RECQL5 works with the transcription-coupled DNA repair complex to regulate transcription elongation rates, providing brake and accelerator functions respectively
During transcription, RNA polymerase II (Pol II) is responsible for converting the information stored in DNA into RNA. Pol II transcription speed is highly dynamic, however abnormally fast transcription can lead to genome instability. To remedy this, the DNA helicase RECQL5 works as a general elongation factor to slow down Pol II, but the underlying mechanism behind this has proved unclear. To illuminate this, Suyang Zhang’s group, in the LMB’s Structural Studies Division, has provided a model mechanism which regulates RECQL5-induced transcription braking and its subsequent reactivation. This study was co-initiated with Ana Tufegdžić Vidaković in the LMB’s PNAC Division.
First, to visualise the interaction between RECQL5 and Pol II, Suyang and her PhD student Luojia Zhang purified and reconstituted transcription elongation complexes with the human helicase RECQL5 and used electron cryomicroscopy (cryo-EM) to determine their structures. This exposed how RECQL5 binds directly to Pol II, utilising a long a-helix which extends toward the downstream DNA in the direction of Pol II translocation. Transcription elongation factors on the surface of Pol II accommodate RECQL5 binding.
Luojia then used biochemical assays to further investigate the role of this a-helix, finding that it is essential for interacting with Pol II where it acts as a brake to slow down transcription elongation. With Yuliya Gordiyenko, a Research Support Officer in Suyang’s group, Luojia comprehensively characterised individual domains of the RECQL5 protein, finding that both the brake helix and the helicase activity of RECQL5 are required for RECQL5-mediated transcription braking. The pair work in tandem, with the brake helix acting as a hindrance for Pol II to proceed with transcription, and the helicase partially unwinding to distort the DNA and block Pol II movement.
Interestingly, the group found that the binding site of RECQL5 on Pol II overlaps with that of the transcription-coupled DNA repair (TCR) complex, a protein complex that is crucial for repairing damaged DNA in actively transcribing genes. Investigating this further, Suyang’s group found that the TCR complex can override the brake helix of RECQL5, allowing Pol II to restore the transcription speed. The TCR complex competes with RECQL5 for the same spot on Pol II while utilizing its translocase activity that works like a motor to ‘push’ Pol II past the braking effect caused by RECQL5. Concurrently, RECQL5 can block the TCR-mediated ubiquitination of Pol II to prevent excessively activating the DNA repair pathway.
Essentially, RECQL5 acts as a brake and the TCR complex as an accelerator, working together to ensure efficient transcription elongation whilst maintaining genome stability. By accurately controlling transcription speed, the pair help prevent transcription-replication collision and allow crucial co-transcriptional events such as co-transcriptional splicing to occur.
This discovery holds wider implications as dysfunctional transcription can lead to many diseases, including cancers and neurodegeneration. By elucidating how cells modulate transcription speed, this work advances our understanding of the complex regulation of gene expression and informs future investigations into how transcription elongation speed influences protein formation and contributes to disease progression.
This work was funded by UKRI MRC.
Further references
Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation. Zhang, L., Gordiyenko, Y., Morgan, T., Franco, C., Tufegdžić Vidaković, A. and Zhang, S. Nature Structural & Molecular Biology
Suyang’s group page
Ana’s group page