Fig. 5: IDR inhibits CHD1-binding to unmodified nucleosome.

a Representative images of nucleosome binding assay showing stronger binding of CHD1^∆NC protein to nucleosomes compared to CHD1^WT. The concentration of indicated CHD1 was tested against 5 nM nucleosomes containing IR dye-labeled DNA, separated by native PAGE, and visualized via IR signal detection. Shifted nucleosome fractions (n = 3 independent experiments) were fitted to a dose-response curve (right). The curves were compared using two-way ANOVA (P < 0.0001). b Schematics illustrating the structure of CHD1^WT, CHD1^∆NC, and CHD1^∆Helicase. Confocal images of HeLa cells expressing WT, ΔNC, and ∆Helicase show negative correlation between CHD1 condensation and its affinity to nucleosomes. Scale bars, 5 µm. Condensate sizes in cells from 10 random fields are represented using violin plots with boxplots, illustrating the mean, median, interquartile range, and 10^th–90^th percentiles denoted by white circles, black bars, grey boxes and thin black lines, respectively. The size of each condensate was plotted as a dot on the right and analyzed using unpaired two-tailed Student’s t-test. c Schematic diagrams showing the nucleosome-binding properties of CHD1^WT, CHD1^∆NC, and CHD1^∆Helicase. CHD1^WT possesses IDRs, which inhibit non-specific binding to unmodified nucleosomes. Condensation driven by the IDR occurs around H3K4me3-nucleosomes, elevating local concentration and ensuring specificity towards H3K4me3-modified regions. CHD1^∆NC exhibits reduced condensation ability, leading to non-specific binding to nucleosomes through the helicase/ATPase domain. CHD1^∆Helicase cannot bind to nucleosomes and forms large condensates. Source data are provided as a Source Data file.