Genome-Wide Analysis of Circular RNA-Mediated ceRNA Regulation in Porcine Skeletal Muscle Development

Abstract

Abstract Background: As a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investigated the role of circRNAs in muscle development in cultivated pigs. Results: In this study, we used RNA-seq to construct circRNA expression profiles in skeletal muscle of Jinfen White pigs at the age of 1, 90, and 180 days. Among the 16,990 identified circRNAs, 584 were differentially expressed, with 255, 477, and 63 DE circRNAs in the 90 d vs. 1 d, 180 d vs. 1 d, and 180 d vs. 90 d groups, respectively. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DE circRNA host genes revealed them to be mainly involved in skeletal muscle fiber-related processes (e.g., muscle contraction, muscle organ development, and muscle system processes) and skeletal muscle fiber-related signaling pathways (e.g., AMPK and cAMP pathways). We also constructed circRNA–miRNA–mRNA co-expression network to screen out circRNAs many involved in the regulation of porcine skeletal muscle growth and development through the competitive endogenous RNA (ceRNA) mechanism. In this network, we predicted circ_0018595 may as a potential sponge of miR-1343 to regulate PGM1 expression, in turn promoting the proliferation of pig skeletal muscle satellite cells. The structure and expression of circ_0018595 were confirmed using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR. Conclusions: This study has identified 584 candidate circRNAs, especially circ_0018595, which may be involved in the growth and development of porcine skeletal muscle, and will therefore serve as a valuable resource for further in-depth study of circRNA regulatory mechanisms in skeletal muscle development.