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Characterization of microRNAs encoded by the Bovine herpesvirus 1 genome

¹ The University of Queensland;
² Queensland Agricultural Biotechnology Centre;
³ Chulalongkorn University;
⁴ CSIRO Livestock Industries

⁵ E-mail: timothy.mahony{at}dpi.qld.gov.au

Bovine herpesvirus 1 (BoHV-1) is a ubiquitous and important pathogen of cattle worldwide. This study reports the identification of ten microRNA (miRNA) genes, Bhv1-mir-1 to Bhv1-mir-10, encoded by the BoHV-1 genome that were processed into 12 detectable mature miRNAs as determined by ultrahigh throughput sequencing bioinformatics analyses of small RNA libraries, and expression studies. We found that four of the miRNA genes were present as two copies in BoHV-1 genome resulting in a total of 14 miRNA-encoding loci. Unique features of the BoHV-1 miRNAs include, evidence of bidirectional transcription and a close association of two miRNA genes with the origin of replication including one miRNA that is encoded within the origin of replication. The miRNA gene Bhv1-mir-5 was encoded on the opposite DNA strand to the latency associated transcript, potentially giving rise to the antisense transcripts originating from this locus. The association of herpesvirus miRNAs with latency appears to be a common feature in the alphaherpesviruses. Analyses of the genome the Bovine herpesvirus 5 for putative miRNA gene orthologues identified a high degree of evolutionary conservation for nine of the BoHV-1 miRNA genes. The possible roles for BoHV-1 miRNAs in the regulation of known BoHV-1 transcription units and the genetics of the BoHV-1 genotypes are also discussed.

Received 10 June 2009; accepted 27 September 2009.