ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length

Abstract

UPF1-mediated decay entails several mRNA surveillance pathways that play a crucial role in cellular homeostasis. However, the precise role of UPF1 in postmitotic neurons remains unresolved, as does its activity in amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease characterized by TDP-43 pathology and disrupted mRNA metabolism. Here, we used human iPSC-derived spinal motor neurons (MNs) to identify mRNAs subject to UPF1 degradation by integrating RNA-seq before and after UPF1 knockdown with RIP-seq to identify RNAs that co-immunoprecipitate with the active form of phosphorylated UPF1. We define a stringent set of bona fide UPF1 targets in MNs that are functionally enriched for autophagy and structurally enriched for GC-rich and long 3' UTRs but not for premature termination codon (PTC)-containing transcripts. TDP-43 depletion in iPSC-derived MNs reduces UPF1 phosphorylation and consequently post-transcriptional upregulation of UPF1 targets, suggesting that TDP-43 dysfunction compromises UPF1-mediated mRNA surveillance. Intriguingly, our datasets reveal that UPF1 and TDP-43 regulate alternative polyadenylation and 3'UTR length of mRNAs associated with synaptic and axonal function, a process that we find to be compromised in ALS models in vitro and ALS patient tissue. Our study provides a comprehensive description of UPF1-mediated mRNA decay activity in neurons, reveals overlapping roles between UPF1 and TDP-43 in regulating 3'UTR length, and offers novel insight into the intricate interplay between RNA metabolism and neurodegeneration in ALS.

Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes

“… 10 , 11 , 12 Notably, TDP-43 binds its own 3′-UTR at a sequence termed Clip34nt to autoregulate its expression. 10 , 13 Binding up to one-third of the mammalian transcriptome, TDP-43 functions prolifically in the regulation of RNA processing, including alternative splicing, 10 , 11 the repression of cryptic exons, 12 , 14 , 15 alternative polyadenylation, 16 , 17 , 18 , 19 , 20 and the processing of miRNA 21 and lncRNAs, including long interspersed nuclear elements (LINEs). 22 …”

Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes

“…10–12 Notably, TDP-43 binds its own 3’-UTR at a sequence termed Clip34nt to autoregulate its expression. 10,13 Binding up to one-third of the mammalian transcriptome, TDP-43 functions prolifically in the regulation of RNA processing, including alternative splicing, 10,11 the repression of cryptic exons, 12,14,15 alternative polyadenylation, 16–20 and the processing of miRNA 21 and lncRNAs, including long interspersed nuclear elements (LINEs). 22…”