DNA-Binding Factor Target Identification by Chromatin Immunoprecipitation (ChIP) in Plants

  • David PoséEmail author
  • Levi Yant
Part of the Methods in Molecular Biology book series (MIMB, volume 1363)


Chromatin immunoprecipitation (ChIP) allows the precise identification of genomic loci that physically interact with a protein of interest, whether that protein is a transcription factor, a core polymerase, a histone, or other chromatin-associated protein. In short, tissue is first cross-linked to freeze a population of DNA-protein interactions at a stage of interest. Chromatin is then extracted, fragmented, and incubated with a specific antibody against the protein of interest. Next, the resultant DNA-protein complexes are immunoprecipitated and captured using beads that bind to the antibody constant region. Samples are finally reverse cross-linked to separate the bound fragments and the DNA is purified. This DNA is analyzed by quantitative PCR for enrichment of genomic regions expected to be bound by the protein under study. The protocol detailed in this chapter has been successfully applied in the identification of target genes for seven transcriptional regulators of diverse classes involved in Arabidopsis thaliana floral transition.

Key words

Chromatin immunoprecipitation ChIP ChIP-seq ChIP-chip Transcription factor Antibody Direct target 



DP was supported by a contract “Ramón y Cajal” (code RYC-2013-12699) from the Ministerio de Economía y Competitividad, Spain.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y MediterráneaUniversidad de Málaga-Consejo Superior de Investigaciones CientíficasMálagaSpain
  2. 2.Department of Cell and Development BiologyJohn Innes Centre, Norwich Research parkNorwichUK

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