cause of fructose-1,6-bisphosphatase deficiency in the two subjects studied. The molecular basis of hepatic fructose-1,6-bisphosphatase deficiency in these subjects remains undetermined but could result from unidentified mutations in the promoter that decrease expression or from mutations in another gene that indirectly lead to decreased fructose-1,6-bisphosphatase activity. 18 refs., 3 figs., 3 tabs.

  10. Differential effects of DRD4 and DAT1 genotype on fronto-striatal gray matter volumes in a sample of subjects with attention deficit hyperactivity disorder, their unaffected siblings, and controls

    NARCIS (Netherlands)

    Durston, S; Fossella, JA; Casey, BJ; Pol, HEH; Galvan, A; Schnack, HG; Steenhuis, MP; Minderaa, RB; Buitelaar, JK; Kahn, RS; van Engeland, H

    2005-01-01

    Genetic influences on behavior are complex and, as such, the effect of any single gene is likely to be modest. Neuroimaging measures may serve as a biological intermediate phenotype to investigate the effect of genes on human behavior. In particular, it is possible to constrain investigations by pri

  11. Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

    Science.gov (United States)

    Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

    2016-01-01

    The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.

  12. TALE-directed local modulation of H3K9 methylation shapes exon recognition.

    Science.gov (United States)

    Bieberstein, Nicole I; Kozáková, Eva; Huranová, Martina; Thakur, Prasoon K; Krchňáková, Zuzana; Krausová, Michaela; Carrillo Oesterreich, Fernando; Staněk, David

    2016-07-21

    In search for the function of local chromatin environment on pre-mRNA processing we established a new tool, which allows for the modification of chromatin using a targeted approach. Using Transcription Activator-Like Effector domains fused to histone modifying enzymes (TALE-HME), we show locally restricted alteration of histone methylation modulates the splicing of target exons. We provide evidence that a local increase in H3K9 di- and trimethylation promotes inclusion of the target alternative exon, while demethylation by JMJD2D leads to exon skipping. We further demonstrate that H3K9me3 is localized on internal exons genome-wide suggesting a general role in splicing. Consistently, targeting of the H3K9 demethylase to a weak constitutive exon reduced co-transcriptional splicing. Together our data show H3K9 methylation within the gene body is a factor influencing recognition of both constitutive and alternative exons.

  13. Identification, characterization and expression of novel Sex Hormone Binding Globulin alternative first exons in the human prostate

    Directory of Open Access Journals (Sweden)

    de Torres Inés

    2009-06-01

    Full Text Available Abstract Background The human Sex Hormone Binding Globulin (SHBG gene, located at 17p13.1, comprises, at least, two different transcription units regulated by two different promoters. The first transcription unit begins with the exon 1 sequence and is responsible for the production of plasma SHBG by the hepatocytes, while the second begins with an alternative exon 1 sequence, which replaces the exon 1 present in liver transcripts. Alternative exon 1 transcription and translation has only been demonstrated in the testis of transgenic mice containing an 11-kb human SHBG transgene and in the human testis. Our goal has been to further characterize the 5' end of the SHBG gene and analyze the presence of the SHBG alternative transcripts in human prostate tissue and derived cell lines. Results Using a combination of in silico and in vitro studies, we have demonstrated that the SHBG gene, along with exon 1 and alternative exon 1 (renamed here exon 1A, contains four additional alternative first exons: the novel exons 1B, 1C, and 1E, and a previously identified exon 1N, which has been further characterized and renamed as exon 1D. We have shown that these four alternative first exons are all spliced to the same 3' splice site of SHBG exon 2, and that exon 1A and the novel exon 1B can be spliced to exon 1. We have also demonstrated the presence of SHBG transcripts beginning with exons 1B, 1C and 1D in prostate tissues and cell lines, as well as in several non-prostatic cell lines. Finally, the alignment of the SHBG mammalian sequences revealed that, while exons 1C, 1D and 1E are very well conserved phylogenetically through non-primate mammal species, exon 1B probably aroused in apes due to a single nucleotide change that generated a new 5' splice site in exon 1B. Conclusion The identification of multiple transcription start sites (TSS upstream of the annotated first exon of human SHBG, and the detection of the alternative transcripts in human prostate

  14. Functional identification of an exon 1 substitution in the myostatin gene and its expression in breast and leg muscle of the Bian chicken.

    Science.gov (United States)

    Zhang, G X; Zhang, T; Wei, Y; Ding, F X; Zhang, L; Wang, J Y

    2015-01-01

    1. The objective of this study was to verify the functional effects of the c.234G>A substitution in the myostatin (MSTN) gene and ascertain the mechanism by which the variant affects growth traits in the Bian chicken. 2. The c.234G>A substitution was detected by PCR-RFLP analysis in the 7th-generation Bian chickens and three genotypes (AA, AG and GG) were identified. Results showed that the substitution was significantly associated with all studied growth traits, except first-d-weight, in female Bian chickens. 3. Based on these results, the substitution was used in gene-assisted selection for growth traits and thus fast-growth (AA genotype) and slow-growth (GG genotype) lines were successfully established. Significant differences in growth traits were detected between the fast-growth and slow-growth lines from 6 to 16 weeks of age. Furthermore, all slaughter traits, except leg muscle rate, were significantly different between the fast-growth and slow-growth lines. 4. Expression analysis showed that the relative expression level of MSTN in chickens with GG and AG genotypes were significantly higher than that in chickens with an AA genotype, both in breast and leg muscle. Chickens in the slow-growth line had significantly higher relative expression level of MSTN compared to chickens in the fast-growth line, both in breast and leg muscle. 5. The results suggest that the c.234G>A substitution in the myostatin (MSTN) gene negatively regulates the expression of MSTN in the Bian chicken and that it may be used in marker-assisted selection to accelerate the chicken breeding process.

  15. Impact of the growth hormone receptor exon 3 deletion gene polymorphism on glucose metabolism, lipids, and insulin-like growth factor-I levels during puberty

    DEFF Research Database (Denmark)

    Sørensen, Kaspar; Aksglaede, Lise; Munch-Andersen, Thor

    2009-01-01

    the impact of the GHRd3 gene polymorphism on insulin sensitivity, insulin secretion, lipids, and IGF-I levels in healthy children and adolescents. DESIGN: This was cross-sectional and was part of the COPENHAGEN puberty study. SETTING: The study was conducted at a tertiary center for pediatric endocrinology...... was associated with higher triglyceride (P = 0.028), but not IGF-I levels. CONCLUSION: The presence of at least one GHRd3 allele was associated with higher insulin secretion for a given degree of insulin sensitivity in healthy children and adolescents during puberty. In addition, the presence of the GHRd3 allele...

  16. Antisense mediated exon skipping therapy for duchenne muscular dystrophy (DMD)

    DEFF Research Database (Denmark)

    Brolin, Camilla; Shiraishi, Takehiko

    2011-01-01

    Duchenne Muscular Dystrophy (DMD) is a lethal disease caused by mutations in the dystrophin gene (DMD) that result in the absence of essential muscle protein dystrophin. Among many different approaches for DMD treatment, exon skipping, mediated by antisense oligonucleotides, is one of the most pr...... oligonucleotides (2'-O-methyl phosphorothioate (2OME-PS), phosphorodiamidate morpholino oligomer (PMO)) and peptide nucleic acid (PNA)....

  17. Carcass and physical meat characteristics of thin tail sheep (TTS based on calpastatin gene (CAST (Locus intron 5 – exon 6 genotypes variation

    Directory of Open Access Journals (Sweden)

    Muhammad Ihsan Andi Dagong

    2012-03-01

    Full Text Available The quality of sheep carcass is mostly determined by the total lean meat production, meat distribution on the carcass and the quality of meat. Calpastatin gene (CAST is known to have an association with carcass and meat quality traits. The objective of this research was to identify the association between CAST polymorphisms and carcass characteristics in Thin Tail Sheep (TTS. Thirty three heads of sheep representing three genotypes of CAST (CAST-11, CAST-12 and CAST-22 were identified for carcass and meat characterisation. There was no significant difference between CAST polymorphisms with meat tenderness, pH, water holding capacity and cooking loss, neither with carcass weight and dressing percentage among genotypes. Shoulder proportion of CAST-11 genotype was larger than that of CAST-12 or CAST-22, but the lean meat proportion of CAST-22 genotype in shoulder, rack and loin were higher than those of CAST-11 but not different from CAST-12. The fat percentage of CAST-11 was the highest among the genotypes. CAST-22 genotype has higher lean meat percentage than the CAST-11. Variation in CAST gene could be used as marker assisted selection in sheep for higher lean meat proportion.

  18. Exon-primed, intron-crossing (EPIC) loci for five nuclear genes in deep-sea protobranch bivalves: primer design, PCR protocols and locus utility.

    Science.gov (United States)

    Jennings, Robert M; Etter, R J

    2011-11-01

    We describe PCR primers and amplification protocols developed to obtain introns from conserved nuclear genes in deep-sea protobranch bivalves. Because almost no sequence data for protobranchs are publically available, mollusk and other protostome sequences from GenBank were used to design degenerate primers, making these loci potentially useful in other invertebrate taxa. Amplification and sequencing success varied across the test group of 30 species, and we present five loci spanning this range of outcomes. Intron presence in the targeted regions also varied across genes and species, often within single genera; for instance, the calmodulin and β-tubulin loci contained introns with high frequency, whereas the triose phosphate isomerase locus never contained an intron. In introns for which we were able to obtain preliminary estimates of polymorphism levels in single species, polymorphism was greater than traditional mitochondrial loci. These markers will greatly increase the ability to assess population structure in the ecologically important protobranchs, and may prove useful in other taxa as well.

