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

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

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2012
Publication Date: 1/17/2012
Citation: Heon Shin, J., Li, R.W., Gao, Y., Baldwin, R.L., Li, C. 2012. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscape alteration in bovine cells. Functional and Integrative Genomics. 12(1):119-130.

Interpretive Summary: Genomic DNA is surrounded by histone. Histone modifications are important regulation mechanisms controlling gene expression. Butyrate can induce histone modification. Using next generation sequencing and chromatin-immunoprecipitation technology, we analyzed histone modification induced by butyrate by mapping the binding sites of normal histone H3 and modified histone H3. The changes of histone binding sites modified by butyrate-induced histone modification reported here is a crucial starting-point for an in-depth evaluation of the mechanisms involved in bovine rumen epithelial epigenomic regulation.

Technical Abstract: Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology, 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. Key words: bovine; butyrate; ChIP-seq; epigenomics; histone acetylation.