Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation

During productive transcription elongation, the speed of RNA polymerase II (Pol II) is highly dynamic within individual genes and varies between different genes ^1,2 . Unregulated rapid transcription elongation can lead to detrimental consequences such as transcription-replication collisions, altered alternative splicing patterns, and genome instability ^1–7 . Therefore, elongating Pol II requires mechanisms to slow its progression, yet the molecular basis of transcription braking remains unclear. RECQL5 is a DNA helicase that functions as a general elongation factor by slowing down Pol II ^8–11 . Here we report cryo-electron microscopy (cryo-EM) structures of human RECQL5 bound to multiple transcription elongation complexes. Combined with biochemical analysis, we identify an α-helix of RECQL5 responsible for Pol II binding and slowdown of transcription elongation. We further reveal that the transcription-coupled DNA repair (TCR) complex allows Pol II to overcome RECQL5-induced transcription braking through concerted actions of its translocase activity and competition with RECQL5 for engaging Pol II. Additionally, RECQL5 inhibits TCR-mediated Pol II ubiquitination to prevent activation of the DNA repair pathway. Our results suggest a model in which RECQL5 and the TCR complex coordinately regulate the transcription elongation rate to ensure transcription efficiency while maintaining genome stability. This work provides a framework for future studies on the regulatory role of elongation speed in gene expression.