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

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.