Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus

Abstract

Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage.

A dementia-associated risk variant nearTMEM106Balters chromatin architecture and gene expression

“…Furthermore, while GWAS causal variants have previously been implicated in specific allele-15! specific long-range chromatin interactions 47,[81][82][83][84] , here we report a variant that may directly 16! affect higher-order chromatin architecture.…”

ANRIL regulates production of extracellular matrix proteins and vasoactive factors in diabetic complications

“…ANRIL is known to function as a recruiter of PRC complexes to facilitate altering of chromatin structure and set the stage for gene regulation (61). Recent "allele-specific" functional genomic studies showed that preferential binding of p300 led to increased interaction of chromatin with ANRIL promoters, thereby activating transcription of the lncRNA (39). We and others have described the regulatory role of ANRIL on the expression of p300, a well-known regulator of FN in diabetic complications (15,24,53).…”

Long non‐coding RNA LINC00261 inhibits cell growth and migration in endometriosis

“…Emerging studies have shown that long non‐coding RNAs (lncRNAs) play important roles in the occurrence and progression of endometriosis . LncRNAs are a class of non‐coding RNA molecules longer than 200 nt that lack the ability to code protein .…”