STK19 positions TFIIH for cell-free transcription-coupled DNA repair
Open accessPublished version of a preprint
Abstract
In transcription-coupled repair, stalled RNA polymerase II (Pol II) is recognized by CSB and CRL4 CSA , which co-operate with UVSSSA and ELOF1 to recruit TFIIH for nucleotide excision repair (TC-NER). To explore the mechanism of TC-NER, we recapitulated this reaction in vitro . When a plasmid containing a site-specific lesion is transcribed in frog egg extract, error-free repair is observed that depends on CSB, CRL4 CSA , UVSSA, and ELOF1. Repair also depends on STK19, a factor previously implicated in transcription recovery after UV exposure. A 1.9 Å cryo-electron microscopy structure shows that STK19 joins the TC-NER complex by binding CSA and the RPB1 subunit of Pol II. Furthermore, AlphaFold predicts that STK19 interacts with the XPD subunit of TFIIH, and disrupting this interface impairs cell-free repair. Molecular modeling suggests that STK19 positions TFIIH ahead of Pol II for lesion verification. In summary, our analysis of cell-free TC-NER suggests that STK19 couples RNA polymerase II stalling to downstream repair events.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Another top ranked hit for SLF1 was RAD18, a known SLF1 interactor that was randomly included as part of the 1,000 protein negative set.
“Notably, in addition to the desired prey SMC6, another top ranked hit for SLF1 was RAD18, a known SLF1 interactor51–53 that was randomly included as part of the 1,000 protein “negative” set.”
From Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions (2025) · cites this paper as [51]
The Discussion section describes a screen for STK19 partners, not SLF1, and the Methods section describes SPOC scoring without addressing this claim. Searches for SLF1, RAD18, SMC6, and the 1,000-protein negative set found no passage in our copy establishing that RAD18 is a known SLF1 interactor or describing its inclusion in that set. (LLM, conf=0.73)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 9,168 · see citing works
Liebschner, D. C., Afonine, P. V., Baker, M. L., Bunkòczi, G., Chen, V. B., Croll, T. I., Hintze, B. J., Hung, L., Jain, S., McCoy, A. J., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319011471 · Cited by 6,709 · see citing works
UCSF ChimeraX: Meeting modern challenges in visualization and analysis
Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018) · Protein Science · doi:10.1002/pro.3235 · Cited by 5,267 · see citing works
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Steinegger, M., & Söding, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3988 · Cited by 4,840 · see citing works
Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808 · see citing works
Normal table of Xenopus laevis (Daudin)
Gurdon, J. B. (1995) · Trends in Genetics · doi:10.1016/s0168-9525(00)89129-5 · Cited by 2,888 · see citing works
Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052 · see citing works
Croll, T. (2018) · Acta Crystallographica Section D: Structural Biology · doi:10.1107/s2059798318002425 · Cited by 1,934 · see citing works
MELLON, I. (1987) · Cell · doi:10.1016/0092-8674(87)90151-6 · Cited by 1,228 · see citing works
Electroporation and RNA interference in the rodent retina in vivo and in vitro
Matsuda, T., & Cepko, C. L. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235688100 · Cited by 1,032 · see citing works
Improved prediction of protein-protein interactions using AlphaFold2
Bryant, P., Pozzati, G., & Elofsson, A. (2021) · doi:10.1101/2021.09.15.460468 · Cited by 1,025 · see citing works
Mammalian DNA nucleotide excision repair reconstituted with purified protein components
Aboussekhra, A., Biggerstaff, M., Shivji, M. K. K., Vilpo, J. A., Moncollin, V., Podust, V. N., Protić, M., Hübscher, U., Egly, J.-M., & Wood, R. D. (1995) · Cell · doi:10.1016/0092-8674(95)90289-9 · Cited by 837 · see citing works
