Mitochondrial diseases, which are the most common genetic metabolic disorders, arise from mutations in either nuclear or mitochondrial genomes. They often start in childhood, affecting around 5 to 15 out of every 100,000 individuals, and often affecting brain and muscles, leading to encephalomyopathies. Among them, diseases caused by ATP6 and ATP8 mtDNA mutations are frequent and remain elusive, despite these two genes encoding subunits of a well-studied mitochondrial enzyme, the F1Fo-ATP synthase. ATP6 and ATP8 proteins originate from a single transcript having overlapping reading frames. Analyses of mitochondrial mRNA folding using a new technique called mitoDMS-MaPseq, which combines DMS labeling, mutational profiling (MaP), and RNA sequencing (RNAseq), have suggested a mechanism controlled by RNA structure (programmed ribosome frameshifting, PRF) that ensures a balanced synthesis of ATP8 and ATP6. Now, we are applying cutting-edge mtDNA gene editing approaches to better dissect the PRF mechanism. Moreover, using mitoDMS-MaPseq, we aim to reveal changes in the structure of ATP8/6 mRNA caused by neuropathy-related mutations, and their role in pathogenesis. By elucidating these changes in mRNA folding, our project promises to uncover new insights into the realm of RNA structural regulation in human diseases. This study can lay the groundwork for new therapies based on controlling mRNA folding and open new avenues for understanding mitochondrial disorders.