Oxidative stress triggers RNAPII arrest through PARylation and DNA damage
Posted on: 1 April 2026
Preprint posted on 6 November 2025
Attachment of ADP-ribose molecules to RNA Polymerase II allows its traffic regulation on transcribed genes in response to oxidative DNA damage
Selected by Élise Jeanne Pouponnot, Pierre Caron
Categories: cell biology
Background
Every day, our cells experience tens of thousands of DNA lesions (1). These include base modifications arising from oxidative stress or from exposure to exogenous agents such as certain anticancer therapies. To counteract these small and non-helix-distorting DNA lesions, cells rely on the Base Excision Repair (BER) pathway (2).
This pathway begins when specialized enzymes called DNA glycosylases (such as 8-Oxoguanine DNA Glycosylase, OGG1) scan DNA for damaged bases caused by oxidation, such as 8-oxodG. Once detected, these enzymes remove the damaged base, leaving behind a missing-base site known as an abasic (AP) site.
These abasic sites are then cut by either DNA glycosylases with additional “cutting” activity or by the enzyme apurinic/apyrimidinic endonuclease 1 (APE1), which produces a small break in one strand of the DNA (2). This break serves as a signal to recruit poly(ADP-ribose) polymerase 1 (PARP1). PARP1 detects the damage and modifies itself and nearby histones with ADP-ribose chains (e.g. PARylation), causing the surrounding chromatin to loosen. This relaxed chromatin environment allows other repair proteins to access the site and complete DNA repair through DNA synthesis and ligation (3).
Approximately 2% of the human genome consists of genes that can be transcribed by the RNA polymerase II complex (RNAPII). When transcribed genes are damaged in their body by DNA double-strand breaks (DSBs) or UV-induced DNA lesions, RNAPII progression is blocked at damage sites and mRNA production is consequently interrupted (4, 5).
Interestingly, whereas some types of base oxidation do not impede RNAPII progression, others do just like repair intermediates of oxidized bases, e.g. AP sites and ssDNA breaks. Although transcription-coupled BER has been the subject of several studies (6, 7), the factors involved, and the regulatory mechanisms remain largely unknown.
In this preprint (8), Thomas and colleagues investigate how oxidative stress affects transcription by mapping RNAPII and nascent transcription in a genome-wide manner. The authors show that active RNAPII is transiently stalled at defined positions within oxidatively damaged genes, with promoter-proximal RNAPII pausing dynamically repositioned in a NELF-dependent manner. Importantly, transcriptional restart requires the removal of PARylation chains by PARG and the efficient repair of oxidative lesions by the BER factors OGG1 and X-Ray Repair Cross Complementing 1 (XRCC1). Together, these findings provide a refined and spatially resolved view of how transcription is dynamically coordinated with BER to enable rapid recovery of gene expression following oxidative stress.
Key findings
- RNAPII arrested within gene bodies can locally resume transcription without new initiation
To determine whether transcriptional recovery requires new RNAPII initiation, the authors combined pharmacological inhibition of promoter escape using the CDK9 inhibitor DRB with genome-wide nascent transcription profiling (TT-seq). By blocking the release of newly initiated RNAPII complexes from promoters, they show that transcriptional recovery still occurred following oxidative stress, demonstrating that RNAPII complexes arrested by oxidative damage can restart transcription directly from within gene bodies. Moreover, TT-seq profiles during recovery revealed a pronounced bias of nascent transcription toward downstream regions of genes, further supporting a local restart mechanism.
Together, these results uncover a mode of transcriptional recovery that bypasses promoter-dependent initiation and enables rapid restoration of gene expression.
- Promoter-proximal regulation of early RNAPII elongation by NELF and PARylation
To dissect the mechanisms underlying transcriptional repression and recovery following oxidative stress, the authors combined genome-wide profiling of RNAPII occupancy (ECLAP-seq) with nascent transcription analysis (TT-seq). At the promoter-proximal region, analysis of RNAPII distribution around transcription start sites (TTS) revealed that oxidative stress induces a redistribution of paused RNAPII complexes (Figure 1A). By depleting the pausing factor NELF, the authors show that NELF is not required for the global shutdown of transcription. Instead, it modulates the positioning of early elongation complexes, promoting a transient shift of RNAPII pausing from the canonical first pause site to a second pause site associated with the +1 nucleosome during stress and recovery. In addition, using pharmacological inhibition of PARP1, the authors demonstrate that PARylation acts as a reversible brake on early RNAPII elongation. High levels of PARylation coincide with transcriptional repression and blocking PARP1 activity promotes the release of RNAPII complexes, without preventing the initial transcriptional shutdown. Finally, transcriptional recovery requires the active removal of PAR chains by the poly(ADP-ribose) glycohydrolase PARG, indicating that PARylation must be rapidly reversed to permit RNAPII reactivation (Figure 1B).
