Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modification
Thai B. Nguyen, Ricardo Miramontes, Carlos Chillón-Marinas, Roy Maimon, Sonia Vazquez‐Sanchez, Alice Lau, Nicolette R. McClure, Zhuoxing Wu, Keona Q. Wang, Whitney England, Monika Singha, Jennifer Stocksdale, Marie Heath, Ki-Hong Jang, Sunhee Jung, Karen Ling, Paymaan Jafar‐Nejad, Jharrayne I. McKnight, Leanne N. Ho, Osama Al‐Dalahmah, Richard L. M. Faull, Joan S. Steffan, Jack C. Reidling, Cholsoon Jang, Gina Lee, Don W. Cleveland, Clotilde Lagier‐Tourenne, Robert C. Spitale, Leslie M. Thompson
Abstract
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.