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Circular RNAs (circRNAs) with regulatory potency activity was identified from varieties of species. Crucian carp (Carassius auratus gibelio) is one of the most freshwater aquaculture species in China. Every year, huge economic damage to the farming was caused by the virus and bacterial infection. Until now, there is any information about circRNA reported from the Crucian carp. In this study, the expression pattern of circRNA in Crucian carp was investigated with transcriptomic analysis. The results showed that only 37 circRNAs were identified from the Crucian carp, and these circRNAs biogenesis was formed with canonical GU-AG splicing mechanism with unevenly distributed on the chromosomes. Wherein, most of the circRNAs were derived from the sense overlapping strategy. Reverse transcript PCR and Sanger sequencing data indicated that these circRNAs were existed authenticity in Crucian carp. The bioinformatics analysis indicated that circRNAs identified from the Crucian carp with potential miRNA sponge regulate the expression level of mRNAs. GO annotation and KEGG pathway analysis of these circRNAs showed that more than 20% circRNAs were related with catalytic activity and binding in the category of molecular function, and these circRNAs were enriched in 9 signaling pathways, such as, Wnt signaling pathway, MAPK signaling pathway, Ubiquitin mediated proteolysis et al. 220 mRNAs would be regulated by the circRNAs via miRNAs mediation. These target mRNAs were further analyzed with functional annotation and KEGG analysis. GO annotation analysis showed that several genes were related with function of nucleotide binding, transcription regulatory activity. KEGG pathway analysis showed that 5 genes were enriched in the pathway of Endocytosis. The circRNA-miRNA-mRNA regulation network indicated that one miRNA can link one or more circRNA and one or more mRNA. Overall, these results will not only help us to further understand the novel RNA transcripts in Crucian carp, but also provide the novel clue to investigate the interaction between host and pathogens from this novel circRNA molecule. • CircRNAs were identified from the Crucian carp with transcriptomic analysis. • CircRNAs biogenesis was formed with canonical GT/AG splicing mechanism. • Most of the circRNAs were derived from the sense overlapping strategy. • These circRNAs were enriched in 9 signaling pathways. • The circRNA-miRNA-mRNA regulation network was constructed. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are novel, single-stranded, non-coding RNAs that play important roles in many biological processes. CircRNAs have not only been identified in eukaryotes, they have also been identified in some DNA viruses. Grass carp reovirus (GCRV) is a dsRNA virus; the genome of this virus contains 11 segmented dsRNAs. Infection of grass carp with GCRV leads to haemorrhagic disease, one of the most serious diseases in the grass carp aquaculture industry. To investigate the expression of circRNAs in this dsRNA virus, and their potential role in viral infection, we performed transcriptome analysis of GCRV-infected Ctenopharyngodon idellus kidney (CIK) cells. In total, 32 GCRV-derived circRNAs (vcircRNAs) were identified using a back-splicing strategy. Thirty-one vcircRNAs were derived from antisense strands of dsRNA segments; only one vcircRNA was derived from the sense strand. Our analysis predicted that some vcircRNAs, with the same 5′ terminal and variable 3′ terminal regions, were generated via alternative splicing events. The expression levels of vcircRNAs increased in CIK cells following GCRV infection. Competing endogenous RNA analysis further showed that the effects of vcircRNAs on host or viral genes may act via miRNAs. Furthermore, some vcircRNAs, that were transfected into cells via in vitro syntheses, caused a significant increase in cell apoptosis when compared with linear sequences of vcircRNAs or circRNA-GFP (as controls). Finally, we found that the expression levels of GCRV genes in CIK cells were significantly suppressed following the transfection of vcircRNAs. Collectively, our findings indicate that vcircRNAs are a novel form of viral transcript that are expressed in virus-infected cells. Our data also indicate that vcircRNAs may sequester the functions of host miRNAs or viral miRNAs in order to regulate genes in the host or virus to inhibit viral infection. • Circular RNAs (viral circRNAs, vcircRNAs) were encoded by the genome of Grass carp reovirus (GCRV), a dsRNA virus. • Thirty-one vcircRNAs were derived from antisense strands and only one from a sense strand of dsRNA segments. • Some vcircRNAs were predicted to be generated by alternative splicing events. • vcircRNAs with activity and the roles played by vcircRNAs on host or viral genes may be through miRNAs. • The replication of GCRV was significantly suppressed by vcircRNAs transfected into cells. [ABSTRACT FROM AUTHOR]