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<p>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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月15日

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  • Eddie Rodriguez-Carballo,
  • Vasilis S. Dionellis,
  • Sotirios G. Ntallis,
  • Lilia Bernasconi,
  • Ezgi G. Keskin,
  • Thanos D. Halazonetis

摘要

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.