Defects in RNA metabolism in mitochondrial disease

The expression of mitochondrially-encoded genes requires the efficient processing of long precursor RNAs at the 5′ and 3′ ends of tRNAs, a process which, when disrupted, results in disease. Two such mutations reside within mt-tRNA^Leu(UUR); a m.3243A > G transition, which is the most common cause of MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), and m.3302A > G which often causes mitochondrial myopathy (MM). We used parallel analysis of RNA ends (PARE) that captures the 5′ terminal end of 5′-monophosphorylated mitochondrial RNAs to compare the effects of the m.3243A > G and m.3302A > G mutations on mitochondrial tRNA processing and downstream RNA metabolism. We confirmed previously identified RNA processing defects, identified common internal cleavage sites and new sites unique to the m.3243A > G mutants that do not correspond to transcript ends. These sites occur in regions of predicted RNA secondary structure, or are in close proximity to such regions, and may identify regions of importance to the processing of mtRNAs.