School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China.
School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China.
Fish Shellfish Immunol. 2019 Nov;94:50-57. doi: 10.1016/j.fsi.2019.08.070. Epub 2019 Aug 27.
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.
环状 RNA（circRNAs）具有调节活性，已从各种物种中鉴定出来。鲫鱼（Carassius auratus gibelio）是中国最主要的淡水养殖鱼类之一。每年，病毒和细菌感染都会给养殖业造成巨大的经济损失。到目前为止，还没有关于鲫鱼 circRNA 的报道。在本研究中，通过转录组分析研究了鲫鱼 circRNA 的表达模式。结果表明，从鲫鱼中仅鉴定出 37 个 circRNA，这些 circRNA 的生物发生是通过非均匀分布在染色体上的典型 GU-AG 剪接机制形成的。其中，大多数 circRNA 来源于有义重叠策略。逆转录 PCR 和 Sanger 测序数据表明，这些 circRNA 在鲫鱼中是真实存在的。生物信息学分析表明，从鲫鱼中鉴定出的具有潜在 miRNA 海绵作用的 circRNA 可以调节 mRNA 的表达水平。这些 circRNA 的 GO 注释和 KEGG 通路分析表明，超过 20%的 circRNA 与分子功能类别中的催化活性和结合有关，这些 circRNA 富集在 9 个信号通路中，如 Wnt 信号通路、MAPK 信号通路、泛素介导的蛋白水解等。220 个 mRNA 将通过 miRNA 介导被 circRNA 调控。这些靶 mRNA 进一步进行了功能注释和 KEGG 分析。GO 注释分析表明，几个基因与核苷酸结合、转录调控活性的功能有关。KEGG 通路分析表明，5 个基因富集在内吞作用通路中。circRNA-miRNA-mRNA 调控网络表明，一个 miRNA 可以连接一个或多个 circRNA 和一个或多个 mRNA。总的来说，这些结果不仅有助于我们进一步了解鲫鱼中的新型 RNA 转录物，而且为从这种新型 circRNA 分子研究宿主与病原体的相互作用提供了新的线索。
