Fig. 3: HCMV extensively reprograms host nascent and steady state transcriptomes.

Mock or infected samples taken at 72 h.p.i. (n = 2) or 96 h.p.i. (n = 4) were pulsed with 4sU and nascent RNA was isolated for TTseq, or total RNA was sequenced (RNAseq). A Comparisons of DE genes identified at the indicated timepoints showing shared and unique genes in TTseq, RNAseq and across both TTseq and RNAseq datasets. The number of shared genes at both times is indicated for each condition. B, C Compartment distributions of DE genes. Genes were assigned to 100 kb binned subcompartment calls, requiring an overlap of 75% of the gene. Alluvial diagram of DE genes showing start (mock) and end (inf) compartment state for up-regulated or down-regulated genes at 96 h.p.i. is shown in B. Interactive version is available at https://public.flourish.studio/visualisation/20359025/. Compartment transition states of core 72/96 h.p.i. DE genes are shown in (C). D diffDomain was used to identify several types of TAD reorganization upon infection (split, single, merge, loss and complex subtypes) and enrichment in each subtype of up- or down-regulated genes identified by DEseq2. See also Supplementary Fig. 5. E, F DEseq2 was used to identify differentially expressed genes between mock and infected samples at 96 h.p.i. n = 4 per condition. Differentially expressed genes were subdivided by Log₂FC below (mid) or above 2 (high) (Log₂FC > 2 & < − 2). E Gene Ontology analysis of statistically significant upregulated or downregulated genes at 96 h.p.i., plotted using clusterProfiler. F EnhancedVolcano plot displaying mid versus high (Log₂FC > 2 & < − 2) expression changes.