ChIP-seq analysis of BRD4 and RNAPII in K562 cells treated with DMSO or JQ1, NUP98 and NUP153 in K562 cells, and H3K27ac in mouse KH2 undifferentiated embryonic stem cells (ESCs) or differentiated embryonic bodies (EBs)

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 endonuclease-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 ß-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease. Overall design: ChIP-seq was performed to determine the BRD4 and RNAPII chromatin occupancy in K562 cells treated with BRD4 inhibitor (JQ1) or vehicle control (DMSO) for 2 or 6 hours, the NUP98 and NUP153 chromatin occupancy in K562 cells, and the H3K27ac mark in mouse KH2 ESCs or differentiated EBs