Fig. 5: Immortalisation alters the DNA replication origin distribution in heterochromatin and at TAD borders.

a Euler diagrams showing the percentage of shared core and stochastic origins identified in untransformed (white) and immortalised (grey) cell lines. b In immortalised cells stochastic origins are markedly increased. Bar plots showing the percentage of core (red) and stochastic (grey) origins identified in each cell type. c Line plot showing the percentage of origins (Q1 to Q10) identified in immortalised (pink) and untransformed (blue) cells. d Percentage of origins in each quantile (untransformed Q1–10 in blue, immortalised Q1–Q10 in pink) that overlap with promoter regions (within ±2 kb of the TSS). The expected chance overlap is shown with dotted lines (paler colours). P-values obtained by Chi-square Goodness-of-Fit test. P-value indicated in blue represent statistical analysis of overlaps in untransformed cells, while pink indicates immortalised cells. e As in d for overlaps with gene body (excluding the TSS + 2 kb region) of GENCODE (v25) genes. f As in d for overlaps with regions enriched for heterochromatin-associated H3K9me3 histone mark (in hESC, left panel) and with regions defined as heterochromatin by HMM in hESC and K265 cells (right panel). g Plot shows the core origin (red) density across topologically associating domains (TADs)⁶⁷. Average origin density per bin (100 bins) across all TADs was plotted (y-axis, in origins/Mb). Core origin density is higher at the TAD borders, creating a “smiley” trend-line. P-values were obtained using the non-parametric Wilcoxon test in R. h Same as in g but for stochastic origins. i Bar plot showing the sum of normalised mean SNS-seq signal (y-axis, total initiation) across 19 samples coming from both core and stochastic origins at TAD borders and TAD centres. The total amount of SNS-seq signal is 1.53-fold higher at TAD borders. j Density of core origins active in HMEC (blue) and ImM-1 cells (orange) across TADs as in g. k Same as in j but for stochastic origins active in HMEC and ImM-1 cells. l As in i for HMEC (parental, in blue) and immortalised ImM-1 (in orange) cell types.