Chromatin Immunoprecipitation to Verify or to Identify In Vivo Protein–DNA Interactions

Yumei Zheng, Sharyn E. Perry

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

5 Scopus citations


Chromatin immunoprecipitation (ChIP) is a valuable tool to detect the interaction in vivo between a DNA-associated protein and DNA fragments. Combined with approaches to assess gene expression in response to accumulation of a transcription factor, it is possible to identify direct responsive targets from targets that are indirectly responsive to accumulation of the transcription factor. ChIP may be used to confirm in vivo association of a transcriptional regulator with suspected target DNA fragments. ChIP may also be used to discover new targets, and when combined with high-throughput approaches to identify DNA fragments associated with a transcription factor, it may provide a tool to study the gene regulatory networks active during plant development and/or response to the environment. Furthermore, ChIP is also a powerful means to map epigenetic modifications within a genome.

Original languageEnglish
Title of host publicationPlant Transcription Factors
Subtitle of host publicationMethods and Protocols
Number of pages15
StatePublished - 2011

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Funding Information:
The authors would like to thank Jeanne Hartman for comments on the manuscript. This work was supported by grants from the National Science Foundation (IBN-9984274 and IOS-0922845).

Publisher Copyright:
© 2011, Springer Science+Business Media, LLC.


  • Chromatin immunoprecipitation
  • DNA modification
  • epigenetics
  • gene regulation
  • protein–DNA interaction
  • transcription
  • transcription factor

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'Chromatin Immunoprecipitation to Verify or to Identify In Vivo Protein–DNA Interactions'. Together they form a unique fingerprint.

Cite this