Gene-specific and genome-wide ChIP approaches to study plant transcriptional networks

Methods Mol Biol. 2009;553:3-12. doi: 10.1007/978-1-60327-563-7_1.


Chromatin immunoprecipitation (ChIP) provides a versatile tool to investigate the in vivo location of DNA-binding proteins on genomic DNA. ChIP approaches are gaining significance in plants, in cases when entire genome sequences are available (e.g., Arabidopsis), for which several high-density oligo arrays have been or are being developed. Nevertheless, plant ChIP and ChIP-chip still present some technical challenges. Here, we describe general methods for ChIP and ChIP-chip, which have been successfully applied to maize and Arabidopsis.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Chromatin Immunoprecipitation / methods*
  • Chromosome Mapping / methods*
  • Cross-Linking Reagents / pharmacology
  • DNA-Binding Proteins / analysis
  • DNA-Binding Proteins / isolation & purification
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks / genetics
  • Gene Regulatory Networks / physiology*
  • Genes, Plant*
  • Genome, Plant / physiology
  • Substrate Specificity / genetics


  • Cross-Linking Reagents
  • DNA-Binding Proteins