Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs

Abstract

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.

MicroRNA-100 suppresses human gastric cancer cell proliferation by targeting CXCR7

“…Dysregulation of miRNAs in diseases especially in tumor has attracted extensive attentions in recent years (7)(8)(9)(10)(11)(12). Mounting evidences have demonstrated that aberrant expression of several miRNAs is associated with survival outcome of cancer patients (27,28) and therefore could be regarded as potential therapeutic targets for these cancers.…”

“…Accumulating evidences have revealed that altered expression of miRNAs play an important role in tumorigenesis of many human cancers (7)(8)(9). In the mean time, studies have demonstrated that a single cancer can be driven by different miRNAs (7,10,11), while a single miRNA can be found aberrant expressed in different cancers (11,12).…”

Contribution of Next-Generation Sequencing to Aquatic and Fish Virology

“…Preliminary bioinformatics analysis of the viral genome suggested the presence of pre-miRNA, and deep sequencing of the microtranscriptome confirmed the existence of some of the predicted miRNAs [131]. Two pre-miRNAs were found in cells infected in vitro and the corresponding miRNAs were detected in infected animals.…”

MicroRNAs in large herpesvirus DNA genomes: recent advances

“…The vast majority of viral miRNAs identified so far were reported to be expressed by members of the Herpesviridae family (8,14,16,26) and at least one member of the Alloherpesviridae family (27). Viral miRNAs were characterized as the most recently discovered weapons in herpesvirus genomes.…”