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.
Liu, Xin; Zhang, Yuannyu; Chen, Yong; Li, Mushan; Zhou, Feng; Li, Kailong; Cao, Hui; Ni, Min; Liu, Yuxuan; Gu, Zhimin; Dickerson, Kathryn E; Xie, Shiqi; Hon, Gary C; Xuan, Zhenyu; Zhang, Michael Q; Shao, Zhen; and Xu, Jian, "In Situ Capture of Chromatin Interactions by Biotinylated dCas9." (2017). Faculty Scholarship for the College of Science & Mathematics. 128.
Xin Liu, Yuanyu Zhang, Yong Chen, Mushan Li, Feng Zhou, Kailong Li, Hui Cao, Min Ni, Yuxuan Liu, Zhimin Gu, Kathryn E. Dickerson, Shiqi Xie, Gary C. Hon, Zhenyu Xuan, Michael Q. Zhang, Zhen Shao, Jian Xu. (2017) In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell 170 (5), 1028-1043.e19.