Fig. 5: Complex CTCF contact networks are altered upon depletion of cohesin factors.
From: Characterization of induced cohesin loop extrusion trajectories in living cells
a, Representation of the collapsed ‘inner’ domain in STAG2-depleted cells (highlighted in orange) as determined from 4C and HMM modeling. The outer TACL domain runs until the original TACL domain boundaries. CTCF binding sites within these domains are categorized by orientation (convergent or divergent relative to TetO) and ChIP–seq signal strength (strong, intermediate or weak). b, Average signal plots of CTCF, FLAG, NIPBL, SMC1, STAG2 and STAG1 ChIP–seq signals at CTCF sites within the inner or outer TACL domains. CTCF sites are categorized by orientation to TetO and CTCF strength. Peaks are plotted as ±1 kb windows centered on the highest ChIP–seq signals. ChIP signals are normalized to the average signal at CTCF sites genome-wide. Number of sites in the inner domain: convergent-strong, n = 77; convergent-intermediate, n = 65; convergent-weak, n = 59; divergent-strong, n = 78; divergent-intermediate, n = 57; divergent-weak, n = 53. Number of sites in the outer domain: convergent-strong, n = 48; convergent-intermediate, n = 42; convergent-weak, n = 35; divergent-strong, n = 32; divergent-intermediate, n = 38; divergent-weak, n = 41. c, Aggregate 4C signal plots of TACL-ON, TACL-OFF and TACL-ON degron depleted cells. Signal is plotted at CTCF sites within the inner and outer TACL domains. Again, CTCF sites are categorized by orientation to TetO and strength. Signals are centered (gray dashed line) around a ±50 kb window. Number of sites in the inner domain: convergent-strong, n = 57; convergent-intermediate, n = 58; convergent-weak, n = 49; divergent-strong, n = 63; divergent-intermediate, n = 44; divergent-weak, n = 44. Number of sites in the outer domain: convergent-strong, n = 48; convergent-intermediate, n = 45; convergent-weak, n = 35; divergent-strong, n = 32; divergent-intermediate, n = 39; divergent-weak, n = 41. d, Average signal plots of FLAG, NIPBL, SMC1 and STAG1 ChIP–seq signals in TACL-ON STAG2-depleted cells. Signal is plotted at TetO-convergent CTCF sites within the inner or outer TACL domains. Sites are categorized based on CTCF strength. Peaks are plotted as ±1 kb windows centered on the highest ChIP–seq signals. Number of sites as indicated in b.
