Transcriptome Characterization by RNA-seq Unravels the Mechanisms of Butyrate-Induced Epigenomic Regulation in Bovine Cells

Abstract

Short-chain fatty acids (SCFAs), especially butyrate, affect cell differentiation, proliferation, and motility. Butyrate also induces cell cycle arrest and apoptosis through its inhibition of histone deacetylases (HDACs). In addition, butyrate is a potent inducer of histone hyper-acetylation in cells. Therefore, this SCFA provides an excellent in vitro model for studying the epigenomic regulation of gene expression induced by histone acetylation. In this study, we analyzed the differential in vitro expression of genes induced by butyrate in bovine epithelial cells by using deep RNA-sequencing technology (RNA-seq). The number of sequences read, ranging from 57,303,693 to 78,933,744, were generated per sample. Approximately 11,408 genes were significantly impacted by butyrate, with a false discovery rate (FDR) <0.05. The predominant cellular processes affected by butyrate included cell morphological changes, cell cycle arrest, and apoptosis. Our results provided insight into the transcriptome alterations induced by butyrate, which will undoubtedly facilitate our understanding of the molecular mechanisms underlying butyrate-induced epigenomic regulation in bovine cells.

Dietary Inhibitors of Histone Deacetylases in Intestinal Immunity and Homeostasis

“…One possibility is that butyrate inhibits deacetylation, but not HDAC activity directly (42). However, earlier studies have addressed the potential of SCFAs to alter epigenetic marks in epithelial cells (43). In particular the SCFA butyrate inhibits all class I HDACs.…”

“…In bovine epithelial cell cultures, RNA sequencing analyses revealed that the expression of HDACs was modulated by butyrate treatment. Whereas the expression of HCACs 7, 8, and 9 are down-regulated, HDACs 5 and 11 are up-regulated (43). It is to be determined why inhibition of enzymatic activities, seemingly regulates their own expression at the mRNA level.…”

“…FFAR2 is expressed in immune cells: mast cells, B lymphocytes, monocytes, eosinophils, and also neutrophils, in which FFAR2 is the only functional receptor for SCFAs in mice. Expression of FFAR2 on immune cells seems to be important in the regulation of immune responses, since mice lacking FFAR2 develop exacerbated inflammation in models for colitis, asthma, and arthritis due to higher production of inflammatory mediators and increased recruitment of immune cells (43, 53). The expression of FFAR2 is also needed for the SCFA-mediated regulation of size and function of the colonic regulatory T-cell pool (54).…”

Short-Chain Fatty Acids Regulate Secretion of IL-8 from Human Intestinal Epithelial Cell Linesin vitro

“…Inhibitory effect of SCFAs, particularly butyrate, on the expression of IL-8 mRNA was evident, resulting in reduction of IL-8 protein in the supernatant, indicating that the mechanism of IL-8 reduction may be mediated through the inhibition of IL-8 gene expression via inhibition of HDAC (Licciardi et al, 2011;Vinolo et al, 2011;Wu et al, 2012;Schilderink et al, 2013). The different effects of SCFAs in normal versus cancerous cells or inflamed cells may be useful in formulation of the more effective drug that inhibit the inflammation, particularly in IBD with stimulate the growth of normal cells and induce apoptosis in cancer cells.…”

Comparative epigenetics: relevance to the regulation of production and health traits in cattle

“…In bovine studies, butyrate-induced IGF2 activation has been shown to be correlated with distinct histone modification changes, identified by ChIP-seq technology (Shin et al 2013). Another recent in vitro mRNA-sequencing study analysed the response of bovine epithelial cells to butyrate and identified 11 408 significantly differentially expressed genes (Wu et al 2012). This confirms that widespread transcriptomic changes are induced by this VFA, some of which are likely to be epigenetically regulated.…”