TDP-43 stable deficiency leads to transcriptional dysregulation and transposable elements activation via global R-loops and 5hmC landscape alteration [micro-C-Seq]

TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in many aspects of RNA metabolism, but its molecular roles in regulating gene and tTransposable eElements (TEs) transcription transcription is not extensively explored. TDP-43 loss-of-function via due to progressive cytoplasmic aggregations serves as a pathological hallmark and potential causality for several neurodegenerative diseases. While rRecent evidence suggest TDP-43 acute knockdown of TDP-43 affects the formation of R-loops formation, a nuclear DNA:RNA hybrid structures implicated in transcription regulation, . However, how its stable and chronic functional perturbation of TDP-43, which more closely resembles age-related neurodegeneration, impact global transcriptome via R-loop dysregulation remains unclear. Here we show demonstrate that stable and prolonged TDP-43 loss-of-function results in slowed impaired cell proliferation and impaired DNA damage response. At the molecular level, TDP-43 stable knockdown impacts key gene expression through concomitantly altering intragenic R-loops dynamics and its crosstalk with and thea DNA covalent modification 5-hydroxymethylcytosine (5hmC) in cis, as well as long- range R-loops-mediated enhancer-promoter interactions in trans. Furthermore, we find TDP-43 stable knockdown induces massive disease-related TEstransposable elements (TEs) activation via influencing R-loop and 5hmC homeostasis in many of these loci. Our results highlight previous underdeveloped transcriptional roles of TDP-43 via R-loops regulation in coding genes, distal regulatory elements and TEs, and suggest that TDP-43 proteinopathies transcriptionally contributes to the etiology of neurodegenerative disorders. TDP-43 knockdown by shRNA, micro-C-seq