Fig. 2
Replication timing correlates with DNA methylation in cancer. a DNA methylation (WGBS) density distributions for early (blue) and late (red) loci per cell line. Adjacent are scatterplots of DNA methylation in relation to replication timing (WA) for all measured 1 kb loci in PrEC and LNCaP. Blue dashed line indicates early (WA > 75) and red dashed line indicates late (WA < 20). b Representative examples of late-replicating regions common to both PrEC and LNCaP (shaded) that become hypomethylated in LNCaP. The correlation between DNA methylation and replication timing values increases from PrEC (Spearman’s 0.3073, p < 2.2e−16) to LNCaP (Spearman’s 0.4985, p < 2.2e−16). Scale bar represents 5 Mb. c Percentage (y-axis) of PrEC early and late regions (1 kb loci) that are hypermethylated (LNCaP-PrEC, ΔWGBS > 0.2) and hypomethylated (LNCaP-PrEC, ΔWGBS < −0.2). Asterisks indicate significantly different percentages between early and late (test of equal proportions, p < 2.2e−16). d Associations between genomic elements and hypo- and hypermethylated 1 kb loci. Association is above zero, and disassociation is below zero. Asterisks indicate significant associations (FDR < 0.05, Fisher’s exact test)
