Significance In recent years, adeno-associated virus (AAV) has attracted considerable attention as a result of its success as a gene therapy vector. However, several aspects of its biology remain elusive. Given that AAV vectors mimic the latent phase of the viral life cycle, defining the mechanisms involved in the regulation of AAV latency is of particular importance. Our studies demonstrate that epigenetic processes are involved in the regulation of viral latency and reveal virus–host interactions and helper functions that are aimed at counteracting the epigenetic repression of the viral genome during the lytic phase of the viral life cycle. These observations will inform the design of future AAV vector technologies.