Fig. 5: HCMV genomes accumulate at euchromatic regions of the host genome.

Viral-host interactions were extracted using HiCPro’s makeviewpoints from combined 72 and 96 h (n = 4) infected HiC datasets to identify regions of enrichment. A Viral-host contacts visualized with dcHiC compartment analysis shows overlap with A compartments using Chromosome 15 as an example. B Viral genome interactions across subcompartments. Top; percent of viral-host reads mapped to subcompartments. Bottom; subcompartments were normalized by size and viral genome coverage. C, D. Enrichment of viral reads in (A) compartments and de-enrichment in (B) compartments (C) is evident in the aggregated signal profile controlling for compartment size. H3K9me3 (repressive mark) CUT&RUN performed on mock-infected or infected NHDFs at 96 h.p.i. (MOI 5, n = 2 per sample) shows the opposing depletion of H3K9me3 reads in A compartments and enrichment in (B) compartments (D). E–H Identification of viral interaction hotspots (VERs) and their interactions with the host genome. E GENOVA-derived heatmaps of trans contacts highlight viral-host reads across Chromosome 17. Parameters = znorm. Mode = difference. The top 10% of 100 kb bins of the host genome most enriched for viral reads, termed VERs, are highlighted in purple on the accompanying chromosome map with viral read plots on the right. F Distribution of A compartments and VERs across all chromosomes displayed with an Ideogram. GDeeptools plotProfile of VERs across subcompartments. Region body length = 100 kb. Bin size = 10. H Percent of Viral Enriched Regions (VERs) within each subcompartment.