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.
Highlights
Mammalian skeletal muscles with different fiber types exhibit various structural and functional properties
We constructed six ribosomal-depleted RNA libraries from biceps femoris (Bf) and Sol muscles, which were denoted as Bf28, Bf35, Bf36, Sol28, Sol35, and Sol36 groups
A typical fasttwitch muscle, is riched in type II muscle fiber, whereas Sol riched in type I muscle fiber is a typical slow-twitch muscle
Summary
Mammalian skeletal muscles with different fiber types exhibit various structural and functional properties. Slow-twitch fibers enrich mitochondria and have high oxidative capacity, and primarily express myosin heavy chain I (MyHC I) (Schiaffino and Reggiani, 2011). Fast-twitch fibers primarily express myosin heavy chain II b (IIb) and display strong glycolytic metabolic capacity (Schiaffino and Reggiani, 2011). As peroxisome-proliferator-activated receptor-γ coactivator (PGC-1α) is a principal factor regulating slow-twitch fiber determination, muscle-specific overexpression of PGC-1α improves the parameters characteristic of Duchenne muscular dystrophy (DMD), a regulatory mechanism mediated by folliculin interacting protein-1 (Fnip 1) (Handschin et al, 2007; Reyes et al, 2015). Skeletal muscles composed of different fiber types vary in postmortem metabolic rates, and are closely linked with color, water-holding capacity, marbling, pH and other meat quality traits (Hwang et al, 2010). A better understanding of the genetics basis of muscle fiber formation could greatly improve both meat quality traits of livestock and treatment of human muscle diseases
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