# Dimer‐Specific FokT‐seq Reveals DNA‐Binding Dimerization and Novel Genomic Targets of TDP‐43

## TL;DR

A new method called FokT-seq helps map DNA binding sites of TDP-43, a protein linked to ALS, by restoring its dimerization ability.

## Contribution

The study introduces FokT-seq, a novel system that enables genome-wide detection of DNA targets bound by dimerized TDP-43.

## Key findings

- FokT-seq reveals DNA-binding dimerization of TDP-43 and identifies novel genomic targets.
- Restoring TDP-43 dimerization reactivates FokI nuclease activity for DNA cleavage at TDP-43 binding sites.
- The system provides a powerful tool for studying dimerized transcription factors and their DNA interactions.

## Abstract

In postmortem brain tissues of patients with sporadic amyotrophic lateral sclerosis (ALS), the dimerization ability of TAR DNA‐binding protein 43 (TDP‐43) is impaired, accompanied by an accumulation of insoluble TDP‐43. Thus, the loss of TDP‐43 dimerization may play a critical driving role in ALS pathogenesis, although its underlying mechanism remains unclear. In this study, the FokT (FokI‐TDP‐43) system is developed, which fuses TDP‐43 protein with FokI nuclease. By restoring TDP‐43 dimerization, this system reactivates FokI nuclease activity, enabling the cleavage of DNA targets bound by TDP‐43. Additionally, the FokT‐seq (FokT combined with genome‐wide unbiased identification of DNA double‐strand breaks enabled by sequencing, Guide‐seq) method is established, allowing genome‐wide detection of DNA sites bound by dimerized TDP‐43. These findings reveal the essential role of TDP‐43 dimerization in DNA binding, identify a series of related targets. Furthermore, this study offers a powerful tool for investigating dimerized transcription factors.

Loss of TDP‐43 dimerization is implicated in ALS, yet its mechanistic role remains elusive. This study introduces FokT, a novel system that restores TDP‐43 dimerization to map its DNA targets via FokT‐seq. The findings uncover key binding sites and offer a versatile tool for exploring dimer‐dependent transcriptional regulation.