Abstract
MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.
Highlights
Hepatic cell proliferation, hepatic metabolism of nutrients, energy metabolism and detoxification[26]
The differential expression P-values for quantitative PCR (qPCR) results were not as low as those for RNAseq, which might be related to sensitivity differences between the two methods regarding profiling gene expression[31], we observed that the Pearson correlation coefficients were high (0.73 – 0.99) between the qPCR and RNAseq profiles and significant (6.79E−03 to 6.00E−10) (Table S5 in the Supplementary File 1), which indicates that the RNAseq results were highly reproducible
With a context++ score percentile > 50, it was revealed that 61.1% (44 differentially expressed (DE) genes), 75.6% (31 DE genes) and 73.7% of the previously identified DE genes were predicted as potential targets of the DE miRNAs in Angus, Charolais, and Kinsella Composite (KC) steers, respectively. These target DE genes are mainly involved in lipid metabolism, molecular transport, small molecule biochemistry, energy production, carbohydrate metabolism, cellular movement, cell-to-cell signaling and interaction, cell death and survival, amino acid metabolism and vitamin and mineral metabolism, implying that these identified DE miRNAs influence feed efficiency through differential modulation of these biological functions in the liver
Summary
Hepatic cell proliferation, hepatic metabolism of nutrients (including lipids, carbohydrates, vitamins and minerals, and proteins and amino acids), energy metabolism and detoxification[26]. Previous transcriptomic studies have revealed the involvement of hepatic tissue in the molecular control of feed efficiency through identification of differentially expressed genes between efficient and inefficient animals[10,11,12,14,15,17,18]. In our most recent studies we detected multiple differentially expressed genes associated with feed efficiency traits, some of which are involved in key hepatic functions such as lipid metabolism, energy production, amino acid metabolism, and carbohydrate metabolism in beef cattle[18,27]. In this study we aimed to profile the hepatic miRNAome of beef steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC), and to identify miRNAs associated with residual feed intake (RFI), a common measurement of feed efficiency, through small RNAseq differential expression analyses
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