Extended Data Fig. 7: Polymer simulations of two genomic locations within the same TAD.
From: Cohesin and CTCF control the dynamics of chromosome folding
A. Radial MSD of TetO random integrations (mean ± s.e.m., purple, see Fig. 1E, n = 271 cells examined over 3 pooled biological replicates) and of targeted LacO and TetO insertions on Chr15 (mean ± s.e.m., dark blue, n = 214 cells examined over 4 replicates) are compared to model predictions for pairs of loci containing extrusion barriers at a distance of 1 Mb (light blue) and 152 kb (red). Note that random TetO insertions often occur on different chromosomes and thus have larger absolute radial MSD than 1 Mb simulations (but similar scaling). B. Radial MSD for cell lines containing multiple random integrations of TetO as shown in Extended Data Fig. 2D (mean ± s.e.m., red, 266 cells examined over 3 pooled replicates) or the targeted integrations of LacO and TetO on chr15 (mean ± s.e.m., orange, n = 277 cells examined over 6 replicates) in the absence of RAD21 compared to the predicted radial MSD of two loci at a distance of 150 kb in the absence of extruders (gray) as predicted from polymer simulations. C. Radial MSD of TetO-LacO distances in mESC lines with or without convergent 3xCTCF sites (or promoters, respectively), either before or after treatment with 500 nM dTag-13 for 2 hours to induce degradation of RAD21 (dt = 30 s). radial MSDs are plotted as mean ± s.e.m. over conditions: +CTCF sites/+RAD21: n = 152 cells examined over 4 replicates, −CTCF sites/+RAD21: n = 214 cells examined over 4 replicates, +CTCF sites/−RAD21: n = 248 cells examined over 7 replicates, −CTCF sites/−RAD21: n = 277 cells examined over 6 replicates, +Promoters/+RAD21: n = 155 cells examined over 3 replicates, +Promoters/−RAD21: n = 170 cells examined over 3 replicates.
