Extended Data Fig. 6. Effect of time since loop extrusion initiation, loop size, DNA end to end length and DNA tension on the loop extrusion blocking probability of CTCF.

a, Time since loop extrusion initiation and N-terminal (blue) and C-terminal (red) CTCF encounters for events which blocked (left part of violin, dark shading) and did not block loop extrusion (right part of violin, light shading). The horizontal line is the median; boxes extend to the quartiles and the whiskers show the range of the data (median-1.5* interquartile range (IQR); median+1.5*IQR). NTD: p = 0.14; CTD: p = 0.89. b, CTCF blocking fraction for N-terminal (blue) and C-terminal (red) encounters for binned times between loop initiation and CTCF encounter. The number of data points per bin is shown on top. Error bars on bar plots denote 95% confidence intervals. c,d, as for (a,b) but for the loop size at encounter (NTD: p = 0.08; CTD: p = 0.90). Error bars on bar plots denote 95% confidence intervals. e,f, as for (a, b) but for the DNA end-to-end length (NTD: p = 5.05 x 10⁻⁵; CTD: p = 0.09). Error bars on bar plots denote 95% confidence intervals. DNAs with a higher end-to-end length are under higher DNA tension due to entropic effects. g, as for (a) but for the DNA tension (NTD: p = 1.38 x 10⁻⁹; CTD: p = 0.02). For a binned representation of the CTCF blocking probability against DNA tension, see Fig. 2g. Thick horizontal lines on boxplots denote median values, the box extends from the lower to upper quartile values and whisker limits denote the range of data within 1.5 times the interquartile range from the median. Error bars on bar plots denote 95% confidence intervals. h, Calculated DNA tension for values of DNA end-to-end length and loop size. The colour scale shows white for DNA tension values of ≥ 0.15 pN (see Supplementary Information). i, Cross-sections through the two-dimensional representation in (h) for specific values of DNA end-to-end length. Even without an extruded loop (loop size = 0 kb), the tethering of the DNA to the surface at the given end-to-end lengths contributes to the DNA tension. For example, a 31.8 kb DNA construct tethered with an end-to-end length of 4 μm (black line) results in a DNA tension of ~0.07 pN. Statistical significance was assessed by a two-sided Mann-Whitney U test without multiple comparison adjustments.