  19. An Association Analysis of Reelin Gene (RELN Exon 22 (G/C, Rs.362691, Polymorphism with Autism Spectrum Disorder among Iranian-Azeri Population

    Directory of Open Access Journals (Sweden)

    Leila Mehdizadeh Fanid

    2016-07-01

    Full Text Available Background Autism spectrum disorder (ASD is a intricate childhood neuropsychiatric disorder that is described by deficits in communication of verbal and non-verbal, reciprocal social interactions, stereotypic behaviors, interests, and activities. The studies of post-mortem neuro-anatomical anomalies have indicated that migration alterations could occur early during development (first trimester in autistic brain. Since the Reelin gene, plays a crucial role in these migratory processes, it is subsequently considered as a potential candidate gene for autism. Materials and Methods In this case-control study, we recruited 74 patients with ASD and 88 healthy controls from Iranian-Azeri Population. Genomic DNA isolated from blood leukocytes of cases and control individuals by the proteinase K and using salt-out method. Single nucleotide polymorphisms (SNP genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP technique. Results The allele and genotype frequencies did not show significant difference between autistic and control groups (P>0.05. No significant relationship was observed between the genders and genotypes in autism group (P>0.05. Conclusion The current study showed that the SNPs rs362691 could not be used as a useful molecular biomarker to predict genetic susceptibility for ASD among Iranian-Azeri patients.

  20. Variation in exon 10 of the ovine calpain 3 gene (CAPN3) and its association with meat yield in New Zealand Romney sheep.

    Science.gov (United States)

    Fang, Q; Forrest, R H; Zhou, H; Frampton, C M; Hickford, J G H

    2013-07-01

    Variation in the ovine CAPN3 gene was analysed using PCR-single strand conformational polymorphism, and its effect on growth and carcass traits was assessed in 513 New Zealand Romney lambs produced by 17 unrelated rams. Among the four allelic variants detected, the presence of variant *02 was found to be associated with an increased proportion of shoulder yield (absent: 32.6±0.01%; present: 33.4±0.03%; P=0.016), and tended to be associated with increased shoulder yield (lean meat yield of the shoulder expressed as a percentage of the hot carcass weight) (absent: 16.6±0.06%; present: 17.02±0.20%; P=0.067). No association was detected with growth traits or other carcass traits.

  1. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA.

    Directory of Open Access Journals (Sweden)

    Stephen H Munroe

    Full Text Available The α-thyroid hormone receptor gene (TRα codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3' end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30 located downstream of the alternative 3'splice site of TRα2 mRNA and antisense to the 3'UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing.

  2. The third exon of the budding yeast meiotic recombination gene HOP2 is required for calcium-dependent and recombinase Dmc1-specific stimulation of homologous strand assimilation.

    Science.gov (United States)

    Chan, Yuen-Ling; Brown, M Scott; Qin, Daoming; Handa, Naofumi; Bishop, Douglas K

    2014-06-27

    During meiosis in Saccharomyces cerevisiae, the HOP2 and MND1 genes are essential for recombination. A previous biochemical study has shown that budding yeast Hop2-Mnd1 stimulates the activity of the meiosis-specific strand exchange protein ScDmc1 only 3-fold, whereas analogous studies using mammalian homologs show >30-fold stimulation. The HOP2 gene was recently discovered to contain a second intron that lies near the 3'-end. We show that both HOP2 introns are efficiently spliced during meiosis, forming a predominant transcript that codes for a protein with a C-terminal sequence different from that of the previously studied version of the protein. Using the newly identified HOP2 open reading frame to direct synthesis of wild type Hop2 protein, we show that the Hop2-Mnd1 heterodimer stimulated Dmc1 D-loop activity up to 30-fold, similar to the activity of mammalian Hop2-Mnd1. ScHop2-Mnd1 stimulated ScDmc1 activity in the presence of physiological (micromolar) concentrations of Ca(2+) ions, as long as Mg(2+) was also present at physiological concentrations, leading us to hypothesize that ScDmc1 protomers bind both cations in the active Dmc1 filament. Co-factor requirements and order-of-addition experiments suggested that Hop2-Mnd1-mediated stimulation of Dmc1 involves a process that follows the formation of functional Dmc1-ssDNA filaments. In dramatic contrast to mammalian orthologs, the stimulatory activity of budding yeast Hop2-Mnd1 appeared to be specific to Dmc1; we observed no Hop2-Mnd1-mediated stimulation of the other budding yeast strand exchange protein Rad51. Together, these results support previous genetic experiments indicating that Hop2-Mnd1 specifically stimulates Dmc1 during meiotic recombination in budding yeast.

  3. A founder synonymous COL7A1 mutation in three Danish families with dominant dystrophic epidermolysis bullosa pruriginosa identifies exonic regulatory sequences required for exon 87 splicing

    DEFF Research Database (Denmark)

    Covaciu, C; Grosso, F; Pisaneschi, E

    2011-01-01

    a previously unrecognized translationally silent exonic COL7A1 mutation that results in skipping of exon 87 and is associated with DDEB-Pr phenotypes in several members of three apparently unrelated Danish families. A haplotype segregation study suggested a common ancestor in these kindred. Functional splicing...... shoulders. DEB-Pr is caused by either dominant (DDEB-Pr) or recessive mutations in the COL7A1 gene encoding type VII collagen (COLVII). The full spectrum of COL7A1 mutations in DEB-Pr remains elusive and the genotype-phenotype correlation is largely incomplete. Here, we report and functionally characterize...... analysis of the mutant exon by a COL7A1 minigene construct and computational prediction for splicing regulatory cis-sequences prove that the mutation alters the activity of an exonic splicing enhancer (ESE) critical for exon inclusion. These findings substantiate for the first time the involvement...

  4. The complete exon-intron structure of the 156-kb human gene NFKB1, which encodes the p105 and p50 proteins of transcription factors NF-{kappa}B and I{kappa}B-{gamma}: Implications for NF-{kappa}B-mediated signal transduction

    Energy Technology Data Exchange (ETDEWEB)

    Heron, E.; Deloukas, P.; van Loon, A.P.G.M. [F. Hoffmann-La Roche Limited, Basel (Switzerland)

    1995-12-10

    The NFKB1 gene encodes three proteins of the NF-{kappa}/Rel and I{kappa}B families: p105, p50, and (in mouse) I{kappa}B-{gamma}. We determined the complete genomic structure of human NFKB1. NFKB1 spans 156 kb and has 24 exons with introns varying between 40,000 and 323 bp in length. Although NFKB2, which encodes p100 and p52, also has 24 exons and has a comparable exon-intron structure, it is 20 times shorter than NFKB1. We propose that the long size of NFKB1 is important for transient activation of NF-{kappa}B complexes containing p50. I{kappa}B-{gamma} corresponds to the carboxyl-terminal half of p105. DNA sequence analysis showed that the 3{prime}-end of human intron 11 and the 5{prime}-end of exon 12 of NFKB1 are colinear with the 5{prime}-untranslated region of mouse I{kappa}B-{gamma} cDNA. I{kappa}B-{gamma} is thus likely to be generated by transcription starting within intron 11 and not by alternative splicing of the mouse mRNA encoding p105 and p50. 71 refs., 5 figs., 1 tab.

  5. Recombinant Exon-Encoded Resilins for Elastomeric Biomaterials

    Science.gov (United States)

    Qin, Guokui; Rivkin, Amit; Lapidot, Shaul; Hu, Xiao; Arinus, Shira B.; Dgany, Or; Shoseyov, Oded; Kaplan, David L.

    2011-01-01

    Resilin is an elastomeric protein found in specialized regions of the cuticle of most insects, providing outstanding material properties including high resilience and fatigue lifetime for insect flight and jumping needs. Two exons (1 and 3) from the resilin gene in Drosophila melanogaster were cloned and the encoded proteins expressed as soluble products in Escherichia coli. A heat and salt precipitation method was used for efficient purification of the recombinant proteins. The proteins were solution cast from water and formed into rubber-like biomaterials via horseradish peroxidase-mediated cross-linking. Comparative studies of the two proteins expressed from the two different exons were investigated by Fourier Transform Infrared Spectroscopy (FTIR) and Circular Dichrosim (CD) for structural features. Little structural organization was found, suggesting structural order was not induced by the enzyme-mediateed dityrosine cross-links. Atomic Force Microscopy (AFM) was used to study the elastomeric properties of the uncross-linked and cross-linked proteins. The protein from exon 1 exhibited 90% resilience in comparison to 63% for the protein from exon 3, and therefore may be the more critical domain for functional materials to mimic native resilin. Further, the cross-linking of the recombinant exon 1 via the citrate-modified photo-Fenton reaction was explored as an alternative dityrosine mediated polymerization method and resulted in both highly elastic and adhesive materials. The citrate-modified photo-Fenton system may be suitable for in-vivo applications of resilin biomaterials. PMID:21963157

  6. Fourier Power Spectrum Analysis of Exons for the Period-3 Behavior

    Institute of Scientific and Technical Information of China (English)

    Yuan Xin TIAN; Chao CHEN; Xiao Yong ZOU; Jian Ding QIU; Pei Xiang CAI; Jin Yuan MO

    2005-01-01

    The period-3 behaviors of 105 exons from 20 genes in human were studied by Fourier power spectrum. The results indicated that not all exons show the period-3 behavior. The exons were adjusted in order to make them accord with the order of the protein translated, and we found that the period-3 character is relation to the length of exons and the bases distribution in the three codon position. Furthermore, as long as the exons with period-3 behavior accord with the order of protein translated, they would exhibit the synonymous codons usage preference, and the codons with g/c at the third position are used in higher frequency. The results are significant to the gene prediction and the research on the introns.

