Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors

Meike Wagner, Johannes Jung, Michael Koslowski, Özlem Türeci, Vijay K. Tiwari, Ugur Sahin

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

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 pro- cess 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 pro- teins and a specifi c 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 (E 2 ) in breast cancer cells as an example.
LanguageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.,U.S.
Pages53-65
Number of pages13
DOIs
Publication statusPublished - 01 Jan 2016

Publication series

NameMethods in Molecular Biology
Volume1366

Fingerprint

Chromatin Immunoprecipitation
Estrogen Receptor alpha
Binding Sites
DNA
Proteins
Breast Neoplasms
Genes
Co-Repressor Proteins
Cytoplasmic and Nuclear Receptors
Epigenomics
DNA Repair
Genetic Recombination
Estradiol
Estrogens
Homeostasis
Transcription Factors
Ligands
Gene Expression
Neoplasms

Keywords

  • Cancer
  • ChIP assay
  • Chromatin
  • DNA-protein interactions
  • Estrogenreceptorα
  • Estrogensignaling
  • Gene regulation

Cite this

Wagner, M., Jung, J., Koslowski, M., Türeci, Ö., Tiwari, V. K., & Sahin, U. (2016). Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors. In Methods in Molecular Biology (pp. 53-65). (Methods in Molecular Biology; Vol. 1366). Humana Press Inc.,U.S.. https://doi.org/10.1007/978-1-4939-3127-9_6
Wagner, Meike ; Jung, Johannes ; Koslowski, Michael ; Türeci, Özlem ; Tiwari, Vijay K. ; Sahin, Ugur. / Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors. Methods in Molecular Biology. Humana Press Inc.,U.S., 2016. pp. 53-65 (Methods in Molecular Biology).
@inbook{e3b4dfad2cb6486ea32c720a28b91f70,
title = "Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors",
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 pro- cess 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 pro- teins and a specifi c 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 (E 2 ) in breast cancer cells as an example.",
keywords = "Cancer, ChIP assay, Chromatin, DNA-protein interactions, Estrogenreceptorα, Estrogensignaling, Gene regulation",
author = "Meike Wagner and Johannes Jung and Michael Koslowski and {\"O}zlem T{\"u}reci and Tiwari, {Vijay K.} and Ugur Sahin",
year = "2016",
month = "1",
day = "1",
doi = "10.1007/978-1-4939-3127-9_6",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.,U.S.",
pages = "53--65",
booktitle = "Methods in Molecular Biology",

}

Wagner, M, Jung, J, Koslowski, M, Türeci, Ö, Tiwari, VK & Sahin, U 2016, Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1366, Humana Press Inc.,U.S., pp. 53-65. https://doi.org/10.1007/978-1-4939-3127-9_6

Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors. / Wagner, Meike; Jung, Johannes; Koslowski, Michael; Türeci, Özlem; Tiwari, Vijay K.; Sahin, Ugur.

Methods in Molecular Biology. Humana Press Inc.,U.S., 2016. p. 53-65 (Methods in Molecular Biology; Vol. 1366).

Research output: Chapter in Book/Report/Conference proceedingChapter

TY - CHAP

T1 - Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors

AU - Wagner, Meike

AU - Jung, Johannes

AU - Koslowski, Michael

AU - Türeci, Özlem

AU - Tiwari, Vijay K.

AU - Sahin, Ugur

PY - 2016/1/1

Y1 - 2016/1/1

N2 - 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 pro- cess 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 pro- teins and a specifi c 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 (E 2 ) in breast cancer cells as an example.

AB - 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 pro- cess 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 pro- teins and a specifi c 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 (E 2 ) in breast cancer cells as an example.

KW - Cancer

KW - ChIP assay

KW - Chromatin

KW - DNA-protein interactions

KW - Estrogenreceptorα

KW - Estrogensignaling

KW - Gene regulation

UR - http://www.mendeley.com/research/chromatin-immunoprecipitation-assay-identify-genomic-binding-sites-regulatory-factors

U2 - 10.1007/978-1-4939-3127-9_6

DO - 10.1007/978-1-4939-3127-9_6

M3 - Chapter

T3 - Methods in Molecular Biology

SP - 53

EP - 65

BT - Methods in Molecular Biology

PB - Humana Press Inc.,U.S.

ER -

Wagner M, Jung J, Koslowski M, Türeci Ö, Tiwari VK, Sahin U. Chromatin immunoprecipitation assay to identify genomic binding sites of regulatory factors. In Methods in Molecular Biology. Humana Press Inc.,U.S. 2016. p. 53-65. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-3127-9_6