Supplementary Figure 8: TAD connectivity dynamics during reprogramming.

(a) Average expression of genes (plotted as an expression percentile) in TADs (n = 1,664) having a low (-0.26;-0.02), average (-0.02;0.1) or high (0.1;0.6) relative domain score (D-score). (b) Boxplots showing relative D-score values for TADs in the A (n = 953-1,039) or B (n = 1,141-1,227) compartment at each timepoint. Statistical significance was assessed using a Wilcoxon rank-sum test. (c) Percentage of expression variance explained by TADs (relative to a linear model, see Supplemental Materials for a detailed explanation) for each timepoint. (d) Collection of all PCA trajectories generated in this study. Points denote average data from two biological replicates. (e) Average D-score and PC1 kinetics during reprogramming for clusters of TADs that gain (n = 705, left) or lose (n = 869, right) D-score. Pearson correlation coefficients (R) are indicated. (f) Top dynamic TADs gaining (n = 279, upper half) or losing (n = 252, lower half) D-score during reprogramming. Line graphs show mean PC1 values for switching and non-switching TADs. Percentages of A-to-B and B-to-A switching for both groups of TADs are depicted by triangles. Tables show selected gene ontology (GO) terms for the genes within the corresponding TADs. (g) Fraction of TADs that switch compartment in groups of TADs with low (0-0.02), average (0.02-0.07) or high (>0.07) absolute changes in D-score for both independent biological replicate experiments. Error bars in all plots denote SEM.