CircRNA Identification and CircRNA–miRNA–mRNA Network in Cynoglossus semilaevis Sexual Size Dimorphism

Abstract

Simple SummaryChinese tongue sole (Cynoglossus semilaevis) typically displays female-biased sexual size dimorphism (SSD), but its epigenetic regulatory mechanisms are poorly understood, especially the role of circRNAs. To explore the function of circRNAs in Chinese tongue sole SSD, we firstly identified differentially expressed circular RNAs (DE circRNAs) in female, male, and pseudo-male C. semilaevis. Secondly, the ceRNA network containing DE circRNAs, miRNAs, and mRNAs in the three genders was constructed. Among the ceRNA network, several circRNAs such as novel_circ_004374 and novel_circ_014597 may regulate hipk2 expression by sponging miR-130-x. It is also worth exploring whether or how novel_circ_008696 regulates setd2 by binding to novel-m0387-3p. The present study provided the cirRNA and its ceRNA network that potentially regulate C. semileavis female-biased SSD for the first time. Sexual size dimorphism (SSD), which is the sexual differences in body size, has been widely reported in various species including fishes. For Chinese tongue sole (Cynoglossus semilaevis), a flatfish exhibiting typically female-biased SSD, little is known for its epigenetic regulation mechanism, especially the role of circRNAs. Here, we identified the differently expressed abundances of circRNAs in females, males, and pseudo-males to explore the potential functions of circRNAs in Chinese tongue sole SSD. In total, 14,745 novel circRNAs were screened, among which 1461 DE circRNAs were identified from the brain, gonad, liver, and muscle in female, male, and pseudo-male individuals. The ceRNA network was subsequently constructed, including 10 circRNAs, 26 mRNAs, and 11 miRNAs. These DE mRNAs were mainly related to the mRNA surveillance pathway, metabolic pathways, and cellular senescence. Importantly, the ceRNA network has revealed that several circRNAs such as novel_circ_004374 and novel_circ_014597 may regulate homeodomain interacting protein kinase 2 (hipk2) expression by sponging miR-130-x. It is also worth exploring whether or how novel_circ_008696 regulates SET Domain Containing 2, histone lysine methyltransferase (setd2), which in turn affects the epigenetic patterns of different sexual individuals. The present study not only enriches the knowledge on the potential roles of circRNA in the physiological process, but also provides new clues for the explanation of fish SSD. In future studies, the precise function and involvement of circRNAs in female-biased SSD will require more efforts.