Fig. 2: Analysis of viral transcription start sites (TiSS).

a Screenshot of our HSV-1 viewer displaying the annotated mRNAs of MinION, PacBio and coverage of read 5’-ends for cRNA-seq and dRNA-seq of the UL22.5-UL25 gene locus. Transcripts in our reference annotation are indicated in blue. b, c Venn diagram depicting the number of Transcription start sites (TiSS) that were identified by cRNA-seq, dRNA-seq and MinION¹⁴ (b) or PacBio¹³ (c) sequencing, respectively. TiSS included into the final annotation are indicated by the black circle. d Histogram depicting the number of TiSS criteria that were fulfilled by the individual viral transcripts. e Sequence logos upstream of viral TiSS with viral TiSS grouped into three equally sized bins according to their transcription rates (top: highest; bottom: lowest). The TATA-box and initiator element (Inr) are shown. f Log fold-change between cytoplasmic and chromatin-associated FPKM-normalized read counts (export index) of cellular (gray) and viral (red and blue) gene clusters compared between wild-type HSV-1 (wt) and a null mutant of the viral RNA export factor ICP27 (ΔICP27). Viral immediate early genes are indicated in blue.