Yuan-Yuan Duan, Xiao-Feng Chen, Ren-Jie Zhu, Ying-Ying Jia, Xiao-Ting Huang et al.
Most of the single-nucleotide polymorphisms (SNPs) associated with insulin resistance (IR)-relevant phenotypes by genome-wide association studies (GWASs) are located in noncoding regions, complicating their functional interpretation. Here, we utilized an adapted STARR-seq to evaluate the regulatory activities of 5,987 noncoding SNPs associated with IR-relevant phenotypes. We identified 876 SNPs with biased allelic enhancer activity effects (baaSNPs) across 133 loci in three IR-relevant cell lines (HepG2, preadipocyte, and A673), which showed pervasive cell specificity and significant enrichment for cell-specific open chromatin regions or enhancer-indicative markers (H3K4me1, H3K27ac). Further functional characterization suggested several transcription factors (TFs) with preferential allelic binding to baaSNPs. We also incorporated multi-omics data to prioritize 102 candidate regulatory target genes for baaSNPs and revealed prevalent long-range regulatory effects and cell-specific IR-relevant biological functional enrichment on them. Specifically, we experimentally verified the distal regulatory mechanism at IRS1 locus, in which rs952227-A reinforces IRS1 expression by long-range chromatin interaction and preferential binding to the transcription factor HOXC6 to augment the enhancer activity. Finally, based on our STARR-seq screening data, we predicted the enhancer activity of 227,343 noncoding SNPs associated with IR-relevant phenotypes (fasting insulin adjusted for BMI, HDL cholesterol, and triglycerides) from the largest available GWAS summary statistics. We further provided an open resource (http://www.bigc.online/fnSNP-IR) for better understanding genetic regulatory mechanisms of IR-relevant phenotypes.
Yuan-Yuan Duan, Xiao-Feng Chen, Ren-Jie Zhu, Ying-Ying Jia, Xiao-Ting Huang, Meng Zhang, Ning Yang, Shan-Shan Dong, Mengqi Zeng, Zhihui Feng, Dong-Li Zhu, Hao Wu, Feng Jiang, Wei Shi, Wei-Xin Hu, Xin Ke, Hao Chen, Yunlong Liu, Rui-Hua Jing, Yan Guo, Meng Li, Tie-Lin Yang. High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes. 2023-07-27. https://doi.org/10.1016/j.ajhg.2023.07.002
An episomal hSTARR-seq_ORI library containing both alleles of selected noncoding IR-associated SNPs was transfected into human Hep-G2 cells for 24 h. Three biological replicates were sequenced as plasmid input and poly(A)+ RNA output libraries.
An episomal hSTARR-seq_ORI library containing both alleles of selected noncoding IR-associated SNPs was transfected into human A-673 cells for 24 h. Three biological replicates were sequenced as plasmid input and poly(A)+ RNA output libraries.
An episomal hSTARR-seq_ORI library containing both alleles of selected noncoding IR-associated SNPs was transfected into human preadipocytes derived from subcutaneous adipose tissue for 24 h. Three biological replicates were sequenced as plasmid input and poly(A)+ RNA output libraries.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 7 files (ZIP)GSE198047_A673-input.output.pairs.SNPs.UMI.count.txt.gzGSE198047_family.soft.gzGSE198047_HepG2-input.output.pairs.SNPs.UMI.count.txt.gzGSE198047_Preadipocyte-input.output.pairs.SNPs.UMI.count.txt.gzmmc1.pdfmmc2.xlsxmmc3.pdf