Figure 2: Viral infection impacts loop-extrusion and phase-separation features at TAD level.

A: Intra-TAD weakening in SARS-CoV-2 infected genome detected from HiC data⁴. B: Polymer model of genome organization at TAD scale envisages chromatin loop-extrusion and interactions between chromatin and proteins (binders). C: TAD boundaries are limited by converging (forward-reverse) anchor points, occurring with a probability (Methods). D: Average contact maps of TADs from the best model for Mock (left) and SARS-CoV-2 conditions, obtained fitting experimental contact probabilities (Methods). Below, best fit and experimental contact probabilities. E: Log2 Fold Change of average contact maps. Below, Log2 Fold Change of contact probabilities in HiC⁴ (blue curve) and model (orange curve). Correlation between the curves is r=0.82. F: Contact maps of best fit models for Mock and SARS-CoV-2 conditions. Below, 3D rendering of polymer structures obtained from MD simulations of Mock and SARS-CoV-2 models. For visualization purposes, only the three central TADs are shown.