A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration to tRNA genes

Integration of transposable elements into the genome is mutagenic. Mechanisms targeting integrations into relatively safe locations hence minimizing deleterious consequences for cell fitness have emerged during evolution. In budding yeast, the integration of the Ty1 LTR retrotransposon upstream of RNA polymerase III (Pol III)-transcribed genes requires the interaction between Ty1 integrase (IN1) and AC40, a subunit common to Pol I and Pol III. Here we identify the Ty1 targeting domain of IN1 that ensures (i) IN1 binding to Pol I and Pol III through AC40, (ii) IN1 genome-wide recruitment to Pol I and Pol III-transcribed genes, and (iii) Ty1 integration at Pol III-transcribed genes only, IN1 recruitment by AC40 being insufficient to target Ty1 integration to Pol I-transcribed genes. Swapping the targeting domain of the Ty5 and Ty1 integrases leads to Ty5 integration at Pol III-transcribed genes. Therefore, the targeting domain of IN1 alone confers Ty1 integration site specificity.