39. Modulation of Histone Dosage and Chromatin Dynamics Regulates AAV Transduction

Abstract

Recombinant adeno-associated vectors (AAVs) have gained momentum due to their combined characteristics of safety and efficiency. Nonetheless, the identity of the host functions intercepting the AAV transduction pathway still needs to be thoroughly understood.To address this issue on a genome-wide scale, we previously performed an unbiased RNAi high throughput screening (HTS; 18,120 human target genes) and identified 710 negative and 414 positive regulators of AAV efficiency. Based on the results obtained and with the purpose to identify factors involved in single-stranded (ss) AAV genome processing, we compared, again in an HTS format, siRNAs affecting ssAAV, but dispensable for scAAV transduction. One of the genes identified was ERI-1. While the effects of this protein were negligible on scAAV transduction, its knock down or overexpression lead to a 5 fold decrease or 2-7 fold increase of ssAAV efficiency, respectively.ERI-1 is a 3’-exoribonuclease known to degrade endogenous miRNAs and histone mRNAs. Indeed, we observed that AAV transduction negatively correlated with histone mRNA levels. Chromatin immunoprecipitation (ChIP) studies aimed at assessing the extent of chromatinization of the AAV genome revealed that the overexpression of ERI-1 determined an over 10-fold, selective reduction on ssAAV genome association with H3 and H4, while changes were negligible for scAAV DNA and for control cellular genes. Consistent with chromatin exerting a repressive role on ssAAV transduction, we also noticed that the downregulation of the main replication-dependent histone chaperone CAF-1 induced an over 20-fold increase in transduction. Increase of ssAAV2 transduction by ERI-1 also decreased the association, with the viral DNA, of proteins of the cellular DNA damage response (DDR; e.g. Nbs1 and Mre11), which our previous work had indicated as inhibitory of AAV transduction.Interestingly, DNA damage per se induced downregulation of histone gene expression. In particular, hydroxyurea, a drug markedly increasing AAV transduction, also determined histone mRNA degradation, an effect that required integrity of ERI-1.These results underline the importance of chromatin and its dynamic regulation in determining the fate of productive AAV transduction. These findings can be exploited for the development of more effective AAV-mediated gene delivery strategies.