Spinal muscular atrophy (SMA) is a fatal neurodegenerative disorder in children, characterized by motor neuron loss and atrophy of muscle. However, SMA affects many organ systems, since the causal gene, SMN1, is expressed in all cells. Recently, an AAV9-mediated gene therapy, Zolgensma, was approved. However, challenges remain. To be effective, the systemically delivered AAV9- SMN1 needs to mimic the native regulation of the genomic SMN1. In fact, recent findings demonstrated that delivery of AAV-SMN1 under the control of the ubiquitous viral promoter CMV found in Zolgensma eventually caused death of neurons in a mouse model of SMA. To date, there has been no systematic categorization of how treatment with SMN1 is regulated in different tissues through development. Furthermore, little is understood about the chromatin changes that occur during SMA, how gene therapy impacts the long-term stability of patient’s epigenomes, or how the AAV-delivered DNA is epigenetically controlled over time. The goal of the proposed work is to understand how the epigenome reacts to gene therapy, using SMA as a model. To do so I will: i) profile the epigenetic changes during SMA disease progression in mice, before and after gene therapy, ii) evaluate the role of various promoter-enhancer structures in the vector on the epigenetic regulation of AAV-delivered episomal DNA and iii) test if endogenous promoter-enhancer combinations can be used to achieved a better tuning of the delivered gene. The proposed project combines the expertise of Dr. Piera Smeriglio in SMA models, neuromuscular disorders and gene therapy with my expertise in epigenetic profiling, gene regulation, functional genomics, and single-cell technologies. AAV gene therapies are poised to have a huge impact on rare diseases, a key priority of the Horizon Europe programme, making now a critical time to understand their effect on the epigenome and cell regulatory networks to increase the efficacy and safety of their use.