Integrating enhancer RNA signatures with diverse omics data identifies characteristics of transcription initiation in pancreatic islets

Identifying active regulatory elements and their molecular signatures is critical to understand gene regulatory mechanisms and subsequently better delineating biological mechanisms of complex diseases and traits. Studies have shown that active enhancers can be transcribed into enhancer RNA (eRNA). Here, we identify actively transcribed regulatory elements in human pancreatic islets by generating eRNA profiles using cap analysis of gene expression (CAGE) across 70 islet samples. We identify 9,954 clusters of CAGE tag transcription start sites (TSS) or tag clusters (TCs) in islets, [~]20% of which are islet-specific when compared to CAGE TCs across publicly available tissues. Islet TCs are most enriched to overlap genome wide association study (GWAS) loci for islet-relevant traits such as fasting glucose. We integrated islet CAGE profiles with diverse epigenomic information such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) profiles of five histone modifications and accessible chromatin profiles from the assay for transposase accessible chromatin followed by sequencing (ATAC-seq), to understand how the underlying islet chromatin landscape is associated with TSSs. We identify that ATAC-seq informed transcription factor (TF) binding sites (TF footprint motifs) for the RFX TF family are highly enriched in transcribed regions occurring in enhancer chromatin states, whereas TF footprint motifs for the ETS family are highly enriched in transcribed regions within promoter chromatin states. Using massively parallel reporter assays in a rat pancreatic islet beta cell line, we tested the activity of 3,378 islet CAGE elements and found that 2,279 ([~]67.5%) show significant regulatory activity (5% FDR). We find that TCs within accessible enhancer show higher enrichment to overlap T2D GWAS loci than accessible enhancer annotations alone, suggesting that TC annotations pinpoint active regions within the enhancer chromatin states. This work provides a high-resolution transcriptional regulatory map of human pancreatic islets.

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