RESEARCH ARTICLE Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs Owen H. Donohoe1,2, Kathy Henshilwood1, Keith Way3, Roya Hakimjavadi2, David M. Stone3, Dermot Walls2* 1 Marine Institute, Rinville, Oranmore, Co. Galway, Ireland, 2 School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland, 3 Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom a11111 *
[email protected] Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional OPEN ACCESS gene regulation. Some viruses encode their own miRNAs and these are increasingly being Citation: Donohoe OH, Henshilwood K, Way K, recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus Hakimjavadi R, Stone DM, Walls D (2015) 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the ONE 10(4): e0125434. doi:10.1371/journal. CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) pone.0125434 genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led Academic Editor: Sebastien Pfeffer, French National to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from Center for Scientific Research - Institut de biologie some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, North- moléculaire et cellulaire, FRANCE ern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 Received: December 15, 2014 expresses two pre-miRNAs during infection in vitro.