Circular RNAs (circRNAs) are functional (mostly) non-coding transcripts produced by head-to-tail splicing in multicellular organisms. They participate in various biological processes by acting as miRNA sponges, RNA-binding protein regulators and protein translation templates. In recent years, There is mounting evidence that circRNAs modulate muscle growth in farmed animals but the regulatory mechanisms of circRNAs in fish are still poorly understood. Thus, this study aimed to investigate the expression of circRNAs in Nile tilapia and explore their regulatory mechanism through a multi-omics approach. We compared the circRNA, mRNA and miRNA transcriptomes in fast muscle collected from fast- and slow-growing Nile tilapia (Oreochromis niloticus) from the third generation of our in-house domestication program.
A total of 1947 mRNAs, 9 microRNAs (miRNAs), and 4 circRNAs were differentially expressed between fast- and slow-growing fish. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that the differentially expressed mRNAs are related to muscle fibre development, striated muscle cell development, and spliceosome. Further, we focused on a novel circRNA (circMef2c) produced from myocyte-specific enhancer factor 2C-like, and verified its expression and back splice junction using reverse transcription quantitative PCR and Sanger sequencing, respectively. As circRNAs participate in biological regulation through competing endogenous RNA (ceRNA), we identified the miRNA targets of circMef2c. In silico prediction showed that circMef2c could bind to 3 miRNAs, and these miRNAs could target 65 mRNAs. Among the genes in this ceRNA network, circMef2c-oni-miR-34-igfbp2, circMef2c-oni-miR-130b-5p-myod1, and circMef2c-oni-miR-202-fgf14 are likely to play a key role in muscle growth. Our results provide a comprehensive overview of a novel ceRNA regulatory network in Nile tilapia muscle. In addition to deepening our knowledge of muscle growth in teleosts, they pave the way for exploring novel growth biomarkers in farmed fish.
Acknowledgements: This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210, 2016) and by the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20, 2016).
Reference: G. Rbbani, A. Nedoluzhko, J. Galindo-Villegas and J.M.O. Fernandes (2021). Function of circular RNAs in fish and their potential application as biomarkers. International Journal of Molecular Sciences 22(13): 7119.