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Status |
Public on Aug 01, 2021 |
Title |
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci [ATAC-seq] |
Organism |
Homo sapiens |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 subcutaneous adipose tissue samples. A set of 15,919 adipocyte-dependent peaks showed stronger enrichment (60.1%) of adipocyte nuclei enhancers than 51,855 adipose tissue peaks (44.6%) or 18,244 preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and differential gene expression. Of 16,167 context-dependent peaks that could be linked to a gene, 5,184 were linked by two or more strategies to 1,675 genes. Among GWAS loci for cardiometabolic traits, adipocyte peaks showed the strongest enrichment for waist-to-hip ratio, coronary artery disease, and HDL-cholesterol, while adipose tissue peaks also showed significant enrichment for LDL-cholesterol and triglyceride levels. We identified 666 peaks linked to 507 genes by two or more methods and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P=0.003) but not preadipocytes (P=0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms.
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Overall design |
ATAC-seq on SGBS preadipocytes and adipocytes at days 0, 2, 4, and 14 of differentiation and bulk adipose tissue from 17 individuals **Please note that the 'adiposeTissue' raw data require controlled access and thus are not provided****
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Contributor(s) |
Perrin HJ, Currin KW, Vadlamudi S, Pandey GK, Ng KK, Wabitsch M, Laakso M, Love MI, Mohlke KL |
Citation missing |
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Submission date |
Jun 23, 2021 |
Last update date |
Aug 02, 2021 |
Contact name |
Karen L Mohlke |
E-mail(s) |
mohlke@med.unc.edu
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Organization name |
University of North Carolina at Chapel Hill
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Department |
Genetics
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Street address |
120 Mason Farm Road
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City |
Chapel Hill |
State/province |
NC |
ZIP/Postal code |
27599-7264 |
Country |
USA |
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Platforms (2) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (44)
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This SubSeries is part of SuperSeries: |
GSE178796 |
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci |
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Relations |
BioProject |
PRJNA740464 |
SRA |
SRP325411 |
Supplementary file |
Size |
Download |
File type/resource |
GSE178794_DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData.gz |
69.7 Mb |
(ftp)(http) |
RDATA |
GSE178794_RAW.tar |
23.0 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
GSE178794_SGBS-day0_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
GSE178794_SGBS-day14_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
GSE178794_SGBS-day2_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
GSE178794_SGBS-day4_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
GSE178794_adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz |
594.7 Kb |
(ftp)(http) |
BED |
GSE178794_adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz |
913.6 Kb |
(ftp)(http) |
BED |
GSE178794_mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz |
2.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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