In-depth profiling and analysis of host and viral microRNAs in Japanese flounder (Paralichthys olivaceus) infected with megalocytivirus reveal involvement of microRNAs in host-virus interaction in teleost fish.

Bao-Cun Zhang,Li Sun,Jian Zhang

doi:10.1186/1471-2164-15-878

Abstract

BackgroundMicroRNAs (miRNAs) regulate gene expression by binding to mRNA transcripts in various biological processes. In mammals and birds, miRNAs are known to play vital parts in both host immune defense and viral infection. However, in lower vertebrates such as teleost, systematic investigations on host and viral miRNAs are lacking.ResultsIn this study, we applied high-throughput sequencing technology to identify and analyze both host and viral miRNAs in Japanese flounder (Paralichthys olivaceus), an economically important teleost fish farmed widely in the world, infected with megalocytivirus at a timescale of 14 days divided into five different time points. The results showed that a total of 381 host miRNAs and 9 viral miRNAs were identified, the latter being all novel miRNAs that have no homologues in the currently available databases. Of the host miRNAs, 251 have been reported previously in flounder and other species, and 130 were discovered for the first time. The expression levels of 121 host miRNAs were significantly altered at 2 d to 14 d post-viral infection (pi), and these miRNAs were therefore classified as differentially expressed host miRNAs. The expression levels of all 9 viral miRNAs increased from 0 d pi to 10 d pi and then dropped from 10 d pi to 14 d pi. For the 121 differentially expressed host miRNAs and the 9 viral miRNAs, 243 and 48 putative target genes, respectively, were predicted in flounder. GO and KEGG enrichment analysis revealed that the putative target genes of both host and viral miRNAs were grouped mainly into the categories of immune response, signal transduction, and apoptotic process.ConclusionsThe results of our study provide the first evidences that indicate existence in teleost fish (i) infection-responsive host and viral miRNAs that exhibit dynamic changes in expression profiles during the course of viral infection, and (ii) potential involvement of miRNAs in host-viral interaction.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-878) contains supplementary material, which is available to authorized users.

Highlights

MicroRNAs regulate gene expression by binding to mRNA transcripts in various biological processes
Our results indicate for the first time that in teleost fish, the expression profiles of both host and viral miRNAs changed dynamically during the course of viral infection, and that miRNAs are most likely involved in the process of host-viral interaction
Identification of host (Japanese flounder) miRNAs In order to identify the miRNAs involved in viral infection and host immune response, Japanese flounder were infected with megalocytivirus for 0 d, 2 d, 6 d, 10 d, and 14 d

Summary

Introduction

MicroRNAs (miRNAs) regulate gene expression by binding to mRNA transcripts in various biological processes. MicroRNAs (miRNAs) are small non-coding RNAs with ~22 nucleotides (nt) in length. They have been recognized as crucial regulators of gene expression in plants and animals through interaction with specific mRNA targets and thereby affecting translation [1]. The host limits viral infection through differentially expressing the miRNAs that target essential viral genes [9,10,11,12]. Viral miRNAs contribute to infection through various mechanisms, notably immune evasion [15,16], induction of anti-apoptosis [17], reducing the antigenicity of viral proteins [16,18], and promoting cell survival, proliferation, and differentiation [14]

Methods

Results

Discussion

Conclusion