Two-step cross-linking for analysis of protein-chromatin interactions

Bing Tian, Jun Yang, Allan R. Brasier

Research output: Chapter in Book/Report/Conference proceedingChapter

51 Citations (Scopus)

Abstract

Eukaryotic gene regulation is controlled, in part, by inducible transcription factor-binding regulatory sequences in a tissue-specific and hormone-responsive manner. The development of methods for the analysis of transcription factor interaction within native chromatin has been a significant advance for the systematic analyses of the timing of gene regulation and studies on the effects of chromatin modifying enzymes on promoter accessibility. Chromatin immunoprecipitation (ChIP) is a specific method involving formaldehyde mediated protein-chromatin fixation to preserve the interaction for subsequent target identification. However, the conventional single-step cross-linking technique does not preserve all protein-DNA interactions, especially for transcription factors in hyper-dynamic equilibrium with chromatin or for coactivator interactions. Here, we describe a versatile, efficient "two-step" XChIP method that involves sequential protein-protein fixation followed by protein-DNA fixation. This method has been used successfully for analysis of chromatin binding for transcription factors (NF-κB, STAT3), polymerases (RNA Pol II), coactivators (CBP/p300, CDK9), and chromatin structural proteins (modified histones). Modifications of DNA extraction and sonication suitable for downstream target identification by quantitative genomic PCR and next generation sequencing are described.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages105-120
Number of pages16
Volume809
DOIs
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
Volume809
ISSN (Print)10643745

Fingerprint

Chromatin
Transcription Factors
Proteins
DNA
p300-CBP Transcription Factors
Sonication
RNA Polymerase II
Chromatin Immunoprecipitation
Histones
Formaldehyde
Genes
Hormones
Polymerase Chain Reaction
Enzymes

Keywords

  • Chromatin immunoprecipitation
  • Next generation sequencing
  • Nuclear factor-κB
  • Polymerase chain reaction

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Tian, B., Yang, J., & Brasier, A. R. (2012). Two-step cross-linking for analysis of protein-chromatin interactions. In Methods in Molecular Biology (Vol. 809, pp. 105-120). (Methods in Molecular Biology; Vol. 809). https://doi.org/10.1007/978-1-61779-376-9_7

Two-step cross-linking for analysis of protein-chromatin interactions. / Tian, Bing; Yang, Jun; Brasier, Allan R.

Methods in Molecular Biology. Vol. 809 2012. p. 105-120 (Methods in Molecular Biology; Vol. 809).

Research output: Chapter in Book/Report/Conference proceedingChapter

Tian, B, Yang, J & Brasier, AR 2012, Two-step cross-linking for analysis of protein-chromatin interactions. in Methods in Molecular Biology. vol. 809, Methods in Molecular Biology, vol. 809, pp. 105-120. https://doi.org/10.1007/978-1-61779-376-9_7
Tian B, Yang J, Brasier AR. Two-step cross-linking for analysis of protein-chromatin interactions. In Methods in Molecular Biology. Vol. 809. 2012. p. 105-120. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-376-9_7
Tian, Bing ; Yang, Jun ; Brasier, Allan R. / Two-step cross-linking for analysis of protein-chromatin interactions. Methods in Molecular Biology. Vol. 809 2012. pp. 105-120 (Methods in Molecular Biology).
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