Fig. 6: TADs and loops are rearranged at different times post-infection while A/B compartments are maintained.

a Contact frequencies (Log10 average normalized counts) as a function of genome-wide distance for individual Hi-C replicates obtained in mock and HSV-1 infected A549 cells at 1, 3 and 8 hpi. b Left. Plots showing the eigenvector (PC1) obtained for chromosome 2 (100 kb resolution) for mock and HSV-1 infected A549 cells at 1, 3, or 8 hpi (compartments: A (blue), B (yellow)). Right. Scatterplots showing the correlation between PC1 values for each bin obtained for mock versus 1, 3, or 8 hpi. c Distribution of the compartmentalization score (Contacts within compartments/Contacts between compartments) for mock and HSV-1 infected A549 cells at 1, 3, or 8 hpi. d Plot showing the average insulation score at TAD boundaries (±300 kb) obtained for mock and HSV-1 infected cells at 1, 3, or 8 hpi. e, g Alluvial plot showing the number of created and maintained TADs (e) and loops (g) in the transitions between mock and HSV-1 infected A549 cells at 1, 3 and 8 hpi, with a tolerance of 50 kb. The yellow portion of the bars represent the TADs or loops present in mock, the blue portion of the bars represent the TADs or loops created at different times post-infection. f, h Plots showing the number of TADs (f) and loops (h) maintained, lost and new at each time point during infection, compared with mock, with a tolerance of 50 kb. Dark yellow represents maintained loops, pale yellow represents lost loops, and blue represents new loops in regards to mock. Source data are provided as a Source Data file.