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Variation in chromatin accessibility is a key determinant of heritable variation in gene expression

ABSTRACT: While it is well established that variation in gene expression levels can be influenced by single nucleotide polymorphisms (SNPs), little is known about the regulatory mechanisms by which this occurs. To address this gap, we used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (LCLs), for which genome-wide genotypes and estimates of gene expression levels based on RNA-sequencing are also available. We obtained a total of 2.8 billion uniquely mapped DNase-seq reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 7,759 locations at which DNase-seq read depth correlates significantly with variation at a nearby SNP or indel (FDR=10%). We call such variants 'chromatin accessibility Quantitative Trait Loci' (or caQTLs). Most caQTLs lie within or very near the target DNaseI hypersensitive sites, and they are strongly enriched within inferred transcription factor binding sites. We find that a substantial fraction (14%) of caQTLs are also significantly associated with variation in the expression levels of nearby genes (namely, these loci are also classified as eQTLs), suggesting that changes in chromatin accessibility or transcription factor binding frequently lead to gene expression changes. Conversely, 12% of eQTL SNPs are also classified as caQTLs and, accounting for incomplete power, we estimate that the true fraction may be as high as 41%. Our observations indicate that caQTLs are abundant in the human genome, and are likely to be significant contributors to phenotypic variation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31388 | GEO | 2012/01/26

SECONDARY ACCESSION(S): PRJNA145917

REPOSITORIES: GEO

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Variation in chromatin accessibility is a key determinant of heritable variation in gene expression

Project description:While it is well established that variation in gene expression levels can be influenced by single nucleotide polymorphisms (SNPs), little is known about the regulatory mechanisms by which this occurs. To address this gap, we used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (LCLs), for which genome-wide genotypes and estimates of gene expression levels based on RNA-sequencing are also available. We obtained a total of 2.8 billion uniquely mapped DNase-seq reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 7,759 locations at which DNase-seq read depth correlates significantly with variation at a nearby SNP or indel (FDR=10%). We call such variants 'chromatin accessibility Quantitative Trait Loci' (or caQTLs). Most caQTLs lie within or very near the target DNaseI hypersensitive sites, and they are strongly enriched within inferred transcription factor binding sites. We find that a substantial fraction (14%) of caQTLs are also significantly associated with variation in the expression levels of nearby genes (namely, these loci are also classified as eQTLs), suggesting that changes in chromatin accessibility or transcription factor binding frequently lead to gene expression changes. Conversely, 12% of eQTL SNPs are also classified as caQTLs and, accounting for incomplete power, we estimate that the true fraction may be as high as 41%. Our observations indicate that caQTLs are abundant in the human genome, and are likely to be significant contributors to phenotypic variation. DNaseI-Seq on 70 YRI Hapmap cell lines. Each individual sequenced on several lanes of a flow cell on the Illumina Genome Analyzer II

2012-01-26 | E-GEOD-31388 | biostudies-arrayexpress

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq]

Project description:DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 *cis* methylation QTLs (meQTLs), i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs. Whole genomic DNA from 10 Yoruba HapMap individuals and spiked in unmethylated lambda phage DNA was bisuflite converted using the Invitrogen MethylCode Bisulfite Conversion Kit and sequenced using a Illumina HiSeq 2000

2014-05-09 | E-GEOD-57471 | biostudies-arrayexpress

Detection of chromatin accessibility in WT and SRC-2-/- mice in liver

Project description:We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq. In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10. DNase-Seq was carried out in WT and SRC-2-/- mice in liver at CT10 using two doses of DNaseI.

2015-12-07 | E-GEOD-67859 | biostudies-arrayexpress

Kidney on a Chip

Project description:<p>We generated primary cultures from mechanically isolated kidney glomeruli (filtration unit of the nephron) which are composed of podocytes and mesangial cells. In parallel, we generated primary kidney cortex tubule cell cultures, which are composed primarily of proximal tubule cells. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-Seq) and gene expression profiling (RNA-Seq). We found thousands of dynamically regulated enhancers in both cell types that potentially regulate nearby and distal target genes that are differentially expressed. These data will be useful for understanding the epigenomic regulation of gene transcription in key kidney cell types.</p>

| phs001720 | dbGaP

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]

2014-05-09 | GSE57481 | GEO

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq]

2014-05-09 | GSE57471 | GEO

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels

Project description:This SuperSeries is composed of the SubSeries listed below. DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 *cis* methylation QTLs (meQTLs), i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.

2014-05-09 | GSE57483 | GEO

Chromatin Accessibility Reveals Insight into Androgen Receptor Activation and Transcriptional Specificity

Project description:Using DNase-seq, mRNA-seq and publicly available ChIP-seq data sets, we examined the role of chromatin accessibility (DNase-seq) in androgen receptor binding to the genome (ChIP-seq) and AR-mediated transcriptional changes (mRNA-seq). Our data reveals genome-wide changes in chromatin structure that correspond to AR binding and differential gene expression. A focused examination of DNase-seq data around androgen receptor motifs within androgen receptor ChIP-seq peaks reveals distinct patterns of protection from DNaseI cleavage. Examination of chromatin accessibility (DNase-seq), AR binding (AR ChIP-seq), and transcription (mRNA-seq) in LNCaP cells before and after 12 hours of 1 nM R1881 treatment This Series represents the RNA-Seq data only. Exon microarray data generated under the same conditions is available through GSE15805. The DNase-seq data is publicly available through GSE32970 as well as the UCSC genome browser (genome.ucsc.edu) under Regulation::ENCODE DNase/FAIRE::Duke DNaseI HS:LNCaP and LNCaP + Andro. The accession numbers for the ChIP-seq experiments used are GSE14097 and GSE28126.

2012-08-14 | E-GEOD-34780 | biostudies-arrayexpress

TE-associated chromatin variation in mice livers

Project description:Chromatin accessibility is a hallmark of active regulatory function in the genome and variation of chromatin accessibility across individuals has been shown to contribute to complex traits and disease susceptibility. However, the mechanisms responsible for chromatin variation among different individuals and how this variation contributes to phenotypic diversity remain poorly understood. We examined chromatin accessibility variation in liver tissue from seven strains of adult mice that have phenotypic diversity in response to a high-fat/high-sucrose diet. Remarkably, nearly 40% of the loci with the greatest degree of chromatin variability across the strains are associated with transposable elements (TEs), with evolutionarily younger TEs being particularly enriched for regions of chromatin variation. We found that evolutionary younger and older TEs have differential chromatin accessibility profiles and are enriched for binding sites of different transcription factors, indicating the role of TEs in the evolution of regulatory networks in the liver. We also demonstrate that TE polymorphisms and epigenetic regulation of TEs contribute to regulatory variation across different strains through providing binding sites for liver transcription factors. Intriguingly, variable chromatin loci that are associated with liver metabolism are primarily TE-associated. We demonstrate that TEs contribute to regulatory variation in liver and have downstream effects on metabolism. Our data reveal TEs as a novel and important contributor to regulatory and phenotypic variation in the liver and suggest that regulatory variation at TEs is a major contributor to phenotypic variation in populations. Examination of chromatin accessibility with FAIRE-seq in livers of male mice (A/J, AKR/J, BALB/cJ, C57BL/6J, C3H/HeJ, CBA/J, DBA/2J, BXH2/TyJ, and BXH19/TyJ) fed a high-fat, high-sucrose diet.

2016-07-14 | E-GEOD-75770 | biostudies-arrayexpress

Chromatin Accessibility Reveals Insight into Androgen Receptor Activation and Transcriptional Specificity

2012-08-14 | GSE34780 | GEO

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