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

Hirofumi Nakaoka,Shigeo Akira,Kazuyoshi Hosomichi,Akihito Yamamoto,Kosuke Yoshihara,Somayeh Ahmadloo,Keisuke Kurose,Waleed H Omer,Ituro Inoue,Takahide Hayano,Aishwarya Gurumurthy,Takayuki Enomoto,Chris Cotsapas

doi:10.1371/journal.pgen.1005893

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.

Highlights

With the advent of genome-wide association studies (GWASs), a large number of single nucleotide polymorphisms (SNPs) associated with human complex diseases have been discovered [1]
A large number of variants associated with human complex diseases have been discovered by genome-wide association studies (GWASs)
These discoveries have been anticipated to be translated into the definitive understanding of disease pathogeneses; functional characterization of the disease-associated SNPs remains a formidable challenge

Summary

Introduction

With the advent of genome-wide association studies (GWASs), a large number of single nucleotide polymorphisms (SNPs) associated with human complex diseases have been discovered [1]. Most of the identified SNPs are located on intergenic regions and introns rather than coding regions [7], suggesting that these non-coding SNPs are associated with the disease risk through regulation of expression levels of nearby genes. A large proportion of the SNPs identified by GWASs or tagged by them were located on DHSs in cell types relevant to the corresponding diseases and overlapped transcription factor (TF) recognition sequences [14]. These systematic analyses present a plausible model in which the disease-associated SNPs alter activities of cis-regulatory elements including promoters, enhancers, insulators, and silencers. It has been reported that mutations on cis-regulatory elements cause severe developmental disorders showing a Mendelian pattern of inheritance [26]

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Discussion

Conclusion