Genome-Wide Characterization of cis Natural Antisense Transcripts during Skeletal Muscle Development of Pigs

Understanding the mechanism of muscle development is very important for meat production. Many studies focused on the characterization of the mRNA expression in the skeletal muscle tissue of pigs, but few studies focused on the cis natural antisense transcripts (cis –NATs). Moreover, there is still lack of understanding on the expression characteristics, biological functions and regulation mechanisms of cis –NATs in different muscle development stages of the pig. In this study, we systematically identified cis –NATs and their expression characteristics in longissimus dorsi muscle by using 26 RNA-seq libraries data of Lantang, an endogenous pig breed of China, Landrace and Yorkshire pig breeds. According to our results, 1790 genes were detected with antisense transcript, which contained 1915 cis natural antisense transcript regions. The Large-scale expression profiling analysis of cis –NATs indicated that more than 1300 cis –NATs were stage-specific expression. We also found significant (p<0.05) correlation, in both breeds, between expression of more than 800 sense and cis –NAT pairs across stages. Moreover, results of function annotation using DAVID Bioinformatics Resources 6.7 displayed that, in both breeds, DE transcripts were significant (p< 0.05) enriched in Glycolysis / Gluconeogenesis, Insulin signaling pathway etc. muscle development related pathways. Also, mitochondria expressed genes of Alzheimer's disease, Huntington's disease and Parkinson's disease were also enriched.