Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscapes alteration in bovine cells

Authors: Li, Congjun - Cj; Li, Robert; GAO, YUAN - Johns Hopkins University; SHIN, JOO-HEON - Johns Hopkins University; Baldwin, Ransom - Randy

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/6/2011
Publication Date: 1/9/2012
Citation: Li, C., Li, R.W., Gao, Y., Shin, J., Baldwin, R.L. 2012. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscapes alteration in bovine cells [abstract]. Annual International Plant & Animal Genome Conference. W. 020.

Interpretive Summary:

Technical Abstract: Volatile short-chain fatty acids (VFAs, acetate, propionate, and butyrate) are nutrients especially critical to ruminants. Beyond their nutritional impact, clear evidence is beginning to link modifications in chromatin structure induced by butyrate to cell cycle progression, DNA replication and overall chromosome stability. Butyrate-induced biological effects in bovine cells provide an example of epigenetic regulation and provide a basis for understanding the full range of the biological roles and molecular mechanisms that butyrate may have in animal cell growth, proliferation and energy metabolism. This study was designed to utilize next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology, to comprehensively, quantitatively and cost-effectively analyze histone modification (acetylation) and to map protein target sites in the bovine genome that are responsive to modulation by VFAs. we analyzed histone modification (acetylation) induced by butyrate and the large-scale mapping of the epigenomic landscape of normal histone H3 and acetylated histone H3K9 and H3K27. 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). The 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. The epigenomic landscape modified by butyrate-induced histone acetylation and reported here is a crucial starting-point for an in-depth evaluation of the mechanisms involved in bovine rumen epithelial epigenomic regulation.