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A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

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posted on 13.04.2021, 20:58 by Arushi Varshney, Yasuhiro Kyono, Venkateswaran Ramamoorthi Elangovan, Collin Wang, Michael R. Erdos, Narisu Narisu, Ricardo D'Oliveira Albanus, Peter Orchard, Michael L. Stitzel, Francis S. Collins, Jacob O. Kitzman, Stephen C. J. Parker
Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (~68%) tested islet CAGE elements (5% FDR). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.

Funding

We acknowledge support from the University of Michigan Rackham Predoctoral Fellowship (A.V.), T32 HG00040 from the National Human Genome Research Institute of the N.I.H. (P.O.), ADA Accelerator grant 1-18-ACE-15 (M.L.S.), NIH intramural support from project ZIA-HG000024 (F.S.C.), ADA Pathway to Stop Diabetes Grant 1-14-INI-07, NIH 1UM1DK126185-01 grant and R01 DK117960 (S.C.J.P.).

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