Fig. 4: HCMV causes transcriptional dysregulation.

A, B Averaged read coverage within and nearby gene bodies for upregulated or downregulated genes between mock and infected conditions, plotted for nascent RNA (TTseq) (A) or total RNA levels (RNAseq) (B). Read counts for “all genes” is also plotted, highlighting the effects of infection on gene expression overall versus up- or down-regulated genes. Data were normalized and replicates combined using Deeptools before display with plotProfile. Region body length = 100 kb. Bin size = 10. C–F ARTDeco was used to characterize read-in (RI) and read-through (RT) in mock versus infected TTseq and RNAseq samples described in A-B above. Rates of RI or RT for the top 1000 expressed genes (C) in individual 72 (n = 2) and 96 (n = 4) h datasets, as well as averaged datasets for effects of infection over both timepoints (dark green, n = 6). Transcriptional profile (D) of upregulated gene categories, high (logFC > 2), mid (0;< logFC > 2), and read-in (log2FC > 2, read-in rate > − 2). E Subcompartment transition state localization of read-in genes shows affected gene flow from the original mock to the final infected states. F Examples of read-in genes visualized in IGV; PLAC8L1 is found in an A compartment that is altered by infection, and C3orf20 is in a weak B (white box) that becomes A upon infection. Both are accompanied by TAD changes during infection. Shown in each are compartments in uninfected and infected cells determined by dcHiC together with DC stats and viral reads (n = 4), H3K4me3 (promoter, n = 2) and H3K9me3 (repressive mark, n = 2) CUT&RUN tracks, average read counts from TTseq at 72 (n = 2) or 96 h (n = 4), up- or down-regulated genes called by DEseq2 (green and orange, respectively), genes upregulated by read-in as identified by ARTDeco (light green) and 20 kb TADs in mock (blue) or infected (purple) cells identified using HiCExplorer.