A p5 integration efficiency element mediates Rep-dependent integration into AAVS1 at chromosome 19

Adeno-associated virus (AAV) undergoes site-specific integration into human chromosome 19 through a deletion-substitution mechanism at the well characterized AAVS1 site. We have shown previously that a cis element within the left end of the AAV genome enhances the efficiency of Rep-mediated site-specific integration into chromosome 19 when present in inverted terminal repeat-containing recombinant AAV (rAAV) plasmids. We now demonstrate that a 138-bp cis element, the p5 integration efficiency element (p5IEE), mediates efficient integration. The p5IEE is not only required for efficient site-specific integration, it is also sufficient. Integration mediated by the p5IEE occurs in the absence of the AAV inverted terminal-repeat elements. The data presented in this study demonstrate that the p5IEE is a multifunctional element, serving as the highly regulatable Rep promoter and the primary substrate for targeted integration.