Comprehensive analysis of the expression profile of circRNAs and their predicted protein-coding ability in the muscle of mdx mice

Abstract

Duchenne muscular dystrophy (DMD) is an X-linked genetic neuromuscular disease that is characterized by progressive muscle wasting and by defects in the regenerative capacity and inflammatory infiltration of muscle. Many noncoding RNAs (ncRNAs) participate in the pathophysiological mechanisms of this disease. To explore the role of circular RNAs (circRNAs), a type of ncRNAs, in DMD, microarray analysis was performed to explore the expression patterns of circRNAs in the gastrocnemius muscles in mdx mice, a DMD animal model, and C57 mice. The microarray data were validated by qRT-PCR. Further, gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to predict the function of the differentially expressed circRNAs (DEcRNAs). A circRNA/microRNA (miRNA) interaction network was predicted by bioinformatics. We also predicted the protein-coding ability of the circRNAs based on their N⁶-methyladenosine motifs and open-reading frames. We identified 197 differentially expressed circRNAs between mdx mice and C57 mice. Of the 197 DEcRNAs, 6 circRNAs were randomly selected to validate the microarray data, and twenty-two circRNAs were randomly selected to construct a circRNA/miRNA interaction network. Bioinformatics analysis showed that the linear counterparts of the DEcRNAs were mainly associated with muscle structure, nervous system development, and the cAMP signaling pathway. A total of 189 circRNAs were predicted to have protein-coding potential, and there were 98 circRNAs that could potentially be translated into polypeptides with 150 or more amino acids. This work described the expression pattern of circRNAs in mdx mice and indicated that circRNAs may play pivotal roles in the pathophysiological mechanisms of DMD.

Keywords: Circular RNAs (circRNAs); Duchenne muscular dystrophy; Expression profile; Muscle; Protein-coding ability; ceRNA.