Fig. 4

Focused replication initiation upstream of the TOP1 transcription start site. A Replication fork direction from published Okazaki fragment sequencing [16] across 1 Mb of the human genome centered on the TOP1 gene transcription start site. The location of Ok-seq determined initiation (dark blue) and termination zones (light blue) are marked. Gray box indicates the 54-kb locus targeted for enrichment via nCATS. B Stacked single-molecule DNAscent DNA replication profiles with fraction BrdU incorporation indicated via the heatmap (300-bp windows). Gene annotations and the location of ORM and Ok-seq IZs are marked above the heatmap. C For each single-molecule DNAscent DNA replication profile, computationally determined replication kinetics are shown: forks with direction (arrows), initiation (light green bars) and termination sites (dark green bars). D Two example single-molecule nanopore sequence reads are plotted with DNAscent BrdU probabilities (black dots) and fractions BrdU incorporated (blue lines) as in Fig. 2. For each read, the respective heatmap and replication kinetics are reproduced from panels B and C. E Ensemble of DNAscent single-molecule replication fork direction across the target enrichment locus. The gray ribbon indicates the 95% confidence limits from 1000 randomizations of individual replication fork directions