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Title: Transcriptome characterization by deep-RNA-sequencing underlies the mechanisms of butyrate-induced epigenomic regulation in bovine cells

Author
item SITAO, WU - University Of California
item Li, Robert
item LI, WIZHONG - University Of California
item Li, Congjun - Cj

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2012
Publication Date: 5/15/2012
Citation: Sitao, W., Li, R.W., Li, W., Li, C. 2012. Transcriptome characterization by deep-RNA-sequencing underlies the mechanisms of butyrate-induced epigenomic regulation in bovine cells. PLoS One. DOI:10.1371/journal.pone.0036940.

Interpretive Summary: Butyrate is an important nutrient for cattle. It also regulates the expression of genes and genomic functions. Using an advanced molecular biology technology (RNA sequencing), we obtained detailed information about the effects of butyrate on induced genomic functions. This detailed information provides a strong basis for understanding the molecular mechanisms of the biological effects of butyrate in normal bovine cells.

Technical Abstract: Volatile short-chain fatty acids (SCFAs, acetate, propionate, and butyrate), especially butyrate, alter cell differentiation, proliferation, motility, and in particular, induce cell cycle arrest and apoptosis through its histone deacetylase (HDAC) inhibition activity. Butyrate is a great inducer of the hyper-acetylation of histone in cells and provides an excellent in vitro model to study the epigenomic regulation of gene expression induced by histone acetylation. In order to achieve a comprehensive understanding of the biological effects caused by butyrate-induced histone acetylation, we analyzed differentially expressed genes detected by deep RNA-sequencing in a controlled MDBK cell cultivation process. RNA-Seq analyses were performed on eight independent replicate RNA samples from both the MDBK cells with or without butyrate treatment. The Illumina Genome Analyzer yielded a total number of reads for each sample ranging from 57,303,693 to 78,933,744. There are 11408 genes that are significantly differentially expressed in both terms of false discovery rate (FDR) and p-value <0.05. Changes of cell functions related the differentially expressed genes are underlying the mechanisms for the essential biological effects of butyrate treatment such as cell morphological changes, cell cycle arrest and apoptosis. Transcriptomic profiling of MDBK cells and a comparison of normal transcription activities and transcription activities in butyrate-treated cell provide a detailed knowledge of changes in gene expression induced by butyrate. This detailed information provides a strong basis for understanding the molecular mechanisms of the biological effects of butyrate in normal cells.