  7. Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements.

    Science.gov (United States)

    Di Giacomo, Daniela; Gaildrat, Pascaline; Abuli, Anna; Abdat, Julie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra

    2013-11-01

    Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing.

  8. Muscle-specific deletion of exons 2 and 3 of the IL15RA gene in mice: effects on contractile properties of fast and slow muscles.

    Science.gov (United States)

    O'Connell, Grant; Guo, Ge; Stricker, Janelle; Quinn, LeBris S; Ma, Averil; Pistilli, Emidio E

    2015-02-15

    Interleukin-15 (IL-15) is a putative myokine hypothesized to induce an oxidative skeletal muscle phenotype. The specific IL-15 receptor alpha subunit (IL-15Rα) has also been implicated in specifying this contractile phenotype. The purposes of this study were to determine the muscle-specific effects of IL-15Rα functional deficiency on skeletal muscle isometric contractile properties, fatigue characteristics, spontaneous cage activity, and circulating IL-15 levels in male and female mice. Muscle creatine kinase (MCK)-driven IL-15Rα knockout mice (mIl15ra(fl/fl)/Cre(+)) were generated using the Cre-loxP system. We tested the hypothesis that IL-15Rα functional deficiency in skeletal muscle would increase resistance to contraction-induced fatigue, cage activity, and circulating IL-15 levels. There was a significant effect of genotype on the fatigue curves obtained in extensor digitorum longus (EDL) muscles from female mIl15ra(fl/fl)/Cre(+) mice, such that force output was greater during the repeated contraction protocol compared with mIl15ra(fl/fl)/Cre(-) control mice. Muscles from female mIl15ra(fl/fl)/Cre(+) mice also had a twofold greater amount of the mitochondrial genome-specific COXII gene compared with muscles from mIl15ra(fl/fl)/Cre(-) control mice, indicating a greater mitochondrial density in these skeletal muscles. There was a significant effect of genotype on the twitch:tetanus ratio in EDL and soleus muscles from mIl15ra(fl/fl)/Cre(+) mice, such that the ratio was lower in these muscles compared with mIl15ra(fl/fl)/Cre(-) control mice, indicating a pro-oxidative shift in muscle phenotype. However, spontaneous cage activity was not different and IL-15 protein levels were lower in male and female mIl15ra(fl/fl)/Cre(+) mice compared with control. Collectively, these data support a direct effect of muscle IL-15Rα deficiency in altering contractile properties and fatigue characteristics in skeletal muscles.

  9. Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon.

    Science.gov (United States)

    Osigus, Hans-Jürgen; Eitel, Michael; Schierwater, Bernd

    2017-01-01

    The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 ("Panama" clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.

  10. Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy.

    Science.gov (United States)

    Yamashita, Yoshihiro; Matsuura, Tohru; Shinmi, Jun; Amakusa, Yoshinobu; Masuda, Akio; Ito, Mikako; Kinoshita, Masanobu; Furuya, Hirokazu; Abe, Koji; Ibi, Tohru; Sahashi, Ko; Sahashi, Koo; Ohno, Kinji

    2012-06-01

    Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data.

  11. Study on the Polymorphism of Porcine Hormone-sensitive Lipase Gene Exon I by PCR-RFLP in Different Breeds%猪品种间HSL基因外显子I PCR-RFLP的研究

    Institute of Scientific and Technical Information of China (English)

    雷明刚; 吴珍芳; 邓昌彦; 熊远著

    2001-01-01

    Hormone-sensitive lipase (HSL) is the key enzyme responsible for the mobilization of free acids from adipose tissue, and it is also the most important enzyme that affects fat deposition. In this paper, the polymorphism of HSL gene in exon I was detected by PCR-RFLP. It revealed a BsaHI-site polymorphism in different pig breeds. There exist two genotypes (AA,AG) in the fat-type Tongcheng pig and Qingping pig with allele frequencies of 0.917A,0.083G and 0.893,0.107,respectively. Duroc has two genotypes (AG,GG) with allele frequencies 0.15A and 0.85G. However, There exists only GG genotype in lean-type Large White and Landrace pig.%激素敏感脂肪酶(Hormone-sensitive lipase,HSL)是负责分解脂肪组织中甘油三酯释放游离脂肪酸的关键酶。本研究利用PCR*.RFLP(polymerase chain reaction-restriction fragment length polymorphism)方法,分析了猪HSL基因外显子I区多态性,发现不同品种猪间存在多态性。瘦肉型大白猪和长白猪全部表现为GG基因型;杜洛克猪表现为AG和GG两种基因型,其等位基因A和G的频率是15%和85%;脂肪型通城猪和清平猪表现为AA和AG两种基因型,其等位基因A、G的频率分别是91.67%、8.33%和89.83%、10.17%。

  12. Developmental differences in early adolescent aggression: a gene × environment × intervention analysis.

    Science.gov (United States)

    Schlomer, Gabriel L; Cleveland, H Harrington; Vandenbergh, David J; Feinberg, Mark E; Neiderhiser, Jenae M; Greenberg, Mark T; Spoth, Richard; Redmond, Cleve

    2015-03-01

    Aggression-related problems such as assault and homicide among adolescents and young adults exact considerable social and economic costs. Although progress has been made, additional research is needed to help combat this persistent problem. Several lines of research indicate that parental hostility is an especially potent predictor of adolescent aggression, although most longitudinal research has focused on clarifying the direction of effects. In this study, we used longitudinal data from the PROSPER project (N = 580; 54.8% female), a primarily rural Caucasian preventative intervention sample, to examine developmental change in early- to mid-adolescent aggressive behavior problems (age 11-16 years). In addition, we examined maternal hostility as a predictor of developmental change in aggression and the PROSPER preventative intervention, designed to reduce substance use and aggression, as a potential influence on this association. Lastly, several studies indicate that variation in the DRD4 7-repeat gene moderates both parenting and intervention influences on externalizing behavior. Accordingly, we examined the potential moderating role of DRD4. As hypothesized, there was a significant maternal hostility by intervention interaction indicating that the intervention reduced the negative impact of maternal hostility on adolescent change in aggressive behavior problems. DRD4 7-repeat status (7+ vs. 7-) further conditioned this association whereby control group 7+ adolescents with hostile mothers showed increasing aggressive behavior problems. In contrast, aggression decreased for 7+ adolescents with similarly hostile mothers in the intervention. Implications for prevention are discussed as well as current perspectives in candidate gene-by-environment interaction research.

  13. The role of exon shuffling in shaping protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    França Gustavo S

    2010-12-01

    Full Text Available Abstract Background Physical protein-protein interaction (PPI is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains, self-interacting (able to interact with another copy of themselves and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

  14. Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

    Directory of Open Access Journals (Sweden)

    Charles W Sugnet

    2006-01-01

    Full Text Available Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.

  15. Functional polymorphism in exon 5 and variant haplotype of the interleukin-1 receptor-associated kinase 1 gene are associated with susceptibility to and severity of sepsis in the Chinese population

    Institute of Scientific and Technical Information of China (English)

    FANG Yu; ZHANG Lu; ZHOU Gang-qiao; WANG Zhi-fu; ZENG Zhao-shu; LUO Zhi-yi; LI Lei; LIU Bao-chi

    2011-01-01

    Background The interleukin-1 (IL-1) receptor-associated kinase 1 (IRAKI) is believed to play an important role in the pathogenesis of sepsis. Recent studies have suggested that the IRAK1 functional genetic variant could affect the severity of sepsis in Caucasians. In this report, we have investigated whether polymorphisms at the IRAK1 gene are associated with the susceptibility to and severity of sepsis among the Chinese population. Methods Haplotype-tagging single nucleotide polymorphisms (htSNPs) were selected from the HapMap database.They were genotyped in 255 patients with sepsis and 260 control subjects by PCR/restriction fragment length polymorphism (RFLP) analysis. The association between the selected htSNPs and the susceptibility to and severity of sepsis were estimated by Logistic regression with adjustments for age, sex, smoking, drinking, chronic disease status,Acute Physiology and Chronic Health Evaluation (APACHE) Ⅱ score and primary diseases. Results rs1059702 was selected to represent the six linked htSNPs for IRAK1. Genotype frequencies of the htSNPs were in Hardy-Weinberg equilibrium for females, as were allele frequencies for both sex groups. Associations were observed in females between the htSNPs C/C genotype and increased susceptibility to sepsis (odds ratio (OR), 5.46;95% confidence interval (Cl), 1.12-26.67; P=0.018), and such associations were also observed between the IRAK1variant haplotype (CC/C-allele) and increased susceptibility to sepsis (OR, 1.68; 95% Cl, 1.05-2.70; P=0.031) when compared with the T/T + T/C genotype and the wild-type haplotype (TC + TT/T-allele). In the multiple organ dysfunction syndrome (MODS) subgroup, the variant haplotype was also associated with increased severity of sepsis (OR, 2.37; 95%Cl, 1.13-4.94; P=0.02) when compared with the wild haplotype. This association was not significant in male patients. Conclusions The functional polymorphism in exon 5 and the variant haplotype of IRAK1 gene mediate

  16. 酸性-α-糖苷酶基因外显子突变与 mRNA 剪接导致Ⅱ型糖贮积病关系%Silent exonic mutation in the acid-alpha-glycosidase gene that causes glycogen storage disease type Ⅱ by affecting mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    米热古丽·买买提; 罗燕飞; 许晨波

    2013-01-01

    Objective To probe the relationship between the Glycogen storage disease type Ⅱ (GSDⅡ) and acid alpha-glycosidase (GAA) .Methods Extract childhood-onset GSD Ⅱ children genomic DNA and total RNA ,using PCR and nucleic acid sequencing methods to study the mutation .Results 3 gene locus muta-tions are found in children patients′GAA ,including two missense mutations (exon 2 c .199G>A mutation and exon 13 and c .1798C> T mutation) and a donor splice site synonymous mutation (exon 2 c .546G> T mutation) .Conclusion GAA gene exon 2 has a new spliceosome mutation which is associated with the at-tack of GSD Ⅱ .%目的探讨Ⅱ型糖原贮积病(GSDⅡ)与酸性α-葡萄糖苷酶基因突变的关系。方法提取儿童期发病的GSDⅡ患儿基因组DNA及总RNA ,采用PCR及核酸测序的方法研究其突变。结果患儿GAA基因3个位点存在突变,包括2个错义突变(第2外显子c .199G>A突变和第13外显子c .1798C> T突变)和1个供体剪接位点的同义突变(第2外显子c .546G> T突变)。结论 GAA基因第2外显子上有1个新的剪接体突变,该突变与GSDⅡ的发病相关。

  17. The emergence of alternative 3' and 5' splice site exons from constitutive exons.

    Directory of Open Access Journals (Sweden)

    Eli Koren

    2007-05-01

    Full Text Available Alternative 3' and 5' splice site (ss events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving, similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.

