The fission yeast S-phase regulator Mcl1, an orthologue of budding yeast Ctf4, is an interacting protein of DNA polymerase alpha and an important factor to ensure DNA replication and sister chromatid cohesion. Deletion of this protein results in severe cohesion defects, however, the function and cellular role of this protein remains elusive. In this study we isolate Mcl1 as an interaction partner of the F-box protein Pof3, which is a component of the ubiquitin ligase complex SCF(Pof3). Comparing the phenotypes of cells lacking pof3+ or mcl1+ we find a broad overlap including the accumulation of DNA damage and activation of the DNA damage pathway. Importantly, we identity a novel, specific role for Mcl1 in the transcriptional silencing and the localisation of CENP-A at the centromeres.