In my PhD thesis I describe the work I've done with my colleagues in Professor David Shore's Lab that led to the next 3 main conclusions. (1) Conserved protein Rif1 is a negative regulator of DNA replication initiation in budding yeast. Rif1 counteracts DDK-dependent activatory phosphorylation at Mcm4 and Sld3 replication initiation proteins by recruiting protein phosphatase PP1 (ScGlc7) through its RVxF/SILK motifs. (2) Replication-restraining activity of Rif1 is important for the maintenance of genome integrity. Cells lacking Rif1 have elevated origin activation in early S phase at ribosomal RNA gene tandem repeat array (rDNA), which leads to destabilization of the array and dependency on DSB repair/fork maintenance factors MRX and Mms22-Ctf4 for survival. (3) Replisome pausing factors Tof1-Csm3 promote pausing at RFB independently of replisome accessory helicase Rrm3. Replication fork pausing at proteinaceous barriers (RFBs) depends on DNA lagging strand synthesis machinery and topoisomerases I and II.