Figure 4.

Effects of condensin and cohesin mutations on domain organizations. (a) Contact maps in the wild-type (WT1) and cut14-208 condensin mutant. (b) Relations between contact scores and genomic distances in WT1 and cut14-208 cells. Dotted lines show the fitting lines against the slopes in the 75–800-kb and >800-kb ranges. (c) Log₂ ratios of contact scores between cut14-208 and WT1 cells plotted against distance. (d) Map showing difference of contact scores between cut14-208 and WT1. (e) Enlarged difference map for the 1.9-Mb area indicated by the open box in d. Dotted lines indicate the large domains. (f) Enlarged contact map at the 40-min time point. (g) Averages and log₂ ratios of contact scores between the cut14-208 mutant and WT1 and between two in situ Hi-C experiments using independent cell cultures (120-min point; inset). Genomic contacts within the large domains (red) were separated from other contacts (gray) and were used in the analysis. 100 combinations of genomic loci were randomly selected from the large domains. Log₂ ratios of contact scores between the cut14-208 mutant and WT1 and between the biological replicates (120-min point) were extracted for the selected 100 combinations and subjected to two-sided paired Student’s t test. Random sampling was repeated 1,000 times and a median of P values is represented. (h) A contact map in the rad21-K1 cohesin mutant. (i) A map showing difference of contact scores between the rad21-K1 mutant and WT2. (j) Relations between contact scores and genomic distances in the WT2 and rad21-K1 mutant. Dotted lines show the fitting lines against the slopes in the <75-kb and >75-kb ranges. (k) Contact maps for the 500-kb region indicated by the open box in i in rad21-K1 (left) and WT2 cells (right). Dotted lines indicate the small domains. (l) Enlarged difference map between the rad21-K1 and WT2 for the same 500 kb-region. (m) Averages and log₂ ratios of contact scores between the rad21-K1 mutant and WT2 and between two in situ Hi-C experiments using independent cell cultures (120-min point; inset). The rad21-K1 and WT2 small domains were subjected to the same statistical analyses as described in g.