Nucleotide Excision Repair in EukaryotesPreprint
Schärer, O. D. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012609 · Cited by 801 · see citing works
A Genetic Map of the Response to DNA Damage in Human Cells
Olivieri, M., Cho, T., Álvarez-Quilón, A., Li, K., Schellenberg, M. J., Zimmermann, M., Hustedt, N., Rossi, S. E., Adam, S., Melo, H., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.040 · Cited by 551 · see citing works
Transcription-Coupled Repair and Human Disease
Hanawalt, P. C. (1994) · Science · doi:10.1126/science.7801121 · Cited by 496 · see citing works
Reconstitution of Human DNA Repair Excision Nuclease in a Highly Defined System
Mu, D., Park, C.-H., Matsunaga, T., Hsu, D. S., Reardon, J. T., & Sancar, A. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.6.2415 · Cited by 476 · see citing works
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf
Yariv, B., Yariv, E., Kessel, A., Masrati, G., Chorin, A. B., Martz, E., Mayrose, I., Pupko, T., & Ben-Tal, N. (2023) · Protein Science · doi:10.1002/pro.4582 · Cited by 387 · see citing works
Structure of paused transcription complex Pol II–DSIF–NELF
Vos, S. M., Farnung, L., Urlaub, H., & Cramer, P. (2018) · Nature · doi:10.1038/s41586-018-0442-2 · Cited by 378 · see citing works
Self-citationThe DNA damage response to transcription stress
Lans, H., Hoeijmakers, J. H. J., Vermeulen, W., & Marteijn, J. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0169-4 · Cited by 321 · see citing works
Near-atomic resolution visualization of human transcription promoter opening
He, Y., Yan, C., Fang, J., Inouye, C. J., Tjian, R., Ivanov, I. N., & Nogales, E. (2016) · Nature · doi:10.1038/nature17970 · Cited by 296 · see citing works
UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair
Schwertman, P., Lagarou, A., Dekkers, D. H. W., Raams, A., van der Hoek, A. C., Laffeber, C., Hoeijmakers, J. H. J., Demmers, J. A. A., Fousteri, M., Vermeulen, W., et al. (2012) · Nature Genetics · doi:10.1038/ng.2230 · Cited by 279 · see citing works
Deep Proteomics of the Xenopus laevis Egg using an mRNA-Derived Reference Database
Wühr, M., Freeman, R. M., Presler, M., Horb, M. E., Peshkin, L., Gygi, S. P., & Kirschner, M. W. (2014) · Current Biology · doi:10.1016/j.cub.2014.05.044 · Cited by 257 · see citing works
Nucleosome–Chd1 structure and implications for chromatin remodelling
Farnung, L., Vos, S. M., Wigge, C., & Cramer, P. (2017) · Nature · doi:10.1038/nature24046 · Cited by 257 · see citing works
Self-citationUbiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair
Nakazawa, Y., Hara, Y., Oka, Y., Komine, O., van den Heuvel, D., Guo, C., Daigaku, Y., Isono, M., He, Y., Shimada, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.010 · Cited by 229 · see citing works
Rational design of a super core promoter that enhances gene expression
Juven-Gershon, T., Cheng, S., & Kadonaga, J. T. (2006) · Nature Methods · doi:10.1038/nmeth937 · Cited by 223 · see citing works
Nakazawa, Y., Sasaki, K., Mitsutake, N., Matsuse, M., Shimada, M., Nardò, T., Takahashi, Y., Ohyama, K., Ito, K., Mishima, H., et al. (2012) · Nature Genetics · doi:10.1038/ng.2229 · Cited by 213 · see citing works
Regulation of the RNAPII Pool Is Integral to the DNA Damage Response
Vidaković, A. T., Mitter, R., Kelly, G. P., Neumann, M., Harreman, M. T., Rodríguez‐Martínez, M., Herlihy, A. E., Weems, J. C., Boeing, S., Encheva, V., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.009 · Cited by 209 · see citing works
Structural basis for the initiation of eukaryotic transcription-coupled DNA repair
Xu, J., Lahiri, I., Wang, W., Wier, A. D., Cianfrocco, M. A., Chong, J. P. C., Hare, A. A., Dervan, P. B., DiMaio, F., Leschziner, A. E., et al. (2017) · Nature · doi:10.1038/nature24658 · Cited by 202 · see citing works
