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  • 1
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    Understanding mechanisms underlying human gene expression variation with RNA sequencing (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-12
    Description: Understanding the genetic mechanisms underlying natural variation in gene expression is a central goal of both medical and evolutionary genetics, and studies of expression quantitative trait loci (eQTLs) have become an important tool for achieving this goal. Although all eQTL studies so far have assayed messenger RNA levels using expression microarrays, recent advances in RNA sequencing enable the analysis of transcript variation at unprecedented resolution. We sequenced RNA from 69 lymphoblastoid cell lines derived from unrelated Nigerian individuals that have been extensively genotyped by the International HapMap Project. By pooling data from all individuals, we generated a map of the transcriptional landscape of these cells, identifying extensive use of unannotated untranslated regions and more than 100 new putative protein-coding exons. Using the genotypes from the HapMap project, we identified more than a thousand genes at which genetic variation influences overall expression levels or splicing. We demonstrate that eQTLs near genes generally act by a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within and near the consensus splice sites. Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089435/" 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/PMC3089435/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pickrell, Joseph K -- Marioni, John C -- Pai, Athma A -- Degner, Jacob F -- Engelhardt, Barbara E -- Nkadori, Everlyne -- Veyrieras, Jean-Baptiste -- Stephens, Matthew -- Gilad, Yoav -- Pritchard, Jonathan K -- GM077959/GM/NIGMS NIH HHS/ -- MH084703-01/MH/NIMH NIH HHS/ -- R01 GM077959/GM/NIGMS NIH HHS/ -- R01 GM077959-05/GM/NIGMS NIH HHS/ -- R01 MH084703/MH/NIMH NIH HHS/ -- R01 MH084703-02/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Apr 1;464(7289):768-72. doi: 10.1038/nature08872. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, The University of Chicago, Chicago 60637, USA. pickrell@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220758" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group/genetics ; Alleles ; Consensus Sequence/genetics ; DNA, Complementary/genetics ; Exons/genetics ; *Gene Expression Profiling ; Gene Expression Regulation/*genetics ; Genetic Variation/*genetics ; Humans ; Nigeria ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; RNA Splice Sites/genetics ; RNA, Messenger/*analysis/*genetics ; Sequence Analysis, RNA ; Transcription, Genetic/*genetics
    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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  • 2
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    DNase I sensitivity QTLs are a major determinant of human expression variation (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-02-07
    Description: The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool for linking genetic variation to changes in gene regulation. However, it remains difficult to identify the causal variants underlying eQTLs, and little is known about the regulatory mechanisms by which they act. Here we show that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to gene expression differences among humans. We used DNase I sequencing to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available. We obtained a total of 2.7 billion uniquely mapped DNase I-sequencing (DNase-seq) reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 8,902 locations at which the DNase-seq read depth correlated significantly with genotype at a nearby single nucleotide polymorphism or insertion/deletion (false discovery rate = 10%). We call such variants 'DNase I sensitivity quantitative trait loci' (dsQTLs). We found that dsQTLs are strongly enriched within inferred transcription factor binding sites and are frequently associated with allele-specific changes in transcription factor binding. A substantial fraction (16%) of dsQTLs are also associated with variation in the expression levels of nearby genes (that is, these loci are also classified as eQTLs). Conversely, we estimate that as many as 55% of eQTL single nucleotide polymorphisms are also dsQTLs. Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501342/" 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/PMC3501342/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Degner, Jacob F -- Pai, Athma A -- Pique-Regi, Roger -- Veyrieras, Jean-Baptiste -- Gaffney, Daniel J -- Pickrell, Joseph K -- De Leon, Sherryl -- Michelini, Katelyn -- Lewellen, Noah -- Crawford, Gregory E -- Stephens, Matthew -- Gilad, Yoav -- Pritchard, Jonathan K -- HG006123/HG/NHGRI NIH HHS/ -- MH084703/MH/NIMH NIH HHS/ -- MH090951/MH/NIMH NIH HHS/ -- R01 HG006123/HG/NHGRI NIH HHS/ -- R01 HG006123-01/HG/NHGRI NIH HHS/ -- R01 HG006123-02/HG/NHGRI NIH HHS/ -- R01 MH090951/MH/NIMH NIH HHS/ -- R01 MH090951-01/MH/NIMH NIH HHS/ -- R01 MH090951-02/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22307276" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/genetics/metabolism ; *DNA Footprinting ; Deoxyribonuclease I/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation/*genetics ; Genetic Variation/*genetics ; Genome, Human/genetics ; Humans ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/*genetics ; Sequence Analysis, DNA ; Transcription Factors/metabolism
    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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  • 3
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    Identification of genetic variants that affect histone modifications in human cells (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-10-19
    Description: Histone modifications are important markers of function and chromatin state, yet the DNA sequence elements that direct them to specific genomic locations are poorly understood. Here, we identify hundreds of quantitative trait loci, genome-wide, that affect histone modification or RNA polymerase II (Pol II) occupancy in Yoruba lymphoblastoid cell lines (LCLs). In many cases, the same variant is associated with quantitative changes in multiple histone marks and Pol II, as well as in deoxyribonuclease I sensitivity and nucleosome positioning. Transcription factor binding site polymorphisms are correlated overall with differences in local histone modification, and we identify specific transcription factors whose binding leads to histone modification in LCLs. Furthermore, variants that affect chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947669/" 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/PMC3947669/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McVicker, Graham -- van de Geijn, Bryce -- Degner, Jacob F -- Cain, Carolyn E -- Banovich, Nicholas E -- Raj, Anil -- Lewellen, Noah -- Myrthil, Marsha -- Gilad, Yoav -- Pritchard, Jonathan K -- GM007197/GM/NIGMS NIH HHS/ -- HG006123/HG/NHGRI NIH HHS/ -- HG007036/HG/NHGRI NIH HHS/ -- MH084703/MH/NIMH NIH HHS/ -- R01 HG006123/HG/NHGRI NIH HHS/ -- R01 MH084703/MH/NIMH NIH HHS/ -- T32 GM007197/GM/NIGMS NIH HHS/ -- U01 HG007036/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):747-9. doi: 10.1126/science.1242429. Epub 2013 Oct 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136359" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites/genetics ; Cell Line, Tumor ; Cells/metabolism ; Chromatin/chemistry/genetics/metabolism ; *Gene Expression Regulation ; *Genetic Variation ; Genome, Human ; Histones/chemistry/genetics/*metabolism ; Humans ; Polymorphism, Genetic ; Promoter Regions, Genetic ; Protein Processing, Post-Translational/*genetics ; Quantitative Trait Loci ; RNA Polymerase II/chemistry/*metabolism ; Transcription Factors/genetics/*metabolism
    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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  • 4
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    The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-12-02
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Extreme adaptation seen in snake genomes [Evolution] (2013)
    National Academy of Sciences
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    Publication Date: 2013-12-18
    Description: Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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