Megalocytivirus Induces Complicated Fish Immune Response at Multiple RNA Levels Involving mRNA, miRNA, and circRNA.

Qian Wu,Xianhui Ning,Li Sun

doi:10.3390/ijms22063156

Abstract

Megalocytivirus is an important viral pathogen to many farmed fishes, including Japanese flounder (Paralichthys olivaceus). In this study, we examined megalocytivirus-induced RNA responses in the spleen of flounder by high-throughput sequencing and integrative analysis of various RNA-seq data. A total of 1327 microRNAs (miRNAs), including 368 novel miRNAs, were identified, among which, 171 (named DEmiRs) exhibited significantly differential expressions during viral infection in a time-dependent manner. For these DEmiRs, 805 differentially expressed target mRNAs (DETmRs) were predicted, whose expressions not only significantly changed after megalocytivirus infection but were also negatively correlated with their paired DEmiRs. Integrative analysis of immune-related DETmRs and their target DEmiRs identified 12 hub DEmiRs, which, together with their corresponding DETmRs, formed an interaction network containing 84 pairs of DEmiR and DETmR. In addition to DETmRs, 19 DEmiRs were also found to regulate six key immune genes (mRNAs) differentially expressed during megalocytivirus infection, and together they formed a network consisting of 21 interactive miRNA-messenger RNA (mRNA) pairs. Further analysis identified 9434 circular RNAs (circRNAs), 169 of which (named DEcircRs) showed time-specific and significantly altered expressions during megalocytivirus infection. Integrated analysis of the DETmR-DEmiR and DEcircR-DEmiR interactions led to the identification of a group of competing endogenous RNAs (ceRNAs) constituted by interacting triplets of circRNA, miRNA, and mRNA involved in antiviral immunity. Together these results indicate that complicated regulatory networks of different types of non-coding RNAs and coding RNAs are involved in megalocytivirus infection.

Highlights

Megalocytivirus is an important viral pathogen to a wide range of aquaculture fish, including Japanese flounder (Paralichthys olivaceus), a valued marine fish
The lengths of the miRNAs in all six groups were distributed in the range 20–23 nt, with a maximum of 22 nt, indicating a high degree of consistency between groups (Figure 1a)
In a previous transcriptome analysis of the same samples used in this study, we identified 16 key immune-related and differentially expressed genes (DEGs) significantly induced by megalocytivirus [33]

Summary

Introduction

Megalocytivirus is an important viral pathogen to a wide range of aquaculture fish, including Japanese flounder (Paralichthys olivaceus), a valued marine fish. Megalocytivirus is a double-stranded DNA virus belonging to the family Iridoviridae. Several types of megalocytivirus have been identified, including infectious spleen and kidney necrosis virus (ISKNV), red seabream iridovirus (RSIV), rock bream iridovirus (RBIV), orange-spotted grouper iridovirus (OSGIV), and turbot reddish body iridovirus (TRBIV) [1,2,3,4,5]. In Japanese flounder, reports have shown that megalocytivirus infection elicits systematic changes in the expression of small non-coding RNAs and mRNAs in the spleen [8]. MicroRNAs (miRNAs) are a class of small endogenous RNAs ranging 21–24 nt in size and play an important role in mRNA translation. MicroRNAs execute post-transcriptional regulation of their target gene expression by binding to the 30 untranslated region (30 -UTR)

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Discussion

Conclusion