RNA-sequencing reveals the metabolism regulation mechanism of sheep skeletal muscle under nutrition deprivation stress.

Although the skeletal muscle is one of the main sites of metabolism, little is known about the molecular mechanisms involving its response to nutrition stress. The aim of the study was to screen the transcriptome of sheep muscle to identify the metabolism-related genes under nutrition deprivation stress. Ten healthy adult female Small-tailed Han sheep with similar age and weight were randomly divided into a normal group and fasted group. After 3 days, three sheep were randomly selected from each group and the semitendinosus samples were subjected to RNA-sequencing (RNA-seq) and a series of analyses and function annotations. Compared with the normal group, 391 differentially expressed genes (DEGs) were identified in the fasted group that had obvious weight loss, including 278 down-regulated and 113 up-regulated genes. Gene Ontology enrichment annotation classified 228 DEGs in the metabolic process, 11 of which were new genes and only Sheep_newGene_4578 had been annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results of Clusters of Orthologous Groups annotation indicated that 11, 9, and 4 DEGs were respectively classified in lipid transport and metabolism, amino acid transport and metabolism, and carbohydrate transport and metabolism. In addition, KEGG enrichment analysis showed that there were not only pathways which were directly related to metabolisms such as protein digestion and absorption pathway, fatty acid metabolism pathway, and biosynthesis pathway of unsaturated fatty acids, but also PI3K-AKT pathway, AMPK pathway, MAPK pathway, and FoxO pathway which were important to metabolism among the top 20 pathways with the lowest significant Q value. The MCODE analysis of protein-protein interaction revealed that two identified subnetworks with top score were closely associated with metabolism. The correlation analysis showed that the mRNA levels of most of DEGs that might be related in the two subnetworks were significantly correlated respectively, and the mRNA levels of most of 10 metabolism-related DEGs including Sheep_newGene_4578 were significantly correlated. Finally, 16 random and 10 metabolism-related DEGs were chosen for confirmation by quantitative real-time PCR, demonstrating the same expression change as determined by RNA-seq. In conclusion, multiple interrelated metabolism-related DEGs in skeletal muscle contributed to the response of sheep to nutritional deprivation stress.