TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk

TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders. [Display omitted] •TDP-43 chronic deficiency reduces R-loops and 5hmC in a group of gene bodies and enhancers•Intragenic R-loop and 5hmC depletion downregulates functional gene expression•Enhancer R-loop and 5hmC depletion downregulates their long-range targets•R-loop and 5hmC ectopic accumulation in TEs contributes to their aberrant derepression Hou et al. report that TDP-43 chronic deficiency alters R-loops and 5hmC at genic regions, enhancers, and transposable element loci to dysregulate critical gene and transposable element expression. This study unravels the genomic and epigenetic roles of TDP-43 and sheds light on the broader molecular mechanisms linking proteinopathies to neurodegenerative disorders.