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

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.