After fertilisation of the oocyte by the sperm an intense period of chromatin remodelling ensues, whereby the two parental chromatins of the gametes are reprogrammed to establish totipotency. This remodelling is essential to start a new developmental programme, whereby a single cell, the one-cell embryo or zygote, will form an entire new organism. Coinciding with these changes in cellular potency, a new epigenetic state must be established, which is accompanied by massive alterations in the nucleus, major transcriptional, chromatin and architectural remodelling, as well as the establishment of the DNA replication landscape. In particular, replication timing is a major epigenetic fingerprint, which is linked to nuclear organisation. Understanding how nuclear organisation and the replication timing programme are first established at the beginning of development is essential to decipher how the first epigenetic regulatory layers are set in place during development and how they are reprogrammed to enable totipotency. I will discuss recent advances in this area, which have informed us on how the early embryo and totipotent-like cells in vitro control DNA replication and its molecular interdependencies with epigenetic regulation and nuclear organisation.