Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus.
Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus.
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DOI：
10.1371/journal.pgen.1005893
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发表时间：
2016-04
期刊：
影响因子：
4.5
通讯作者：
Inoue I
中科院分区：
文献类型：
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作者：
Nakaoka H;Gurumurthy A;Hayano T;Ahmadloo S;Omer WH;Yoshihara K;Yamamoto A;Kurose K;Enomoto T;Akira S;Hosomichi K;Inoue I
全基因组关联研究（GWAS）发现了许多与人类复杂疾病相关的单核苷酸多态性（SNP）。然而，疾病相关SNP的功能表征仍然是一个巨大的挑战。在此，我们利用等位基因特异性功能基因组学方法探讨了与子宫内膜异位症相关的染色体9 p21上SNP的调控机制。通过重新测序9 p21区域的1.29 Mb，并仔细检查来自ENCODE项目的DNase-seq数据，我们优先考虑rs 17761446作为候选功能变体，其与原始GWAS SNP（rs 10965235）处于完美连锁不平衡，并位于DNase I超敏感位点。染色体构象捕获后的高通量测序结果显示，rs 17761446的保护性G等位基因与ANRIL启动子产生了更强的染色质相互作用。通过生物信息学和染色质免疫沉淀（ChIP）分析，我们证明了保护性等位基因对TCF 7 L2和EP 300表现出优先结合亲和力。组蛋白H3赖氨酸27乙酰化和RNA聚合酶II的ChIP测定增强了SNP位点的增强子活性。在位子宫内膜组织和子宫内膜癌细胞系的等位基因特异性表达分析表明，rs 17761446是一个顺式调节变体，其中G等位基因与ANRIL表达增加相关。我们的工作阐明了9 p21子宫内膜异位症风险基因座的分子机制是由染色质相互作用介导的从因子结合到基因表达的一系列转录调控中的等位基因失衡。常见疾病的功能基因组学将在后GWAS阶段揭示基因型-表型相关性的功能方面。全基因组关联研究（GWAS）发现了大量与人类复杂疾病相关的变异。这些发现有望转化为对疾病发病机制的明确理解;然而，疾病相关SNP的功能表征仍然是一个巨大的挑战。在这里，我们探讨了与子宫内膜异位症，一种常见的妇科疾病，染色体9 p21变异的调控机制。通过仔细研究连锁不平衡结构和DNA酶I超敏位点的风险位点，我们优先考虑rs 17761446作为候选的因果变异。我们的“等位基因特异性”功能基因组学方法的结果揭示了9 p21子宫内膜异位症风险位点的调控机制，其中TCF 7 L2及其共激活因子EP 300与rs 17761446的保护性G等位基因的优先结合导致与ANRIL启动子的更强的染色质相互作用，这反过来激活非编码RNA的转录。基于TCF 7 L2是Wnt信号通路的关键转录因子这一事实，我们推测Wnt信号的诱导激活了ANRIL和细胞周期抑制剂CDKN 2A/2B的表达水平。常见疾病的功能基因组学将在后GWAS阶段揭示基因型-表型相关性的功能方面。
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 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; however, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a variant on chromosome 9p21 associated with endometriosis, a common gynecological disorder. By scrutinizing linkage disequilibrium structure and DNase I hypersensitive sites across the risk locus, we prioritized rs17761446 as a candidate causal variant. The results of our “allele-specific” functional genomic approaches sheds light on regulatory mechanisms underlying 9p21 endometriosis risk locus, in which preferential bindings of TCF7L2 and its coactivator EP300 to the protective G allele of rs17761446 lead to stronger chromatin interaction with the promoter of ANRIL, which in turn activate transcription of the non-coding RNA. Motivated by the fact that TCF7L2 was a key transcription factor of Wnt signaling pathway, we postulated that the induction of Wnt signaling activated expression levels of ANRIL and cell cycle inhibitors, CDKN2A/2B. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage.