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Herpes simplex virus 1 (HSV-1) has been shown to encode 29 microRNAs (miRNAs) differentially expressed during productive and/or latent infection, whose functions are yet to be revealed. The functions of miRNAs are defined by their sequences, as only one nucleotide difference can dramatically change the specificity of miRNA for its target. However, the exact sequences of HSV-1 miRNAs have not been determined even ten years after the first discovery, since the discrepancies in miRNA sequences in different data sets compared to the reference sequences in miRBase are frequently found. It is also possible that different strains express different miRNAs. Thus, to comprehensively and critically evaluate HSV-1 expressed miRNAs and their biogenesis, we analysed more than 500 million high quality reads obtained from different laboratories, in experiments with different virus strains, and different host species. In addition, we sequenced several miRNA libraries of human samples. Using biological approaches and advanced bioinformatics tools we determined a reliability-score for each HSV-1 miRNA and based on the score HSV-1 miRNAs were grouped into three categories: true miRNAs, tentative miRNAs and miRNAs that need confirmation. In addition, we show that sequences of a subset of HSV-1 miRNAs differ from the sequences in miRBase. Interestingly, our results show that the frequency of isomiRs (sequence variations at 5’ or 3’) is significantly higher for HSV-1 miRNAs than host miRNAs. The molecular basis for this observation is not known, however, our preliminary results indicate that this is not an intrinsic property of HSV-1 pre-miRNA sequence, but rather regulated by viral gene product or cellular factors induced by infection. Furthermore, we describe a substantial neuron- specific posttranscriptional editing of certain HSV-1 miRNAs, which might significantly change the targeting of these miRNAs. These results indicate that the virus is using cellular processes to expand the repertoire of possible miRNA targets or to affect their stability. Our analysis is not only revealing discrepancies with the reference miRBase, which will significantly facilitate functional analyses, but also sheds light on a peculiar HSV-1 miRNA processing that is yet to be fully investigated. |
