TY - CHAP
T1 - In Vivo ChIP-Seq of nuclear receptors
T2 - A rough guide to transform frozen tissues into high-confidence genome-wide binding profiles
AU - Mir, Ashfaq Ali
AU - Dyar, Kenneth Allen
AU - Greulich, Franziska
AU - Quagliarini, Fabiana
AU - Jouffe, Céline
AU - Hubert, Michaël Jean
AU - Hemmer, Marie Charlotte
AU - Uhlenhaut, Nina Henriette
N1 - Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2019.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - ChIP-seq
KW - Chromatin immunoprecipitation
KW - Data analysis
KW - In vivo
KW - Nuclear receptors
UR - http://www.scopus.com/inward/record.url?scp=85065419332&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-9195-2_5
DO - 10.1007/978-1-4939-9195-2_5
M3 - Chapter
C2 - 31041738
AN - SCOPUS:85065419332
T3 - Methods in Molecular Biology
SP - 39
EP - 70
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -