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Scott, Laura J; Erdos, Michael R; Huyghe, Jeroen R; Welch, Ryan P; Beck, Andrew T; Wolford, Brooke N; Chines, Peter S; Didion, John P; Narisu, Narisu; Stringham, Heather M; Taylor, D Leland; Jackson, Anne U; Vadlamudi, Swarooparani; Bonnycastle, Lori L; Kinnunen, Leena; Saramies, Jouko; Sundvall, Jouko; Albanus, Ricardo D'Oliveira; Kiseleva, Anna; Hensley, John; Crawford, Gregory E; Jiang, Hui; Wen, Xiaoquan; Watanabe, Richard M; Lakka, Timo A; Mohlke, Karen L; Laakso, Markku; Tuomilehto, Jaakko; Koistinen, Heikki A; Boehnke, Michael; Collins, Francis S; Parker, Stephen C J
Nature communications, 06/2016, Volume: 7, Issue: 1Journal Article
Type 2 diabetes (T2D) results from the combined effects of genetic and environmental factors on multiple tissues over time. Of the >100 variants associated with T2D and related traits in genome-wide association studies (GWAS), >90% occur in non-coding regions, suggesting a strong regulatory component to T2D risk. Here to understand how T2D status, metabolic traits and genetic variation influence gene expression, we analyse skeletal muscle biopsies from 271 well-phenotyped Finnish participants with glucose tolerance ranging from normal to newly diagnosed T2D. We perform high-depth strand-specific mRNA-sequencing and dense genotyping. Computational integration of these data with epigenome data, including ATAC-seq on skeletal muscle, and transcriptome data across diverse tissues reveals that the tissue-specific genetic regulatory architecture of skeletal muscle is highly enriched in muscle stretch/super enhancers, including some that overlap T2D GWAS variants. In one such example, T2D risk alleles residing in a muscle stretch/super enhancer are linked to increased expression and alternative splicing of muscle-specific isoforms of ANK1.
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