Extended Data Fig. 2: Chromosome dynamics is modulated by degradation of factors involved in loop extrusion.
From: Cohesin and CTCF control the dynamics of chromosome folding
A. Mean Square Displacement (MSD) of trajectories from TetO insertions within the same cell (MSD, mean ± s.e.m., n = 45 tracks) before (cyan) and after applying cell motion (light blue, n = 45 tracks) and localisation error correction (dark blue, n = 45 tracks). B. Scaling exponents (α) and generalized diffusion coefficients (D) across all conditions and cell lines were fitted by pooling all three biological replicates. Shown are the numbers for the best fit ± error of the fit. C. MSD (mean ± s.e.m.) plots for a single clonal cell line (biological replicate) when looking at removal of 3xCTCF sites (top row) next to the array or degrading all CTCF (bottom row). D. MSD (mean ± s.e.m.) in the cell lines (n = 3 replicates per clonal cell line, three cell lines) where the 3xCTCF cassette was excised. Shown are the MSDs for cells either depleted of RAD21 for 90 min (red, 266 cells, 9,020 trajectories analyzed) or not (blue, 271 cells, 11,082 trajectories analyzed). Global depletion of RAD21 increases mobility. p-values in panel E. E. Distributions of α and D fitted based on single trajectory MSD and significance test for differences in generalized diffusion coefficients (D) and scaling exponents (α). The p-value is calculated using Student t-test (two-sided) (see Methods). F. Same as in C for a single clonal cell line (biological replicate) with integrations with 3xCTCF-TetO (top row) or without 3xCTCF-TetO (bottom row) when degrading RAD21. Global depletion of RAD21 increases mobility. G. Same as in D in the cell lines that contain integrations of 3xCTCF-TetO and the Tir1 protein, but do not contain any AID-tag for targeted degradation. MSDs for cells either treated with auxin for 90 min (red, 97 cells, 2,155 trajectories analyzed) or not (blue, 111 cells, 3,711 trajectories analyzed). No significant changes were detected. p-values in panel E.
