Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci

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-se...

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Autores principales:	Hannah J. Perrin, Kevin W. Currin, Swarooparani Vadlamudi, Gautam K. Pandey, Kenneth K. Ng, Martin Wabitsch, Markku Laakso, Michael I. Love, Karen L. Mohlke
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/18b6484704474b5f9bc3936b6a808459
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id	oai:doaj.org-article:18b6484704474b5f9bc3936b6a808459
record_format	dspace
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Hannah J. Perrin Kevin W. Currin Swarooparani Vadlamudi Gautam K. Pandey Kenneth K. Ng Martin Wabitsch Markku Laakso Michael I. Love Karen L. Mohlke Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
description	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 human 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 human subcutaneous adipose tissue samples. We identified 58,387 context-dependent chromatin accessibility peaks and 3,090 context-dependent genes between all timepoint comparisons (log2 fold change>1, FDR<5%) with 15,919 adipocyte- and 18,244 preadipocyte-dependent peaks. Adipocyte-dependent peaks showed increased overlap (60.1%) with Roadmap Epigenomics adipocyte nuclei enhancers compared to 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 context-dependent gene expression. Of 16,167 context-dependent peaks linked to a gene, 5,145 were linked by two or more strategies to 1,670 genes. Among GWAS loci for cardiometabolic traits, adipocyte-dependent peaks, but not preadipocyte-dependent peaks, showed significant enrichment (LD score regression P<0.005) for waist-to-hip ratio and modest enrichment (P < 0.05) for HDL-cholesterol. We identified 659 peaks linked to 503 genes by two or more approaches and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. To identify variants that may alter chromatin accessibility between timepoints, we identified 582 variants in 454 context-dependent peaks that demonstrated allelic imbalance in accessibility (FDR<5%), of which 55 peaks also overlapped GWAS variants. 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. Author summary Cardiovascular and metabolic diseases are widespread, and an increased understanding of genetic mechanisms behind these diseases could improve treatment. Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and genetic mechanisms for disease traits. A relevant context for cardiovascular and metabolic disease traits is adipocyte differentiation. To identify regulatory elements and genes that display differences in activity during adipocyte differentiation, we profiled chromatin accessibility and gene expression in a human cell model of preadipocytes and adipocytes. We identified chromatin regions that change accessibility during differentiation and predicted genes they may affect. We also linked these chromatin regions to genetic variants associated with risk of disease. At one genomic region linked to fatty acids, a chromatin region more accessible in adipocytes linked to a fatty acid synthesis gene and exhibited allelic differences in transcriptional activity in adipocytes but not preadipocytes. These results demonstrate that chromatin regions and genes that change during cell context can guide discovery of regulatory variants and aid identification of disease mechanisms.
format	article
author	Hannah J. Perrin Kevin W. Currin Swarooparani Vadlamudi Gautam K. Pandey Kenneth K. Ng Martin Wabitsch Markku Laakso Michael I. Love Karen L. Mohlke
author_facet	Hannah J. Perrin Kevin W. Currin Swarooparani Vadlamudi Gautam K. Pandey Kenneth K. Ng Martin Wabitsch Markku Laakso Michael I. Love Karen L. Mohlke
author_sort	Hannah J. Perrin
title	Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
title_short	Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
title_full	Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
title_fullStr	Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
title_full_unstemmed	Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
title_sort	chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic gwas loci
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/18b6484704474b5f9bc3936b6a808459
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spelling	oai:doaj.org-article:18b6484704474b5f9bc3936b6a8084592021-11-11T06:20:07ZChromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci1553-73901553-7404https://doaj.org/article/18b6484704474b5f9bc3936b6a8084592021-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8570510/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Chromatin 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 human 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 human subcutaneous adipose tissue samples. We identified 58,387 context-dependent chromatin accessibility peaks and 3,090 context-dependent genes between all timepoint comparisons (log2 fold change>1, FDR<5%) with 15,919 adipocyte- and 18,244 preadipocyte-dependent peaks. Adipocyte-dependent peaks showed increased overlap (60.1%) with Roadmap Epigenomics adipocyte nuclei enhancers compared to 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 context-dependent gene expression. Of 16,167 context-dependent peaks linked to a gene, 5,145 were linked by two or more strategies to 1,670 genes. Among GWAS loci for cardiometabolic traits, adipocyte-dependent peaks, but not preadipocyte-dependent peaks, showed significant enrichment (LD score regression P<0.005) for waist-to-hip ratio and modest enrichment (P < 0.05) for HDL-cholesterol. We identified 659 peaks linked to 503 genes by two or more approaches and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. To identify variants that may alter chromatin accessibility between timepoints, we identified 582 variants in 454 context-dependent peaks that demonstrated allelic imbalance in accessibility (FDR<5%), of which 55 peaks also overlapped GWAS variants. 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. Author summary Cardiovascular and metabolic diseases are widespread, and an increased understanding of genetic mechanisms behind these diseases could improve treatment. Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and genetic mechanisms for disease traits. A relevant context for cardiovascular and metabolic disease traits is adipocyte differentiation. To identify regulatory elements and genes that display differences in activity during adipocyte differentiation, we profiled chromatin accessibility and gene expression in a human cell model of preadipocytes and adipocytes. We identified chromatin regions that change accessibility during differentiation and predicted genes they may affect. We also linked these chromatin regions to genetic variants associated with risk of disease. At one genomic region linked to fatty acids, a chromatin region more accessible in adipocytes linked to a fatty acid synthesis gene and exhibited allelic differences in transcriptional activity in adipocytes but not preadipocytes. These results demonstrate that chromatin regions and genes that change during cell context can guide discovery of regulatory variants and aid identification of disease mechanisms.Hannah J. PerrinKevin W. CurrinSwarooparani VadlamudiGautam K. PandeyKenneth K. NgMartin WabitschMarkku LaaksoMichael I. LoveKaren L. MohlkePublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 10 (2021)

Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci

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