Extended Data Fig. 10: Klf4 transition from adsorbed to condensed layer and from low to high sequence specificity on DNA upon MBP cleavage.

a, Representative examples of kymograph ROIs corresponding to the 3 C dependent MBP-Klf4 condensation. Each example corresponds to a different experimental realization. b, c, Example kymographs of MBP-Klf4 and Klf4 coated DNA when transferred to the assay buffer (which does not contain the 3 C protease). d, Coefficient of variation (CV, top) and mean (bottom) of the distribution of intensity values along the DNA over time after cleavage. An increase in the CV while the mean intensity decays in a similar way for all conditions indicates a rearrangement of material on the DNA that leads to local enrichment of cleaved Klf4-GFP. Solid lines, mean, shaded area, standard error of the mean at 95% confidence. The number of experiments (N) is indicated. e, Representative kymographs corresponding to the 3 C dependent MBP-Klf4 condensation process. The coarse-grained binding energy profile is shown at the bottom as a guide to the eye (see Fig. 2h and Methods). f, Red, average intensity profile along λ-DNA for N = 22 experiments binned at the indicated time after transfer of the bead-DNA system to a solution containing the 3 C protease. Shaded area, standard error of the mean at 95% confidence. The coarse-grained binding energy profile is shown in blue (see Fig. 2h and Methods). The Pearson’s correlation between the average intensity and the binding energy profiles, increases from 𝜌=0.51 at t = 0 s to 𝜌=0.69 at t = 450 s. g, h, Average intensity profile along λ-DNA for N experiments binned in the indicated concentration range (red) for Klf4 (g) and MPB-Klf4 (h). Shaded area, standard error of the mean at 95% confidence. The coarse-grained binding energy profile is shown in blue (see Fig. 2h and Methods). The correlation between the average intensity profile and the binding energy profile, quantified by Pearson’s correlation coefficient (𝜌), is indicated in each case.