Fig. 4: RIF1 regulates the activity of early origins of replication in B cells.

a Scatter plot of IS density in log2 RPM (reads per million) in WT and Rif1^−/− CH12 cells identified from SNS-seq. Data were obtained from two replicates (n = 2), as shown in Supplementary Fig. 4a. b Bar plots showing the percentage of upregulated (1.5-fold), unchanged or downregulated (1.5-fold) ISs in shMcm6 cells relative to shLacZ cells and in Rif1^−/− cell relative to WT cells. The shMcm6 and shLacZ data are from our previous study (ref. 13). c Heatmaps spanning a 4 kb region centered on the IS peak summit providing an overview of the location of ISs relative to regions of DNase hypersensitivity (DHS)-seq and histone modifications (H3K36me3 and H3K9me3). All heatmaps display read densities as RPM. Within each heatmap, the ordering is based on decreasing SNS-seq fold-change (Rif1^−/−/WT). d ISs in CH12 cells were split into five equal classes (quintiles) based on their fold-change of read densities (log2 Rif1^−/−/WT) such that class 1 contained the most downregulated ISs and class 5 contained the most upregulated ISs, respectively, in Rif1^−/− cells. The violin plots show the IS read density within each class in WT and Rif1^−/− cells. Number of IS per class: class 1 = 7827, class 2 = 7819, class 3 = 7824, class 4 = 7828, class 5 = 7817. The violins represent kernel density estimates of the value distribution. The inner boxes and whiskers represent the same data as a boxplot where the dot represents the median, the minimum and maximum of the box represent the 1^st and the 3^rd quartile, and the minimum and maximum of the whiskers are the 1^st and 3^rd quartile ± 1.5 times the interquartile distance. e ISs were classified into five classes as in d. The violin plots show the RT values within each IS class.