Fig. 5: Model of DNA replication regulation in early mouse embryos.

During the embryonic S phase in 1- and 2-cell embryos, DNA replication proceeds gradually and uniformly across the entire genome in the absence of Mb-sized RT domain structure. This is achieved by numerous replication forks with a median IOD of 12–22 kb that travel extremely slowly, with the majority estimated to move at <33 bp per min bidirectionally (or <66 bp per min assuming unidirectional forks). The only exceptions are the centromeres in 1- and 2-cell embryos and the sperm-derived heterochromatin in 1-cell embryos, which replicate later in S phase. At the 4-cell stage, a somatic-cell-like RT program commences abruptly, which is accompanied by a marked strengthening of nuclear compartments. Despite this abrupt switch, the forks were still extremely slow and the median IOD was still around 12 kb, giving rise to a transitional 4-cell S phase, in which the RT regulation mode is somatic, while the replisome-level regulation mode is still embryonic. This uncoordinated regulatory state led to S phase extension in 4-cell embryos, and the cells with the most extended S phase frequently showed chromosome breaks during the 4-to-8-cell division that probably arose due to under-replication of late-replicating domains after an S phase with increased replication stress, DNA damage and repair. After the 8-cell stage, forks accelerate (approximately 0.76 kb per min), IODs become larger (median, 56.1 kb) and DNA replication proceeds in a coordinated manner again, resulting in a reduction in genomic instability (somatic S phase).