Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo

  • Smitha Pillai
  • Piyali Dasgupta
  • Srikumar P. ChellappanEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1288)


Studies in the past decade have shown that differential gene expression depends not only on the binding of specific transcription factors to discrete promoter elements but also on the epigenetic modification of the DNA as well as histones associated with the promoter. While techniques like electrophoretic mobility shift assays could detect and characterize the binding of specific transcription factors present in cell lysates to DNA sequences in in vitro binding conditions, they were not effective in assessing the binding in intact cells. Development of chromatin immunoprecipitation technique in the past decade enabled the analysis of the association of regulatory molecules with specific promoters or changes in histone modifications in vivo, without overexpressing any component. ChIP assays can provide a snapshot of how a regulatory transcription factor affects the expression of a single gene, or a variety of genes at the same time. Availability of high quality antibodies that recognizes histones modified in a specific fashion further expanded the use of ChIP assays to analyze even minute changes in histone modification and nucleosomes structure. This chapter outlines the general strategies and protocols used to carry out ChIP assays to study the differential recruitment of transcription factors as well as histone modifications.

Key words

Chromatin immunoprecipitation Histone modification Methylation Acetylation 



Work in the Chellappan lab is supported by the grants CA139612 and CA127725 from the NCI.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Smitha Pillai
    • 1
  • Piyali Dasgupta
    • 1
    • 2
  • Srikumar P. Chellappan
    • 1
    Email author
  1. 1.Department of Tumor BiologyH. Lee Moffitt Cancer Center and Research InstituteTampaUSA
  2. 2.Department of Pharmacology, Physiology, and ToxicologyMarshall UniversityHuntingtonUSA

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