Xenbase Image ID: 176226

Fig. 3. Changes in the replication origin repertoire upon G4 stabilization by PhenDC3. a PhenDC3 formula. b Volcano plot of origins affected by incubation of mouse ES cells with PhenDC3. After identification of the bound sites in all SNS-seq samples, differential binding analysis was performed. For each origin, the corrected p values (false discovery rates, −log10(FDR)) and the log2 fold change (FC) of control and PhenDC3-treated samples were plotted. The horizontal and vertical lines correspond to the thresholds for detecting differential origins. On the basis of the FC and peak reproducibility, origins were classified in five different classes, according to PhenDC3 effect (suppressed, reduced, reinforced, new, and insensitive), as described in “Methods” section. c Examples of the activity of origins in the indicated classes after incubation with PhenDC3 or in control cells. The corresponding genomic region is indicated and the origin color is according to the corresponding class in the Volcano plot. d Heatmap showing the read densities in origins affected by G4 stabilization (PhenDC3-treated vs. Control). The heatmap indicates the signal strength (number of reads) and density around each origin and was performed on 7 kb regions on each side of origins, as previously described4. The intensity (brown) is proportional to the read counts per 100 bp bins. Origins were sorted on the basis of the FC in signal strength. e Activity of origins (reads number) in each class in control (−) and PhenDC3-treated (+) cells Image published in: Prorok P et al. (2019) © The Author(s) 2019. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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