  18. CoNVaDING: Single Exon Variation Detection in Targeted NGS Data.

    Science.gov (United States)

    Johansson, Lennart F; van Dijk, Freerk; de Boer, Eddy N; van Dijk-Bos, Krista K; Jongbloed, Jan D H; van der Hout, Annemieke H; Westers, Helga; Sinke, Richard J; Swertz, Morris A; Sijmons, Rolf H; Sikkema-Raddatz, Birgit

    2016-05-01

    We have developed a tool for detecting single exon copy-number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control (QC) metric, that excludes or flags low-quality exons. Since this QC shows exactly which exons can be reliably analyzed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high-quality targets in 320 samples analyzed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions.

  19. Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis

    Directory of Open Access Journals (Sweden)

    Whistler Toni

    2010-09-01

    Full Text Available Abstract Background The contribution of alternative splicing and isoform expression to cellular response is emerging as an area of considerable interest, and the newly developed exon arrays allow for systematic study of these processes. We use this pilot study to report on the feasibility of exon array implementation looking to replace the 3' in vitro transcription expression arrays in our laboratory. One of the most widely studied models of cellular response is T-cell activation from exogenous stimulation. Microarray studies have contributed to our understanding of key pathways activated during T-cell stimulation. We use this system to examine whole genome transcription and alternate exon usage events that are regulated during lymphocyte proliferation in an attempt to evaluate the exon arrays. Results Peripheral blood mononuclear cells form healthy donors were activated using phytohemagglutinin, IL2 and ionomycin and harvested at 5 points over a 7 day period. Flow cytometry measured cell cycle events and the Affymetrix exon array platform was used to identify the gene expression and alternate exon usage changes. Gene expression changes were noted in a total of 2105 transcripts, and alternate exon usage identified in 472 transcript clusters. There was an overlap of 263 transcripts which showed both differential expression and alternate exon usage over time. Gene ontology enrichment analysis showed a broader range of biological changes in biological processes for the differentially expressed genes, which include cell cycle, cell division, cell proliferation, chromosome segregation, cell death, component organization and biogenesis and metabolic process ontologies. The alternate exon usage ontological enrichments are in metabolism and component organization and biogenesis. We focus on alternate exon usage changes in the transcripts of the spliceosome complex. The real-time PCR validation rates were 86% for transcript expression and 71% for

  20. Studies on mutations of exon 7,11,12 of phenylalanine hydroxylase gene of children with phenylketonuria in the south region of Xinj iang Uygur Autonomous Region%新疆南疆地区苯丙酮尿症患儿苯丙氨酸羟化酶基因第7,11,12外显子突变研究

    Institute of Scientific and Technical Information of China (English)

    王昌敏; 唐承波; 王慧琴; 依布拉音

    2015-01-01

    Objective To study the characteristics of mutations of exon 7,1 1,12 in phenylalanine hydroxylase(PAH ) gene of children with phenylketonuria (PKU ) in south region of Xinjiang Uygur Autonomous Region.Methods A total of 42 children who made a definite diagnosis as PKU by different levels of medical institutions in the south region of Xinjiang by neonatal PKU screening from March 2009 to December 2013 were chosen as study subjects.The mutations of exon 7,1 1,12 of PAH gene were analyzed by detect heelstick blood or venous blood through polymerase chain reaction(PCR)and PAH gene DNA sequencing.The study protocol was approved by the Ethical Review Board of Investigation in Human Being of different levels of medical institutions in the south region of Xinjiang Uygur Autonomous Region,such as People′s Hospital of Xingjiang Uygur Autonomous Region.Informed consent was obtained from the parents of each participant.Results There were 7 types of mutation of PAH gene,and a total of 46 mutational sites were detected in 42 pairs of PAH alleles in 42 PKU children.There were 23 silent mutations of exon 7:c.735G> A (p.Val245Val),8 missense mutations of exon 7:c.728G > A (p.Arg243Gln),2 nonsense mutations of exon 7:c.781C>T(p.Arg261X),1 missense mutations of exon 7:c.782G>A(p.Arg261Gln), 6 silent mutations of exon 1 1:c.1 1 55G>C (p.Leu385Leu),5 missense mutations of exon 12:c.1238G>C(p.Arg413Pro)and 1 missense mutation of exon 12:c.1252A>C(p.Thr418Pro).The exon 7:c.735G>A(p.Val245Val)mutational site has the highest detection ratio [50.00% (23/46 )]in this study,and the mutation frequency was 27.38% (23/84).Mutation detection rate of PAH alleles was 54.76% (46/84). Conclusions The mutational characteristic in exon 7,1 1,12 of PAH gene in PKU children in south region of Xinjiang is silent mutational and missense mutation are major mutation types,and mutation types and amount of exon 7 are the most frequent.%目的:探讨新疆南疆地区苯丙酮尿症(PKU)

  1. 普氏野马与两种新疆地方品种马的ELA-DRA*exon2的多态性分析%Polymorphisms of the Gene ELA-DRA * exon 2 in Przewalski's Horse (Equus Przewalskii) and Two Kinds of Xinjiang Local Breeds

    Institute of Scientific and Technical Information of China (English)

    于丽娟; 恩特马克; 凌英会; 马月辉; 马合木提·哈力克

    2011-01-01

    To understand the polymorphism and allele frequency distribution of ELA-DRA * exon2 in Przewalski,s horse(Equus PrzewaLskii) , Kazakh and Yanqi horse, ELA-DRA * exon2 in three types of horses was genotyped by PCR-SSCP methods. Both the nucleotide and the amino acid sequences of the different alleles were analyzed in these horses. The results showed that seven genotypes were detected in 127 horses: three homozygotes named AA, BB and CC, four heterozygotes named AB, BC, AC and AD. AA genotype was dominant in Kazakh and Yanqi horses.CC was the dominant genotype in Przewalski's horse(Equus Przewalskii). The chi-square analysis suggested that the allele and genotype frequencies were in Hardy-Weinberg equilibrium in the three horse types. The analysis of PIC and He showed that the three horse types belonged to intermediate polymorphism. The values of PIC and He in Przewalski's horse(Equus Przewalskii)were lower than that in Kazakh and Yanqi horses.%为了解普氏野马、哈萨克马与焉耆马的ELA-DRA*exon2的多态性以及等位基因频率分布.本研究采用PCR-SSCP技术对普氏野马、哈萨克马与焉耆马的ELA-DRA*exon2进行分型,并对不同等位基因进行核苷酸与氨基酸分析.结果显示:127匹马中共出现7种基因型,3种纯合子分别记为AA、BB、CC;4种杂合子分别记为AB、AC、BC、AD.AA基因型为哈萨克马与焉耆马的优势基因型,普氏野马以CC基因型为主.经x2检验后,3种类型马的等位基因频率和基因型频率均处于Hardy-Weinberg平衡状态.PIC值与He值分析表明,3种类型马均属于中度多态,且普氏野马的PIC值与He值比哈萨克马与焉耆马低.

  2. Sm10.3, a member of the micro-exon gene 4 (MEG-4 family, induces erythrocyte agglutination in vitro and partially protects vaccinated mice against Schistosoma mansoni infection.

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    Vicente P Martins

    2014-03-01

    Full Text Available BACKGROUND: The parasitic flatworm Schistosoma mansoni is a blood fluke that causes schistosomiasis. Current schistosomiasis control strategies are mainly based on chemotherapy, but many researchers believe that the best long-term strategy to control disease is a combination of drug treatment and immunization with an anti-schistosome vaccine. Numerous antigens that are expressed at the interface between the parasite and the mammalian host have been assessed. Among the most promising molecules are the proteins present in the tegument and digestive tract of the parasite. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we evaluated the potential of Sm10.3, a member of the micro-exon gene 4 (MEG-4 family, for use as part of a recombinant vaccine. We confirmed by real-time PCR that Sm10.3 was expressed at all stages of the parasite life cycle. The localization of Sm10.3 on the surface and lumen of the esophageal and intestinal tract in adult worms and lung-stage schistosomula was confirmed by confocal microscopy. We also show preliminary evidence that rSm10.3 induces erythrocyte agglutination in vitro. Immunization of mice with rSm10.3 induced a mixed Th1/Th2-type response, as IFN-γ, TNF-α, and low levels of IL-5 were detected in the supernatant of cultured splenocytes. The protective effect conferred by vaccination with rSm10.3 was demonstrated by 25.5-32% reduction in the worm burden, 32.9-43.6% reduction in the number of eggs per gram of hepatic tissue, a 23.8% reduction in the number of granulomas, an 11.8% reduction in the area of the granulomas and a 39.8% reduction in granuloma fibrosis. CONCLUSIONS/SIGNIFICANCE: Our data suggest that Sm10.3 is a potential candidate for use in developing a multi-antigen vaccine to control schistosomiasis and provide the first evidence for a possible role for Sm10.3 in the blood feeding process.