Zhang, X., Horibata, K., Saijo, M., Ishigami, C., Ukai, A., Kanno, S.-I., Tahara, H., Neilan, E. G., Honma, M., Nohmi, T., et al. (2012) · Nature Genetics · doi:10.1038/ng.2228 · Cited by 201 · see citing works
Multiomic Analysis of the UV-Induced DNA Damage Response
Boeing, S., Williamson, L. M., Encheva, V., Gori, I., Saunders, R. E., Instrell, R., Aygün, O., Rodríguez‐Martínez, M., Weems, J. C., Kelly, G. P., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.047 · Cited by 199 · see citing works
Enoiu, M., Jiricny, J., & Schärer, O. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks670 · Cited by 183 · see citing works
The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
van der Weegen, Y., Golan-Berman, H., Mevissen, T. E. T., Apelt, K., González‐Prieto, R., Goedhart, J., Heilbrun, E. E., Vertegaal, A. C. O., van den Heuvel, D., Walter, J. C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15903-8 · Cited by 177 · see citing works
Self-citationStructural basis of TFIIH activation for nucleotide excision repair
Kokic, G., Chernev, A., Tegunov, D., Dienemann, C., Urlaub, H., & Cramer, P. (2019) · Nature Communications · doi:10.1038/s41467-019-10745-5 · Cited by 163 · see citing works
Li, C., Gołębiowski, F., Onishi, Y., Samara, N. L., Sugasawa, K., & Yang, W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.08.012 · Cited by 155 · see citing works
Cip1 inhibits DNA replication but not PCNA-dependent nucleotide excision—repair
Shivji, M. K. K., Grey, S. J., Strausfeld, U. P., Wood, R. D., & Blow, J. J. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00244-x · Cited by 149 · see citing works
Initiation of DNA repair mediated by a stalled RNA polymerase IIO
Lainé, J., & Egly, J. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600933 · Cited by 147 · see citing works
Structural basis of human transcription–DNA repair coupling
Kokić, G., Wagner, F., Chernev, A., Urlaub, H., & Cramer, P. (2021) · Nature · doi:10.1038/s41586-021-03906-4 · Cited by 137 · see citing works
Gradia, S., Ishida, J. P., Tsai, M.-S., Jeans, C., Tainer, J. A., & Fuss, J. O. (2017) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2017.03.008 · Cited by 127 · see citing works
Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways
Okuda, M., Nakazawa, Y., Guo, C., Ogi, T., & Nishimura, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx970 · Cited by 124 · see citing works
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid, E. W., & Walter, J. C. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.034 · Cited by 120 · see citing works
Self-citationMoreno, N. N., Olthof, A. M., & Svejstrup, J. Q. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052621-091205 · Cited by 115 · see citing works
ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation
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., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00688-9 · Cited by 114 · see citing works
Self-citationIn silico protein interaction screening uncovers DONSON’s role in replication initiation
Lim, Y., Tamayo-Orrego, L., Schmid, E., Tarnauskaite, Z., Kochenova, O. V., Gruar, R., Muramatsu, S., Lynch, L., Schlie, A. V., Carroll, P. L., et al. (2023) · Science · doi:10.1126/science.adi3448 · Cited by 112 · see citing works
Self-citationStructures of mammalian RNA polymerase II pre-initiation complexes
Aibara, S., Schilbach, S., & Cramer, P. (2021) · Nature · doi:10.1038/s41586-021-03554-8 · Cited by 109 · see citing works
Transcription-Coupled DNA Repair: From Mechanism to Human Disorder
van den Heuvel, D., van der Weegen, Y., Boer, D. E. C., Ogi, T., & Luijsterburg, M. S. (2021) · Trends in Cell Biology · doi:10.1016/j.tcb.2021.02.007 · Cited by 105 · see citing works
Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability
