Genome-Wide Profiling of Histone Modifications with ChIP-Seq

Methods Mol Biol. 2020:2072:101-117. doi: 10.1007/978-1-4939-9865-4_9.

Abstract

Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a widely used method for mapping the genome-wide locations of chromatin-associated proteins. This protocol has been developed and utilized to perform ChIP on histone covalent modifications in various plant species including cereals. DNA and chromatin-associated proteins are crosslinked with formaldehyde. Chromatin is then isolated from nuclei and sheared via sonication. Antibodies targeting the histone modification of interest are incubated with the sheared chromatin and nonspecific interactions are washed away. DNA is purified via phenol-chloroform extraction, end-repaired, ligated to sequencing adapters, and PCR-amplified.

Keywords: Antibody; Cereals; Chip-seq; Chromatin immunoprecipitation; Epigenomics; Histone modification; Nuclei; Plant.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatin / genetics*
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation Sequencing* / methods
  • Epigenesis, Genetic
  • Gene Expression Regulation, Plant
  • Genome-Wide Association Study* / methods
  • High-Throughput Nucleotide Sequencing
  • Histones / metabolism*
  • Plants / genetics
  • Polymerase Chain Reaction
  • Protein Processing, Post-Translational*
  • Sequence Analysis, DNA

Substances

  • Chromatin
  • Histones