Fig. 3: ICP22 is sufficient to induce dOCRs upon ICP27-induced read-through transcription.

a Number of genes in Cluster 5 from Fig. 1b for which dOCRs reach at least a length greater than the value indicated on the x-axis in T-HF-ICP22 cells, T-HF-ICP27 cells, and T-HF-ICP22/ICP27 cells ± Dox treatment. b Example gene (HNRNPA2B1) showing induction of dOCRs after Dox-induced ICP22 and ICP27 expression in T-HF-ICP22/ICP27 cells. Tracks show total RNA-seq (strand-specific) and Omni-ATAC-seq (non-strand-specific) read coverage (normalized to a total number of mapped human reads; averaged between replicates). Below each Omni-ATAC-seq track, the figure shows open chromatin regions (OCRs) identified with F-Seq as well as the dOCR regions calculated from the OCRs as described in Methods. For simplification, OCRs and dOCRs are shown only for the first replicate. Gene annotation is indicated at the top. Boxes represent exons, lines introns, and gene direction is indicated by arrowheads. Genomic coordinates are shown at the bottom. c Scatter plot correlating downstream FPKM in total RNA against dOCR length (average of two replicates) for Dox-induced combined ICP22 and ICP27 expression (T-HF-ICP22/ICP27 cells + Dox). Shown are all analyzed genes with a downstream FPKM ≥ 0.05. Colors indicate the density of points from high (red) to low (blue). The red line indicates a linear fit of log10(dOCR length) against log10(downstream FPKM). The slope of the fit and p-values for the slope of the linear regression estimate being ≠ 0 were calculated using the lm function in R and are indicated on top of each figure. The error bands around the red line indicate the 95% confidence level interval for predictions from the lm linear model. Example genes with high induction of dOCRs in HSV-1 infection are highlighted. The corresponding scatter plot for T-HF-ICP22/ICP27 cells without Dox treatment is shown in Supplementary Fig. 8f. Source data are provided as a Source Data file.