Replication in Hydroxyurea: It's a Matter of Time

Abstract

Hydroxyurea (HU) is a DNA replication inhibitor that negatively affects both the elongation and initiation phases of replication and triggers the “intra-S phase checkpoint.” Previous work with budding yeast has shown that, during a short exposure to HU, MEC1/RAD53 prevent initiation at some late S phase origins. In this study, we have performed microarray experiments to follow the fate of all origins over an extended exposure to HU. We show that the genome-wide progression of DNA synthesis, including origin activation, follows the same pattern in the presence of HU as in its absence, although the time frames are very different. We find no evidence for a specific effect that excludes initiation from late origins. Rather, HU causes S phase to proceed in slow motion; all temporal classes of origins are affected, but the order in which they become active is maintained. We propose a revised model for the checkpoint response to HU that accounts for the continued but slowed pace of the temporal program of origin activation.

SUPPLEMENTAL MATERIAL

We thank the Fangman/Brewer/Raghuraman laboratory members, past and present, for support and helpful discussions. We are grateful to Wenyi Feng and Kim Lindstrom for critical review of the manuscript and to Dan Butler for valuable insight in designing the origin analysis tool used in the study. We also thank the crew at the FHCRC Genomics Facility for technical assistance. G.M.A. is especially grateful to Walt Fangman for his time spent as her mentor.

This work was supported by NIGMS grant 18926 to W. L. Fangman, B.J.B. and M.K.R.