In Situ Capture of Chromatin Interactions by Biotinylated dCas9

Cell. 2017 Aug 24;170(5):1028-1043.e19. doi: 10.1016/j.cell.2017.08.003.

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.

Keywords: CRISPR/Cas9; DNA looping; biotinylation; chromatin; cis-regulatory elements; enhancers; proteomics; super-enhancers.

MeSH terms

  • Animals
  • Biotinylation
  • CRISPR-Cas Systems*
  • Cells, Cultured
  • Embryonic Stem Cells / metabolism
  • Endonucleases / genetics
  • Endonucleases / metabolism*
  • Enhancer Elements, Genetic
  • Genetic Techniques*
  • Humans
  • K562 Cells
  • Mice
  • RNA, Guide / metabolism
  • Regulatory Elements, Transcriptional*
  • Telomere / metabolism
  • beta-Globins / genetics

Substances

  • RNA, Guide
  • beta-Globins
  • Endonucleases