From Simple Bacterial and Archaeal Replicons to Replication N/U-Domains

The Replicon Theory proposed 50years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~50% of the human genome is organized as ~1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution. [Display omitted] •Replicons were defined as autonomous units containing an initiator and a replicator.•Bacterial chromosomes consist of single replicons.•Archaeal chromosomes may comprise several distinct replicator/initiator systems.•Eukaryal chromosomes have many degenerate replicators regulated by one initiator.•Mammalian N/U-domains replicate by cascades of origin firing from master origins.