The yeast retrotransposon Ty5 integrates preferentially into heterochromatin at the telomeres and HM loci. Target specificity is mediated by a six amino acid sequence motif (the targeting domain, TD) of integrase that interacts with Sir4p, a structural component of heterochromatin. When tethered to CEN plasmids as part of a Gal4p DNA binding domain (GBD) fusion protein, TD destabilizes plasmid segregation in a manner similar to that observed for CEN + HM or CEN +TEL antagonism. This instability is caused by the ability of TD to nucleate components of heterochromatin on the CEN plasmid, because CEN +TD antagonism is abrogated by sir2, sir3 and sir4 mutations and by TD mutations that prevent interaction with Sir4p. In strains that acquire resistance to CEN +TD antagonism, the CEN plasmid has either recombined with a 2 μ plasmid or sustained deletions in sequences required to bind GBD-TD. CEN +TD and CEN + HM antagonism is exacerbated by mutations in components of the Ku-mediated non-homologous end-joining pathway. These observations suggest that CEN antagonism is caused by DNA breaks that result from competition between CEN - and Sir-specific segregation pathways.
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Acknowledgements We thank Rolf Sternglanz for providing many of the strains used in this study. This research was funded by grants to D.F.V. from the American Cancer Society (RPG9510106MBC) and the National Institutes of Health (GM51425).