Geijer, M. E., Zhou, D., Selvam, K., Steurer, B., Mukherjee, C., Evers, B., Cugusi, S., van Toorn, M., van der Woude, M., Janssens, R. C., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00692-z · Cited by 91 · see citing works
Lesion recognition by XPC, TFIIH and XPA in DNA excision repair
Kim, J., Li, C., Chen, X., Cui, Y., Gołębiowski, F., Wang, H., Hanaoka, F., Sugasawa, K., & Yang, W. (2023) · Nature · doi:10.1038/s41586-023-05959-z · Cited by 90 · see citing works
Fei, J., & Chen, J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.398131 · Cited by 70 · see citing works
Molecular Mechanisms of Transcription-Coupled Repair
Selby, C. P., Lindsey‐Boltz, L. A., Li, W., & Sancar, A. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-041522-034232 · Cited by 67 · see citing works
Tsutakawa, S. E., Tsai, C.-L., Yan, C., Bralić, A., Chazin, W., Hamdan, S. M., Schärer, O. D., Ivanov, I. N., & Tainer, J. A. (2020) · DNA repair · doi:10.1016/j.dnarep.2020.102972 · Cited by 58 · see citing works
Kokić, G., Yakoub, G., van den Heuvel, D., Wondergem, A. P., van der Meer, P. J., van der Weegen, Y., Chernev, A., Fianu, I., Fokkens, T. J., Lorenz, S., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01207-0 · Cited by 54 · see citing works
Xenopus egg extract: A powerful tool to study genome maintenance mechanisms
Hoogenboom, W. S., Douwel, D. K., & Knipscheer, P. (2017) · Developmental Biology · doi:10.1016/j.ydbio.2017.03.033 · Cited by 52 · see citing works
Jia, N., Guo, C., Nakazawa, Y., van den Heuvel, D., Luijsterburg, M. S., & Ogi, T. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103192 · Cited by 50 · see citing works
Thymine DNA Glycosylase Is a CRL4Cdt2 Substrate
Slenn, T. J., Morris, B. L., Havens, C. G., Freeman, R. M., Takahashi, T. S., & Walter, J. C. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.574194 · Cited by 49 · see citing works
Self-citationExtracts for Analysis of DNA Replication in a Nucleus-Free System.Preprint
Sparks, J. L., & Walter, J. (2019) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot097154 · Cited by 48 · see citing works
Self-citationEvidence That STK19 Is Not an NRAS-dependent Melanoma Driver
Rodríguez‐Martínez, M., Boissiére, T., González, M. N., Litchfield, K., Mitter, R., Walker, J., Kjœr, S., Ismail, M., Downward, J., Swanton, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.014 · Cited by 31 · see citing works
Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase
Shabek, N., Ruble, J., Waston, C. J., Garbutt, K. C., Hinds, T. R., Li, T., & Zheng, N. (2018) · Cell Discovery · doi:10.1038/s41421-018-0064-8 · Cited by 29 · see citing works
Heubes, S., & Stemmann, O. (2007) · Journal of Cell Science · doi:10.1242/jcs.006924 · Cited by 26 · see citing works
Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair
Sarsam, R. D., Xu, J., Lahiri, I., Gong, W., Li, Q., Oh, J., Zhou, Z., Hou, P., Chong, J. P. C., Hao, N., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2314245121 · Cited by 21 · see citing works
Pines, A., Schiffmacher, D. L., Lee, S.-H., Kliza, K., Theil, A., Akita, M., Helfricht, A., Bezstarosti, K., Gonzalo-Hansen, C., Attikum, H. V., et al. (2023) · doi:10.21203/rs.3.rs-3385435/v1 · Cited by 19 · see citing works
The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics
Llerena Schiffmacher, D. A., Lee, S.-H., Kliza, K. W., Theil, A. F., Akita, M., Helfricht, A., Bezstarosti, K., Gonzalo-Hansen, C., van Attikum, H., Verlaan-de Vries, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50584-7 · Cited by 19 · see citing works
STK19 is a DNA/RNA-binding protein critical for DNA damage repair and cell proliferation
Li, Y., Gong, Y., Zhou, Y., Xiao, Y., Huang, W., Zhou, Q., Tu, Y., Zhao, Y., Zhang, S., Dai, L., et al. (2023) · The Journal of Cell Biology · doi:10.1083/jcb.202301090 · Cited by 17 · see citing works
