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Fig. 1 | Genome Biology

Fig. 1

From: Transcription shapes DNA replication initiation to preserve genome integrity

Fig. 1

NAIL-seq identified DNA early replication initiation zones (ERIZs). a Schematic showing the ERIZs identified by NAIL-seq. Nascent DNA labeled with EdU is red, while that labeled with BrdU is green. The origin indicated by the gray arrows was identified by EdU/HU, but not by EdU and BrdU. The light blue boxes show the procedures for the indicated NAIL-seq libraries. CDKi is the CDK4/6 inhibitor, palbociclib. Rel., release; ERIZ, early replication initiation zone. b Early replication signals from NAIL-seq libraries in K562 cells. Bar plots show the distribution of EdU (red) or BrdU (green) signals in the indicated region. The early DNA replication regions identified by Repli-seq are shown in gray. For the dual-labeled samples, the G1-arrested K562 cells were released for 2.5 h to reach the G1/S transition and then sequentially labeled with EdU and BrdU, each for 15 min. The E-B panel shows the BrdU-subtracted EdU signals; red represents the EdU-dominant signal and green represents the BrdU-dominant signal. E-B peaks called by the RepFind pipeline are shown underneath. For EdU/HU, G1-arrested cells were released into medium supplied with 10 mM HU and 10 μM EdU for 12 h before harvesting. EdU/HU signals are shown in dark red with the identified ERIZs in blue underneath. The pink shadow box highlights a non-ERIZ region, while the cyan box highlights a typical region where EdU/HU displays a higher resolution than E-B. c The width distribution of NAIL-seq identified replication peaks and Repli-seq revealed early replicated regions in K562 cells. The Wilcoxon Rank-sum test was applied for statistical analysis. d Venn diagram showing the overlapping peaks of E-B and EdU/HU in K562 cells. The cyan circle represents the total number of E-B peaks and the orange circle represents the EdU/HU peaks. The EdU/HU peaks overlapping with E-B peaks are defined as ERIZs. e Replication timing analysis for the two categories of EdU/HU peaks in K562 cells. EdU/HU peaks are categorized as ERIZs (n = 2,265, red, overlapping with E-B peaks) and non-ERIZs (n = 891, black, independent of E-B peaks). The replication timing of each peak is defined by the mean of the wavelet-smoothed signals from six fractions of the ENCODE Repli-seq profile. f The peak width distribution of ERIZs in K562 and GM12878 cells. The total number (N) and the median width of ERIZs are shown in the legends

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