ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus

Cell Rep. 2012 Jul 26;2(1):198-205. doi: 10.1016/j.celrep.2012.06.019. Epub 2012 Jul 20.


The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that provide for the localization of a defined protein or posttranslationally modified protein to specific chromosomal sites. While these approaches have helped us conceptualize epigenetic mechanisms, the field has been limited by the inability to define features such as the proteome and histone modifications at a specific genomic locus in an unbiased manner. We developed an unbiased approach whereby a unique native genomic locus was isolated, which was followed by high-resolution proteomic identification of specifically associated proteins and histone posttranslational modifications. This chromatin affinity purification with mass spectrometry (ChAP-MS) technique was used to specifically enrich a ~1,000 base pair section of GAL1 chromatin under transcriptionally active and repressive conditions, as well as to identify the specifically bound proteins and histone posttranslational modifications. ChAP-MS should yield insight into the regulatory mechanisms of transcription and help identify factors that epigenetically control chromatin function.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Cells, Cultured
  • Chromatin Immunoprecipitation / methods*
  • Chromatography, Affinity / methods*
  • Chromosomes, Fungal / chemistry
  • Chromosomes, Fungal / metabolism
  • Combinatorial Chemistry Techniques / methods
  • Fungal Proteins / analysis
  • Fungal Proteins / chemistry
  • Fungal Proteins / metabolism
  • Galactokinase / genetics
  • Galactokinase / metabolism
  • Gene Silencing / physiology
  • Histones / analysis
  • Histones / chemistry
  • Histones / metabolism*
  • Mass Spectrometry / methods*
  • Models, Biological
  • Protein Processing, Post-Translational*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism


  • Fungal Proteins
  • Histones
  • Saccharomyces cerevisiae Proteins
  • GAL1 protein, S cerevisiae
  • Galactokinase