title: 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.
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Nakaoka
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Aishwarya
authors.initials: A
authors.lastname: Gurumurthy
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Takahide
authors.initials: T
authors.lastname: Hayano
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Somayeh
authors.initials: S
authors.lastname: Ahmadloo
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Waleed H
authors.initials: WH
authors.lastname: Omer
authors.affiliation: Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan.
authors.forename: Kosuke
authors.initials: K
authors.lastname: Yoshihara
authors.affiliation: Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan.
authors.forename: Akihito
authors.initials: A
authors.lastname: Yamamoto
authors.affiliation: Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Kurose
authors.affiliation: Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Enomoto
authors.affiliation: Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan.
authors.forename: Shigeo
authors.initials: S
authors.lastname: Akira
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.|Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Hosomichi
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Ituro
authors.initials: I
authors.lastname: Inoue
mesh_terms: D022981:Allelic Imbalance; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics*; D002899:Chromosomes, Human, Pair 9; D050881:E1A-Associated p300 Protein / Q000378:metabolism; D004715:Endometriosis / Q000235:genetics*; D005260:Female; D055106:Genome-Wide Association Study; D006239:Haplotypes; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D058118:Transcription Factor 7-Like 2 Protein / Q000378:metabolism
chemical_list: C561518:CDKN2B antisense RNA, human; D002843:Chromatin; D062085:RNA, Long Noncoding; C544894:TCF7L2 protein, human; D058118:Transcription Factor 7-Like 2 Protein; D050881:E1A-Associated p300 Protein; C494360:EP300 protein, human