Pluripotency factors enhance the firing efficiency of late DNA replication origins in mouse embryonic stem cells

DNA replication initiates at genomic loci known as origins, which fire according to a spatiotemporal program, still not yet well-defined in mammals. Here, we investigated whether pluripotent mouse embryonic stem cells (mESCs), which proliferate rapidly and have very short G1 phases, have a different spatiotemporal origin firing program than differentiated cells. Using EdU-seq combined with various cell cycle synchronization methods, we identified DNA replication initiation zones (IZs) in mESCs, mesenchymal stem cells and mouse embryo fibroblasts (MEFs). Similar profiles of IZs were present in the early-replicating genomic domains in all cell types. Uniquely in mESCs, we observed, within 1-2 hours of entry into S phase, origin firing at IZs that mapped to the mid and late-replicating genomic domains. This change in the replication timing program, which did not lead to shortening of the length of S phase, was driven by pluripotency transcription factors, notably OCT4, as documented by examining mESCs in which OCT4 expression was transiently suppressed. We propose that pluripotency factors in mESCs bind to IZs at mid and late-replicating genomic domains to enhance chromatin accessibility, which in turn leads to changes in the replication timing program. These results provide an example of how transcription factors control DNA replication in a cell type-specific manner.