a Representative profile from chromosome 1, comparing RT (RT = log2(Early/Late)) in HeLa cells, A/B compartments as defined by the eigenvector calculated from Hi-C data from HeLa cells, and FANCM and GFP-DONSON distribution (enrichment = log2(ChIP/input)) in HeLa cells stably expressing GFP-DONSON. Some examples are shadowed in red of late-replicating regions aligning with FANCM enriched genomic regions. Some early-replicating regions are highlighted in blue showing correspondence with GFP-DONSON-enriched regions. In the RT profile, positive and negative values correspond to early and late replication, respectively. In the eigenvector profile, they correspond to the A and B compartments. Regions containing fragile sites are marked by red bars above the profiles. b Violin plot displaying the distribution of replication timing of 50-Kb genomic windows enriched in FANCM or GFP-DONSON ChIP (log2[ChIP/Input] > 0) and the A and B Hi-C compartments (eigenvector >0, <0, respectively), each compared with a matching number of randomly selected genomic windows of the same size. The box plot inside the violin plot shows the median (center line), the upper (Q3) and lower (Q1) quartiles (box bounds) and the highest and lowest values excluding outliers (extreme lines). c Coverage of H3K9me3, H3K4me3, FANCM, and GFP-DONSON of 50-Kb genomic windows within 25 replication-timing quantiles, going from late- to early-replicating regions, in HeLa cells expressing GFP-DONSON. d Coverage of H3K9me3, H3K4me3, FANCM, and GFP-DONSON of 50-kb genomic windows within 25 eigenvector quantiles, going from B to A Hi-C compartments in HeLa cells expressing GFP-DONSON. In the box plots in c, d, the center line represents the median, the box bounds represent the upper (Q3) and lower (Q1) quartiles, the extreme lines represent the highest and lowest value excluding outliers, and the black dot represents the mean.