  3. Exon circularization in mammalian nuclear extracts.

    Science.gov (United States)

    Pasman, Z; Been, M D; Garcia-Blanco, M A

    1996-06-01

    Correct ligation of exons in pre-mRNA splicing requires splice site juxtaposition (splice site pairing), usually involving a 5' splice site and a downstream 3' splice site. Splicing of a 5' splice site to an upstream 3' splice site, however, is predicted to result in a circular RNA. This mode of splice site pairing across the axon has been hypothesized to account for rare RNAs containing scrambled exons (Nigro JM et al., 1991, Celt 64:607-613; Cocquerelle C et al., 1992, EMBO J 11:1 095-1098). Additionally, this mode of splice site pairing has been postulated to explain the formation of SRY circular transcripts in mouse testis (Capel B et al., 1993, Celt 73:1019- 1030). Here we show that splice site pairing across the exon can result in exon circularization in vitro. These results indicate that spliceosome-mediated axon circularization indeed can account for the formation of scrambled exons and circular RNAs. Exon circularization efficiency decreased dramatically as the length of the exon was increased from 95 nt to 274 nt. Circularization of this longer exon was restored, however, when intronic complementary sequences were included in the RNA substrate. These complementary sequences could form a stem that served to bring the splice sites into proximity and thereby promote splice site pairing. Therefore, the splicing of this structured RNA recapitulated SRY-like exon circularization in vitro.

  4. BoLA-DQA、DRB3* exon2多态性及其与奶牛乳房炎的关联分析%Analysis of Polymorphisms of BoLA-DQA and DRB3 * exon2 and the Relationship between the Gene and Mastitis in Dairy Cattle

    Institute of Scientific and Technical Information of China (English)

    高树新; 许尚忠; 李金泉; 高雪; 任红艳; 陈金宝; 马云

    2006-01-01

    采用PCR-SSCP技术,检测到9种中国荷斯坦牛BoLA-DQA*exon2基因基因型、15种BoLA-DRB3*ex-on2基因的基因型和3种单体型,分析比较了各基因型、单体型与奶牛乳房炎的关联性.结果在中国荷斯坦牛中,没有发现与乳房炎易感性或抗性有关联的基因和基因型,但发现DQA-B/DRB3-C、DQA-G/DRB3-F两种单体型可能与奶牛乳房炎易感性有关,而DQB-F/DRB3-E单体型可能与奶牛乳房炎抗性有关.

  5. Tracking the evolution of alternatively spliced exons within the Dscam family

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    Vision Todd J

    2006-02-01

    Full Text Available Abstract Background The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17, potentially generating 38,016 protein isoforms. This degree of transcript diversity has not been found in mammalian homologs of Dscam. We examined the molecular evolution of exons within this gene family to locate the point of divergence for this alternative splicing pattern. Results Using the fruit fly Dscam exons 4, 6, 9 and 17 as seed sequences, we iteratively searched sixteen genomes for homologs, and then performed phylogenetic analyses of the resulting sequences to examine their evolutionary history. We found homologs in the nematode, arthropod and vertebrate genomes, including homologs in several vertebrates where Dscam had not been previously annotated. Among these, only the arthropods contain homologs arranged in tandem arrays indicative of mutually exclusive splicing. We found no homologs to these exons within the Arabidopsis, yeast, tunicate or sea urchin genomes but homologs to several constitutive exons from fly Dscam were present within tunicate and sea urchin. Comparing the rate of turnover within the tandem arrays of the insect taxa (fruit fly, mosquito and honeybee, we found the variants within exons 4 and 17 are well conserved in number and spatial arrangement despite 248–283 million years of divergence. In contrast, the variants within exons 6 and 9 have undergone considerable turnover since these taxa diverged, as indicated by deeply branching taxon-specific lineages. Conclusion Our results suggest that at least one Dscam exon array may be an ancient duplication that predates the divergence of deuterostomes from protostomes but that there is no evidence for the presence of arrays in the common ancestor of vertebrates. The different patterns of conservation and turnover among the Dscam exon arrays

  6. 家兔MITF基因部分外显子多态性的PCR-SSCP分析%PCR-SSCP Polymorphism of Parts of Exons in MITF Gene in Rabbit

    Institute of Scientific and Technical Information of China (English)

    何孟颉; 李挺; 王晓明; 潘雨来; 吴信生

    2012-01-01

    小眼畸形相关转录因子MITF是色素细胞的发育成熟中的重要因子,可调控酪氨酸基因家族的表达,参与黑素生成的调控,从而影响动物的毛色.本实验采用PCR-SSCP技术,检测白色獭兔、海狸色獭兔和闽西南黑兔群体中家兔MITF基因的5个外显子和部分内含子区域的多态性,结果发现,引物1、2、5、7的扩增片段均未表现出多态,在获得的大小为255 bp的引物4扩增片段中发现一个SNP (C43T)位点,在各群体中表现为3种等位基因型AA、BB、AB.测序结果表明第4外显子扩增片段的突变位于5′端的内含子区域,不影响氨基酸序列.统计结果显示,白色獭兔群体不处在哈代温伯格平衡状态(P<0.05),其余群体则均处于平衡状态.闽西南黑兔群体表现出中度多态(0.5>PIC>0.25),其余群体为低度多态.%Microphthalmia-Associtated Transcription Factor plays an important role in the growth of pigment cells,which affects the furriery colors by controling the expression of tyrosinase gene family,and participating the regulation of melanin producting.In this study,the polymorphism five exons and parts of introns of MITF gene were detected by PCR-SSCP in three rabbit populations include White Rex rabbit,Chinchilla Rex rabbit and Minxinan Black rabbit.The results indicated that the primers 1,2,5 and 7 did not display polymorphism,and a 255 bp polymorphism segment was obtained by primer 4.The polymorphism of the segment obtained by primer 4 was controlled by A and B alleles and formed three genotypes, namely AA, BB, AB.The result of cloning and sequencing showed that there was one single nucleotide mutation (C/T) at 43bp in 5'end of the extended segment, and it did not change the encoding amino acid. Statistical results showed that the MITF gene SSCP sites in White rabbite population was at Hardy-Weinberg disequilibrium (PPIC>0.25),others were of low polymorphism.

  7. Exon skipping and Duchenne muscular dystrophy: Hope, hype and how feasible?

    Directory of Open Access Journals (Sweden)

    Wilton Steve

    2008-01-01

    Full Text Available Duchenne muscular dystrophy (DMD, the most common and serious form of childhood muscle wasting is generally caused by protein-truncating mutations in the large DMD gene. Specific removal of an exon from a defective DMD gene transcript has the potential to allow synthesis of a semi-functional dystrophin, thereby reducing the severity and presumably progression of muscle wasting. The efficacy of this treatment will vary greatly between the different mutations that preclude the synthesis of a functional dystrophin. Restoration of the reading frame from a large multi-exon genomic deletion, typically greater than 36 exons, may lead to synthesis of a protein with only partial function and limited clinical benefit, whereas excising a nonsense mutation in a redundant exon should generate a near normal dystrophin. A clinical trial has recently confirmed proof-of-principle that exclusion of Exon 51 from human dystrophin mRNAs, carrying frame-shifting deletions adjacent to this exon, results in dystrophin expression. No major side-effects after local administration of the antisense oligomer were reported. Additional trials are underway, targeting the same exon but using an oligomer of different backbone chemistry. If functional dystrophin synthesis is demonstrated, and safety issues are addressed, subsequent trials will involve systemic delivery. Great challenges are ahead, some technical; establishing an effective delivery regimen, some ethical; choosing subsequent targets for therapy, and others of an administrative and regulatory nature.

