Fig. 9: Effects of CAP-H2 depletion on A/B compartmental organizations.

a Contact maps for chromosome 4 in CAP-H2 KD (#1) (top right) and OIS (bottom left) cells at 200 kb resolution. Cells were prepared as in Fig. 7a. Histone H3K9me3 ChIP-seq data (GEO accession#, GSE38448) are shown at top. b Difference of contact probabilities for the data shown in panel a. Red and blue dots indicate that contact probabilities were higher in CAP-H2 KD and OIS cells, respectively. Red and blue dotted lines represent reduced and elevated contact scores in A and B compartments, respectively. The 50 Mb genomic region indicated by open box is enlarged in Fig. 10b. c PCA scores in OIS and CAP-H2 KD cells plotted along chromosome 4. SAHF were defined as genomic regions with PCA scores <−20; locations are indicated by black bars at left. d An example of the BAB compartmental transitions. The BAB transitions indicate regions that underwent BA transitions upon OIS and AB transitions upon CAP-H2 KD. PCA scores in the indicated cell types are plotted along a 4 Mb region in chromosome 1. CAP-H2 and H3K9me3 ChIP-seq data are shown beneath. e Overlap of genomic regions (40 kb bins) undergoing BA transitions upon OIS and AB transitions upon CAP-H2 KD (hypergeometric distribution test). f GSEA of genes (n = 395) located at genomic regions undergoing BAB transitions. Human genes were ranked by expression fold changes (FC), where expression levels of genes in OIS cells were divided by those in growing cells. g GSEA of genes (n = 232) located at genomic regions undergoing BAB transitions and upregulated upon OIS. Human genes were ranked as expression levels in CAP-H2 KD cells were divided by those in OIS cells. h Average ChIP-seq enrichment of CAP-H2 and H3K9me3 at BA and BAB regions. Genomic regions that belonged to the compartmental categories (BA and BAB) were analyzed as in Fig. 4c. 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. i PCA scores of 40 kb bins from BA (gray) or BAB (red) genomic regions plotted against H3K9me3 ChIP-seq enrichment in OIS cells.