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A high‐resolution whole‐genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells
Author(s) -
Shin J. H.,
Xu L.,
Li R. W.,
Gao Y.,
Bickhart D.,
Liu G. E.,
Baldwin R.,
Li C.J.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12147
Subject(s) - epigenomics , biology , chromatin immunoprecipitation , histone , genetics , histone h3 , histone h4 , histone code , h3k4me3 , computational biology , nucleosome , gene , promoter , dna methylation , gene expression
Summary This report presents a study utilizing next‐generation sequencing technology, combined with chromatin immunoprecipitation (Ch IP ‐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‐Ch IP ‐seq, trimethy‐H3K9, histone H4 Ch IP ‐seq, acetyl‐H4K5 Ch IP ‐seq, acetyl‐H4K12 Ch IP ‐seq, acetyl‐H4K16 Ch IP ‐seq, histone H3 Ch IP ‐seq, acetyl H3H9 Ch IP ‐seq, acetyl H3K27 Ch IP ‐seq and tetra‐acetyl H4 Ch IP ‐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 Ch IP ‐seq datasets discovered numerous motifs from each of the Ch IP ‐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.