Making sense of eukaryotic DNA replication origins

Abstract

DNA replication is the process by which cells make one complete copy of their genetic information before cell division. In bacteria, readily identifiable DNA sequences constitute the start sites or origins of DNA replication. In eukaryotes, replication origins have been difficult to identify. In some systems, any DNA sequence can promote replication, but other systems require specific DNA sequences. Despite these disparities, the proteins that regulate replication are highly conserved from yeast to humans. The resolution may lie in a current model for once-per-cell-cycle regulation of eukaryotic replication that does not require defined origin sequences. This model implies that the specification of precise origins is a response to selective pressures that transcend those of once-per-cell-cycle replication, such as the coordination of replication with other chromosomal functions. Viewed in this context, the locations of origins may be an integral part of the functional organization of eukaryotic chromosomes.

Fig. 1

Structure of genetically dissected replication origins in eukaryotes. Consensus ORC binding sites are indicated in red. Additional sequences important for origin activity are shown in brown. Transcription units and regulatory sequences are shown in green. Sites of ORC binding, where known, are indicated. Sites of initiation of replication are indicated with a bidirectional arrow passing through a bubble.

Fig. 2

Once-per-cell-cycle genome duplication is independent of the positions or density of replication origins. (A) Duplication of DNA exactly once-per-cell division is achieved with two mutually exclusive periods of the cell cycle during which either pre-RCs can be assembled but replication cannot initiate or replication can initiate but pre-RCs cannot be assembled. Regardless of where pre-RCs assemble, DNA is completely replicated and cannot be re-replicated until after cell division. (B) The assembly of extraneous pre-RCs can ensure that the entire segment of DNA is replicated in a timely fashion, without the need for specific DNA sequences to optimize origin spacing. Any pre-RCs that do not initiate are destroyed by passage of the replication fork and so cannot re-initiate on the replicated strands.

Fig. 3

Exclusion of pre-RCs from specific regions could create the need for origin focusing mechanisms. In this model, passage of the transcription apparatus before replication depletes transcription units (black boxes) of pre-RCs (yellow stars). (A) Without transcription, there is no selective pressure to focus initiation to specific sites as the assembly of pre-RCs at many sites ensures timely genome replication. (B) When transcription units are sparse, the assembly of multiple pre-RCs at many sites within the intergenic regions is sufficient to accomplish genome replication. (C) When intergenic regions are few and far between, specific DNA sequence recognition elements are required to ensure that at least one pre-RC is assembled at intervals appropriate to accomplish the timely replication of the DNA segment.