Fig. 3: Effects of cnd1-K658E condensin mutation and Pmc4 mediator depletion on 3D chromosome organization during mitosis.

a Genome-wide contact maps of mitotic cells from the wild-type strain (cnd1-WT; left) and the cnd1-K658E mutant strain (cnd1-K658E; right). ICE-normalized matrices at 20 kb resolution were used for data representation. Mitotic cells were prepared as described in Supplementary Fig. 3a. b Difference map showing changes in contact scores between cnd1-K658E and cnd1-WT cells. The Hi-C data shown in (a) were used to calculate the difference scores. c Relationships between contact scores and genomic distances in cnd1-WT and cnd1-K658E cells. Contact matrices at 10-kb resolution were used for this analysis. d Enlarged difference map of a 1.9 Mb region of chromosome I (dotted box in (b)). Data representation is explained in Supplementary Fig. 3e. e Averages and log₂ ratios of contact scores between cnd1-K658E and the cnd1-WT cells, and between biological replicates from mitotic cell cultures (inset). Analysis was performed as described in Supplementary Fig. 3f. f Contact maps of mitotic cells expressing wild-type Pmc4 from a plasmid (Pmc4 WT; left) and cells lacking exogenous Pmc4 expression (Pmc4 depletion; right). Endogenous Pmc4 proteins were degraded using the AID system. Mitotic cells were prepared as in Supplementary Fig. 3a. g Genome-wide difference map showing changes in contact scores between Pmc4-depleted and Pmc4 WT cells. h Relations between contact scores and genomic distances in Pmc4 WT and Pmc4-depleted cells. i Enlarged difference map of the 1.9 Mb region on chromosome I (dotted box in (g)) comparing Pmc4-depleted and Pmc4 WT cells. Border strength in each sample was calculated as described³⁸. The difference in the border strength scores between the two samples is shown on the right. Arrows mark domain boundaries impaired by Pmc4 depletion. j Averages and log₂ ratios of contact scores between Pmc4-depleted and Pmc4 WT cells. The analysis was performed as described in Supplementary Fig. 3f. Insets show biological replicates from mitotic cell cultures. Across the entire study, the same conditions were used for representing Hi-C matrices, generating difference maps, plotting distance curves, and performing statistical analyses of condensin domains.