  8. PCR-SSCP Detection and DNA Sequence Analysis of MHC-DRB1 Gene Exon 3 in Tibetan Sheep%藏绵羊MHC-DRB1基因第3外显子的PCR-SSCP检测及其序列分析

    Institute of Scientific and Technical Information of China (English)

    徐飞; 成述儒; 刘秀; 王继卿; 胡江; 罗玉柱

    2011-01-01

    为了研究藏绵羊DRB1基因第3外显子多态性,确定其等位基因数、核苷酸多态位点、变异类型和各等位基因间的遗传关系,本研究采用PCR-SSCP方法,分析了500只藏绵羊(Ovis aries )DRB1基因第3外显子多态性,并对不同等位基因进行克隆和测序.结果表明,藏绵羊DRB1基因第3外显子表现了8个等位基因,8个单倍型序列分析发现了15个核苷酸多态位点,与GenBank序列对比分析,有7个DRB1的等位基因是首次发现.8个DRB1第3外显子的单倍型序列NJ系统发育树呈2支分化趋势.3个种群藏绵羊中B均为优势等位基因,该位点PIC> 0.5,为高度多态且显著偏离Hardy-Weinberg平衡状态.研究认为,藏绵羊DRB1基因第3外显子具有丰富的多态性;藏绵羊DRBI基因最初是由2个等位基因突变分化成两大类等位基因.%In order to study DRB1 gene exon 3 polymorphism in Tibetan sheep, The number of alleles, single nucleotide polymorphisms (SNPs) sites, variation type, the genetic relationship and evolutionary significance of the alleles had been analyzed. Variation in the 500 Tibetan sheep (Ovis aries) DRB1 gene exon 3 was investigated by PCR-SSCP method, followed by cloning and DNA sequencing. The results showed that 8 alleles were identified, 15 nucleotide polymorphism sites were identified in 8 sheep DRB1 gene haplotypes and 7 novel DRB1 exon 3 alleles were found comparison with GenBank sequences. The phylogenetic tree results showed that the 8 haplotypes of Tibetan sheep DRB1 exon 3 could divide into two clusters. Allele B was the most common allele in three Tibetan sheep populations, and that allelic and genotype frequency were significantly deviated from Hardy-Weinberg balanced. The polymorphism was higher with PIC more man 0.5 at DRB1 gene exon 8 in three Tibetan sheep populations. The results suggest that Tibetan sheep DRB1 gene exon 3 has high level of sequence polymorphism, Tibetan sheep DRB1 gene is differentiated into two

  9. Genetic Polymorphisms in Exon 4 of IGF2 Gene of Red Cattle and Its Genetic Effects%草原红牛IGF2基因外显子4的遗传多态性及遗传效应分析

    Institute of Scientific and Technical Information of China (English)

    牛伟萍; 刘晶; 张金玉; 张明军; 杨润军; 赵志辉

    2011-01-01

    The method of PCR - SSCP was used to study the genetic polymorphism of IGF2 gene exon 4 in Red Cattle. Using the linear model, the correlations of different genotypes of mutation points with the naked body and meat quality traits was analyzed. The results showed that there is a SNP site (C250G) in exon 4. The gene has two genotypes, AA and AB. In rid fat weight, genotype AB is 3.1% higher than genotype AA( P < 0.05). Meanwhile, in bone weight and eye muscle area, genotype AB is 15.7% and 46.05 % lower than genotype AA, respectively ( P < O. 01). The genetic polymorphism of the IGF2 gene Exon4 probably has direct genetic effects on meat quality traits in Red Cattle.%运用PCR-SSCP方法检测草原红牛IGF2基因第4外显子的多态性,采用最小二乘法拟合线性模型将突变位点的不同基因型与牛胴体和肉质性状进行关联分析.结果表明:在外显子4上有1个SNP位点(C250G),该基因具有AA和AB 2种基因型,草原红牛AB基因型个体肋脂质量比AA基因型个体高3.1%(P<0.05),骨质量和眼肌面积较AA基因型个体分别低15.7%和46.05%(P<0.01).IGF2基因的遗传多态性可能直接影响草原红牛的肉质性状.

  10. Genetic Polymorphism of the Exon 2 of MHC-DQB Gene in Yunnan Humped Cattle%云南高峰牛MHC-DQB基因外显子2遗传多态性分析

    Institute of Scientific and Technical Information of China (English)

    禹文海; 鲁绍雄; 和占龙; 刘红文; 陆润峰; 金建斌

    2011-01-01

    本研究采用PCR直接测序和PCR-RFLP法研究了云南高峰牛MHC-DQB基因外显子2(DQB.2)的遗传多态性,并利用DNAMAN软件分析了云南高峰牛与部分物种DQB.2相应核苷酸序列的同源性.结果发现,共检测到了17个等位基因,其中HaeⅢ酶切位点存在10种基因型,由A、B、C、D和E5个复等位基因控制;RsaⅠ酶切位点存在22种基因型,由A、B、C、D、E、F、G、H、I、J和K共11个复等位基因控制;Taq Ⅰ酶切位点只出现了1种基因型.分析发现,云南高峰牛DQB.2基因的12、25、63、96、106、126、152、156、165、204位的碱基表现出了多态性.所分析的物种该基因片段大小相同均为270 bp,云南高峰牛第224位碱基缺失及236位碱基插入现象.云南高峰牛与人、猪、马、绵羊、黄牛×瘤牛的核苷酸序列的同源性分别为81.4%、83.3%、78.1%、87.7%、86.6%.经x2检验结果表明,HaeⅢ和Taq Ⅰ酶切位点处于Hardy-Weinberg平衡状态(P>0.05),而RsaⅠ酶切位点则未达到Hardy-Weinberg平衡状态(P<0.05).%In this paper, the genetic polymorphism of the exon 2 of MHC-DQB gene was investigated by directly sequencing and PCR-RFLP in Yunnan humped cattle. Homology of the nucleotide acid sequences was analysis by DNAMAN software. The results showed that 17 alleles were found in this experiment, 10 kinds of genotypes and 5 (At B, C. D. E) alleles were found with enzyme Hae Ⅲ;22 kinds of genotypes and 11 (A, B, C, D, E, F, G, H, I, J, K) alleles were found with enzyme Rsa I;ionly one kind of genotype were found with enzyme Taq I . Polymorphic sites were detected at base position 12, 25, 63, 96, 106, 126, 152, 156, 165 and 204. The results showed that there were same lengths (270 bp) of gene fragment in various species, but there was a nucleotide missing at position 224 and a nucleotide insertion at position 236 in Yunnan humped cattle. The homology between Yunnan humped cattle and human, swine, horse, sheep, Yellow

  11. 再生障碍性贫血患者PIG-A基因外显子2、4、5突变及粒细胞CD 55、CD 59的表达%Mutations of PIG-A gene Exons 2,4,5 and Granulocytic Expressions of CD55 and CD59 in Patients with Aplastic Anemia

    Institute of Scientific and Technical Information of China (English)

    李玉云; 昝丽娜; 王卫国

    2009-01-01

    背景与目的:探讨再生障碍性贫血(aplastic anemia,AA)患者PIG-A基因外显子2、4、5的突变及粒细胞表面CD55、CD59锚蛋白表达的情况. 材料与方法:从30例AA患者及20例正常对照组人群外周血提取基因组DNA,采用PCR扩增PIC-A基因外显子2、4、5,再将纯化的PCR产物双向测序检测基因序列;并用流式细胞术检测两组人群外周血粒细胞中CD55、CD59的表达. 结果:30例从患者中11例发现PIG-A基因外显子2突变,包括碱基替代、缺失、插入;PIG-A基因外显子4和外显子5突变各5例,仅为碱基替代;共5例患者有2个或2个以上外显子存在突变,正常对照组未发现突变.粒细胞CD55和CD59的表达率在AA患者PIG-A基因突变者中分别为(86.57 4±5.90)%、(88.174±5.90)%,在PIG-A基因未突变者中分别为(91.874±4.79)%、(94.24±3.76)%.均较正常对照组(97.864±1.52)%、(98.824±1.42)%显著降低(P均<0.05).结论:再生障碍性贫血患者存在PIG-A基因突变和粒细胞CD55、CD59表达缺失的现象,提示再障患者可能存在造血的克隆源性异常.%BACKGROUND AND AIM: To explore mutations of PIG-A gene exon2, exon4, exon5 and expression of CD55 and CD59 in granulocytes of patients with aplastic anemia. MATERIALS AND METHODS: Genomic DNA from peripheral blood of 30 aplastic anemia patients and 20 normal controls were extracted, and PIG-A gene exon2, exon4, exon5 were then examined with polymerase chain reaction (PCR) , nucleotide sequences were analyzed by bidirectional sequencing after PCR products were purified. The expressions of CD55 and CD59 in granulocytes from peripheral blood of the two groups above were detected by flow cytometry. RESULTS: The mutations of PIG-A gene exon2 including base substitution, deletion, insertion occurred in 11 of 30 aplastic anemia patients , the mutations of exon4, exon5 were also found in five aplastic anemia patients, with only base substitution. Two or more exon mutations were found in 5

  12. Genomic V exons from whole genome shotgun data in reptiles.

    Science.gov (United States)

    Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

    2014-08-01

    Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

  13. The Correlation Analysis between Chinese Merino Sheep OLA-DQB1 Gene Exon 2 Genetic Polymorphism and Brucellosis Susceptibility%中国美利奴羊OLA-DQB1基因exon 2遗传多态性与布鲁氏菌病易感性的关联分析

    Institute of Scientific and Technical Information of China (English)

    王文文; 许万云; 胡梦薇; 李建华; 刘朋涛; 高剑峰

    2015-01-01

    本试验采用PCR-SSCP方法对148只布鲁氏菌阴性和60只布鲁氏菌阳性中国美利奴羊白细胞表面抗原DQB1 (OLA-DQB1)基因exon 2单核苷酸多态性(SNPs)进行了检测,之后挑选不同等位基因进行PCR产物测序,旨在确定该基因的多态性位点,并对每个SNP位点的等位基因频率、基因型频率进行统计分析,从而分析其多态性与布鲁氏菌病易感性的相关性.测序结果表明,在270 bp的序列内共检测到43个SNPs,其中G196A位点的等位基因频率在病例组和对照组中的分布存在极显著差异(P<0.01),其基因型频率存在显著差异(P<0.05);C211T位点的等位基因频率在病例组和对照组中存在显著差异(P<0.05).由此表明,OLA-DQB1基因exon 2多态性与中国美利奴羊布鲁氏菌病易感性呈显著相关.

  14. Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA.

