DOI: 10.1101/475483Nov 23, 2018Paper

Interpreting coronary artery disease risk through gene-environment interactions in gene regulation

BioRxiv : the Preprint Server for Biology
Anthony FindleyFrancesca Luca

Abstract

GWAS and eQTL studies identified thousands of genetic variants associated with complex traits and gene expression. Despite the important role of environmental exposures in complex traits, only a limited number of environmental factors are measured in these studies. Measuring molecular phenotypes in tightly controlled cellular environments provides a more tractable setting to study gene-environment interactions in the absence of other confounding variables. We performed RNA-seq and ATAC-seq in endothelial cells exposed to retinoic acid, dexamethasone, caffeine, and selenium to model genetic and environmental effects on gene regulation in the vascular endothelium, a common site of pathology in cardiovascular disease. We found that genes near regions of differentially accessible chromatin were more likely to be differentially expressed (OR = [3.41, 6.52], p < 10^-16). Furthermore, we confirmed that environment-specific changes in transcription factor binding are a key mechanism for cellular response to environmental stimuli. SNPs in these transcription response factor footprints for dexamethasone, caffeine, and retinoic acid were enriched in GTEx eQTLs from artery tissues indicating that these environmental conditions are latently...Continue Reading

Related Concepts

Caffeine
Cardiovascular Diseases
Chromatin
Dexamethasone
Endothelium, Vascular
Environment
Gene Expression
Genes
Pathology
Retinoids

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