High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes

Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis

“…To systematically assess putative regulatory activities on 5,642 promoter chromatin interaction osteoporosis-associated SNPs ( Table S4 ), we utilized an adapted STARR-seq using hSTARR-seq_ORI vector with ORI as core promoter based on synthesized oligonucleotide sequences ( Figure 2 A, STAR Methods ). We synthesized 150-bp oligonucleotide sequences centered on reference and alternative allele of each of the 5,642 SNPs to assess their enhancer activities according to our previous report 19 ( Figure 2 A; Tables S5 and S6 ). The library containing all SNP oligonucleotides was cloned into hSTARR-seq_ORI vector and transfected into human osteoblast-like cell line U2OS, with plasmid library (input) and transcribed products (output) measured by sequencing ( Figure 2 A).…”

“…We have recently employed an adapted STARR-seq to assess biased enhancer activity of 5,987 noncoding SNP-associated insulin-resistance-relevant phenotypes. 19 Other studies employing STARR-seq have also successfully elucidated regulatory disease risk variants with enhancer activity effect on several other complex diseases, such as prostate cancer, 20 coronary artery disease, 21 and atrial fibrillation. 22 Nevertheless, there is no systematic measurement of enhancer regulatory activities for GWAS SNPs associated with osteoporosis-relevant phenotypes.…”

“…Here, we adopted an integrative strategy combing Hi-C profiling, 17 high-throughput enhancer measurement, 19 and multi-layer analytical and experimental explorations to systematically dissect enhancer-modulating regulatory SNPs conferring risk for osteoporosis via enhancer-promoter interactions ( Figure 1 ). We firstly fine-mapped 5,642 candidate osteoporosis-associated SNPs with significant chromatin interactions to nearby gene promoters in osteoblasts.…”

“…We firstly fine-mapped 5,642 candidate osteoporosis-associated SNPs with significant chromatin interactions to nearby gene promoters in osteoblasts. Secondly, by utilizing an adapted STARR-seq 19 in human osteoblast-like cell line U2OS, we identified 319 SNPs with allelic enhancer regulatory activities, which showed active epigenetic enrichment in osteoblasts and prevailing genetic regulatory roles for osteoporosis. Thirdly, we identified several candidate regulatory transcription factors (TFs) for osteoporosis etiologies and underscored YY2 as a putative key controlling one through combing allelic motif enrichment and TF-gene regulatory network analyses.…”

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs

“…Candidate SNPs with regulatory functions were identified using a previously reported STARR-Seq strategy [ 35 , 61 ]. Initially, custom primers for the 22 enhancer elements containing candidate SNPs were designed and synthesized by Sangon Biotech Co., Ltd (Shanghai, China) (see Additional file 3 : Table S2).…”