Abstract
The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed similar individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution: Footprints in budding yeast were more sharply focused compared to the other three organisms, consistent with the relative sequence specificity of replication origins in S. cerevisiae. Nonetheless, with some clear exceptions, most notably the inactive X-chromosome, much of the fluctuation in replication timing along the chromosomes in all four organisms reflected uneven chromosomal distribution of pre-replication complexes.
Highlights
Eukaryotes organize the replication of their genomes according to programs that ensure that certain regions of the genome complete replication earlier in S phase than others [1,2,3,4,5]
Gene-rich regions of the genome tend to replicate earlier in S phase than do repetitive and other non-genic regions. This may be an evolutionary consequence of the fact that replication later in S phase is associated with higher frequencies of mutation and genome rearrangement
To determine the relative importance of these two mechanisms, here we identify both the binding sites and the abundance of a key component of the origin licensing machinery in budding yeast, fission yeast, mice, and humans, namely the replicative helicase complex
Summary
Eukaryotes organize the replication of their genomes according to programs that ensure that certain regions of the genome complete replication earlier in S phase than others [1,2,3,4,5]. The importance of replication timing is underscored by the observation that it is sometimes modulated according to the utility of the region being replicated: For example, some chromosomal regions containing developmentally regulated genes replicate early only during those developmental phases during which they are activated [12,13,14]. The two main mechanisms for cellular control of replication timing are the regulation of (1) loading and (2) activation of the replicative helicase complex, referred to as origin licensing and firing, respectively: Only sites where the replicative helicase has been loaded during G1 are capable of initiating replication during the subsequent S phase, and only a subset of these loaded helicases are activated [3,18]. Despite the biological importance of replication timing, the relative importance of helicase loading versus helicase activation in its control has not been established
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