Second and third categories, which we subsume for clarity of presentation

    Dirk Espensen
    By Dirk Espensen
    Pending Moderator Review

    Though antisense CPI-1205 get transcription from viral genomes has been described previously, e.g., in HIV-1 [17], and was also observed in our sequencing information in the HSV-1 genome, to our know-how, modulation of host cell antisense transcription by virus infections has not been studied so far. Making use of replication inhibitor and knockout viruses we show that overexpression of viral ICP4 alone is enough to induce expression of a subset of antisense transcripts. Analysis of published RNA-seq information from other herpesviruses revealed that, although induction of a subset of antisense transcripts is conserved within the Alphaherpesvirinae subfamily, infection with extra distantly connected herpesviruses will not bring about detectable upregulation of antisense transcripts. Applying a reporter assay, we showed that the sequence area upstream from the BBC3as antisense transcript functions as a promoter induced upon infection. In addition, we offer evidence that the induced antisense transcript impairs transcription from the BBC3 sense mRNA in cis. We propose that induction of antisense transcripts represents a previously undescribed method of how the virus modulates host gene expression.ResultsDetection of antisense transcripts in RNA-seq information from HSV-1-infected cellsTo investigate GS-9973 cost transcriptional regulatory events in PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28381880 HSV1-infected cells we sequenced mRNA from key lung fibroblasts (WI-38 cells) at various timepoints until late into the lytic infection cycle (Fig. 1a). Two key phenomena emerged when analyzing host cell transcripts upon infection, namely transcriptional readthrough as observed previously [8] as well as the widespread induction of antisense transcription.For the detection of antisense transcripts, we additionally relied on directional RNA-sequencing data from human foreskin fibroblasts of rRNA-depleted total RNA and 4-thiourdine pulse-labeled and subsequently purified newly transcribed RNA (4sU-RNA) [8] (Fig. 1a). For maximal sensitivity, the information from 4sU-RNA was analyzed with a newly created algorithm to detect antisense transcripts. Right after initial definition of transcribed regions outside of annotated genes, transcriptional read-throughs have been filtered out (see "Methods"). Applying a running sum algorithm, we defined 12,863 transcribed regions either annotated as antisense transcripts in Ensembl or not annotated at all. Of those, 9765 regions were designated as read-through regions. The remaining 3098 loci have been grouped by their expression profiles into ten clusters (Fig. 1b; Added file 1: Figure S1a; Added file 2: Table S1). Depending on their place, transcripts have been categorized as divergent, convergent, or internal antisense transcripts (Fig. 1d), or, in the event the transcription start web page (TSS) in the antisense transcript was not inside ten kb of a TSS of a transcript on the opposite strand, and if it didn't overlap a gene physique, it was categorized as "undefined". From the 3098 antisense transcripts, 1517 showed no less than two-fold upregulation upon infection.Second and third categories, which we subsume for clarity of presentation as "antisense transcripts" in our text. Whilst antisense transcription from viral genomes has been described previously, e.g., in HIV-1 [17], and was also observed in our sequencing information in the HSV-1 genome, to our know-how, modulation of host cell antisense transcription by virus infections has not been studied so far. Here, we set out to investigate antisense transcription in the host genome after HSV1 infection, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26266977 and identified around 1000 antisense transcripts particularly upregulated upon HSV-1 infection.