Comprehensive analysis of lncRNAs and circRNAs reflects the functional specialization in oxidative and glycolytic skeletal muscles

The biochemical and functional differences between oxidative and glycolytic muscles affect human muscle health and animal meat quality, but the epigenetic regulation with respect to lncRNAs and circRNAs remains largely unknown. Here, we employed porcine oxidative and glycolytic skeletal muscles, at growth curve inflection point, to survey variant global lncRNAs and circRNAs expression using RNA-seq. In total, we obtained 540 million raw reads approximately 81.02 Gb of high quality data. After a strict filtering process, 4,046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including oxidation-reduction process, glycolytic process, fatty acid metabolic, PPAR signaling pathway, which are closely related to the different phenotypes between oxidative and glycolytic muscles. Additional, we also identified 810 circRNAs, 137 of them were differentially expressed (p < 0.05). The host genes of circRNAs were related to motor activity, transition between fast and slow fiber and ATP metabolic process by function enrichment analysis. Interestingly, we found circRNA290-miR27b-Foxj3 and circRNA9210-miR-23a-MEF2C taken as two competing endogenous network, which was closely linked to muscle fiber-type switching. circRNA41-miR-217-SIRT1 network was connected with mitochondria biogenesis in muscle. Furthermore, we found 44.69%, 39.19% and 54.01% of differentially expressed mRNAs, lncRNAs and circRNAs were siginificantly enriched pig QTL regions (traits of meat quality and growing development), respectively. Togeter, this study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological function, which improve understanding of muscle metabolism and development from epigenetic perspectives. Overall design: lncRNA profiles of porcine oxidative and glycolytic skeletal muscles were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 4000.

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Shen L, Gan M, Tang Q, Tang G, Jiang Y, Li M, Chen L, Bai L, Shuai S, Wang J, Li X, Liao K, Zhang S, Zhu L