Figure 4.

Increased Correlation between Chromatin Compartments and RT in Terminally Differentiated Cells Compared to Early Stages of Differentiation

(A) Left: boxplot of RT for 50-kb windows that are constitutively early replicating (yellow) or late replicating (blue) in all cell types (Experimental Procedures). Right: boxplot of compartment (PC1) values for the 50-kb bins in top panel.

(B) Correlation between RT and compartments (PC1) in undifferentiated ESCs (red), early differentiation intermediates (blue), and terminally differentiated cells (gray). Left panel shows data from individual differentiation states or cell lines (average of replicates). Right panel shows all replicates grouped into undifferentiated, intermediate, or terminal differentiation. Differences were significant with ^∗∗p = 0.004, ^∗∗∗p = 2.595 × 10⁻⁶ (t test). Error bars indicate SEM.

(C) Scatterplot showing correlation between changes in RT and changes in PC1 for each differentiation stage (compared with undifferentiated state). R is Pearson’s correlation. MED is mesendoderm.

(D) Exemplary plots show discordance between RT and compartments in ESC and early differentiation stages, but becomes concordant in IMR90 (terminally differentiated cell line). For all panels except the individual tracks in (D), plots of samples 24 and 48 h, IMR90, K562, H1ESC, and mesendoderm are average of two independent differentiations or cell collections, IMR90 is average of four independent cell collections.