Supplementary Figure 2: Subnuclear compartmentalization dynamics during reprogramming.
(a) Representative in-situ Hi-C contact maps (50kb resolution) of a 22.5 Mb region on chromosome 3. (b) Pearson correlation coefficient (R2) heatmap of PC1 value comparisons between timepoints. (c) Line chart depicting genome fractions assigned to A or B compartments at the different time points. Regions that could not be assigned (PC1 = 0, e.g. telomeric regions) are shown in gray. (d) Overall contact enrichment for 100kb bins within the A (left) or B (middle) compartment or between A and B (right) compartments during reprogramming. (e) Fraction of the genome that switches compartment at any point during the time course. Bar graph depicts switching percentages per timepoint. (f) Overlay of principal component analyses for gene expression (blue) and compartmentalization (red) dynamics reveals similar trajectories. Sample sizes are indicated in Fig.1d and Fig.2c. (g) Gene expression changes for genes in bins that switch compartment at any timepoint (n = 2,676 for A-to-B; n = 2,667 for B-to-A) or do not switch (‘stable’, n = 21,027) during reprogramming (*P<2.2e-16, Wilcoxon rank-sum test). (h) Gene ontology terms associated with the two categories of switching genes. (i) Average absolute PC1 score of switching or non-switching (‘stable) bins as a function of their distance to the nearest A/B compartment border. Samples sizes as in panel g. (j) Average distance to the nearest compartment border of non-switching stable bins divided by the average distance of the two types of switching bins. Switching bins are significantly closer to borders than stable bins at all timepoints (Poisson regression, P<4.97e-31). (k) Cartoon summarizing characteristics of compartment switching dynamics: compartmentalization dynamics are highest in regions of low PC1 and near compartment domain borders. Error bars in all plots denote 95% CI.
