Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Bojiang Li; Di Yin; Pinghua Li; Zengkai Zhang; Xiying Zhang; Hongqiang Li; Rongyang Li; Liming Hou; Honglin Liu; Wangjun Wu

doi:10.3389/fcell.2020.00322

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Front Cell Dev Biol. 2020 May 26:8:322. doi: 10.3389/fcell.2020.00322. eCollection 2020.

Authors

Bojiang Li¹, Di Yin², Pinghua Li², Zengkai Zhang², Xiying Zhang², Hongqiang Li^{2

3}, Rongyang Li², Liming Hou², Honglin Liu², Wangjun Wu²

Affiliations

¹ College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
² Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
³ College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China.

Abstract

The different skeletal muscle fiber types exhibit distinctively different physiological and metabolic properties, and have been linked to both human metabolic diseases and meat quality traits in livestock. Circular RNAs (circRNAs) are a new class of endogenous RNA regulating gene expression, but regulatory mechanisms of skeletal muscle fibers involved in circRNAs remain poorly understood. Here, we constructed circRNA expression profiles of three fast-twitch biceps femoris (Bf) and three slow-twitch soleus (Sol) muscles in pigs using RNA-seq and identified 16,342 distinct circRNA candidates. Notably, 242 differentially expressed (DE) circRNAs between Bf and Sol muscles were identified, including 105 upregulated and 137 downregulated circRNAs, and are thus potential candidates for the regulation of skeletal muscle fiber conversion. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of host genes of DE circRNAs revealed that host genes were mainly involved in skeletal muscle fiber-related GO terms (e.g., muscle contraction, contractile fiber part, and Z disk) and skeletal muscle fiber-related signaling pathways (e.g., AMPK and cGMP-PKG). We also constructed co-expression networks of DE circRNA-miRNA-mRNA using previously acquired high-throughput sequencing mRNA and miRNA data, from which 112 circRNA-miRNA and 95 miRNA-mRNA interactions were identified. Multiple circRNAs essentially serve as a sponge for miR-499-5p, which is preferentially expressed in slow-twitch muscle and reduces the severity of Duchenne muscular dystrophy (DMD). Taken together, a series of novel candidate circRNAs involved in the growth and development of porcine skeletal muscle was identified. Furthermore, they provide a comprehensive circRNA resource for further in-depth research on the regulatory mechanisms of circRNA in the formation of skeletal muscle fiber, and may provide insights into human skeletal muscle diseases.

Keywords: circular RNA; expression profile; fast-twitch biceps femoris muscle; pig; slow-twitch soleus muscle.