Expression of circular RNAs during C2C12 myoblast differentiation and prediction of coding potential based on the number of open reading frames and N6-methyladenosine motifs

Abstract

The importance of circular RNAs (circRNAs) as regulators of muscle development and muscle-associated disorders is becoming increasingly apparent. To explore potential regulators of muscle differentiation, we determined the expression profiles of circRNAs of skeletal muscle C2C12 myoblasts and myotubes using microarray analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore circRNA functions. We also established competing endogenous RNA (ceRNA) networks using bioinformatics methods and predicted the coding potential of differentially expressed circRNAs. We found that 581 circRNAs were differentially regulated between C2C12 myoblasts and myotubes. Bioinformatics analysis suggested that the primary functions of the linear transcripts of the circRNAs were linked with organization of the cytoskeleton, calcium signaling, cell cycle, and metabolic pathways. ceRNA networks showed that the myogenic-specific genes myogenin, myocyte enhancer factor 2a, myosin heavy chain (Myh)-1, Myh7, and Myh7b could combine with 91 miRNAs and the top 30 upregulated circRNAs, forming 239 edges. According to the number of open reading frames and N-methyladenosine motifs, we identified 224 circRNAs with coding potential, and performed GO and KEGG analyses based on the linear counterparts of 75 circRNAs. We determined that the 75 circRNAs were related to regulation of the actin cytoskeleton and metabolic pathways. We established expression profiles of circRNAs during C2C12 myoblast differentiation and predicted the function of differentially expressed circRNAs, which might be involved in skeletal muscle development. Our study offers new insight into the functions of circRNAs in skeletal muscle growth and development.

Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

“…Myh1 was important for the fast-twitch muscle fibers, Myh7 contributed to the slow-twitch muscle fibers, while Myh2 acted as an intermediator between Myh1 and Myh7 [44,45]. Myh1, Myh2, and Myh7 were the signature genes of myoblast differentiation [46]. Our data displayed that the up-regulated expression of miR-133a inhibited the expression of two potential target genes (Myh1 and Myh7) with age.…”

Roles of lncRNAs and circRNAs in regulating skeletal muscle development

“…102 circFGFR4 binding to miR-107 promotes cell differentiation by targeting Wnt3a in bovine primary myoblasts. 95 Our research group has identified the coding potentials and known functional domains of 75 circRNAs during mouse C2C12 myoblast differentiation, 30 as well as 71 circRNAs with coding potential and known functional domains during pathological conditions of Co (II) ion-induced myocytotoxicity in mouse skeletal 108 In the future, other circRNAs encoding proteins involved in muscle development may be discovered. 104 Moreover, circSNX29 sponges miR-744 to facilitate bovine myoblasts differentiation and inhibit cell proliferation by activating the Wnt5a/Ca 2+ signalling pathway.…”

“…107 In addition to promoting proliferation, circ-ZNF609 is translated into a protein, but the function of the flagged protein is unknown in human myoblasts. 95 Our research group has identified the coding potentials and known functional domains of 75 circRNAs during mouse C2C12 myoblast differentiation, 30 as well as 71 circRNAs with coding potential and known functional domains during pathological conditions of Co (II) ion-induced myocytotoxicity in mouse skeletal 108 In the future, other circRNAs encoding proteins involved in muscle development may be discovered.…”

“…22,23 Although proteins are major regulators of cell function, a great deal of non-protein coding processes are also operating. 29,30 Understanding the functions and mechanisms of lncRNAs and circRNAs during skeletal muscle development and pathophysiological conditions will therefore facilitate therapeutic treatments for muscle disorders. 24,25 Non-coding RNAs are still known not to code proteins, but they may have a significant influence on organisms.…”

“…In our previous studies, 2922 lncRNAs and 581 circRNAs were differentially regulated during C2C12 differentiation, indicating their potential involvement in muscle development. 29,30 Understanding the functions and mechanisms of lncRNAs and circRNAs during skeletal muscle development and pathophysiological conditions will therefore facilitate therapeutic treatments for muscle disorders. As recent reports have indicated the importance of lncRNAs and circRNAs in skeletal muscle development and disease, a systematic review of these studies is necessary to provide a broad and deeper understanding of the subject.…”