Figure 1. Illustrating the complexity of transcriptional outputs from gene loci from two unrelated DNA viruses.

Alignment of dRNA-Seq data against viral genomes can be used to produce coverage plots (beige, blue-gray) integrated with pileup analyses of sequence read termini (5’ end – red, 3’ end – black). Peak-calling of the pileup data yields putative transcription start site (TSS, red vertical boxes) and cleavage and polyadenylation sites (CPAS, black boxes) that are filtered to remove artefacts occurring at splice junctions (yellow boxes). Full length mRNAs identified by dRNA-seq are depicted in green with untranslated regions (UTRs) shown as narrow horizontal boxes and coding sequences (CDS) shown as broader boxes. Spliced introns are shown as narrow lines. (A) Example of shared TSS. The adenovirus strain 5 (Ad5) E3 locus specifies at least eight distinct polyadenylated RNAs, each encoding a unique protein product (Price, Hayer, Depledge, et al., 2019). They share a common transcription start site (TSS) but differ in their splicing patterns and sites of cleavage and polyadenylation (CPAS). Non-E3 transcripts that overlap in this region are shown in gray. (B) Example of shared CPAS. HSV-1 produces transcripts that differ in their TSS and splicing patterns but that make use of a shared CPAS. This is exemplified in the gene cluster encoding transcripts for UL24, UL25, and UL26. (C) Example of readthrough-derived fusion transcripts. HSV-1 also produces fusion transcripts that are generated following readthrough transcription and splicing. This is exemplified using transcripts spanning the RL2 (ICP0) and clustered UL1/UL2/UL3 loci (Depledge et al., 2019).