Fig. 6: Low occupancy sites of CTCF and cohesin are susceptible to developmental regulation and Matr3 loss.

a Cumulative probability distribution of the distance to the nearest enhancer for up- and down-regulated genes versus stable genes in Matr3 KO compared to parental cells. Genes whose expression was altered upon Matr3 deletion resided at shorter genomic distances under a two-sided Kolmogorov-Smirnov (KS) test (up vs. stable: p = 3.62e-06, down vs. stable: p = 1.93e-09, up vs. down: p = 0.495, respectively). b Differently occupied regions of CTCF and Rad21 in Matr3 KO compared to parental cells nearby H3K27Ac marked chromatin associate with genes whose expression was altered upon Matr3 loss during differentiation. Significance of enrichment was calculated using the one-sided Fisher’s exact test. The odds ratios for significant enrichment for CTCF and Rad21 were 2.01 (95% confidence interval (c.i.) = 1.7–2.4) and 2.03 (95% c.i. = 1.7–2.5), respectively. c ChIP-seq data sets of CTCF and Rad21 from uninduced (unt) and differentiated (diff) cells were quantitatively compared³⁸, and the results of at least two independent experiments were combined to generate a more stringent peak list. d After classification of regions into altered (uniq) and maintained (common) during differentiation (Fig. 6c), the enrichment of the peaks in each experiment was investigated using⁸⁶ (p < 2.2e-16, p < 2.2e-16, respectively, by two-sided t test; Cohen’s d = 1.48, Cohen’s d = 1.24, respectively). The results were confirmed in 2-3 independent experiments (Fig. S5a-c). e Percentage of sites with reduced CTCF and Rad21 binding during differentiation in the binding regions lost in Matr3 KO compared to parental cells. f After classification of binding regions into maintained (common) and altered (uniq) upon Matr3 loss (Fig. 4d), the enrichment of the peaks in each experiment was measured (p < 2.2e-16, p < 2.2e-16, respectively, by two-sided t test; Cohen’s d = 1.22, Cohen’s d = 1.26, respectively). The results were confirmed in 2-3 independent experiments (Fig. S5d-f). In box plots, the centre line represents the median, box limits show upper and lower quartiles, and whiskers extend to 1.5 × interquartile range.