Cell-free transcription in Xenopus egg extract
Barrows, J. K., & Long, D. T. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011350 · Cited by 11 · see citing works
Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19
Li, J., Ma, X., Wang, X., Hu, X., Fang, S., Jin, G., Liu, K., & Dong, Z. (2024) · Scientific Reports · doi:10.1038/s41598-024-64840-9 · Cited by 9 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid, E. W., & Walter, J. C. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.034 · Cited by 120 · see citing works
Self-citationTan, Y., Gao, M., Huang, Y., Zhan, D., Wu, S., An, J., Zhang, X., & Hu, J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae787 · Cited by 31 · see citing works
Chromatin Transcription Elongation – A Structural Perspective
Farnung, L. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168845 · Cited by 18 · see citing works
Self-citationTranscription-coupled AID deamination damage depends on ELOF1-associated RNA polymerase II
Dai, P., Tan, Y., Luo, Y., Liu, T., Huang, Y., Shang, Y., Huang, M. E., Liu, X., Zhang, S., Wang, Y., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.02.006 · Cited by 17 · see citing works
Recent progress and future challenges in structure-based protein-protein interaction prediction
Yuan, R., Zhang, J., Zhou, J., & Cong, Q. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.04.003 · Cited by 20 · see citing works
RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease
Kuldell, J. C., & Kaplan, C. D. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168770 · Cited by 15 · see citing works
The molecular basis of human transcription-coupled DNA repair
van der Meer, P. J., & Luijsterburg, M. S. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01715-9 · Cited by 17 · see citing works
Mechanisms of transcription-coupled repair and DNA damage surveillance in health and disease
van Sluis, M., Gonzalo-Hansen, C., Li, Q., Lans, H., Wang, D., & Marteijn, J. A. F. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00915-3 · Cited by 21 · see citing works
Transcription-coupled repair of DNA–protein crosslinks
Carnie, C. J., Jackson, S. P., & Stingele, J. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.11.003 · Cited by 16 · see citing works
Transcription-Coupled Nucleotide Excision Repair: A Faster Solution or the Only Option?
Khobta, A., & Sarmini, L. (2025) · Biomolecules · doi:10.3390/biom15071026 · Cited by 12 · see citing works
Molecular model of TFIIH recruitment to the transcription-coupled repair machinery
Paul, T., Yan, C., Yu, J., Tsutakawa, S. E., Tainer, J. A., Wang, D., & Ivanov, I. N. (2025) · Nature Communications · doi:10.1038/s41467-025-57593-0 · Cited by 11 · see citing works
Transcription-Coupled Repair and R-Loop Crosstalk in Genome Stability
Jeon, J., & Kang, T. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26083744 · Cited by 8 · see citing works
Transcription‐coupled repair: tangled up in convoluted repair
Schiffmacher, D. A. L., Pai, Y. J., Pines, A., & Vermeulen, W. (2025) · FEBS Journal · doi:10.1111/febs.70104 · Cited by 9 · see citing works
Hierarchical mechanisms control the clearance of DNA lesion–stalled RNA polymerase II
van der Meer, P. J., Yakoub, G., Tsukada, K., Nakazawa, Y., Ogi, T., & Luijsterburg, M. S. (2026) · Nature Communications · doi:10.1038/s41467-026-68413-4 · Cited by 9 · see citing works
Proteome-wide in silico screening for human protein-protein interactionsPreprint
Schmid, E. W., Zhu, H., Ryu, E., Lim, Y., Smogorzewska, A., Brown, A., & Walter, J. C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.10.687652 · Cited by 12 · see citing works
Self-citationStructure and function of IWS1 in transcription elongation
Syau, D., Steinruecke, F., Roth, S., Schmid, E., Adelman, K., Walter, J. C., & Farnung, L. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag357 · Cited by 5 · see citing works
