Fig. 5: Cohesin and CTCF control contact dynamics inside a TAD.
From: Cohesin and CTCF control the dynamics of chromosome folding
a, Representative trajectories of radial distance (gray) and occurrences of the proximal state called by HMM (colored bars). The HMM was fitted on data with convergent 3 × CTCF sites and RAD21 (top left) to find the proximal state which was then imposed on the other three samples. b, Left, radial distance distribution in cells with convergent 3 × CTCF sites and RAD21 overlaid with those of proximal and distal states called by HMM on the same sample. Right, same as in the left panel but normalized and with the additional display of the distance distribution from a control cell line where TetO and LacO signals perfectly co-localize. c, Fraction of time spent in the proximal state called by HMM in the four experimental conditions (no. of replicates as indicated in Fig. 4e). Shown are averages across experimental conditions; error bars represent bootstrapped (n = 10,000) standard deviations. d, Average durations of proximal states (mean ± 95% confidence interval (CI), n = 680 (−3 × CTCF/+RAD21); n = 287 (+3 × CTCF/+RAD21); n = 268 (−3 × CTCF/−RAD21); n = 114 (+3 × CTCF/−RAD21)). P values (two-sided Kolmogorov–Smirnov): *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. Exact P values can be found in Supplementary Table 2. e, Average rates of contact formation—time elapsed between the end of a proximal state and the beginning of the next (mean ± 95% CI, n = 726 (−3 × CTCF/+RAD21); n = 323 (+3 × CTCF/+RAD21); n = 268 (−3 × CTCF/−RAD21); n = 138 (+3 × CTCF/−RAD21)). P values as in panel d.
