Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs.
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA-offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
Marine Institute, Rinville, Oranmore, Co. Galway, Ireland; School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
Owen H
OH
Donohoe
Marine Institute, Rinville, Oranmore, Co. Galway, Ireland.
Kathy
K
Henshilwood
Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom.
Keith
K
Way
School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
Roya
R
Hakimjavadi
Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom.
David M
DM
Stone
School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
Dermot
D
Walls
D000818:Animals; D002347:Carps; D005393:Fish Diseases / Q000821:virology*; D006564:Herpesviridae / Q000235:genetics* / Q000472:pathogenicity; D006566:Herpesviridae Infections / Q000821:virology*; D035683:MicroRNAs / Q000235:genetics*
D035683:MicroRNAs