MPI-NAT Seminar: Molecular mechanisms at the crossroad of transcription termination, R-loops and neuronal identity

Transcription is an essential step of gene expression, yet it can interfere with DNA replication and repair when termination is defective. In particular contexts, the nascent RNA may reanneal to its DNA template, forming three-stranded structures known as R-loops. While R-loops can contribute to the regulation of gene expression and other physiological processes, their persistence leads to DNA damage and genome instability. Maintaining their balance is therefore critical, and relies on a network of regulatory factors. Among these, the RNA/DNA helicase senataxin (SETX) has been implicated in both transcription termination and R-loop metabolism, although its precise role in these processes remain debated. In the first part of this talk, I will present biochemical and structural insights into SETX molecular functions, identifying key determinants that underlie its activity in transcription termination and R-loop resolution. In the second part, I will address how SETX dysfunction contributes to neurodegeneration, focusing on ALS4, a juvenile form of amyotrophic lateral sclerosis. We show that ALS4-associated SETX mutations induce motor neuron axonal degeneration and widespread transcriptomic alterations, including reduced expression and altered splicing of genes/transcripts essential for neuronal function. ALS4 motor neurons exhibit a coherent transcriptional signature marked by cellular stress, aberrant cell cycle re-entry, and compromised neuronal identity. Mechanistically, these defects are partly driven by aberrant activation of the TGF-β signaling pathway, whose pharmacological inhibition significantly rescues axonal phenotypes. Finally, our data suggest that ectopic SETX activity at R-loops directly contributes to the observed alterations in RNA expression and splicing. Altogether, our work reveals how perturbations at the interface of transcription termination and R-loop metabolism can reshape neuronal identity and drive disease.