cDNA of the yeast retrotransposon Ty5 preferentially recombines with substrates in silent chromatin

The yeast retrotransposon Ty5 preferentially integrates into regions of sil ent chromatin. Ty5 cDNA also recombines with homologous sequences, generati ng tandem elements or elements that have exchanged markers between cDNA and substrate. In this study, we demonstrate that Ty5 integration depends upon the conserved DD(35)E domain of integrase and cis-acting sequences at the end of the long terminal repeat (LTR) implicated in integrase binding, cDNA recombination requires Rad52p, which is responsible for homologous recombi nation. Interestingly, Ty5 cDNA recombines at least three times more freque ntly with substrates in silent chromatin than with a control substrate at a n internal chromosomal locus. This preference depends upon the Ty5 targetin g domain that is responsible for integration specificity, suggesting that l ocalization of cDNA to silent chromatin results in the enhanced recombinati on. Recombination with a telomeric substrate occasionally generates highly reiterated Ty5 arrays, and mechanisms for tandem element formation were exp lored by using a plasmid based recombination assay. Point mutations were in troduced into plasmid targets, and recombination products were characterize d to determine recombination initiation sites. Despite our previous observa tion of the importance of the LTR in forming tandem elements, recombination cannot simply be explained by crossover events between the LTRs of substra te and cDNA. We propose an alternative model based on single-strand anneali ng, where single-stranded cDNA initiates tandem element formation and the L TR is required for strand displacement to form a looped intermediate. Retro transposons are increasingly found associated with chromosome ends, and amp lification of Ty5 by both integration and recombination exemplifies how ret roelements can contribute to telomere dynamics.