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

K. Kaufmann, J.M. Muiño, M. Østerås, L. Farinelli, P. Krajewski, G.C. Angenent

Research output: Contribution to journalArticleAcademicpeer-review

202 Citations (Scopus)

Abstract

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 ~7 d
Original languageEnglish
Pages (from-to)457-472
JournalNature protocols
Volume5
Issue number3
DOIs
Publication statusPublished - 2010

Keywords

  • cross-linking
  • arabidopsis-thaliana
  • wide analysis
  • dna
  • protein
  • binding
  • genes
  • identification
  • association
  • methylation

Fingerprint Dive into the research topics of 'Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)'. Together they form a unique fingerprint.

Cite this