Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Nat Commun. 2021-09-02;12(1):5242.
- 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.
- Consortium data used in this publication
- Code used for analysis in this paper is available at https://github.com/UcarLab/ MPRA_Khetan and linked to Zenodo at https://doi.org/10.5281/zenodo.4974390. All datasets generated and analyzed during the current study are publicly available in GEO under Accession GSE145643 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE145643), which includes fastq files containing barcode sequences in the 3′UTR of gfp in the plasmid library and MIN6 RNA samples and processed files containing the sum of all barcode counts for each test construct in the plasmid DNA and MIN6 RNA samples. Human islet ATAC-seq data were obtained from NCBI Sequence Read Archive Accession SRP117935. Summary InsPIRE Consortium73 islet eQTL statistics were obtained from https://zenodo.org/record/3408356 and SNP2TFBS predictions for transcription factor motifs altered by MPRA-modulating SNP alleles were obtained from https://ccg.epfl.ch/snp2tfbs/.
- Data summary
- Linked to Zenodo