Pluripotency factor OCT4 enhances the firing efficiency of late DNA replication origins in mouse em-bryonic stem cells [EdUseq]
DNA replication initiates at specific genomic regions known as initiation zones (IZs), which follow a defined spatiotemporal program partially dependent on cell type. Here, we examined the replication initiation patterns of pluripotent mouse embryonic stem cells (mESCs), which are characterized by a very short G1 phase and rapid entry into S phase. Using EdU-seq combined with cell cycle synchroni-zation and Repli-seq, we identified IZs, that are activated during S phase in mESCs and classified them as early, mid, or late, according to the replication timing (RT) domain to which they mapped. Remarka-bly, we found that some IZs mapping to mid or late RT domains were activated within 1–2 hours of entry into S phase. Chromatin and nascent transcriptome profiling revealed that these IZs were associated with regions of open chromatin structure that were bound by the pluripotency factor OCT4. Transient OCT4 depletion was associated with reduced chromatin accessibility and replication initiation efficiency at these sites. These results provide an example of a pioneer factor, OCT4, facilitating DNA replication initiation by promoting local chromatin accessibility. Overall design: Monitor DNA replication by EdUseq