Fig. 2: Compartmental reorganization and SAHF formation upon OIS.

a Contact maps for chromosome 4 in OIS (top right) and growing cells (bottom left) at 200 kb resolution. Contact maps were plotted as detailed in Supplementary Fig. 3. b Difference of contact probabilities between OIS and growing cells. Red and blue dots indicate that contact probabilities are higher in OIS and growing cells, respectively. c PCA (principal component analysis) scores in OIS and growing cells plotted along chromosome 4. PCA scores were calculated as described in Methods. SAHF were defined as genomic regions with PCA scores <−20; locations are indicated by black bars at left. d Occupancy of A and B compartments in growing and OIS cells (for replicate #1). Rightmost column shows compartmental switching (AB or BA) or not (AA and BB) between growing and OIS cells. Details are in Supplementary Fig. 4b. e Left: Size distributions of A and B compartments in growing and OIS cells (for the same data as in panel d; two-sided Mann–Whitney U test) shown as boxplots (central bar represents the median with boxes indicating the upper and lower quartiles, and whiskers extend to the data points, which are no more than 1.5× the interquartile range from the box; outliers shown as circles). Numbers of A and B compartments are shown at top. Right: Size distributions and numbers of genomic regions that belong to the respective compartmental categories. f Correlation between PCA score, H3K9me3 enrichment and chromatin compartment. PCA scores of every 40 kb bin across the human genome were plotted against histone H3K9me3 enrichment score in growing and OIS cells (for replicate #1). Dot colors represent genomic regions that belong to the indicated compartmental categories. g Size distribution of the SAHF defined in panel f. h FISH visualization of the SAHF-forming heterochromatic (P1 and P2 probes) and BA-switching loci (P3 and P4 probes) in OIS cells (Methods). Probe positions are shown in Supplementary Fig. 4h. Left: Examples of FISH images for the P1 and P3 probes. SAHF were visualized by DAPI staining. Right: The distance between a center of DAPI-dense area and FISH signal was measured in the indicated numbers of cells (top). Distance distributions shown as boxplots (central bar represents the median with boxes indicating the upper and lower quartiles, and whiskers extend to the data points, which are no more than 1.5× the interquartile range from the box) were compared between the SAHF and BA-switching loci (two-sided Mann–Whitney U test). DAPI signals were used to measure radiuses of SAHF.