A CRISPR-based approach for proteomic analysis of a single genomic locus

Epigenetics. 2014 Sep;9(9):1207-11. doi: 10.4161/epi.29919. Epub 2014 Jul 18.


Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epiproteome. However, defining local epiproteomes has been limited by a lack of effective technologies to isolate discrete sections of chromatin and to identify with precision specific proteins and histone posttranslational modifications (PTMs). We report the use of the Cas9 and guide RNA (gRNA) components of the CRISPR system for gRNA-directed purification of a discrete section of chromatin. Quantitative mass spectrometry provides for unambiguous identification of proteins and histone PTMs specifically associated with the enriched chromatin. This CRISPR-based Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) approach revealed changes in the local epiproteome of a promoter during activation of transcription. CRISPR-ChAP-MS thus has broad applications for discovering molecular components and dynamic regulation of any in vivo activity at a given chromosomal location.

Keywords: affinity purification; epigenetics; epiproteome; histone; posttranslational modification; proteomics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin / genetics
  • Chromatin / metabolism
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Genetic Loci*
  • Histones / metabolism*
  • Mass Spectrometry
  • Protein Processing, Post-Translational
  • Proteome / genetics
  • Proteome / metabolism*
  • RNA, Guide, CRISPR-Cas Systems / metabolism
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*


  • Chromatin
  • Histones
  • Proteome
  • RNA, Guide, CRISPR-Cas Systems
  • Saccharomyces cerevisiae Proteins