TY - CHAP
T1 - Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell—Part 1
T2 - Epigenomics Assays
AU - Cheng, Keren
AU - McCarrey, John R.
N1 - Publisher Copyright:
© 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2023
Y1 - 2023
N2 - Epigenomics encompasses analyses of a variety of different epigenetic parameters which, collectively, make up the epigenetic programming that dictates cell fate and function. Here, protocols are provided for four different epigenomic methods including whole-genome bisulfite sequencing (WGBS) to assess DNA methylation patterns, chromatin immunoprecipitation-sequencing (ChIP-seq) to assess genomic patterns of either specific histone modifications or bound transcription factors, the assay for transposase-accessible chromatin-sequencing (ATAC-seq) to assess genomic patterns of chromatin accessibility, and high-throughput chromosome conformation capture-sequencing (Hi-C-seq) to assess three-dimensional interactions among distant genomic regions, plus computational methodology to integrate data from those four methodologies using Chromatin State Discovery and Characterization (ChromHMM) to obtain the most comprehensive overall assessment of epigenetic programming.
AB - Epigenomics encompasses analyses of a variety of different epigenetic parameters which, collectively, make up the epigenetic programming that dictates cell fate and function. Here, protocols are provided for four different epigenomic methods including whole-genome bisulfite sequencing (WGBS) to assess DNA methylation patterns, chromatin immunoprecipitation-sequencing (ChIP-seq) to assess genomic patterns of either specific histone modifications or bound transcription factors, the assay for transposase-accessible chromatin-sequencing (ATAC-seq) to assess genomic patterns of chromatin accessibility, and high-throughput chromosome conformation capture-sequencing (Hi-C-seq) to assess three-dimensional interactions among distant genomic regions, plus computational methodology to integrate data from those four methodologies using Chromatin State Discovery and Characterization (ChromHMM) to obtain the most comprehensive overall assessment of epigenetic programming.
KW - Assay for transposase-accessible chromatin-sequencing (ATAC-seq)
KW - Chromatin State Discovery and Characterization (ChromHMM)
KW - Chromatin immunoprecipitation-sequencing (ChIP-seq)
KW - Epigenomic profiling
KW - High-throughput chromosome conformation capture (Hi-C)
KW - Multiparametric integrative analysis
KW - Whole-genome bisulfite sequencing (WGBS)
UR - http://www.scopus.com/inward/record.url?scp=85160876635&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85160876635&partnerID=8YFLogxK
U2 - 10.1007/978-1-0716-3139-3_5
DO - 10.1007/978-1-0716-3139-3_5
M3 - Chapter
C2 - 37249867
AN - SCOPUS:85160876635
T3 - Methods in Molecular Biology
SP - 71
EP - 108
BT - Methods in Molecular Biology
PB - Humana Press
ER -