Fig. 2: Chd4 alters contact ___domain interactions and compartmentalization.

a (Left) Hi-C contact matrix of a contact ___domain on chromosome 13 and the flanking region. Below is a genome-browser snapshot of the region corresponding to the Hi-C contact matrix displaying the ChIP-seq profiles of H3K4me1, H3K27ac, and Smc1 as well as DNaseI-seq from the control and Chd4 cKO cerebellum. (Right) Juicebox browser snapshot of the Pearson’s correlation matrix of a region on chromosome 13 surrounding the contact ___domain. Below is the eigenvalue of the corresponding region on chromosome 13 in 150 kb bins, with the region surrounding the contact ___domain highlighted. b Density plot comparing the change in contact ___domain DNaseI-seq with the change in Hi-C contacts within the ___domain in the control and Chd4 cKO cerebellum. Pearson’s r, p < 0.001. c Change in Hi-C contacts within domains with increased (Log₂FC > 0.585), unchanged (−0.585 < Log₂FC < 0.585), and decreased (−0.585 < Log₂FC) accessibility in the Chd4 cKO cerebellum. Points represent average of domains in individual biological replicates (n = 3). One-way ANOVA with Tukey’s post hoc HSD test. **p < 0.01. d, e Density plot comparing the change in contact ___domain (e) H3K27ac and (f) Smc1 ChIP-seq with the change in Hi-C contacts within the ___domain in the control and Chd4 cKO cerebellum. Pearson’s r, p < 0.001. f Spearman’s Rho comparing the difference in eigenvalue among contact domains and the change in ___domain contacts or other epigenomic features (Chd4 cKO/Ctrl).