In Vivo ChIP-Seq of nuclear receptors: A rough guide to transform frozen tissues into high-confidence genome-wide binding profiles

Ashfaq Ali Mir, Kenneth Allen Dyar, Franziska Greulich, Fabiana Quagliarini, Céline Jouffe, Michaël Jean Hubert, Marie Charlotte Hemmer, Nina Henriette Uhlenhaut

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

7 Scopus citations

Abstract

Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-seq) is a powerful tool to map context-dependent genome-wide binding of nuclear hormone receptors and their coregulators. This information can provide important mechanistic insight into where, when and how DNA–protein interactions are linked to target gene regulation. Here we describe a simple, yet reliable ChIP-seq method, including nuclear isolation from frozen tissue samples, cross-linking DNA–protein complexes, chromatin shearing, immunoprecipitation, and purification of ChIP DNA. We also include a standard ChIP-seq data analysis pipeline to elaborate and analyze raw single-end or paired-end sequencing data, including quality control steps, peak calling, annotation, and motif enrichment.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages39-70
Number of pages32
DOIs
StatePublished - 2019
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1966
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • ChIP-seq
  • Chromatin immunoprecipitation
  • Data analysis
  • In vivo
  • Nuclear receptors

Fingerprint

Dive into the research topics of 'In Vivo ChIP-Seq of nuclear receptors: A rough guide to transform frozen tissues into high-confidence genome-wide binding profiles'. Together they form a unique fingerprint.

Cite this