Functional & Integrative Genomics

, Volume 12, Issue 1, pp 119–130

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

Authors

  • Joo Heon Shin
    • Lieber Institute for Brain DevelopmentJohns Hopkins University
  • Robert W. Li
    • Bovine Functional Genomics Laboratory, Animal and Natural Resources InstituteARS, USDA
  • Yuan Gao
    • Lieber Institute for Brain DevelopmentJohns Hopkins University
  • Ransom BaldwinVI
    • Bovine Functional Genomics Laboratory, Animal and Natural Resources InstituteARS, USDA
    • Bovine Functional Genomics Laboratory, Animal and Natural Resources InstituteARS, USDA
Original Paper

DOI: 10.1007/s10142-012-0263-6

Cite this article as:
Shin, J.H., Li, R.W., Gao, Y. et al. Funct Integr Genomics (2012) 12: 119. doi:10.1007/s10142-012-0263-6

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

BovineButyrateChIP-seqEpigenomicsHistone acetylation

Supplementary material

10142_2012_263_MOESM1_ESM.bmp (12.6 mb)
High-resolution image file (BMP 12,870 kb)
10142_2012_263_MOESM2_ESM.xls (771 kb)
ESM 1XLS 771 kb
10142_2012_263_MOESM3_ESM.xls (417 kb)
ESM 2XLS 416 kb
10142_2012_263_MOESM4_ESM.xls (2.2 mb)
ESM 3XLS 2,298 kb

Copyright information

© Springer-Verlag (outside the USA) 2012