Fig. 3: Subcellular localization of viral transcripts.
From: Integrative functional genomics decodes herpes simplex virus 1
a Read levels 500 bp upstream (left) and downstream (right) of the Poly(A)-site (PAS) of viral genes for wild-type HSV-1. Gray bars indicate overlapping parts with other genes, for which reads could not be uniquely assigned. In the cytoplasmic RNA fraction, read levels dropped substantially immediately downstream of the PAS. p-values were calculated using a one-sided paired t-test over the mean fold-change of read levels 500 bp before against after the PAS (Cytoplasmic to Nucleoplasmic: p-value = 8.157 × 10−4, Cytoplasmic to chromatin-associated: p-value = 6.956 × 10−8, Cytoplasmic to total p-value = 4.06 × 10−4). b Screenshot of our HSV-1 viewer depicting poly(A) read-through at the UL30 PAS in cRNA-seq data at 2, 4, and 8 h post infection (hpi) of replicate 1. The annotated transcripts (mRNA), proteins (Proteins) and read coverage (Coverage) for chromatin-associated, nucleoplasmic, cytoplasmic and total reads are shown for the positive strand only. Read-through transcription is schematically indicated in red. Downstream of the UL30 PAS, chromatin-associated and nucleoplasmic reads show substantial read-through, whereas cytoplasmic reads drop down to only a fraction of what they were before (blue arrow).