Self-citationRobu, M., Shah, R. G., van den Heuvel, D., Coulombe, Y., Bazin, M., van der Woude, M., Kragten, A., Lans, H., Pascal, J. M., Masson, J., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1303 · Cited by 6 · see citing works
Targeting DNA Damage and Repair Pathways in Cerebral Ischemic Stroke: From Bench to Bedside
Xie, Z., Luo, Y., & Han, Z. (2026) · Translational Stroke Research · doi:10.1007/s12975-025-01394-6 · Cited by 4 · see citing works
Integrator subunit INTS12 links ribotoxic stress to transcription-coupled nucleotide excision repair
Li, Z., Li, R., Yang, M., Huang, Y., Yang, J., Zhu, Q., Shao, Y., Zhao, W., Fu, H., Xiao, Y.-X., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-026-01766-y · Cited by 4 · see citing works
Ao, Q., Tang, L., Bao, Y., Wang, M., Zhu, J., Chen, Y., Zhu, H., & Gao, J. (2026) · Phytomedicine · doi:10.1016/j.phymed.2026.158065 · Cited by 3 · see citing works
STK19: a critical factor coordinating transcription-coupled DNA repair
Li, S., & Li, W. (2025) · Protein & Cell · doi:10.1093/procel/pwaf007 · Cited by 3 · see citing works
Jones, K., Dye, E., Gilkes, N., Xia, D., Jiang, S., & Li, W. (2025) · Journal of Environmental Science and Health Part C · doi:10.1080/26896583.2025.2545086 · Cited by 2 · see citing works
Search, verify and excise-lesion recognition in NER
Kuper, J., & Kisker, C. (2026) · DNA repair · doi:10.1016/j.dnarep.2026.103922 · Cited by 2 · see citing works
Kim, M., Jeong, E., Park, J., D’Souza, A., Tsai, M.-S., Yan, C., Ivanov, I., Chazin, W. J., Kim, H. S., & Schärer, O. D. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag078 · Cited by 2 · see citing works
Harnessing AI to decode protein kinases: Structural, functional, and therapeutic design perspectives
Gomari, M. M., Ntwali, P. V. M., Choupani, E., & Ashayeri, N. (2026) · New Biotechnology · doi:10.1016/j.nbt.2026.02.010 · Cited by 2 · see citing works
PAF1C restores transcription after DNA damage independently of promoting histone mark deposition
van Schie, J. J. M., de Groot, B. A. F. J., van den Heuvel, D., & Luijsterburg, M. S. (2026) · EMBO Reports · doi:10.1038/s44319-026-00761-0 · Cited by 2 · see citing works
Recruitment and release of XPG during NER is controlled by pre- and post-incision factors and EXO1
Muniesa-Vargas, A., Ribeiro-Silva, C., Davó-Martínez, C., Raams, A., Geverts, B., van de Grint, J., Ganpat, M. M. P., Thijssen, K. L., Pothof, J., Houtsmuller, A. B., et al. (2026) · The Journal of Cell Biology · doi:10.1083/jcb.202602121 · Cited by 2 · see citing works
Unlocking transcription-coupled DNA repair with the STK19 key
Kuper, J., Kisker, C., & Houten, B. V. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.027 · Cited by 2 · see citing works
Nascent RNA Folding and RNP Assembly Revealed by Single-molecule Microscopy
Bustamante, A., Carrocci, T. J., Nicholson, D. A., & Rodgers, M. L. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169365 · Cited by 2 · see citing works
Molecular basis for CSB stimulation of the SNM1A DNA repair nucleasePreprint
Roddan, R., Schaich, M. A., Nathan, W. J., Kis, I., Pierangelini, A., Henderson, L. R., van Wee, R., Martin, L., El-Sagheer, A. H., Kukura, P., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.05.611390 · Cited by 2 · see citing works
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
Preparation of Nucleoplasmic Extract and Its Application in DNA End Processing
Nishiguchi, D., Tatsukawa, K., & Takahashi, T. S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4714-1_14 · Cited by 2 · see citing works
Structure of cytoplasmic RNA polymerase II
Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., & Bernecky, C. (2026) · Nature Communications · doi:10.1038/s41467-026-75416-8 · Cited by 1 · see citing works
Topology Resetting During Transcription-Coupled Nucleotide Excision Repair
