Fig. 5: Condensin has pronounced effect on the conformation of ChrIII and ChrXII.

Hi-C contact matrices for ChrIII (A) and ChrXII (B) in G1-arrested WT strain and Smc4-AID strain ±IAA. Key loci on these chromosomes, including centromeres (block dot), HML, RE, MAT, HMR, and rDNA, are labeled. Log2 fold change between Smc4-AID +IAA and WT is shown on the right. The intersection of the two yellow dashed lines in A marks the interaction between HML/RE and MAT, which is decreased in Smc4 +IAA. The one in (B) corresponds to the interaction between CICI pair 13 (C), which is increased in Smc4 +IAA. C Schematic configuration of intra-chromosomal CICI pair 13, with one array on each side of rDNA. D Mean dot distance and CFT for pair 13 in WT and Brn1-AID strain ±IAA. Brn1 (another condensin subunit) is depleted instead of Smc4 because the SMC4 gene is located very close to the LacO array of pair 13, making it difficult to genetically manipulate without interfering with the locus. Same statistical test is used as in Fig. 3. Error bars represent the standard error of the dot distance and 95% confidence interval of the CFT fit. N = 955, 997, 1131 cells for the dot distance measurement of WT, Brn1-AID strain -IAA, and Brnd1-AID strain +IAA. N = 848, 488, 491 cells for the CFT measurement of WT, Brn1-AID strain -IAA, and Brnd1-AID strain +IAA. Error bars represent the standard error of the dot distance and 95% confidence interval of the CFT fit. For CFT, statistical significance was determined using bootstrap resampling with replacement for 100,000 iterations. For dot distance, statistical analysis is based on two-tailed students’ t test. E Mean dot distance and CFT vs Hi-C contact frequency for all CICI pairs tested. The data taken in WT and Smc4+IAA condition are shown in black and red. The power-law fits of these data are shown in gray curves: \({dis}=0.068{({cf}+0.0008)}^{-0.33}+0.1\), where 0.1 μm represents the finite size of the arrays (same as in Fig. 2F), and \({{{\rm{CFT}}}}=\,0.075{({cf}+0.0008)}^{-0.9}\). Error bars represent the standard error of the dot distance and 95% confidence interval of the CFT fit.