Abstract
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.
Original language | English (US) |
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Pages (from-to) | 1028-1043.e19 |
Journal | Cell |
Volume | 170 |
Issue number | 5 |
DOIs | |
State | Published - Aug 24 2017 |
Keywords
- CRISPR/Cas9
- DNA looping
- biotinylation
- chromatin
- cis-regulatory elements
- enhancers
- proteomics
- super-enhancers
ASJC Scopus subject areas
- General Biochemistry, Genetics and Molecular Biology