Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

Nat Protoc. 2010 Mar;5(3):457-72. doi: 10.1038/nprot.2009.244. Epub 2010 Feb 18.


Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNA amplification and purification. We also provide a guide for primary data analysis of ChIP-SEQ data. The complete protocol for ChIP-SEQ/ChIP-CHIP sample preparation starting from plant harvest takes approximately 7 d.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / isolation & purification
  • Arabidopsis Proteins / metabolism
  • Binding Sites / genetics
  • Chromatin Immunoprecipitation / methods*
  • DNA, Plant / genetics*
  • DNA, Plant / metabolism*
  • Genome, Plant
  • In Situ Hybridization
  • Oligonucleotide Array Sequence Analysis / methods
  • Plant Proteins / isolation & purification*
  • Plant Proteins / metabolism*
  • Sequence Analysis, DNA
  • Transcription Factors / isolation & purification*
  • Transcription Factors / metabolism*


  • Arabidopsis Proteins
  • DNA, Plant
  • Plant Proteins
  • Transcription Factors