Fig. 4
Viral polyadenylated RNAs initiate at single or multiple locations. To visualize transcription start sites, the extreme 5′ end of each nanopore read was plotted against the HSV-1 genome. Datasets correspond to NHDF infected with HSV-1 strain Patton for 6 hpi (upper track), strain F Δvhs for 6 hpi (middle track), and strain Patton for 18 hpi (lower track). Peaks corresponding to clustered 5′ ends, are referred to as proximal transcription start sites (pTSS) and likely differ by only a few nucleotides from the actual capped 5′ end. In 13 cases, the pTSS is positioned 30–48 bp downstream of a canonical TATA box. Upper panel: top strand. Lower panel: bottom strand. Inset boxes: a Transcription of the HSV-1 UL26.5 gene initiates at a single location throughout infection. b UL48 transcription initiates at multiple locations, one of which is internal to the canonical UL48 ORF, suggesting transcripts encoding a truncated or alternative protein. Canonical HSV-1 ORFs are colored according to kinetic class (IE—green, E—yellow, L—red, and undefined—gray), while polycistronic transcriptional units are indicated by hatched boxes
