Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells

Joo Heon Shin, Robert W. Li, Yuan Gao, Ransom Baldwin VI, Cong Jun Li

Research output: Contribution to journalArticle

Abstract

Butyrate-induced histone acetylation plays an important role in the regulation of gene expression. However, the regulation mechanisms of histone modification remain largely unclear. To comprehensively analyze histone modification induced by butyrate, we utilized chromatin immunoprecipitation (ChIP) technology combined with next-generation sequencing technology (ChIP-seq) to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3 and acetylated histone H3K9 and H3K27 on a large scale. To determine the location of histone H3, acetyl-H3K9, and acetyl-H3K27 binding sites within the bovine genome, we analyzed the H3-, acetyl-H3K9-, and acetyl-H3K27-enriched binding regions in the proximal promoter within 5 kb upstream, or at the 5′ untranslated region (UTR) from the transcriptional start site (TSS), exon, intron, and intergenic regions (defined as regions 25 kb upstream or 10 kb downstream from the TSS). Our analysis indicated that the distribution of histone H3, acetyl-H3K9, and acetyl-H3K27 correlated with transcription activity induced by butyrate. Using the GADEM algorithm, several motifs were generated for each of the ChIP-seq datasets. A de novo search for H3, acetyl-H3K9, and acetyl-H3K27 binding motifs indicated that histone modification (acetylation) at various locations changes the histone H3 binding preferences. Our results reveal that butyrate-induced acetylation in H3K9 and H3K27 changes the sequence-based binding preference of histone H3 and underlies the potential mechanisms of gene expression regulation induced by butyrate.

Original languageEnglish (US)
Pages (from-to)119-130
Number of pages12
JournalFunctional and Integrative Genomics
Volume12
Issue number1
DOIs
StatePublished - Mar 1 2012

Fingerprint

Butyrates
Chromatin Immunoprecipitation
Acetylation
Histones
Histone Code
Genome
Gene Expression Regulation
Technology
Intergenic DNA
5' Untranslated Regions
Epigenomics
Introns
Exons
Binding Sites

Keywords

  • Bovine
  • Butyrate
  • ChIP-seq
  • Epigenomics
  • Histone acetylation

ASJC Scopus subject areas

  • Genetics

Cite this

Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. / Shin, Joo Heon; Li, Robert W.; Gao, Yuan; Baldwin VI, Ransom; Li, Cong Jun.

In: Functional and Integrative Genomics, Vol. 12, No. 1, 01.03.2012, p. 119-130.

Research output: Contribution to journalArticle

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