|Shin, Joo Heon - Johns Hopkins University|
|Xu, Lingyang - University Of Maryland|
|Gao, Yuan - Johns Hopkins University|
|Liu, Ge - George|
|Baldwin, Ransom - Randy|
Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2014
Publication Date: 7/1/2014
Citation: Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.
Interpretive Summary: Butyrate is an important nutrient for cattle. It also can regulate how genes behave by affecting histones on DNA. Histones are proteins that surround DNA and allow it to be greatly folded and compacted. They are important in gene regulation, DNA repair, and cell division. The DNA-histone complex is called the ‘epigenome.’ To better understand how butyrate affects gene regulation and the epigenome, we used a modern technology called ChIP-sequencing to construct the first detailed map of histone interactions with the cattle genome, known as epigenetic landscape mapping. This map provides a new framework and resource for scientists testing the role of the epigenome in gene function of cattle.
Technical 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, 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’untranslateded region (UTR) 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 data sets. 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 was also 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.