Fig. 6: Microtubule forces alter virus-host genomic interactions and effects on host chromatin compartments.

A, B Mock or HCMV-infected (MOI 5) NHDFs were treated with control non-targeting siRNAs or siRNAs targeting SUN1 or ATAT1. Samples were harvested at 96 h.p.i. and then processed for HiC. n = 3 independent experiments. A GENOVA-derived heatmaps of trans contacts highlight viral-host reads across Chromosomes 17 and 19, as examples. Shown are mock versus infected (left) alongside mock versus control siRNA (siC)-treated infected samples or infected samples treated with control siRNA versus ATAT1 or SUN1 siRNAs. Parameters = znorm. Mode = difference. VERs are highlighted in purple on chromosome maps with viral read plots on the right. Note that VERs distributions are altered, and many normally weak viral contacts become stronger, resulting in blue colors in subtraction plots of infected control versus ATAT1 knockdown samples. A more broadly mixed phenotype is seen for SUN1 depletion. B Differences in local A-A, B-B or A-B contacts visualized using saddle plots, with A-A and B-B contacts decreasing during infection. Depletion of SUN1 or ATAT1 results in stronger A-A contacts and weaker B-B contacts in infected cells compared to control conditions. GENOVA resolution = 100 kb. Bins = 25. C HCMV-infected NHDFs were treated with either of two independent control non-targeting siRNAs or siRNAs targeting SUN1 or ATAT1. Samples were pulsed with 4sU and then harvested at 72 h.p.i. (n = 2) or 96 h.p.i. (n = 4) for TTSeq. Volcano plots illustrate the effects of target depletion on host gene expression compared to control siRNA-treated infected cells identified using DESeq. Adjusted p-value cutoff = 0.05, Log₂FC cutoff = 0. D Ideograms displaying the chromosome locations of Viral Enriched Regions (VERs) and significantly affected ATAT1 and SUN1 knockdown-sensitive genes identified in TTseq datasets at 96 h.p.i. n = 4 per condition.