Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell—Part 1: Epigenomics Assays

Keren Cheng, John R. McCarrey

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press
Pages71-108
Number of pages38
DOIs
StatePublished - 2023
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume2656
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Assay for transposase-accessible chromatin-sequencing (ATAC-seq)
  • Chromatin State Discovery and Characterization (ChromHMM)
  • Chromatin immunoprecipitation-sequencing (ChIP-seq)
  • Epigenomic profiling
  • High-throughput chromosome conformation capture (Hi-C)
  • Multiparametric integrative analysis
  • Whole-genome bisulfite sequencing (WGBS)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Fingerprint

Dive into the research topics of 'Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell—Part 1: Epigenomics Assays'. Together they form a unique fingerprint.

Cite this