    Science.gov (United States)

    Fu, Yan; Bannach, Oliver; Chen, Hao; Teune, Jan-Hendrik; Schmitz, Axel; Steger, Gerhard; Xiong, Liming; Barbazuk, W Brad

    2009-05-01

    Identifying conserved alternative splicing (AS) events among evolutionarily distant species can prioritize AS events for functional characterization and help uncover relevant cis- and trans-regulatory factors. A genome-wide search for conserved cassette exon AS events in higher plants revealed the exonization of 5S ribosomal RNA (5S rRNA) within the gene of its own transcription regulator, TFIIIA (transcription factor for polymerase III A). The 5S rRNA-derived exon in TFIIIA gene exists in all representative land plant species but not in green algae and nonplant species, suggesting it is specific to land plants. TFIIIA is essential for RNA polymerase III-based transcription of 5S rRNA in eukaryotes. Integrating comparative genomics and molecular biology revealed that the conserved cassette exon derived from 5S rRNA is coupled with nonsense-mediated mRNA decay. Utilizing multiple independent Arabidopsis overexpressing TFIIIA transgenic lines under osmotic and salt stress, strong accordance between phenotypic and molecular evidence reveals the biological relevance of AS of the exonized 5S rRNA in quantitative autoregulation of TFIIIA homeostasis. Most significantly, this study provides the first evidence of ancient exaptation of 5S rRNA in plants, suggesting a novel gene regulation model mediated by the AS of an anciently exonized noncoding element.

  15. Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.

    Science.gov (United States)

    Liu, Li-Yu Daisy; Charng, Yuh-Chyang

    2012-01-01

    Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. Previously, we performed the first experimental assessment of TE exonization by inserting a Ds element into each intron of the rice epsps gene. Exonization of Ds in plants was biased toward providing splice donor sites from the beginning of the inserted Ds sequence. Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron. The current study involved genome-wide computational analysis of Ds exonization events in the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). Up to 71% of the exonized transcripts were putative targets for the nonsense-mediated decay (NMD) pathway. The insertion patterns of Ds and the polymorphic splice donor sites increased the transcripts and subsequent protein isoforms. Protein isoforms contain protein sequence due to unspliced intron-TE region and/or a shift of the reading frame. The number of interior protein isoforms would be twice that of C-terminal isoforms, on average. TE exonization provides a promising way for functional expansion of the plant proteome.

  16. Determination of Single Nucleotide Polymorphism of Exon 21 in GARS-AIRS-GART Gene in Three Chicken Breeds%3个鸡种GARS-AIRS-GART基因第21号外显子的SNPs检测

    Institute of Scientific and Technical Information of China (English)

    龚琳琳; 常国斌; 喻礼怀; 徐琪; 栾德琴; 刘艳; 陈国宏

    2011-01-01

    采用PCR-SSCP和DNA测序法对安卡鸡、文昌鸡和如皋鸡中GARS-AIRS-GART基因的第21号外显子进行SNPs检测.结果发现该外显子含4个核苷酸多态位点:G29943A、C29968T、T30011C和C30017T,其中3处为非同义突变,分别为:29 943处天冬氨酸(Asp)→天冬酰胺(Asn)、30 011处色氨酸(Trp)→精氨酸(Arg)、30 017处精氨酸(Arg)→半胱氨酸(Cys);另一处为同义突变.对多态位点进行单倍型分析,发现12种单倍型,其中两种单倍型(5号和6号)的频率超过10%,分别为0.330 0和0.162 8,1号、3号、9号和10号单倍型频率介于1%~10%之间,其余都小于1%.另外共检测到11种基因型,存在5种等位基因,安卡鸡的D和E等位基因的基因频率较高,基因型与其它两个鸡品种之间都存在着极显著的差异(P<0.01),表明我国地方鸡种和外来鸡种在遗传组成上存在着差异.本研究将为鸡肉品质相关研究积累基础数据,为今后深入开展肉品质的开发利用奠定理论基础.%The PCR-SSCP technology and DNA sequencing were conducted to detect single nucleotide polymorphisms (SNPs) of exon 21 in GARS-AIRS-GART genes in three breeds, Wenchang chicken, Rugao chicken and Anka chiken. 4 SNPs were founded, including 1 synonymous mutation, C29968T, and 3 non-synonymous mutations, G29943A, T30011C and C30017T, resulting in amino acid sequence altered from Asp to Asn, Trp to Arg and Arg to Cys, respectively. 12 haplotypes were detected in the 3 chicken breeds. The frequency of number 5 and number 6 haplotypes were 0.330 0 and 0.162 8, respectively, the frequencies of number 1, 3, 9, and 10 haplotype were between l%~10%, and the others were less than 1%. In addition, 11 genotypes and 5 alleles were founded. The alleles of D and E in Anka chicken were higher than that of other two breeds, and there existed significant difference (P<0.01) in genotype distributions between Anka and the other two breeds, Wenchang and Rugao which indicated Chinese local

  17. Determination of Single Nucleotide Polymorphism of Exon 21 in GARS- AIRS-GART Gene in Three Chicken Breeds%3个鸡种GARS-AIRS-GART基因第21号外显子的SNPs检测

    Institute of Scientific and Technical Information of China (English)

    龚琳琳; 常国斌; 喻礼怀; 徐琪; 栾德琴; 刘艳; 陈国宏

    2011-01-01

    The PCR-SSCP technology and DNA sequencing were conducted to detect single nucleotide polymorphisms (SNPs) of exon 21 in GARS-AIRS-GART genes in three breeds, Wenchang chicken, Rugao chicken and Anka chiken. 4 SNPs were founded, including 1 synonymous mutation, C29968T, and 3 non-synonymous muta- tions, G29943A, T30011C and C30017T, resulting in amino acid sequence altered from Asp to Asn, Trp to Arg and Arg to Cys, respectively. 12 haplotypes were detected in the 3 chicken breeds. The frequency of number 5 and number 6 haplotypes were 0.330 0 and 0.162 8, respectively, the frequencies of number 1, 3, 9, and 10 haplotype were between 1%-10%, and the others were less than 1%. In addition, 11 genotypes and 5 alleles were founded. The alleles of D and E in Anka chicken were higher than that of other two breeds, and there existed significant difference (P〈0.01) in genotype distributions between Anka and the other two breeds, Wenchang and Rugao which indicated Chinese local chicken breeds were different from alien breeds in genetic composition. This paper should be provided the base for the study and exploitation of meat quality in chicken.%采用PCR.SSCP和DNA测序法对安卡鸡、文昌鸡和如皋鸡中GARS-AIRS-GART基因的第21号外显子进行SNPs检测。结果发现该外显子含4个核苷酸多态位点:G29943A、C29968T、T30011C和C30017T,其中3处为非同义突变,分别为:29943处天冬氨酸(Asp)→天冬酰胺(Asn)、30011处色氨酸(Trp)→精氨酸(Arg)、30017处精氨酸(Arg)→半胱氨酸(cys);另一处为同义突变。对多态位点进行单倍型分析,发现12种单倍型,其中两种单倍型(5号和6号)的频率超过10%,分别为0.3300和0.1628,1号、3号、9号和10号单倍型频率介于1%~10%之间,其余都小于l%。另外共检测到11种基因型,存在5种等位基因,安卡鸡的D和E等位基因的基因频率较高,基因型与其它两个

  18. Computational analysis and prediction for exons of PAC579 genomic sequence

    Institute of Scientific and Technical Information of China (English)

    黄弋; 覃文新; 万大方; 赵新泰; 顾健人

    2001-01-01

    To isolate the novel genes related to human hepatocellular carcinoma (HCC), we sequenced P1-derived artificial chromosome PAC579 (D17S926 locus) mapped in the minimum LOH (loss of heterozygosity) deletion region of chromosome 17p13.3 in HCC, Four novel genes mapped in this genomic sequence area were isolated and cloned by wet-lab experiments, and the exons of these genes were located. 0-60 kb of this genomic sequence including the genes of interest was scanned with five different computational exon prediction programs as well as four splice site recognition programs. After analyzing and comparing the computationally predicted results with the wet-lab experiment results, some potential exons were predicted in the genomic sequence by using these programs.

  19. Remarkable selective constraints on exonic dinucleotide repeats.

    Science.gov (United States)

    Haasl, Ryan J; Payseur, Bret A

    2014-09-01

    Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome-wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near-absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short-term intolerance for any change to repeat length and a long-term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome--a 10 x CA repeat in fibroblast growth factor receptor-like 1 (FGFRL1)--that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  20. Molecular Diagnosis of Duchenne/Becker Muscular Dystrophy: Analysis of Exons Deletion and Carrier Detection

    Directory of Open Access Journals (Sweden)

    Mohammad Taghi Akbari

    2010-01-01

    Full Text Available Objective: Duchenne and Becker Muscular Dystrophy (DMD and BMD are X-linked conditionsresulting from a defect in the dystrophin gene located at Xp21.2. DMD is the mostfrequent neuromuscular disease in humans (1/3500 male newborns. In approximately65% of DMD and BMD patients, deletions in the dystrophin gene have been identified asthe molecular determinant. The frequency and distribution of dystrophin gene deletions inDMD/BMD patients from different populations are different.The aim of this study was to delineate various types of deleted exons and their frequencyin affected male patients and identification of carrier females by linkage analysis.Materials and Methods: In this study 100 unrelated patients with DMD/BMD were studiedfor intragenic deletions in 28 exons and the promoter region of the dystrophin geneusing multiplex PCR. We also performed linkage analysis within the dystrophin gene utilizing8 short tandem repeat markers.Results: Fifty-two (52% patients showed intragenic deletions. A total of 81% of the deletionswere located at the distal hot spot region (44-55 exons and 19% of the deletionswere located at the proximal region (exon 2-19. The most frequent deleted exons were47(16%, 48 and 46 (11%.Most of the STR markers showed heterozygosity in the families studied. The linkageanalysis was useful for detecting carrier status.Conclusion: The present study suggests that intragenic dystrophin gene deletions occurwith the same frequency in Iranian patients compared with other ethnic groups.

