Dynamics of DNA replication in a eukaryotic cell

Significance All eukaryotic cells initiate DNA replication at multiple genomic sites. For most cell types these sites lack a well-defined sequence signature, so it is not understood how they are selected. To analyze the factors that influence initiation site selection and determine the dynamics of replication throughout the genome, we developed an integrative computational model of DNA replication in the model organism Schizosaccharomyces pombe. This analysis showed that the locations of initiation sites are determined not only by the sequence preferences of the S. pombe origin recognition complex (ORC), but also by the interference of transcription with the formation of prereplication complexes. Our findings suggest that transcription has influenced evolution of the binding properties of ORC and replication dynamics in eukaryotes. Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.

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