Fig. 6. Detection of common compartmental reorganizations upon OIS and RS.

a Contact maps for chromosome 4 in IMR90 RS (top right) and growing (bottom left) cells at 200 kb resolution. Histone H3K9me3 distribution in IMR90 growing cells is shown at top. PCA scores along chromosome 4 for RS and growing cells (G) are shown at right. b Contact maps for chromosome 4 in BJ RS (top right) and growing (bottom left) cells at 200 kb resolution. c Overlap of genomic regions undergoing BA transitions upon OIS and RS in IMR90 cells. Genomic regions undergoing BA transitions that were common between the IMR90 OIS biological replicates were compared to those shared between the IMR90 RS biological replicates (hypergeometric distribution test). d Overlap of genomic regions undergoing BA transitions upon RS in IMR90 and BJ cells. Genomic regions undergoing BA transitions that were common between the IMR90 RS biological replicates were compared to those shared between the BJ RS biological replicates (hypergeometric distribution test). e GSEA of genes (n = 811) located at genomic regions undergoing BA transitions that were common between OIS and RS in IMR90 cells. All human genes were ranked by expression fold changes (FC), calculated as levels of gene expression in RS (left)⁶⁸ or OIS cells (right) divided by those in growing cells (blue distributions). f GSEA of genes (n = 362) located at genomic regions undergoing BA transitions upon RS that were common between IMR90 and BJ cells. g ChIP-seq enrichment of the indicated proteins and epigenetic marks at genomic regions in the respective compartmental categories (AA, BB, AB, and BA). Genomic regions that belonged to the same compartmental categories in IMR90 OIS and RS cells were analyzed as in Fig. 4c. G and S indicate growing and senescent (OIS and RS) cells, respectively. ChIP-seq data were derived from IMR90 growing and OIS cells. For 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. h An example showing the BA transition conserved between OIS and RS. PCA scores are plotted along a 5 Mb region in chromosome 6. i Same as panel h, but a 5 Mb region in chromosome 18 is shown. The AB transition conserved upon OIS and RS is centered.