A rapid micro chromatin immunoprecipitation assay (microChIP)

Nat Protoc. 2008;3(6):1032-45. doi: 10.1038/nprot.2008.68.


Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antibodies
  • Cell Count
  • Chromatin Immunoprecipitation / methods*
  • Cross-Linking Reagents
  • DNA / genetics
  • DNA / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Histones / genetics
  • Histones / immunology
  • Histones / metabolism
  • Humans
  • Microchemistry / methods
  • Polymerase Chain Reaction
  • RNA Polymerase II / immunology
  • RNA Polymerase II / metabolism
  • Time Factors


  • Antibodies
  • Cross-Linking Reagents
  • DNA-Binding Proteins
  • Histones
  • DNA
  • RNA Polymerase II