Dissecting Locus-Specific Chromatin Interactions by CRISPR CAPTURE

Giovanni A. Botten, Michael Lee, Jian Xu

Research output: Chapter in Book/Report/Conference proceedingChapter


The spatiotemporal control of tissue-specific gene expression is coordinated by cis-regulatory elements (CREs) and associated trans-acting factors. Despite major advances in genome-wide annotation of candidate CREs, the in situ regulatory composition of the vast majority of CREs remain unknown. To address this challenge, we developed the CRISPR affinity purification in situ of regulatory elements (CAPTURE) toolbox that employs an in vivo biotinylated nuclease-deficient Cas9 (dCas9) protein and programmable single-guide RNAs (sgRNAs) to identify CRE-associated macromolecular complexes and chromatin looping. In this chapter, we provide a detailed protocol for implementing the latest iteration of the CRISPR-based CAPTURE methods to interrogate the molecular composition of locus-specific chromatin complexes and configuration in a mammalian genome.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages29
StatePublished - 2023

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Biotinylated dCas9
  • CAPTURE-3C-seq
  • CAPTURE-Proteomics
  • Chromatin looping
  • cis-regulatory elements
  • Enhancer
  • Gene regulation
  • Noncoding genome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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