Extended Data Figure 2: A/B compartments changes are concordant with topological ___domain boundaries.

a, Genome browser image of the A/B compartments determined using the previously described 1-Mb bin algorithm (1-Mb track) compared with the 40-kb sliding window approach used in our analysis (40-kb sliding window track). b, Pie-charts demonstrating the fraction of the genome in the A (blue) or B (yellow) compartments in each of the six lineages studied. Shown in black are regions with a PC1 of zero, often corresponding to centromeric and telomeric regions of the chromosomes. c, Percentage of the genome that changes A/B compartment upon differentiation of ES cells into each of the five differentiated lineages. d, Cumulative density plot of the distance between topological ___domain boundaries and transition points between the A and B compartments. The red line represents the observed distances and the grey line represents distances for randomly generated topological ___domain boundaries. Domain boundaries are closer to A/B compartment transitions when compared with random (P value 2.2 × 10⁻¹⁶, Wilcoxon rank sum test). e, K-means clustering of PC1 values in human ES cells and differentiated lineages surrounding topological ___domain boundaries. Similar to Fig. 1c, ___domain boundaries correspond to the transition points between the A/B compartments, and changes in A/B compartments that occur during differentiation tend occur at ___domain boundaries. Regions that stay as A or B compartment are termed stable A or stable B. Regions that stay as A/B compartment switching are labelled as stable switch. Regions where the boundary becomes a new switching point for the A/B compartment are labelled new switch. Regions that previously were A/B compartment switching but are no longer after differentiation are labelled switch loss. Regions that entirely switch from A to B or vice versa are labelled as switch A/B.