engleski

The transcriptome of herpes simplex virus 1

Herpes simplex virus 1 (HSV-1) is an intensively studied human pathogen for a number of years, however many of its biological properties remain unknown. Although, several HSV-1 strains have been completely sequenced, and partial transcriptomes of the virus have been assigned, the exact transcriptional activity of the virus is yet to be elucidated. Importantly, previous analyses have mainly focused on the transcripts containing open reading frames (ORFs), which might represent a huge underestimation of functional transcripts, namely with regards to recently discovered non-coding RNAs, including regulatory long-non-coding RNAs (lncRNAs) and microRNAs (miRNAs). Several HSV-1 encoded lncRNAs have been detected using traditional techniques, such as Northern blot, and function of most of these have not been elucidated. On the other hand, HSV-1 miRNAs have been discovered very recently and their number is still increasing. For many HSV-1 miRNAs the primary transcripts and the regulation of their promoters are unknown. To generate a comprehensive map of the HSV-1 transcriptome, including the non-coding transcriptome, we analyzed total RNA from cells infected with HSV-1 at different time points using automated NGS library preparation massive parallel sequencing on Illumina platform. We have generated high quality sequence data set (according to FastQC quality control tool) with approx. 25 million reads per sample, and our work in progress shows majority of known virus transcripts. Currently we are trying to map all reads on the virus genome, delineate non-coding transcripts and generate an interactive map of all transcripts. Our specific focus is on the precursors of virus miRNAs, and we investigated thoroughly the potential precursors of miR-H1 and miR-H6 by Northern blot and RACE, which will be now complemented with the transcriptome profile. In addition, we are performing a re-analyses of our miRNA sequencing data sets to evaluate previously and newly discovered miRNA. Of note, many reads obtained by sequencing might falsely satisfy miRNA criteria but represent only the degradation products. We hypothesized that a careful analysis of the transcriptome will also greatly help to define the exact HSV-1 miRNAs.

Herpes simplex virus 1

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