Subcellular localization of read-through transcripts in HSV-1 infection.

<p>(a) Boxplots indicating the distribution of the percentage of transcription downstream of genes identified before infection in total, cytoplasmic, nucleoplasmic and chromatin-associated RNA. Numbers in boxes indicate median values. (b) Boxplots indicating the distribution of read-through at 8h p.i. HSV-1 infection in all RNA fractions. Numbers in boxes indicate median values. (c) Boxplots indicating the distribution of log2 ratios of nucleoplasm enrichment (= gene FPKM in nucleoplasmic RNA/ gene FPKM in cytoplasmic RNA) at 8h p.i. compared to uninfected cells. Ratios are shown separately for groups of genes with different amounts of read-through in 7-8h p.i. 4sU-RNA. The value for IRF1 is highlighted in red. (d) Heatmap of read counts (sum of 2 replicates) in total, cytoplasmic, nucleoplasmic and chromatin-associated RNA for the intergenic splicing events shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006954#ppat.1006954.g003" target="_blank">Fig 3C</a>. Results for the intergenic splicing junction connecting SRSF2 and JMJD6 are highlighted by a blue box. (e) Spearman correlation between read-through (calculated from 4sU-seq data) in all conditions and the percentage of transcription downstream of genes identified in chromatin-associated RNA of uninfected/untreated cells. Correlation to mock read-through values is shown below. Mock read-through values were calculated as described in methods and correlations were averaged for each condition. (f) Mapped sequencing reads (negative strand) for total (light/dark pink), cytoplasmic (light/dark green), nucleoplasmic (light/dark red) and chromatin-associated RNA (light/dark cyan) in uninfected cells (light colors) and at 8h p.i. (dark colors) for the IRF1 gene. Read coverage ranges and RefSeq gene annotation are indicated as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006954#ppat.1006954.g001" target="_blank">Fig 1C</a>. (g) Scatterplot of read-through at 2-3h p.i. against the percentage of transcription downstream of genes identified in chromatin-associated RNA of uninfected/untreated cells. Colors indicate density of points (red = highest density, blue = lowest density).