Chromatin Immunoprecipitation Assay to Identify Genomic Binding Sites of Regulatory Factors

Part of the Methods in Molecular Biology book series (MIMB, volume 1366)

Abstract

DNA–protein interactions are vital to fundamental cellular events including transcription, replication, DNA repair, and recombination. Thus, their study holds the key to our understanding of mechanisms underlying normal development and homeostasis as well as disease. Transcriptional regulation is a highly complex process that involves recruitment of numerous factors resulting in formation of multi-protein complexes at gene promoters to regulate gene expression. The studied proteins can be, for example, transcription factors, epigenetic regulators, co-activators, co-repressors, or ligand-activated nuclear receptors as estrogen receptor-α (ERα) bound either directly to the DNA or indirectly by interaction with other DNA-bound factors. Chromatin immunoprecipitation (ChIP) assay is a powerful method to study interactions of proteins and a specific genomic DNA region. Recruitment of ERα to promoters of estrogen-dependent genes is a common mechanism to activate or enhance gene transcription in breast cancer thus promoting tumor progression. In this chapter, we demonstrate a stepwise protocol for ChIP assay using binding of ERα to its genomic targets after stimulation with 17β-estradiol (E2) in breast cancer cells as an example.

Key words

Chromatin ChIP assay DNA–protein interactions Gene regulation Estrogensignaling Cancer Estrogenreceptorα 

Notes

Acknowledgements

Research in the laboratory of V.K.T. is supported by the Wilhelm Sander Stiftung 2012.009.2, EpiGeneSys RISE1 program, Marie Curie CIG 322210 and Deutsche Forschungsgemeinschaft (DFG) Grant TI 799/1-1.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Meike Wagner
    • 1
    • 2
  • Johannes Jung
    • 3
  • Michael Koslowski
    • 2
  • Özlem Türeci
    • 4
  • Vijay K. Tiwari
    • 3
  • Ugur Sahin
    • 1
    • 2
    • 5
  1. 1.Division of Experimental and Translational Oncology, Institute of ImmunologyUniversity Medical Center of the Johannes Gutenberg University MainzMainzGermany
  2. 2.TRON gGmbH-Translational OncologyUniversity Medical Center of the Johannes Gutenberg University MainzMainzGermany
  3. 3.Institute of Molecular Biology (IMB)MainzGermany
  4. 4.Ganymed Pharmaceuticals AGMainzGermany
  5. 5.BioNTech AGMainzGermany

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