Lee, T.-H., Jeon, J., Jo, S.-G., & Kang, T. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27167244 · Cited by 1 · see citing works
Topoisomerase IIIα resolves inter- and intra-molecular intertwines during DNA replicationPreprint
Ravenstein, S. X. V., Campos, L. V., Harami, G. M., Heintzman, D. R., Dahmen, S. N., Dunphy, W. G., Neuman, K. C., & Dewar, J. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.30.735647 · Cited by 1 · see citing works
Muniesa-Vargas, A., Ribeiro-Silva, C., Geverts, B., Davó-Martínez, C., van de Grint, J., Ganpat, M. M. P., Thijssen, K. L., Pothof, J., Houtsmuller, A. B., Theil, A. F., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.06.627128
van Schie, J. J. M., de Groot, B. A. F. J., & Luijsterburg, M. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.23.666359
Patel, S., Moser, M., Miller, N., Guo, G., McElroy, C. A., & Hester, M. E. (2026) · Developmental Biology · doi:10.1016/j.ydbio.2026.03.019
Effect of DNA Methylation Modulators on UV Damage Formation and Repair
Jones, K., Rajbhandari, R., & Li, W. (2026) · Genes · doi:10.3390/genes17040487
Li, Y., Gong, Y., Chen, P., Tang, M., Zhao, Y., Dai, L., & Sun, Q. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152338
TWH19 scaffolds AURKB to phosphorylate C-RAF and activate MAPK signalingPreprint
Sun, Q., Li, Y., Li, Y., Chen, P., Wang, C., & Guo, L. (2026) · Research Square · doi:10.21203/rs.3.rs-9362063/v1
Fukushima, Y., Kinoshita, C., Negishi, L., Kujirai, T., Kobayashi, Y., Ogasawara, M., Ehara, H., Sekine, S., Kagawa, W., Kurumizaka, H., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-73500-7
Residual CSB activity explains mild UV-sensitive syndrome phenotype caused by CSB mutations
Gonzalo-Hansen, C., Häckes, D., Avramidou, G., Janssens, R. C., Bezstarosti, K., Demmers, J., Lans, H., & Marteijn, J. A. F. (2026) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2026.06.1281 · Cited by 1 · see citing works
RNA polymerase II removal: transcription quality control and gene regulation
Haworth, B., Abyaneh, P., & Vidaković, A. T. (2026) · Transcription · doi:10.1080/21541264.2026.2698182
Passaretti, P., & Gambus, A. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5360-9_7
Reconstitution of genome remodeling using Xenopus egg extracts
Lenz, K. G., & Zhou, C. Y. (2026) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2026.1932329
Glutamine metabolism and its roles in tumor radiotherapy by regulating DNA damage repair
Huang, Y., Wang, H., Zhang, S., Jiang, Z., Shen, R., Chang, W., & Jiang, X. (2026) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2026.1915673
Dilsiz, P., & Hapil, F. Z. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5547-4_2
Xu, T., Shen, Y., Dai, X., Shao, Y., Yuanting, Z., Zhang, Y., Wang, G., & Li, N. (2026) · Molecular Biology Reports · doi:10.1007/s11033-026-12816-5
- Authors
- Mevissen, T. E. T., Kümmecke, M., Schmid, E. W., Farnung, L., & Walter, J. C.
- Affiliations
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Corresponding author
- Farnung, Lucas
- Walter, Johannes C.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2024-12
- Volume
- 187
- Issue
- 25
- Pages
- 7091-7106.e24
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC11291053
- OpenAlex
- W4404374986
- Cited by
- 50
- References
- 69
- Citations by year
- 2026: 26 · 2025: 16 · 2024: 8
- FWCI
- 6.81
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health
- Howard Hughes Medical Institute
- American Cancer Society
- EMBO
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- TFIIH, transcription-coupled repair, XPD, RNA polymerase II, RPB1, CSA, UV-induced DNA damage, protein complex structure, DNA repair
About these checks
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 ›
Are you an author, or do you see a problem with this page? Request a review
