Feb 15, 2017

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

Proceedings of the National Academy of Sciences of the United States of America
Arushi VarshneyMichael L Stitzel

Abstract

Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps. Additional integration with chromatin-state maps for islets and other diverse tissue types revealed that cis-eQTLs for islet-specific genes are specifically and significantly enriched in islet stretch enhancers. High-resolution chromatin accessibility profiling using assay for transposase-accessible chromatin sequencing (ATAC-seq) in two islet samples enabled us to identify specific transcription factor (TF) footprints embedded in active regulatory elements, which are highly enriched for islet cis-eQTL. Aggregate allelic bias signatures in TF footprints enabled us de novo to reconstruct TF binding affinities genetically, which support the high-quality nature ...Continue Reading

Mentioned in this Paper

Establishment and Maintenance of Localization
Isl1
Genome-Wide Association Study
RFX1
Diabetes Mellitus, Non-Insulin-Dependent
RFXANK protein, human
Quantitative Trait Loci
Neonatal Diabetes Mellitus
KCNK16
Transposase

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