A map of open chromatin in human pancreatic islets

Abstract

Tissue-specific transcriptional regulation is central to human disease1. To identify regulatory DNA active in human pancreatic islets, we profiled chromatin by FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements)2–4 coupled with high-throughput sequencing. We identified ~80,000 open chromatin sites. Comparison of islet FAIRE-seq to five non-islet cell lines revealed ~3,300 physically linked clusters of islet-selective open chromatin sites, which typically encompassed single genes exhibiting islet-specific expression. We mapped sequence variants to open chromatin sites and found that rs7903146, a TCF7L2 intronic variant strongly associated with type 2 diabetes (T2D)5, is located in islet-selective open chromatin. We show that rs7903146 heterozygotes exhibit allelic imbalance in islet FAIRE signal, and that the variant alters enhancer activity, indicating that genetic variation at this locus acts in cis with local chromatin and regulatory changes. These findings illuminate the tissue-specific organization of cis-regulatory elements, and show that FAIRE-seq can guide identification of regulatory variants important for disease.

Application of a systems approach to study developmental gene regulation

“…Open chromatin is much more likely to be sensitive to action of DNase I digestion, therefore DHS are typical of open chromatin. A similar technology of DNase-seq is called FAIRE-seq (Gaulton et al 2010). …”

Redundant enhancers and causal variants in the TCF7L2 gene

“…1,2 The rs7903146 single-nucleotide polymorphism (SNP), located in intron 3 and the one with the strongest association to T2D risk, has been the most widely studied TCF7L2 variant. Current evidence suggests that rs7903146 may affect risk of T2D through its effects on enhancer activity 3,4 resulting in higher TCF7L2 gene expression. [3][4][5] The rs7903146 SNP has been found located inside islet-selective open chromatin sites using either formaldehyde-assisted isolation of regulatory elements coupled with high throughput sequencing (FAIRE-seq), 3 or histone H3 lysine methylation modifications as marks of regulatory elements.…”

“…Current evidence suggests that rs7903146 may affect risk of T2D through its effects on enhancer activity 3,4 resulting in higher TCF7L2 gene expression. [3][4][5] The rs7903146 SNP has been found located inside islet-selective open chromatin sites using either formaldehyde-assisted isolation of regulatory elements coupled with high throughput sequencing (FAIRE-seq), 3 or histone H3 lysine methylation modifications as marks of regulatory elements. 4 In addition, the T-allele of rs7903146 (ie, the allele associated with higher risk of T2D) has been found associated with higher TCF7L2 gene expression in human pancreatic islets, 5 and in luciferase reporter assays in the mouse pancreatic MIN6 cell line, 3,4 and the rat pancreatic 832/13 cell line.…”

“…[3][4][5] The rs7903146 SNP has been found located inside islet-selective open chromatin sites using either formaldehyde-assisted isolation of regulatory elements coupled with high throughput sequencing (FAIRE-seq), 3 or histone H3 lysine methylation modifications as marks of regulatory elements. 4 In addition, the T-allele of rs7903146 (ie, the allele associated with higher risk of T2D) has been found associated with higher TCF7L2 gene expression in human pancreatic islets, 5 and in luciferase reporter assays in the mouse pancreatic MIN6 cell line, 3,4 and the rat pancreatic 832/13 cell line. 3 More recently Savic et al 6,7 reported that the TCF7L2 gene harbors several highly conserved cis-regulatory elements that show both in vitro and in vivo enhancer activity.…”

“…4 In addition, the T-allele of rs7903146 (ie, the allele associated with higher risk of T2D) has been found associated with higher TCF7L2 gene expression in human pancreatic islets, 5 and in luciferase reporter assays in the mouse pancreatic MIN6 cell line, 3,4 and the rat pancreatic 832/13 cell line. 3 More recently Savic et al 6,7 reported that the TCF7L2 gene harbors several highly conserved cis-regulatory elements that show both in vitro and in vivo enhancer activity. These enhancer elements are located in a 92-kb interval that harbors all the TCF7L2 SNPs, not just rs7903146, associated with T2D risk.…”