The Adeno-Associated Virus 2 (AAV2) genome and Rep 68/78 proteins interact with cellular sites of DNA damage.

We have previously developed a modified iteration of a viral chromosome conformation capture (V3C-seq) assay to show that the autonomous parvovirus Minute Virus of Mice (MVM) localizes spatially with cellular sites of DNA damage to establish viral replication centers. Similar V3C-seq assays to map AAV genome localization show that both replicating and non-replicating AAV2 genomes in the absence of helper virus colocalize with cellular sites of DNA damage. The AAV non-structural protein Rep 68/78, when ectopically expressed in the absence of viral infection or during AAV2 infection in the absence of helper proteins also localizes to cellular sites of DNA damage. Strikingly however, recombinant AAV gene therapy vector genomes derived from AAV do not colocalize with AAV and Rep at cellular DDR sites. Identification of cellular interaction site of the dependoparvovirus AAV2, and the localization of the resultant DNA damage response. Independent replicates of chromosome conformation capture (designated as V3C in the file name) and ChIP-seq experiments (the target epitope provided in the name) have been performed. For each time-point or treatment, at least two independent replicates of the indicated assays have been performed. ChIP-seq assays have been normalized to total input DNA prior to rpm normalization. Chromosome conformation capture assays have been rpm normalized. A total number of 96 samples have been deposited. "hpd" designates hours post induction with doxycycline, and "hpi" designates hours post infection with the dependoparvovirus Adeno-associated Virus 2 or with recombinand AAV (rAAV).