Protocol

Estrogen Receptors

Volume 1366 of the series Methods in Molecular Biology pp 53-65

Chromatin Immunoprecipitation Assay to Identify Genomic Binding Sites of Regulatory Factors

  • Meike WagnerAffiliated withDivision of Experimental and Translational Oncology, Institute of Immunology, University Medical Center of the Johannes Gutenberg University MainzTRON gGmbH-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz
  • , Johannes JungAffiliated withInstitute of Molecular Biology (IMB)
  • , Michael KoslowskiAffiliated withTRON gGmbH-Translational Oncology, University Medical Center of the Johannes Gutenberg University Mainz
  • , Özlem TüreciAffiliated withGanymed Pharmaceuticals AG
  • , Vijay K. TiwariAffiliated withInstitute of Molecular Biology (IMB) Email author 
  • , Ugur SahinAffiliated withDivision of Experimental and Translational Oncology, Institute of Immunology, University Medical Center of the Johannes Gutenberg University MainzTRON gGmbH-Translational Oncology, University Medical Center of the Johannes Gutenberg University MainzBioNTech AG Email author 

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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 Estrogen signal ing Cancer Estrogen receptor α