Figure 1. (from fig. 1.g and fig. 5.c, Thomas et al. 2025).
(A) Metagene profiles of nascent transcription measured by TT-chem-seq across protein-coding genes in untreated cells (dark line) or following H₂O₂-induced oxidative stress (red line). Oxidative damage induces a strong and global reduction of RNA synthesis along gene bodies while preserving RNAPII occupancy at transcription start sites (TSS), consistent with transcriptional arrest without RNAPII dissociation.
(B) Dot blot analysis of 4-thiouridine (4sU)–labelled nascent RNA in control (DMSO), PARP-inhibited (PARPi) or PARG-inhibited (PARGi) cells following oxidative stress and during recovery. In control cells, nascent transcription is transiently reduced after stress and progressively recovers over time. PARP inhibition accelerates this recovery, whereas inhibition of PARG strongly impairs transcriptional restart. These results indicate that dynamic PARylation, and in particular the timely removal of PAR chains, is required for efficient transcriptional recovery. Methylene blue staining is shown as a loading control.
- DNA repair–dependent restart of RNAPII within gene bodies
Remarkably, the authors also unveil that the recovery of transcription depends on DNA repair. Using XRCC1-deficient cells and pharmacological inhibition of the DNA glycosylase OGG1, the authors show that efficient repair of oxidative DNA lesions is required to relieve RNAPII blocks within gene bodies. Their activity enables RNAPII to locally resume transcription from within genes, independently of new transcription initiation.
Together, the findings described in sections 2 and 3 show that transcriptional recovery relies on two coordinated layers of regulation: PARylation-dependent control of early RNAPII elongation near promoters, and DNA repair–dependent removal of physical blocks that enables RNAPII to restart within gene bodies.
What I like about this preprint
By combining methods that measure nascent RNA synthesis with approaches that map RNAPII occupancy, the authors can distinguish changes in transcriptional activity from changes in polymerase binding to chromatin. This strategy provides a clear view of how RNAPII behavior is dynamically regulated after oxidative stress and helps link transcriptional regulation with DNA repair in a spatially resolved manner.
I really liked this preprint for several reasons, such as the fact that it elevates BER/SSBR from “genome maintenance” to active regulators of transcriptional dynamics and it shows that “global repression” doesn’t mean “global chaos.” It’s structured, modular, and reversible. What really got me excited isn’t just the data, it is that the story feels right, it explains a big, common biological phenomenon (oxidative stress) without invoking exotic machinery.
Question for the authors
Q1: What do you think is the direct PARylation target responsible for restricting early RNAPII release?
Q2: Do you think PARP2 could also be involved in the RNAPII positioning on damaged genes?
References
- LINDAHL,T. and BARNES,D.E. (2000) Repair of Endogenous DNA Damage. Cold Spring Harb Symp Quant Biol, 65, 127–134.
- Krokan,H.E. and Bjoras,M. (2013) Base Excision Repair. Cold Spring Harb Perspect Biol, 5, a012583–a012583.
- Özdemir,C., Purkey,L.R., Sanchez,A. and Miller,K.M. (2024) PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst), 140, 103711.
- Lesage,E., Clouaire,T. and Legube,G. (2021) Repair of DNA double-strand breaks in RNAPI- and RNAPII-transcribed loci. DNA Repair (Amst), 104, 103139.
- van der Meer,P.J. and Luijsterburg,M.S. (2025) The molecular basis of human transcription-coupled DNA repair. Nat Cell Biol, 10.1038/s41556-025-01715-9.
- Bilkis,R., Lake,R.J., Cooper,K.L., Tomkinson,A. and Fan,H.-Y. (2023) The CSB chromatin remodeler regulates PARP1- and PARP2-mediated single-strand break repair at actively transcribed DNA regions. Nucleic Acids Res, 51, 7342–7356.
- Heine,G.F., Horwitz,A.A. and Parvin,J.D. (2008) Multiple Mechanisms Contribute to Inhibit Transcription in Response to DNA Damage. Journal of Biological Chemistry, 283, 9555–9561.
- Thomas,Q.A., Wu,L., Lesage,E., Iversen,H.K.M., López Martínez,D., Kompocholi,S., Liu,H., Nieto Moreno,N. and Gregersen,L.H. (2025) Oxidative stress triggers RNAPII arrest through PARylation and DNA damage. 10.1101/2025.11.06.686939.
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