Fig. 3: Compartment A–B mixing and epigenome reprogramming.
a, Saddle plots showing chromatin compartmentalization between genomic regions ranked by their E1 scores (genome was divided into 50 total bins). A–A homotypic interactions are shown in the lower right; A–B interactions are in the upper right and lower left. Differential compartmental interactions are shown on the right as log2FC, SARS-CoV-2/Mock. b, Western blots showing the abundances of total histone H3 or several modifications in Mock and SARS-CoV-2-infected (24 hpi) cells. Total histone H3 served as a sample processing control and was run on a separate membrane with the same amount of protein loaded. Quantification was done by ImageJ and is shown at the bottom. Rep #1 and #2 are two replicates. c,d, Boxplots showing the log2FC of calibrated ChIP-seq signals of H3K27ac (c) (from left to right, n = 896, 1,116, 16,877, 25,535, 3,739 and 3,990 peaks) and H3K9me3 (d) (from left to right, n = 1,333, 1,332, 10,660, 10,660, 1,332 and 1,333 bins) for the six categories of genomic bins with varying compartmental changes (as in Fig. 2e). For boxplots, the centre lines represent medians; box limits indicate the 25th and 75th percentiles; and whiskers extend 1.5 times the IQR from the 25th and 75th percentiles.
