ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation
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Abstract
Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4 CSA ubiquitin ligase. How CRL4 CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4 CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.
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ELOF1 and LEO1 were identified among cisplatin sensitization hits.
“Notably, ELOF1, a recently identified transcription elongation factor that plays an important role in transcription-coupled nucleotide-excision repair47, and LEO1, a subunit of the polymerase-associated factor 1 (Paf1) complex RNA polymerase that is required for RNA polymerase II removal in response to DNA damage, were identified48,49.”
From Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions (2025) · cites this paper as [47]
In Results, ‘A CRISPR screen identifies ELOF1 as a putative TCR gene’ (page not provided), ELOF1 was a hit in an Illudin S screen, and ELOF1-knockout cells were sensitive to cisplatin in a separate drug-sensitivity assay. The cited paper does not establish that ELOF1 was a cisplatin-screen hit or identify LEO1 as one. (LLM, conf=0.85)
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“Notably, ELOF1 , a recently identi fi ed transcription elongation factorthatplays animportant rolein transcription-coupled nucleotide-excision repair 47 , and LEO1 , a subunit of the polymerase-associated factor 1 (Paf1) complex RNA polymerase that is required for RNA polymerase II removal in…”
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MMS22L-TONSL functions in sister chromatid cohesion in a pathway parallel to DSCC1-RFC
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Hierarchical mechanisms control the clearance of DNA lesion–stalled RNA polymerase II
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Clearance of DNA damage-arrested RNAPII is selectively impaired in Cockayne syndrome cellsPreprint
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Tools for Decoding Ubiquitin Signaling in DNA Repair
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Elf1 promotes transcription-coupled repair in yeast by using its C-terminal domain to bind TFIIH
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Transcription and genome integrity
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Self-citationTargeting Genome Stability to Mitigate Human Aging and Disease
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Integrator subunit INTS12 links ribotoxic stress to transcription-coupled nucleotide excision repair
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A Practical Site-specific Method for the Detection of Bulky DNA Damages
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Search, verify and excise-lesion recognition in NER
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PAF1C restores transcription after DNA damage independently of promoting histone mark deposition
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Self-citationPolymerase face-off: emerging concepts in transcription-replication coordination
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Evidence that ARK2N is not a core factor in transcription-coupled DNA repair
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Self-citationStabilization of AFF1 by PARylation ensures transcriptional restart after DNA damage
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Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recoveryPreprint
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ELOF1 is a core component of the promoter-proximal paused RNA polymerase II complexPreprint
Nunez, R. J. V., Bressin, A., Shao, Z., Mayer, A., & Vos, S. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.26.728003 · Cited by 2 · see citing works
Transcription-coupled repair: protecting genome across generations
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The Role of TFIIH Complex in Nucleotide Excision RepairPreprint
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Ubiquitylation of RNA Polymerase II Controls Early Stages of the Transcription CyclePreprint
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Finding novel vulnerabilities of hypomorphic BRCA1 allelesPreprint
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RNA Polymerase II subunits overexpressions induce genome instability and deregulate transcriptionPreprint
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Bypass of Blocking Lesions by RNAPII Impairs the Transcriptional DNA Damage ResponsePreprint
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Self-citationA Splicing Variant in XPA Results in Delayed Onset of Clinical Features of Xeroderma Pigmentosum
van den Heuvel, A., Wondergem, A. P., Kim, M., Breet, I., Kim, H. S., Fawcett, H., Fassihi, H., Lehmann, A. R., Schärer, O. D., & Luijsterburg, M. S. (2025) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2025.08.047
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Self-citation
- Authors
- van der Weegen, Y., de Lint, K., van den Heuvel, D., Nakazawa, Y., Mevissen, T. E. T., van Schie, J. J. M., San Martin Alonso, M., Boer, D. E. C., González-Prieto, R., Narayanan, I. V., Klaassen, N. H. M., Wondergem, A. P., Roohollahi, K., Dorsman, J. C., Hara, Y., Vertegaal, A. C. O., de Lange, J., Walter, J. C., Noordermeer, S. M., Ljungman, M., Ogi, T., Wolthuis, R. M. F., & Luijsterburg, M. S.
- Affiliations
- Research Institute of Environmental Medicine, Nagoya University (JP)
- Howard Hughes Medical Institute (US)
- Leiden University Medical Center (NL)
- University of Michigan (US)
- Amsterdam University Medical Centers (NL)
- Corresponding author
- Wolthuis, Rob M. F.
- Luijsterburg, Martijn S.
- ORCID
- Nakazawa, Yuka
- Mevissen, Tycho E. T.
- Boer, Daphne E. C.
- González-Prieto, Román
- Narayanan, Ishwarya V.
- Klaassen, Noud H. M.
- Wondergem, Annelotte P.
- Dorsman, Josephine C.
- Hara, Yuichiro
- Vertegaal, Alfred C. O.
- de Lange, Job
- Walter, Johannes C.
- Noordermeer, Sylvie M.
- Ljungman, Mats
- Ogi, Tomoo
- Wolthuis, Rob M. F.
- Luijsterburg, Martijn S.
- Venue
- Nature Cell Biology
- Published
- 2021-06
- Volume
- 23
- Issue
- 6
- Pages
- 595-607
- ISSN
- 1465-7392 (ISSN-L)
- 1476-4679
- PMC
- PMC8890769
- OpenAlex
- W3170184056
- Cited by
- 114
- References
- 64
- Citations by year
- 2026: 22 · 2025: 29 · 2024: 27 · 2023: 17 · 2022: 11 · 2021: 8
- FWCI
- 4.94
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Cell Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Leiden Repository (Leiden University) (submittedVersion)
- Pure Amsterdam UMC (submittedVersion, cc-by)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Amsterdam University Medical Centers
- Universiteit Leiden
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (ALW.016.161.320, 016.161.320, VI.Vidi.192.039, OCENW.KLEIN.090)
- Leids Universitair Medisch Centrum
- Japan Society for the Promotion of Science (18H03372, 20H00629, 21H02399, 21K19844)
- National Heart, Lung, and Blood Institute (R01HL098316)
- National Human Genome Research Institute (UM1HG009382)
- National Cancer Institute (R01CA213214)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- transcription-coupled repair, CSB, transcription elongation, R-loops, replication stress, transcriptional stress response, DNA damage response
- MeSH terms
- Poly-ADP-Ribose Binding Proteins, DNA Damage, DNA Repair, DNA Helicases, Humans, Protein Binding, RNA Polymerase II, Transcription Factors, Peptide Elongation Factor 1, Ubiquitin-Protein Ligases, DNA Repair Enzymes, Cell Line, Tumor, Receptors, Interleukin-17, Protein Interaction Domains and Motifs, Ubiquitination, Transcription Elongation, Genetic, CRISPR-Cas Systems
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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