OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells

Abstract

Abstract DNA replication initiates at specific genomic regions known as initiation zones (IZs), which follow a defined spatiotemporal program that is partially dependent on cell type. Here, we examine 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 synchronization and Repli-seq, we identify IZs that activate during S phase in mESCs and classify them as early, mid, or late according to the replication-timing (RT) domain to which they map. Remarkably, we find that some IZs mapping to mid or late RT domains activate within 1–2 hours of entry into S phase. Chromatin and nascent-transcriptome profiling reveal that these IZs associate with regions of open chromatin structure that are bound by the pluripotency factor OCT4. Transient OCT4 depletion reduces both 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.