A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells

J. H. Shin, L. Xu, R. W. Li, Y. Gao, D. Bickhart, G. E. Liu, R. Baldwin, C. J. Li

Research output: Contribution to journalArticle

Abstract

Summary This report presents a study utilizing next-generation sequencing technology, combined with chromatin immunoprecipitation (ChIP-seq) technology to analyze histone modification induced by butyrate and to construct a high-definition map of the epigenomic landscape with normal histone H3 and H4 and their variants in bovine cells at the whole-genome scale. A total of 10 variants of histone H3 and H4 modifications were mapped at the whole-genome scale (acetyl-H3K18-ChIP-seq, trimethy-H3K9, histone H4 ChIP-seq, acetyl-H4K5 ChIP-seq, acetyl-H4K12 ChIP-seq, acetyl-H4K16 ChIP-seq, histone H3 ChIP-seq, acetyl H3H9 ChIP-seq, acetyl H3K27 ChIP-seq and tetra-acetyl H4 ChIP-seq). Integrated experiential data and an analysis of histone and histone modification at a single base resolution across the entire genome are presented. We analyzed the enriched binding regions in the proximal promoter (within 5 kb upstream or at the 5′-untranslated region from the transcriptional start site (TSS)), and the exon, intron and intergenic regions (defined by regions 25 kb upstream and 10 kb downstream from the TSS). A de novo search for the binding motif of the 10 ChIP-seq datasets discovered numerous motifs from each of the ChIP-seq datasets. These consensus sequences indicated that histone modification at different locations changes the histone H3 and H4 binding preferences. Nevertheless, a high degree of conservation in histone binding also was presented in these motifs. This first extensive epigenomic landscape mapping in bovine cells offers a new framework and a great resource for testing the role of epigenomes in cell function and transcriptomic regulation.

Original languageEnglish (US)
Pages (from-to)40-50
Number of pages11
JournalAnimal Genetics
Volume45
Issue numberSUPPL.1
DOIs
StatePublished - Jan 1 2014

Keywords

  • ChIP-seq
  • butyrate
  • epigenetics
  • epigenomics
  • gene
  • histone acetylation
  • histone modification
  • regulation

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

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    Shin, J. H., Xu, L., Li, R. W., Gao, Y., Bickhart, D., Liu, G. E., Baldwin, R., & Li, C. J. (2014). A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics, 45(SUPPL.1), 40-50. https://doi.org/10.1111/age.12147