  1. 应用SYBR GreenⅠ实时荧光定量聚合酶链反应检测常染色体隐性遗传早发性帕金森综合征的parkin基因外显子重排突变%Analysis of exon rearrangements in the parkin gene in patients with autosomal recessive early-onset parkinsonism using SYBR Green Ⅰ Real-time PCR

    Institute of Scientific and Technical Information of China (English)

    唐北沙; 严新翔; 聂利珞; 郭纪锋; 张海南; 张学伟; 王磊; 沈璐; 江泓; 夏昆

    2009-01-01

    目的 建立应用SYBR GreenⅠ实时荧光定量聚合酶链反应(Real-time PCR,RT-PCR)检测parkin基因外显子重排突变的技术平台,应用该技术对常染色体隐性遗传早发型帕金森综合征(autosomal recessive early-onset parkinsonism,AREP) 家系进行parkin基因外显子重排突变分析.方法 应用SYBR GreenⅠRT-PCR技术对32个中国AREP家系进行parkin基因外显子重排突变分析.结果 14个家系先证者存在parkin基因外显子重排突变,其中3个为纯合缺失突变、3个为复杂杂合缺失突变和8个杂合缺失突变,未发现外显子重复突变,突变主要累及第2~4号外显子.结论 建立了应用SYBR GreenⅠRT-PCR技术检测parkin基因外显子重排突变的基因检测平台;中国AREP 家系的parkin基因外显子重排突变频率为43.8%,与国外报道相似.%Objective To develop a method of detection exon rearrangements in the parkin gene (PARK2) using SYBR Green Ⅰ real-time PCR and to analyze PARK2 exon rearrangement mutations in families with autosomal recessive early-onset parkinsonism (AREP) using this method. Methods Exon rearrangement in PARK2 was screened by SYBR Green Ⅰ real-time PCR in 32 families with AREP. Results Exon rearrangement mutations were found in 14 families, including 3 compound heterozygous deletions;3 homozygous deletions;and 8 heterozygous deletions. No duplication mutation was found. Hotspot for exon rearrangements clustered in exons 2 through 4. Conclusions We have developed a gene test method using SYBR Green Ⅰ Real-time PCR to detect exon rearrangements in the gene PARK2. The frequency of PARK2 mutation is 43.8% in Chinese families with AREP. This frequency is similar to reported findings in other countries.

  2. Exon Shuffling and Origin of Scorpion Venom Biodiversity

    Directory of Open Access Journals (Sweden)

    Xueli Wang

    2016-12-01

    Full Text Available Scorpion venom is a complex combinatorial library of peptides and proteins with multiple biological functions. A combination of transcriptomic and proteomic techniques has revealed its enormous molecular diversity, as identified by the presence of a large number of ion channel-targeted neurotoxins with different folds, membrane-active antimicrobial peptides, proteases, and protease inhibitors. Although the biodiversity of scorpion venom has long been known, how it arises remains unsolved. In this work, we analyzed the exon-intron structures of an array of scorpion venom protein-encoding genes and unexpectedly found that nearly all of these genes possess a phase-1 intron (one intron located between the first and second nucleotides of a codon near the cleavage site of a signal sequence despite their mature peptides remarkably differ. This observation matches a theory of exon shuffling in the origin of new genes and suggests that recruitment of different folds into scorpion venom might be achieved via shuffling between body protein-coding genes and ancestral venom gland-specific genes that presumably contributed tissue-specific regulatory elements and secretory signal sequences.

  3. CLONING AND ANALYSIS OF SEQUENCES OF MHC-DRB3 EXON2 GENES IN ALXABACTRIAN CAMEL AND SUNIT BACTRIAN CAMEL%阿拉善驼与苏尼特驼MHC-DRB3 exon2基因克隆及序列分析

    Institute of Scientific and Technical Information of China (English)

    亢孝珍; 姜建强; 包花尔; 王瑞; 王秀珍; 李盈; 额尔敦木图

    2015-01-01

    通过DNA测序,分别对两个品种双峰驼MHC-Ⅱ类基因DRB3外显子2的基因序列进行分析.通过序列比对,发现阿拉善双峰驼有83个突变位点,79个多态位点,苏尼特双峰驼有47个突变位点和43个多态位点;两个品种双峰驼共检测到DRB3 exon2的等位基因34种,等位基因的分布具有品种特异性,各等位基因之间存在大量的多态位点.在氨基酸序列中,阿拉善双峰驼共检测到44个变异位点,苏尼特双峰驼检测到25个变异位点;在阿拉善双峰驼氨基酸序列中有11个抗原结合位点,苏尼特双峰驼氨基酸序列中有9个抗原结合位点.

  4. NF1 single and multi-exons copy number variations in neurofibromatosis type 1.

    Science.gov (United States)

    Imbard, Apolline; Pasmant, Eric; Sabbagh, Audrey; Luscan, Armelle; Soares, Magali; Goussard, Philippe; Blanché, Hélène; Laurendeau, Ingrid; Ferkal, Salah; Vidaud, Michel; Pinson, Stéphane; Bellanne-Chantelot, Christine; Vidaud, Dominique; Wolkenstein, Pierre; Parfait, Béatrice

    2015-04-01

    Neurofibromatosis type 1 (NF1) is caused by dominant loss-of-function mutations of the tumor suppressor NF1 containing 57 constitutive coding exons. A huge number of different pathogenic NF1 alterations has been reported. The aim of the present study was to evaluate the usefulness of a multiplex ligation-dependent probe amplification (MLPA) approach in NF1 patients to detect single and multi-exon NF1 gene copy number variations. A genotype-phenotype correlation was then performed in NF1 patients carrying these types of genetic alterations. Among 565 NF1 index cases from the French NF1 cohort, single and multi-exon deletions/duplications screening identified NF1 partial deletions/duplications in 22 patients (~4%) using MLPA analysis. Eight single exon deletions, 11 multiple exons deletions, 1 complex rearrangement and 2 duplications were identified. All results were confirmed using a custom array-CGH. MLPA and custom array-CGH allowed the identification of rearrangements that were missed by cDNA/DNA sequencing or microsatellite analysis. We then performed a targeted next-generation sequencing of NF1 that allowed confirmation of all 22 rearrangements. No clear genotype-phenotype correlations were found for the most clinically significant disease features of NF1 in patients with single and multi-exons NF1 gene copy number changes.

  5. Cloning and Sequence Analysis of 5′Flanking Region and Exon of Inhibin α Precursor Gene in Goats%山羊抑制素α前体基因5′侧翼区及外显子的克隆和序列分析

    Institute of Scientific and Technical Information of China (English)

    何远清; 马晓珂; 张春霞

    2009-01-01

    [Objective] The aim of this study was to reveal the relationship between inihibin (INH) α precursor gene and seasonal reproduction of goats, and investigate the evolutionary conservation of INHα precursor gene. [Method] Cloning and sequence analysis of 5′ flanking region and exon of inihibinα (INHα) precursor gene in twenty ewes between non-seasonal estrous breed (Haimen goats) and seasonal estrous breed (Anhui white goats) was analyzed in this study. [Result] Compared with Anhui white goats, INHα precursor gene in Haimen goats had three SNP but no amino acid change, while its nucleotide homology was 99.7% and amino acid homology was 100%. The nucleotide homology of INHα precursor gene in goat, cattle, pig, person, chicken, horse, rat and dog ranged from 12.7% to 96.5%. [Conclusion] INHα precursor gene tends to be highly conserved in species, and any change of nucleotide and amino acid maybe directly influence the function of the whole gene coding and regulation.

  6. Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

    Directory of Open Access Journals (Sweden)

    Obed Ramírez-Sánchez

    2016-12-01

    Full Text Available Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt]. Streptophyta have on average only ∼5.7 exons of medium size (∼230 nt. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt. Among subcellular compartments, membrane proteins are the largest (∼520 aa, whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240 aa. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

  7. An Exon-Capture System for the Entire Class Ophiuroidea.

    Science.gov (United States)

    Hugall, Andrew F; O'Hara, Timothy D; Hunjan, Sumitha; Nilsen, Roger; Moussalli, Adnan

    2016-01-01

    Exon-capture studies have typically been restricted to relatively shallow phylogenetic scales due primarily to hybridization constraints. Here, we present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures approximately 90% of the 1,552 exon target, across all major lineages of the quarter-billion-year-old extant crown group. Key features of our system are 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map, or align; 2) use of multiple artificial representatives based on ancestral state reconstructions rather than exemplars to improve capture and mapping of the target; 3) mapping reads to a multi-reference alignment; and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences, and sample contamination. The resulting data give a well-resolved tree (currently standing at 417 samples, 275,352 sites, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.

  8. Variants affecting exon skipping contribute to complex traits.

    Directory of Open Access Journals (Sweden)

    Younghee Lee

    Full Text Available DNA variants that affect alternative splicing and the relative quantities of different gene transcripts have been shown to be risk alleles for some Mendelian diseases. However, for complex traits characterized by a low odds ratio for any single contributing variant, very few studies have investigated the contribution of splicing variants. The overarching goal of this study is to discover and characterize the role that variants affecting alternative splicing may play in the genetic etiology of complex traits, which include a significant number of the common human diseases. Specifically, we hypothesize that single nucleotide polymorphisms (SNPs in splicing regulatory elements can be characterized in silico to identify variants affecting splicing, and that these variants may contribute to the etiology of complex diseases as well as the inter-individual variability in the ratios of alternative transcripts. We leverage high-throughput expression profiling to 1 experimentally validate our in silico predictions of skipped exons and 2 characterize the mole