A Genome-Wide Screen Reveals a Replication-Independent Role of Dbf4-Dependent Kinase in Localization of the Centromeric Histone H3 Variant for Genome Stability

Authors

• JR Eisenstatt
• L Boeckmann
• WC Au
• V Garcia
• L Bursch
• J Warren
• M Costanzo
• M Weinreich
• R Sclafani
• A Baryshnikova
• C Meyers
• C Boone
• R Baker
• MA Basrai

Abstract

The evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENPA in humans) is essential for faithful chromosome segregation. CENPA is observed to be overexpressed and mislocalized in various cancers, which is associated with a poor prognosis. We therefore aimed to identify novel therapeutic targets for tumors overexpressing CENPA (CENPA-OE). Synthetic lethal (SL) interaction partners were identified in a genome-wide screen using budding yeast as a model system, an approach that has not yet been exploited. Strains with conditional mutant alleles of essential genes with overexpressed Cse4 (Cse4-OE) were assayed for colony growth size; smaller colonies indicated a SL interaction. Validation of the screen was provided by independent confirmation using growth assays for SL. Gene Ontology analysis of significant negative interactors identified categories related to ubiquitin-mediated proteolysis, chromosome segregation, chromatin binding, and DNA replication. Among the top fifteen hits of essential gene conditional mutant alleles with a negative interaction with Cse4-OE, we identified five alleles of the Cdc7-Dbf4 kinase complex, which is evolutionarily conserved and essential for DNA replication initiation. Biochemical analysis showed defects in degradation, ubiquitination, and localization of Cse4 in cdc7 mutants. Defects in Cse4 localization and chromosome segregation as well as SL in the presence of Cse4-OE were also observed in cdc7 mcm5 mutant strains which do not exhibit defects in DNA replication. These data indicate that Cdc7 regulates Cse4 localization independently of its role in the initiation of DNA replication. Furthermore, Cdc7 and Cse4 interacted in vivo, and in vitro kinase assays showed that the Cdc7-Dbf4 kinase complex phosphorylates Cse4. In summary, we have identified potential therapeutic targets for CENPA-OE tumors and provide insights into a novel mechanistic role of Cdc7 in regulating CENP-A/Cse4 levels for genome stability.

Scientific Focus Area: Chromosome Biology

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