A role for human senataxin in contending with pausing and backtracking during transcript elongation

Abstract

Senataxin (SETX) regulates RNA polymerase II (RNAPII) transcription and helps maintain genome stability, at least partly by suppressing R-loops. However, despite its importance in human disease, the precise function of SETX has remained unclear. Employing the degradation tag system for acute protein depletion, we demonstrate that SETX loss perturbs RNAPII elongation but does not markedly influence transcription termination at the end of genes. Through in vitro reconstitution of elongation, we show that SETX uses ATP-dependent RNA translocation to drive RNAPII forward across challenging DNA sequences, reminiscent of how bacterial ribosomes help mitigate RNAP pausing. In vivo, SETX depletion accordingly results in increased RNAPII pausing or backtracking, particularly during early elongation, with a corresponding, time-dependent local increase in R-loop formation. Together, these findings redefine our understanding of SETX's role in transcription and provide a mechanistic framework for interpreting R-loops and the causes of neurological disorders associated with SETX mutation.

Keywords: DNA-RNA hybrid; DSIF; PAF1C; R-loop; RNA polymerase II; SETX; SPT5; SPT6; Sen1; TFIIS; biochemical reconstitution; genome-wide analysis; senataxin; transcript elongation; transcription termination.