The genetic regulatory signature of type 2 diabetes in human skeletal muscle
Laura J Scott 1, Michael R Erdos 2, Jeroen R Huyghe 1, Ryan P Welch 1, Andrew T Beck 1, Brooke N Wolford 2, Peter S Chines 2, John P Didion 2, Narisu Narisu 2, Heather M Stringham 1, D Leland Taylor 2 3, Anne U Jackson 1, Swarooparani Vadlamudi 4, Lori L Bonnycastle 2, Leena Kinnunen 5, Jouko Saramies 6, Jouko Sundvall 5, Ricardo D'Oliveira Albanus 7, Anna Kiseleva 7, John Hensley 7, Gregory E Crawford 8 9, Hui Jiang 1, Xiaoquan Wen 1, Richard M Watanabe 10 11, Timo A Lakka 12 13 14, Karen L Mohlke 4, Markku Laakso 15 16, Jaakko Tuomilehto 17 18 19 20, Heikki A Koistinen 5 21 22, Michael Boehnke 1, Francis S Collins 2, Stephen C J Parker 7 23
Affiliations
Affiliations
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
- Department of Health, National Institute for Health and Welfare, P.O. Box 30, Helsinki FI-00271, Finland.
- South Karelia Central Hospital, Lappeenranta 53130, Finland.
- Department of Computational Medicine &Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.
- Center for Genomic &Computational Biology, Duke University, Durham, North Carolina 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27708, USA.
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, California 90089, USA.
- Department of Physiology and Biophysics, Keck School of Medicine of USC, Los Angeles, California 90089, USA.
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio FI-00100, Finland.
- Kuopio Research Institute of Exercise Medicine, Kuopio FI-00100, Finland.
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio FI-00100, Finland.
- Department of Medicine, University of Eastern Finland, Kuopio FI-00100, Finland.
- Kuopio University Hospital, Kuopio FI-00100, Finland.
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, P.O. Box 30, Helsinki FI-00271, Finland.
- Center for Vascular Prevention, Danube University Krems, Krems 3500, Austria.
- Diabetes Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
- Dasman Diabetes Institute, Dasman 15461, Kuwait.
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, P.O. Box 340, Haartmaninkatu 4, Helsinki FI-00029, Finland.
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki FI-00290, Finland.
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Abstract
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.
Figures
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