Alternative splicing regulated by butyrate in the bovine epithelial cell

As a signaling molecule and a potent inhibitor of histone deacetylases (HADCs), butyrate exerts its impacts on a broad of biological processes, such as apoptosis and cell proliferation, in addition to its critical role in energy metabolism in ruminants. In this study, we examined the effect of butyrate on alternative splicing in the bovine epithelial cell using RNA-seq technology. Junction reads account for 11.28 and 12.32% of total mapped reads between the butyrate-treated (BT) and control groups (P<0.001). 201,326 potential splicing junctions detected were supported by = 3 junction reads. Approximately 94% of these junctions conformed to the consensus sequence (GT/AG) while ~ 3% were GC/AG junctions. No AT/AC junctions were observed. A total of 2,834 exon skipping events, supported by a minimum of 3 junction reads, were detected. At least 7 genes, their mRNA expression significantly affected by butyrate, also had exon skipping events differentially regulated by butyrate. COL5A3, which was induced 310-fold by butyrate (FDR <0.001) at the gene level, had significantly higher number of junction reads mapped to Exon#8 (Donor) and Exon#11 (Acceptor) in BT. This event had potential to result in the formation of a COL5A3 mRNA isoform with 2 of the 69 exons missing. In addition, 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 suggest that butyrate also differentially regulated the expression of HDACs at gene- and isoform- levels. In addition, thirteen gene fusion events differentially affected by butyrate were identified. Our results provided a snapshot into complex transcriptome dynamics regulated by butyrate, which will facilitate our understanding of biological effect of butyrate and other HDAC inhibitors.