Submitted to: Gordon Research Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: July 15, 2009
Publication Date: August 9, 2009
Citation: Li, C., Li, R.W., Elsasser, T.H. 2009. Epigenetic mechanisms of nutrient-induced modulation of gene expression and cellular functions. Gordon Research Conference Proceedings. Epigenetics. August 9-14, Holderness, NH.
Utilizing next-generation sequencing technology in combination with chromatin immunoprecipitation (ChIP) technology, our study provides systematic and novel insights into the relationships between nutrition and epigenetics. One paradigmatic example of nutrient-epigenetic-phenotype relationship is that of volatile fatty acids (VFA) and their gene expression regulation activities. VFA fulfill up to 70% of energy requirements in ruminant species. Our previous studies also revealed that VFA, especially butyrate, participate in metabolism as nutrients and also as inhibitors of histone deacetylases (HDAC), which are one of the most important types of epigenetic regulators. The profound changes in gene expression induced by butyrate in bovine cells elucidate the pleiotropic effects of histone acetylation. Using antibodies against nine conserved histone acetylation sites on H3 and H4 (K5, K8, K12 and K16 on H4 and K9, K14, K18, K23 and K27 on H3) and In-Cell Western Assay (LI-COR Biosciences) we demonstrated that major acetyl sites on H3 and H4 in bovine cells are responding to butyrate treatment in a dose-dependent manner.
Procedures for both X-ChIP (with cross-linking) and N-ChIP (native –ChIP) have been established in our lab using the Active Motif ChIP It Express Kit (Active Motif, Carlsbad, CA). From 10 million cultured MDBK cells and 50 microgram of antibodies (anti-H3 and acetyl H3 K9 and K27 respectively) we obtained 1 to 3 microgram of DNA which is sufficient for sequencing using Illumina’s Genome Analyzer II. Three DNA samples from ChIP generated chromatin (anti-acetyl H3 K9 and K27 from butyrate treated cells and anti-H3 from normal cells) were extracted. These DNA samples were sequenced using Illumina’s Genome Analyzer II (in house) and analyzed. 780, 219 and 358 Mb (mega bases) of sequences have been generated for ChIP samples of acetyl-H3 K9, acetyl-H3 K27 and H3 respectively. Initial analysis of selected sequence reads revealed widespread regulation of transcription. For example, the catenin alpha 3 and bitter taste receptor loci are among those potentially regulated by the H3 K9 acetylation.