In fission yeast, the replication checkpoint is enforced by the kinase Cds1 (human Chk2), which regulates both cell cycle progression and DNA repair factors to ensure that the genome is faithfully duplicated prior to mitosis. Cds1 contains a forkheadassociated domain that mediates its interaction with phosphorylated residues in target proteins. One target of Cds1 is the essential nuclear protein Rad60, which contains the unique structural feature of tandem SUMO homology domains at its C terminus. Hypomorphic mutants of Rad60 cause profound defects in DNA repair and replication stress tolerance. To explore the physiological significance of the Cds1-Rad60 interaction, we have examined the phosphorylation of Rad60 by Cds1 in vitro and the in vivo phosphorylation of Rad60 in response to replication blocks. We find that the N terminus but not the SUMO-like domain of Rad60 is phosphorylated in both conditions. Genome integrity is threatened by multiple sources of damage throughout the cell cycle. A major problem cells have to cope with is perturbations from endogenous or exogenous sources that negatively affect replication fork progression during S phase (1). To mitigate DNA damage associated with such perturbations, the replication checkpoint is activated and regulates multiple factors involved in replication, repair, and transcription (1). One such factor is the homologous recombination repair protein Rad60, which is regulated via direct interaction with the replication checkpoint kinase Cds1 (2, 3). When replication is blocked, Rad60 undergoes Cds1-dependent phosphorylation and delocalization from its normal nuclear localization (2). A Rad60 mutant, Rad60-4, which is apparently refractory to regulation by the replication checkpoint, causes cellular hypersensitivity to inhibition of DNA replication (2). Such regulation of a recombination repair factor is reminiscent of the Cds1-dependent regulation of the structure-specific endonuclease Mus81-Eme1 (4, 5). Uncoupling the interaction between Cds1 and Mus81-Eme1 results in the unscheduled presence of Mus81-Eme1 on chromatin during replication arrest and the subsequent initiation of recombinogenic processes (5). Apparent negative regulation of recombination repair proteins by the replication checkpoint is consistent with the failure to observe recombination repair foci in wild-type fission yeast during hydroxyurea-induced replication arrest (6). Notably, recombination repair foci are observed following release from replication arrest and entry into G 2 phase or during the arrest if Cds1 is deleted (6).Rad60 is the founding member of a family of eukaryotic proteins that have a unique structural organization. Rad60 contains a SUMO homology domain at its C terminus and a largely unstructured N terminus enriched in acidic residues (2). Despite very low sequence conservation, structural and perhaps functional homologues (supported by shared genetic interactions) were identified in budding yeast and mammalian cells, called Esc2p and Nip45, respectively (2). This family was re...