Fig. 3. Swr1p modulates 3D genome organization in a manner that depends on the chromosomal context and/or cell cycle stage.

a–c Contact maps (1-kb resolution) of chromosome 1, 13, and 4, respectively, for SWR1-AID strain arrested at G₂ phase. The left panel shows the ICE-normalized matrix and the right panel shows the log₂ ratio matrix of contact maps for knockdown versus control samples for each chromosome. d Zoom-in log₂ ratio-interaction map of chromosome 13 (0.6–0.65 Mb region) for SWR1-AID strain at G₂ phase. Schematic representations including genomic distances and position are displayed on the left side of d. The yellow dots indicate the point centromere of the chromosome. The yellow box highlights a locus within 0.62–0.64 Mb. e (top) IGV data visualizing the localization of Scc1p on chromosome 13 under nocodazole-induced G2/M arrest. Pink, cyan, and yellow-green boxes indicate the Scc1p peak loci called the cohesin-associated region (CAR). Data deposited under accession number GSM4577764 was used for data analysis. (bottom) Arc plot displaying intra-chromosomal interactions within the 0.62–0.64 Mb region of chromosome 13. The red lines highlight contacts that showed >2-fold higher contact scores in +IAA samples compared to control samples, while orange lines highlight contacts that showed >1.5-fold higher contact scores in +IAA samples. f Boxplot comparing the interaction score of intra-chromosomal interactions (n = 170) within the 0.62-0.64 Mb region of chromosome 13 between control and +IAA samples. The p-value was calculated by a one-sided Wilcoxon rank-sum test. (***p-value < 0.001). Boxplot show median; box limits, upper and lower quartiles; whiskers. g The number of intra-chromosomal interactions within the 0.62–0.64 Mb region of chromosome 13 in control and +IAA samples. Total 168 contacts were divided into four groups (25%) by interaction score; (1) <1st Quantile, (2) >1st but <2nd Quantile (median), (3) >2nd but <3rd Quantile, and (4) >3rd Quantile. h The relative of intra-chromosomal interaction counts along the interaction distance within the 0.62–0.64 Mb region of chromosome 13.