engleski

Comprehensive analysis of herpes simplex virus 1 encoded miRNAs and host miRNAs during productive and latent infection - the need for a revision

Herpes simplex virus 1 (HSV-1) encodes 27 mature miRNAs, some of which are differentially expressed during productive and/or latent infection. The function of miRNAs strongly relies on the sequence complementarity and only one nucleotide difference can dramatically change the specificity of miRNA for its target. Although, HSV-1 miRNAs have been discovered more than 10 years ago, the discrepancies in miRNA sequences in different data sets compared to the reference sequences in miRBase are frequently found, which hampers functional analyses. It is also possible that different strains express different miRNAs. Thus, to comprehensively address these issues and to determine the exact sequence of HVS-1 miRNAs, we analysed 22 data sets (total of ~500 million reads) obtained from different laboratories and using different virus strains. In our analysis, the first 19 nucleotides of the read were used for the alignment, allowing one nt mismatch, and mapped all reads to the host and HSV-1 genome, selecting the most dominant sequence. For each miRNA a reliability-score was determined based on eight parameters: the total read count (RC), length, presence in the productively and latently infected samples, presence in more than one host species, Drosha/Dicer dependence, a proper hairpin folding, and 5' fluctuation. Based on the score HSV-1 miRNAs were grouped into three categories, miRNAs that completely satisfy the miRNA criteria (A – miRNAs), group which partially satisfies the criteria (B – likely reliable miRNAs) and the ones which do not meet the criteria (C – miRNAs that need confirmation). These results might indicate that some of previously described miRNAs might not be the genuine regulatory molecules, but rather degradation products or sequencing artefacts. To test this, we are currently analysing miRNAs bound to the RNA silencing complex (RISC) and preliminary results show that only a subset of host miRNAs is loaded into RISC complex during productive or latent infection. Curiously, in contrast to host miRNAs, HSV-1 miRNAs show a significant frequency of 5’ variants, and importantly, for a number of miRNAs the sequences of the most prevalent variant differ from the miRNA sequence in the miRBase. 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 and host miRNA deregulation that is yet to be fully investigated.

Herpes simplex virus 1, microRNAs

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