Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting.
Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting.
复制标题
识别 1p22 处常见的非编码变异，这些变异对非综合征性口面裂有功能
DOI：
10.1038/ncomms14759
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发表时间：
2017-03-13
影响因子：
16.6
通讯作者：
Cornell RA
中科院分区：
文献类型：
--
作者：
Liu H;Leslie EJ;Carlson JC;Beaty TH;Marazita ML;Lidral AC;Cornell RA
全基因组关联研究（GWAS）不区分单核苷酸多态性（SNP）是因果关系，那些只是在因果突变的连锁不平衡。在这里，我们描述了一个通用的，功能管道，并将其应用于单核苷酸多态性在1 p22，一个位点在几个GWAS确定的非综合征性唇腭裂或腭裂（NS CL/P）。首先，我们扩增了包含10个最高风险相关SNP的DNA元件，并在体外测试了它们的增强子活性，确定了3个对这种活性具有等位基因依赖性效应的SNP。然后，我们使用体内报告基因分析来测试这些增强子的组织特异性，染色质构型捕获来测试增强子-启动子相互作用，体外基因组编辑来显示等位基因特异性对ARHGAP 29表达和细胞迁移的影响。我们的研究结果进一步表明，两个SNP影响CL/P相关转录因子的结合，一个影响染色质构型。这些结果将风险转化为潜在的发病机制。
Genome-wide association studies (GWAS) do not distinguish between single nucleotide polymorphisms (SNPs) that are causal and those that are merely in linkage-disequilibrium with causal mutations. Here we describe a versatile, functional pipeline and apply it to SNPs at 1p22, a locus identified in several GWAS for non-syndromic cleft lip with or without cleft palate (NS CL/P). First we amplified DNA elements containing the ten most-highly risk-associated SNPs and tested their enhancer activityin vitro, identifying three SNPs with allele-dependent effects on such activity. We then usedin vivoreporter assays to test the tissue-specificity of these enhancers, chromatin configuration capture to test enhancer–promoter interactions, and genome editingin vitroto show allele-specific effects on ARHGAP29 expression and cell migration. Our results further indicate that two SNPs affect binding of CL/P-associated transcription factors, and one affects chromatin configuration. These results translate risk into potential mechanisms of pathogenesis.