title: A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells.
abstract: 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.
authors.affiliation: Lieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe Street, Suite 102, Baltimore, MD, 21205, USA.
authors.forename: J H
authors.initials: JH
authors.lastname: Shin
authors.forename: L
authors.initials: L
authors.lastname: Xu
authors.forename: R W
authors.initials: RW
authors.lastname: Li
authors.forename: Y
authors.initials: Y
authors.lastname: Gao
authors.forename: D
authors.initials: D
authors.lastname: Bickhart
authors.forename: G E
authors.initials: GE
authors.lastname: Liu
authors.forename: R
authors.initials: R
authors.lastname: Baldwin
authors.forename: C-J
authors.initials: CJ
authors.lastname: Li
mesh_terms: D000818:Animals; D002087:Butyrates / Q000494:pharmacology*; D002417:Cattle / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000662:veterinary; D057890:Epigenomics / Q000379:methods*; D016678:Genome / Q000187:drug effects* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000662:veterinary; D006657:Histones / Q000187:drug effects / Q000378:metabolism*
chemical_list: D002087:Butyrates; D006657:Histones
keywords: ChIP-seq; butyrate; epigenetics; epigenomics; gene; histone acetylation; histone modification; regulation