Initiation of eukaryotic DNA replication requires phosphorylation of the MCM 
complex by Dbf4-dependent kinase (DDK), composed of Cdc7 kinase and its 
activator, Dbf4. We report here that budding yeast Rif1 (Rap1-interacting factor 
1) controls DNA replication genome-wide and describe how Rif1 opposes DDK 
function by directing Protein Phosphatase 1 (PP1)-mediated dephosphorylation of 
the MCM complex. Deleting RIF1 partially compensates for the limited DDK 
activity in a cdc7-1 mutant strain by allowing increased, premature 
phosphorylation of Mcm4. PP1 interaction motifs within the Rif1 N-terminal 
domain are critical for its repressive effect on replication. We confirm that 
Rif1 interacts with PP1 and that PP1 prevents premature Mcm4 phosphorylation. 
Remarkably, our results suggest that replication repression by Rif1 is itself 
also DDK-regulated through phosphorylation near the PP1-interacting motifs. 
Based on our findings, we propose that Rif1 is a novel PP1 substrate targeting 
subunit that counteracts DDK-mediated phosphorylation during replication. 
Fission yeast and mammalian Rif1 proteins have also been implicated in 
regulating DNA replication. Since PP1 interaction sites are evolutionarily 
conserved within the Rif1 sequence, it is likely that replication control by 
Rif1 through PP1 is a conserved mechanism.