# TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability

## TL;DR

TDP-43 prevents certain mRNAs from accumulating in neurites by making them less stable, and its loss or mutations linked to ALS cause these mRNAs to mislocalize.

## Contribution

TDP-43 directly regulates mRNA localization and stability in neurites through specific 3’-UTR motifs, and this mechanism is disrupted in ALS.

## Key findings

- Loss of TDP-43 increases neurite accumulation of hundreds of mRNAs.
- TDP-43 binds specific 3’-UTR motifs that regulate mRNA localization and stability.
- ALS-associated TDP-43 mutations cause similar mRNA mislocalization as TDP-43 loss.

## Abstract

The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanisms that govern their localization are unknown. Here, using subcellular fractionation and single-molecule RNA FISH, we found that loss of TDP-43 results in increased accumulation of hundreds of mRNAs in neurites. Using high-throughput functional assays in cells and high-throughput binding assays in vitro, we subsequently identified specific regions within these mRNAs that mediate their TDP-43-dependent localization and interaction with TDP-43. We found that the same regions also mediated TDP-43-dependent mRNA instability, suggesting a mechanism by which TDP-43 regulates mRNA localization. ALS-associated mutations in TDP-43 resulted in similar mRNA mislocalization phenotypes as did TDP-43 loss in mouse dorsal root ganglia and human iPS-derived motor neurons. These findings establish TDP-43 as a direct negative regulator of mRNA abundance in neurites and suggest that mislocalization of specific transcripts may occur in ALS patients.

The ALS-linked RNA binding protein TDP-43 regulates the pre-mRNA splicing and subcellular mRNA localization in neurons. Here, TDP-43 is found to bind a subset of mRNAs to inhibit their accumulation in neurites, possibly through promoting their degradation.

Dozens of mRNAs become significantly more neurite-enriched upon loss of TDP-43.These mRNAs are highly enriched for TDP-43 binding sites in their 3′-UTRs.Specific motifs within these UTRs are necessary and sufficient for TDP-43-dependent mRNA localization and directly bind recombinant TDP-43 in vitro.The same motifs also regulate mRNA stability in a TDP-43-dependent manner.mRNA mislocalization upon loss of TDP-43 is partially recapitulated by the expression of ALS-associated TDP-43 mutants.

Dozens of mRNAs become significantly more neurite-enriched upon loss of TDP-43.

These mRNAs are highly enriched for TDP-43 binding sites in their 3′-UTRs.

Specific motifs within these UTRs are necessary and sufficient for TDP-43-dependent mRNA localization and directly bind recombinant TDP-43 in vitro.

The same motifs also regulate mRNA stability in a TDP-43-dependent manner.

mRNA mislocalization upon loss of TDP-43 is partially recapitulated by the expression of ALS-associated TDP-43 mutants.

TDP-43 directly binds a subset of neuronal mRNAs at specific sequences in their 3’-UTR and reduces their stability.