Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here, we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single-copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally regulated super-enhancers reveals spatial features that causally control gene transcription. Thus, comprehensive and unbiased analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

中文翻译：

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通过生物素化的dCas9原位捕获染色质相互作用。

相关的染色质特征通常识别顺式调节元件（CRE），但染色质中绝大多数CRE的分子组成仍然未知。在这里，我们描述了一种CRISPR亲和力原位纯化的调控元件（CAPTURE）方法，可以无偏地识别基因座特异性的染色质调控蛋白复合物和远距离DNA相互作用。使用体内生物素化的核酸酶缺陷Cas9蛋白和序列特异性的指导RNA，我们在单拷贝基因组位点显示了染色质相互作用的高分辨率和选择性分离。使用CAPTURE纯化人类端粒可识别已知和新的端粒因子。原位捕获控制人类β-珠蛋白基因的增强子簇的各个组成部分，为基于组成的分层组织建立了证据。此外，在疾病相关的顺式元件和发育调控的超级增强子上的染色质相互作用的无偏分析显示了因果关系控制基因转录的空间特征。因此，对基因座特异性调控成分的全面，无偏见的分析提供了对发育和疾病中基因组结构和功能的机械洞察力。