Fig. 3.

Transcription relocates early replication in K562 cells and mESCs. a, c Heatmaps of early replication signals (from EdU/HU) around ERIZ-associated non-TRs in K562 cells treated with the indicated concentrations of α-amanitin (a) or DRB (c). Cells were treated as shown in Additional file 1: Figure S4a. Non-TR, non-transcribed region. TR, transcribed region. Legends are depicted as described in Fig. 2d. b, d Box-plots showing the log2 ratio of read density between early replication in the ERIZ-associated non-TRs and that in the flanked transcribed regions in the A compartments of K562 cells treated with the indicated concentrations of α-amanitin (b) or DRB (d). The Wilcoxon rank-sum test was applied for statistical analysis. e Heatmaps of early replication signals (from EdU/HU) around the ERIZ-associated non-TRs in mESCs with or without RNA polymerase II. Cells were treated as illustrated in Additional file 1: Figure S4h. Endogenous RNA polymerase II tagged with mAID is marked as Pol II. Non-transcribed regions (non-TRs) are ranked by width and centered on the midpoint flanked by two transcribed genes in mESCs. The non-TRs within A compartments, 20–100 kb in width, are displayed. Each line represents a non-TR. f The log2 ratio of read density between early replication in ERIZ-associated non-TRs and that in the flanked transcribed regions within the A compartments of mESCs. WT, wild-type. The Wilcoxon rank-sum test was employed for statistical analysis. g Distribution pattern of early replication initiation with or without RNA polymerase II in mESCs