Fig. 5

Distribution of CTCF and PolII binding on 3D models of the Xa and Xi. a 3D models of the Xa (left) and Xi (right) at 1 Mb resolution in mouse F1 brain colored to display the density of allelic CTCF binding (red indicates more binding). CTCF binding tends to be denser at the periphery of the Xi 3D structure, possibly on one face of the model. White dots indicate chromosome ends, orange dot Dxz4, green dots escape genes. b Box plots for the Xa (left) and the Xi (right) showing allele-specific CTCF-peak density at 1 Mb resolution grouped by the corresponding distances of the 1 Mb regions to the Xa chromosomal center or to the Xi superdomain centers, and empirical cumulative curves of 1 Mb regions binned based on their distance to the Xa chromosomal center or to the Xi superdomain centers for the CTCF-rich (red line, top 25 % CTCF-binding regions) and CTCF-poor regions (blue line, bottom 25 %). The empirical cumulative density as a function of the distance to the chromosome or superdomain centers for the feature-rich and feature-poor regions were compared using one-side Wilcoxon rank-sum test. c, d Same analysis for allelic PolII occupancy. Like CTCF, PolII occupancy tends to be higher at the periphery of the Xi 3D structure