Epigenetic control of DNA replication origin assembly regulates vertebrate development and nuclear reprogramming

DNA replication is highly regulated process. However, the molecular and spatio-temporal control of DNA replication in metazoans are poorly understood as replication origins lack defined consensus sequences, thus invoking the involvement of different genomic features in their selection and activation. During early embryonic development in several metazoan organisms, DNA replication is ensured by high number of replication origins, densely distributed on the genome. These ensure fast DNA replication, coordinated with rapid cell divisions. This program switches to a lower number of origins at a developmental stage known as mid-blastula transition (MBT). At MBT in Xenopus laevis embryos cell length increases and gene transcription starts. Consistent with developmental regulation, post-MBT somatic nuclei incubated in an interphase extract derived from Xenopus laevis eggs replicate with lower efficiency compared to sperm DNA. This suggests the existence of an epigenetic memory on somatic nuclei that prevents full scale formation of replication origins at all available sites on the genome when incubated in egg extract. This memory can be erased through a single passage through unfertilized mitotic arrested eggs, eliminating the somatic pattern of replication origin spacing. Here, we identify the molecular determinants of this epigenetic memory dictating replication origin assembly in somatic cells and the molecules responsible for the nuclear reprogramming of somatic nuclei when these are exposed to egg cytoplasm. Collectively, we uncovered novel molecular mechanisms regulating replication origins, showing that the organization and the maintenance of specific chromatin configurations couple DNA replication, cell cycle and organisms development.