Comprehensive analysis of circRNA expression pattern and circRNA-mRNA-miRNA network in Ctenopharyngodon idellus kidney (CIK) cells after grass carp reovirus (GCRV) infection
Comprehensive analysis of circRNA expression pattern and circRNA-mRNA-miRNA network in Ctenopharyngodon idellus kidney (CIK) cells after grass carp reovirus (GCRV) infection
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DOI：
10.1016/j.aquaculture.2019.734349
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发表时间：
2019-10-15
期刊：
影响因子：
4.5
通讯作者：
Gong, Chengliang
中科院分区：
文献类型：
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作者：
Liu, Bo;Yuan, Rui;Gong, Chengliang
草鱼呼肠孤病毒(GCRV)引起草鱼出血性疾病，是草鱼养殖中最具破坏性的因素之一。到目前为止，GCRV感染的机制在很大程度上还不清楚。为了探讨CIK细胞对GCRV感染的分子反应，我们利用高通量测序技术研究了CIK细胞中CircRNA、mRNA和miRNA的表达模式以及CircRNA-miRNA-mRNA网络。与未感染细胞相比，共鉴定出76个CircRNAs、798个mRNAs和186个miRNAs，其中40个CircRNAs、658个mRNAs和146个miRNAs上调，36个CircRNAs、140个mRNAs和40个miRNAs下调(折叠式变化2，p<；0.05)。对DE CircRNA亲本基因、mRNAs和miRNA靶基因进行了基因本体(GO)分析。De CircRNAs的亲本基因、De mRNAs和De miRNAs的靶基因分别主要富含与金属离子结合、免疫和DNA复制相关的项目。KEGG途径分析表明，DE CircRNA亲本基因、DE mRNAs和miRNA靶基因分别在内吞、免疫和感染相关途径中显著富含。还预测了miRNA与靶分子的相互作用，并基于DE RNAs构建了内源RNA的竞争调控网络。我们的预测结果提示，CircRNA-2780/CIK-miRNA-7796/KAT6B、CircRNA1351/CIK-miRNA-10648/B2L14和CircRNA1591/CIK-miR-8141/AMPD3轴可能与GCRV感染有关。这项研究表明，CircRNAs和它们竞争的mRNAs之间的串扰在GCRV感染中起着至关重要的作用。
Grass carp reovirus (GCRV) causes grass carp hemorrhage disease and is one of the most damaging factors in the culture of grass carp (Ctenopharyngodon idellus). Until now, the mechanisms underlying GCRV infection have been largely unknown. To explore the molecular responses to GCRV infection in C. idellus kidney (CIK) cells, we used high-throughput sequencing to investigate the circRNA, mRNA, and miRNA expression patterns and the circRNA-miRNA-mRNA network. A total of 76 circRNAs, 798 mRNAs, and 186 miRNAs were identified as differentially expressed (DE) RNAs in GCRV-infected cells compared with uninfected cells, of which 40 circRNAs, 658 mRNAs, and 146 miRNAs were upregulated, and 36 circRNAs, 140 mRNAs, and 40 miRNAs were downregulated (fold change > 2, p < .05). A Gene Ontology (GO) analysis of the DE circRNA parental genes, mRNAs, and miRNA target genes was performed. The parental genes of the DE circRNAs, the DE mRNAs, and the target genes of the DE miRNAs were mainly enriched in metal-ion-binding-, immune-, and DNA-replication-related items, respectively. A KEGG pathway analysis showed that the DE circRNA parental genes, DE mRNAs, and miRNA target genes were predominantly enriched in endocytosis-, immune-, and infection-related pathways, respectively. The miRNA-target interactions were also predicted and competing regulatory networks of endogenous RNAs were constructed based on the DE RNAs. Our prediction results suggest that the circRNA-2780/cik-miRNA-7796/KAT6B, circRNA-1351/cik-miRNA-10648/B2L14 and circRNA-1591/cik-miR-8141/AMPD3 axes may be associated with GCRV infection. This study suggests that the crosstalk between circRNAs and their competing mRNAs play crucial roles in GCRV infection.