RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia

Abstract Methylation of RNA at the N6 position of adenosine (m6A) is one of the most common RNA modifications, impacting RNA stability as well as its transport and translation. Previous studies uncovered RNA destabilization in models of amyotrophic lateral sclerosis (ALS), in association with accumulation of the RNA-binding protein TDP43, which is itself mislocalized from the nucleus in >95% of those with ALS. Here, we show that TDP43 recognizes m6A-modified RNA, and that RNA methylation is critical for both TDP43 binding and autoregulation. We also observed extensive hypermethylation of coding and non-coding transcripts in ALS spinal cord, many of which overlap with methylated TDP43 target RNAs. Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via a single-cell CRISPR/Cas9 candidate-based screen in primary neurons. The most promising genetic modifier among these—the canonical m6A reader YTHDF2— accumulated within spinal motor neurons in ALS postmortem sections, and its knockdown prolonged the survival of human neurons carrying ALS-associated mutations. Collectively, these data show that m6A modifications modulate RNA binding by TDP43, and that m6A is pivotal for TDP43-related neurodegeneration in ALS.