The immune-related circRNA-miRNA-mRNA ceRNA regulatory network in the liver of turbot (Scophthalmus maximus L.) induced by Vibrio anguillarum

生物 多宝鱼 鳗弧菌 小RNA 小桶 竞争性内源性RNA 生物信息学 基因 转录组 计算生物学 基因调控网络 免疫系统 先天免疫系统 遗传学 基因表达 弧菌 核糖核酸 长非编码RNA 渔业 细菌
作者
Xin Cai,Chengbin Gao,Alan J. Lymbery,Nicola J. Armstrong,Le Ma,Chao Li
出处
期刊:Fish & Shellfish Immunology [Elsevier BV]
卷期号:132: 108506-108506 被引量:6
标识
DOI:10.1016/j.fsi.2022.108506
摘要

Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.
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