biostudies-literatureNguyen TBU.S. Department of DefenseU.S. Department of Defense (United States Department of Defense)ALS AssociationNIAAA NIH HHSNINDS NIH HHSNCI NIH HHSU.S. Department of Health & Human Services | National Institutes of Health (NIH)Hereditary Disease FoundationDake Family FoundationChan Zuckerberg InitiativeU.S. Department of Health & Human Services | National Institutes of Health280-292https://www.ebi.ac.uk/biostudies/studies/S-EPMC11802453biostudies-literatureUnknown28(2)Huntington's disease (HD) is caused by a CAG repeat expansion in the HTT gene, leading to altered gene expression. However, the mechanisms leading to disrupted RNA processing in HD remain unclear. Here we identify TDP-43 and the N6-methyladenosine (m6A) writer protein METTL3 to be upstream regulators of exon skipping in multiple HD systems. Disrupted nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 occurs in HD mouse and human brains, with TDP-43 also co-localizing with HTT nuclear aggregate-like bodies distinct from mutant HTT inclusions. The binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in the striatum of HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a mechanism underlying alternative splicing in HD.Nature neuroscienceAberrant splicing in Huntington's disease accompanies disrupted TDP-43 activity and altered m6A RNA modification.PMC11802453NS112503R01 AA029124TS200022NS116872R01 NS124203K22 CA234399NS27036F31 NS124293R35 NS116872NS124203F31NS124293T32R01 NS112503R01 NS027036AA029124K22CA234399Nguyen TBMcClure NRWang KQMcKnight JILagier-Tourenne CEngland WESpitale RCLee GWu ZSingha MChillon-Marinas CVazquez-Sanchez SHeath MJang CFaull RLMSteffan JSCleveland DWDalahmah OAMiramontes RLing KJafar-Nejad PHo LNStocksdale JTLau ALReidling JCJang KHJung SMaimon RThompson LMfalseAberrant splicing in Huntington's disease accompanies disrupted TDP-43 activity and altered m6A RNA modification.Huntington's disease (HD) is caused by a CAG repeat expansion in the HTT gene, leading to altered gene expression. However, the mechanisms leading to disrupted RNA processing in HD remain unclear. Here we identify TDP-43 and the N6-methyladenosine (m6A) writer protein METTL3 to be upstream regulators of exon skipping in multiple HD systems. Disrupted nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 occurs in HD mouse and human brains, with TDP-43 also co-localizing with HTT nuclear aggregate-like bodies distinct from mutant HTT inclusions. The binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in the striatum of HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a mechanism underlying alternative splicing in HD.2025-01-01T00:00:00Z2025 Feb2026-06-02T00:12:23.123Z2025-04-04T13:11:38.796ZS-EPMC118024533976266010.1038/s41593-024-01850-w