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Originally published as Genetics Published Articles Ahead of Print on October 1, 2008.
Genetics, Vol. 180, 1833-1847, December 2008, Copyright © 2008
doi:10.1534/genetics.108.094359
The Temporal Program of Chromosome Replication: Genomewide Replication in clb5
Saccharomyces cerevisiae
Heather J. McCune*,1,
Laura S. Danielson*,2,
Gina M. Alvino*,
David Collingwood
,
Jeffrey J. Delrow
,
Walton L. Fangman*,
Bonita J. Brewer* and
M. K. Raghuraman*,3
* Department of Genome Sciences and Department of Mathematics, University of Washington, Seattle, Washington 98195 and Department of Genomic Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
3 Corresponding author: University of Washington, Department of Genome Sciences, Box 355065, S041E Foege Bldg., Seattle, WA 98195.
E-mail: raghu{at}u.washington.edu
Temporal regulation of origin activation is widely thought to explain the pattern of early- and late-replicating domains in the Saccharomyces cerevisiae genome. Recently, single-molecule analysis of replication suggested that stochastic processes acting on origins with different probabilities of activation could generate the observed kinetics of replication without requiring an underlying temporal order. To distinguish between these possibilities, we examined a clb5
strain, where origin firing is largely limited to the first half of S phase, to ask whether all origins nonspecifically show decreased firing (as expected for disordered firing) or if only some origins ("late" origins) are affected. Approximately half the origins in the mutant genome show delayed replication while the remainder replicate largely on time. The delayed regions can encompass hundreds of kilobases and generally correspond to regions that replicate late in wild-type cells. Kinetic analysis of replication in wild-type cells reveals broad windows of origin firing for both early and late origins. Our results are consistent with a temporal model in which origins can show some heterogeneity in both time and probability of origin firing, but clustering of temporally like origins nevertheless yields a genome that is organized into blocks showing different replication times.
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Genetics 2008 180: NP.
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