Genetic Effects on Enhancer Activity in Human Pancreatic Islets

Abstract

Genome-wide association studies (GWAS) have identified >100 single nucleotide polymorphisms (SNPs) that modulate risk for type 2 diabetes (T2D) and related traits. Using functional genomic profiling, we and others have shown that T2D GWAS SNPs are significantly enriched to overlap pancreatic islet stretch enhancer chromatin states, implicating these regulatory elements as biological mediators of disease risk. Recent studies that integrate genetic variation and islet gene expression have identified expression quantitative trait loci (eQTL) that nominate target effector transcripts for T2D GWAS SNPs. However, the subset of causal regulatory SNPs that mediate genetic control of gene expression are unknown. To help close this gap in knowledge, we have performed capped analysis of gene expression (CAGE) on RNA enriched for active enhancers (eRNA-CAGE) across 40 human islet samples. Comparison of these profiles to previously published islet chromatin maps revealed significant enrichment for active chromatin states (P<0.001). Interestingly, we observe unbalanced bidirectional transcription at chromatin-defined intronic enhancer regions, where the predominant direction of enhancer transcription is concordant with the transcribed direction of the endogenous gene, suggesting interactions between gene and enhancer activity. One such example is an ABCC8 intronic enhancer that we previously functionally validated using a mouse transgenic reporter assay. We further performed genotyping and imputation, which allowed us to run an eRNA-QTL scan. We identified 4associations (P<0.for beta distribution adjusted P-value; QTLtools package), which are significantly enriched (P=7.3x10-7) to occur in islet active enhancer chromatin states. Notably, we found islet eRNA-QTL that overlap T2D GWAS SNPs and islet eQTL. Together, these results form a genetic map of human islet enhancer activity that is a foundation for interpreting regulatory mechanisms at T2D GWAS loci. Disclosure A. Varshney: None. S. Parker: None.