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  • 1
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    Common regulatory variation impacts gene expression in a cell type-dependent manner (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-01
    Description: Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 individuals. We detected cell type-specific genetic effects, with 69 to 80% of regulatory variants operating in a cell type-specific manner, and identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type-specific eQTLs were found at larger distances from genes and at lower effect size, similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867218/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867218/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dimas, Antigone S -- Deutsch, Samuel -- Stranger, Barbara E -- Montgomery, Stephen B -- Borel, Christelle -- Attar-Cohen, Homa -- Ingle, Catherine -- Beazley, Claude -- Gutierrez Arcelus, Maria -- Sekowska, Magdalena -- Gagnebin, Marilyne -- Nisbett, James -- Deloukas, Panos -- Dermitzakis, Emmanouil T -- Antonarakis, Stylianos E -- 077011/Wellcome Trust/United Kingdom -- 077046/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Sep 4;325(5945):1246-50. doi: 10.1126/science.1174148. Epub 2009 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19644074" target="_blank"〉PubMed〈/a〉
    Keywords: Allelic Imbalance ; B-Lymphocytes ; Cell Line ; Enhancer Elements, Genetic ; Fibroblasts ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Frequency ; Genotype ; Humans ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; RNA, Messenger/genetics/metabolism ; *Regulatory Elements, Transcriptional ; Statistics, Nonparametric ; T-Lymphocytes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-19
    Description: DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation, we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-range, and long-range allelic coordination among the studied molecular phenotypes. We observed genetic influence on most of these phenotypes, with histone modifications exhibiting strong context-dependent behavior. Our results implicate transcription factors as primary mediators of sequence-specific regulation of gene expression programs, with histone modifications frequently reflecting the primary regulatory event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kilpinen, Helena -- Waszak, Sebastian M -- Gschwind, Andreas R -- Raghav, Sunil K -- Witwicki, Robert M -- Orioli, Andrea -- Migliavacca, Eugenia -- Wiederkehr, Michael -- Gutierrez-Arcelus, Maria -- Panousis, Nikolaos I -- Yurovsky, Alisa -- Lappalainen, Tuuli -- Romano-Palumbo, Luciana -- Planchon, Alexandra -- Bielser, Deborah -- Bryois, Julien -- Padioleau, Ismael -- Udin, Gilles -- Thurnheer, Sarah -- Hacker, David -- Core, Leighton J -- Lis, John T -- Hernandez, Nouria -- Reymond, Alexandre -- Deplancke, Bart -- Dermitzakis, Emmanouil T -- GM25232/GM/NIGMS NIH HHS/ -- HG004845/HG/NHGRI NIH HHS/ -- R01 HG004845/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):744-7. doi: 10.1126/science.1242463. Epub 2013 Oct 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136355" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Base Sequence/genetics ; Binding Sites/genetics ; Chromatin/chemistry/*metabolism ; DNA/chemistry/*metabolism ; *Gene Expression Regulation ; *Genetic Variation ; Histones/chemistry/metabolism ; Humans ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Transcription Factors/*metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Transcriptome genetics using second generation sequencing in a Caucasian population (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-12
    Description: Gene expression is an important phenotype that informs about genetic and environmental effects on cellular state. Many studies have previously identified genetic variants for gene expression phenotypes using custom and commercially available microarrays. Second generation sequencing technologies are now providing unprecedented access to the fine structure of the transcriptome. We have sequenced the mRNA fraction of the transcriptome in 60 extended HapMap individuals of European descent and have combined these data with genetic variants from the HapMap3 project. We have quantified exon abundance based on read depth and have also developed methods to quantify whole transcript abundance. We have found that approximately 10 million reads of sequencing can provide access to the same dynamic range as arrays with better quantification of alternative and highly abundant transcripts. Correlation with SNPs (small nucleotide polymorphisms) leads to a larger discovery of eQTLs (expression quantitative trait loci) than with arrays. We also detect a substantial number of variants that influence the structure of mature transcripts indicating variants responsible for alternative splicing. Finally, measures of allele-specific expression allowed the identification of rare eQTLs and allelic differences in transcript structure. This analysis shows that high throughput sequencing technologies reveal new properties of genetic effects on the transcriptome and allow the exploration of genetic effects in cellular processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836232/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836232/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Montgomery, Stephen B -- Sammeth, Micha -- Gutierrez-Arcelus, Maria -- Lach, Radoslaw P -- Ingle, Catherine -- Nisbett, James -- Guigo, Roderic -- Dermitzakis, Emmanouil T -- 077046/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 1;464(7289):773-7. doi: 10.1038/nature08903. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211 Switzerland. stephen.montgomery@unige.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220756" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Alternative Splicing/genetics ; European Continental Ancestry Group/*genetics ; Exons/genetics ; Gene Expression Profiling/*methods ; Haplotypes/genetics ; Homozygote ; Humans ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/*analysis/*genetics ; Sequence Analysis, DNA/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies (2010)
    Oxford University Press
    Details
    Publication Date: 2010-08-10
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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