Original Paper

Functional & Integrative Genomics

, Volume 12, Issue 1, pp 119-130

First online:

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

  • Joo Heon ShinAffiliated withLieber Institute for Brain Development, Johns Hopkins University
  • , Robert W. LiAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, ARS, USDA
  • , Yuan GaoAffiliated withLieber Institute for Brain Development, Johns Hopkins University
  • , Ransom BaldwinVIAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, ARS, USDA
  • , Cong-jun LiAffiliated withBovine Functional Genomics Laboratory, Animal and Natural Resources Institute, ARS, USDA Email author 

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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.

Keywords

Bovine Butyrate ChIP-seq Epigenomics Histone acetylation