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United States Department of Agriculture

Agricultural Research Service

Research Project: Understanding Genetic and Physiological Factors Affecting Nutrient Use Efficiency of Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

Title: In vitro and in vivo study of transcriptome alternation induced by butyrate in cattle using deep RNA-seq

Authors
item LI, CONGJUN
item LI, ROBERT

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: November 28, 2012
Publication Date: January 11, 2013
Citation: Li, C., Li, R.W. 2013. In vitro and in vivo study of transcriptome alternation induced by butyrate in cattle using deep RNA-seq. Meeting Abstract. PAG XX Meeting.

Technical Abstract: Short-chain fatty acids (SCFAs,), especially butyrate, affect cell differentiation, proliferation, and motility. Furthermore, butyrate induces cell cycle arrest and apoptosis through its inhibition on histone deacetylases (HDACs). Butyrate is a potent inducer of histone hyper-acetylation in cells and provides an excellent in vitro/in vivo model to study the epigenomic regulation of gene expression induced by histone acetylation. We analyzed in vitro differential expression of genes induced by butyrate and the effect of butyrate on alternative splicing induced by butyrate in the bovine epithelial cell in vitro using deep RNA-sequencing technology (RNA-seq). In addition, the in vivo transcriptional effect of butyrate on the transcriptome of the rumen epithelium was quantified via serial biopsy sampling using high-throughput RNA-seq technology and bioinformatic tools. The initial reaction of the rumen epithelium to elevated exogenous butyrate may represent a stress response because Gene Ontology (GO) terms significantly enriched were predominantly related to biological processes such as response to bacteria and biotic stimuli. 216 differentially expressed transcript isoforms regulated by butyrate were detected. For example, Isoform 1 of ORC1 was strongly repressed by butyrate while Isoform 2 remained unchanged. Butyrate is a potent inhibitor of major HADCs. Our results also suggest that butyrate differentially regulated the expression of HDACs at gene- and isoform- levels. Our findings provide insight into the regulation of butyrate transport and metabolism in the rumen epithelium and transcriptome dynamics, which will guide our future efforts in exploiting potential beneficial effect of butyrate in animal well-being and human health.

Last Modified: 9/10/2014
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