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The genetic regulatory signature of type 2 diabetes in human skeletal muscle.

Publication ,  Journal Article
Scott, LJ; Erdos, MR; Huyghe, JR; Welch, RP; Beck, AT; Wolford, BN; Chines, PS; Didion, JP; Narisu, N; Stringham, HM; Taylor, DL; Jackson, AU ...
Published in: Nat Commun
June 29, 2016

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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Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

June 29, 2016

Volume

7

Start / End Page

11764

Location

England

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA, Messenger
  • Polymorphism, Single Nucleotide
  • Muscle, Skeletal
  • Male
  • Humans
  • Genome-Wide Association Study
  • Genetic Predisposition to Disease
  • Gene Expression Regulation
  • Female
 

Citation

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Scott, L. J., Erdos, M. R., Huyghe, J. R., Welch, R. P., Beck, A. T., Wolford, B. N., … Parker, S. C. J. (2016). The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Nat Commun, 7, 11764. https://doi.org/10.1038/ncomms11764
Scott, Laura J., Michael R. Erdos, Jeroen R. Huyghe, Ryan P. Welch, Andrew T. Beck, Brooke N. Wolford, Peter S. Chines, et al. “The genetic regulatory signature of type 2 diabetes in human skeletal muscle.Nat Commun 7 (June 29, 2016): 11764. https://doi.org/10.1038/ncomms11764.
Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, et al. The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Nat Commun. 2016 Jun 29;7:11764.
Scott, Laura J., et al. “The genetic regulatory signature of type 2 diabetes in human skeletal muscle.Nat Commun, vol. 7, June 2016, p. 11764. Pubmed, doi:10.1038/ncomms11764.
Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, Chines PS, Didion JP, Narisu N, Stringham HM, Taylor DL, Jackson AU, Vadlamudi S, Bonnycastle LL, Kinnunen L, Saramies J, Sundvall J, Albanus RD, Kiseleva A, Hensley J, Crawford GE, Jiang H, Wen X, Watanabe RM, Lakka TA, Mohlke KL, Laakso M, Tuomilehto J, Koistinen HA, Boehnke M, Collins FS, Parker SCJ. The genetic regulatory signature of type 2 diabetes in human skeletal muscle. Nat Commun. 2016 Jun 29;7:11764.

Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

June 29, 2016

Volume

7

Start / End Page

11764

Location

England

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA, Messenger
  • Polymorphism, Single Nucleotide
  • Muscle, Skeletal
  • Male
  • Humans
  • Genome-Wide Association Study
  • Genetic Predisposition to Disease
  • Gene Expression Regulation
  • Female