Document Type
Article
Publication Date
9-2-2021
Publication Title
Nat Commun
Keywords
JGM, JMG, Alleles, Animals, Cell Line, Chromatin, Diabetes Mellitus, Type 2, Endoplasmic Reticulum Stress, Genome-Wide Association Study, Humans, Insulin-Secreting Cells, Mice, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Short Interspersed Nucleotide Elements, Transcriptional Activation
JAX Source
Nat Commun 2021 Sep 2; 12(1):5241
Volume
12
Issue
1
First Page
5242
Last Page
5242
ISSN
2041-1723
PMID
34475398
DOI
https://doi.org/10.1038/s41467-021-25514-6
Grant
The Jackson Laboratory Director’s Innovation Fund, W81XWH-18-0401, R01DK118011, R00HG008179
Abstract
Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) at >250 loci in the human genome to type 2 diabetes (T2D) risk. For each locus, identifying the functional variant(s) among multiple SNPs in high linkage disequilibrium is critical to understand molecular mechanisms underlying T2D genetic risk. Using massively parallel reporter assays (MPRA), we test the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 β cells under steady state and pathophysiologic endoplasmic reticulum (ER) stress conditions. We identify 1,982/6,621 (29.9%) SNP-containing elements that activate transcription in MIN6 and 879 SNP alleles that modulate MPRA activity. Multiple T2D-associated SNPs alter the activity of short interspersed nuclear element (SINE)-containing elements that are strongly induced by ER stress. We identify 220 functional variants at 104 T2D association signals, narrowing 54 signals to a single candidate SNP. Together, this study identifies elements driving β cell steady state and ER stress-responsive transcriptional activation, nominates causal T2D SNPs, and uncovers potential roles for repetitive elements in β cell transcriptional stress response and T2D genetics.
Recommended Citation
Khetan S,
Kales S,
Kursawe R,
Jillette A,
Ulirsch J,
Reilly S,
Ucar D,
Tewhey R,
Stitzel ML.
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation. Nat Commun 2021 Sep 2; 12(1):5241
Comments
We thank members of the Stitzel and Ucar labs for helpful discussion and critiquesduring study design and execution and Francis S. Collins, D. Leland Taylor, Cassandra Spracklen, Christine Beck, and Taneli Helenius for helpful comments on the manuscript.
This article is licensed under a Creative Commons Attribution 4.0 International License.