Chromatin immunoprecipitation using microarrays

Methods Mol Biol. 2009;529:279-95. doi: 10.1007/978-1-59745-538-1_18.


Chromatin immunoprecipitation (ChIP) is a powerful procedure to investigate the interactions between proteins and DNA. ChIP-chip combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in vivo. This genome-wide analysis of protein-DNA association is carried out in several steps including chemical cross-linking, cell lysis, DNA fragmentation and immunoaffinity purification that allow the identification of DNA interactions and provide a powerful tool for genome-wide investigations. Immunoprecipitated DNA fragments associated with the desired protein are amplified, labelled and hybridized to DNA microarrays to detect enriched signals compared to a labelled reference sample.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / metabolism
  • Chromatin Immunoprecipitation / methods*
  • Formaldehyde
  • Microspheres
  • Nuclear Proteins / isolation & purification
  • Oligonucleotide Array Sequence Analysis / methods*
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Schizosaccharomyces / metabolism*
  • Sonication
  • Tissue Fixation


  • Chromatin
  • Nuclear Proteins
  • Formaldehyde