The DNA damage response to transcription stress

The Hallmarks of Aging

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RNA m6A methylation regulates the ultraviolet-induced DNA damage response

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The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate

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Probing the interaction of an antiviral drug 8-methoxy-3-nitro-2-(4-methoxyphenyl)-2H-chromene (MNC) with DNA by experimental and computational approach

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Elf1 promotes transcription-coupled repair in yeast by using its C-terminal domain to bind TFIIH

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Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

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Camptothecin compromises transcription recovery and cell survival against cisplatin and ultraviolet irradiation regardless of transcription-coupled nucleotide excision repair

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CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters

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The hardwired transcriptional response to DNA damage

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Oxidative stress triggers RNAPII arrest through PARylation and DNA damage

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Integrator subunit INTS12 links ribotoxic stress to transcription-coupled nucleotide excision repair

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A pooled analysis of host factors that affect nucleotide excision repair in humans

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The m6A reader IGF2BP3 facilitates myogenesis by activating the CAMK2B-MEF2C axis

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Age Deceleration and Reversal Gene Patterns in Dauer Diapause

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Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein

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Methods for Assessment of Nucleotide Excision Repair Efficiency

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Dysregulation of the low-level replication stress response in transformed cell lines

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QTMP, a Novel Thiourea Polymer, Causes DNA Damage to Exert Anticancer Activity and Overcome Multidrug Resistance in Colorectal Cancer Cells

Bai, Z., Zhou, Q., Zhu, H., Ye, X., Wu, P., & Ma, L. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.667689 · Cited by 4

Smart Health Based on Internet of Things (IoT) and Smart Devices

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Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA

Mistry, H., & Gupta, G. D. (2023) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2023.109515 · Cited by 4

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

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Adding a transcription-coupled repair pathway

Saponaro, M. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01399-7 · Cited by 4

Histone variant H2A.Z is needed for efficient transcription-coupled NER and genome integrity in UV challenged yeast cells

Gaillard, H., Ciudad, T., Aguilera, A., & Wellinger, R. E. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011300 · Cited by 3

TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data

Kosugi, S., & Terao, C. (2025) · Genome biology · doi:10.1186/s13059-025-03718-z · Cited by 3

Genomic investigation of innate sensing pathways in the tumor microenvironment

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Body Composition and Metabolic Changes in a Lyon Hypertensive Congenic Rat and Identification of Ercc6l2 as a Positional Candidate Gene

Clark, K. C., Wagner, V. A., Holl, K. L., Reho, J. J., Tutaj, M., Smith, J. R., Dwinell, M. R., Grobe, J. L., & Kwitek, A. E. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.903971 · Cited by 3

RNAPII Degradation Factor Def1 Is Required for Development, Stress Response, and Full Virulence of Magnaporthe oryzae

Zhang, X., Li, D., Zhu, J., Zheng, J., Li, H., He, Q., Peng, J., Chen, S., Chen, X., & Wang, W. (2023) · Journal of Fungi · doi:10.3390/jof9040467 · Cited by 3

Analysis of RNA Polymerase II Chromatin Binding by Flow Cytometry

Bay, L. T. E., Stokke, T., Syljuåsen, R. G., & Landsverk, H. B. (2023) · BIO-PROTOCOL · doi:10.21769/bioprotoc.4659 · Cited by 3

Comprehensive analysis identifies DNA damage repair-related gene HCLS1 associated with good prognosis in lung adenocarcinoma

Liu, T., Hu, A., Chen, H., Li, Y., Wang, Y., Guo, Y., Liu, T., Zhou, J., Li, D., & Chen, Q. (2023) · Translational Cancer Research · doi:10.21037/tcr-23-921 · Cited by 3

The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer

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A Sample Preparation Method for the Simultaneous Profiling of Signaling Lipids and Polar Metabolites in Small Quantities of Muscle Tissues from a Mouse Model for Sarcopenia

He, Y., van Mever, M., Yang, W., Huang, L., Ramautar, R., Rijksen, Y., Vermeij, W. P., Hoeijmakers, J. H. J., Harms, A. C., Lindenburg, P. W., et al. (2022) · Metabolites · doi:10.3390/metabo12080742 · Cited by 3

The Emerging Role of (p)ppGpp in DNA Repair and Associated Bacterial Survival against Fluoroquinolones

Sivapragasam, S. (2024) · Gene Expression · doi:10.14218/ge.2024.00033 · Cited by 2

Crosstalk between chromatin state and ATM signalling in DNA damage-induced transcription stress

Salas‐Armenteros, I., Klunder, M., Vermeulen, W., & Tresini, M. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00537-7 · Cited by 2

Comparative toxicity of flame retardants on reproduction, antioxidant system, and energy metabolism of brackish water flea Diaphanosoma celebensis

Yoo, J.-W., Park, C., Choi, T.-J., Kim, C.-B., & Lee, Y.-M. (2026) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2026.119904 · Cited by 2

Oxidation-driven mtDNA B-Z transition activates ZBP1 to mediate acetaminophen hepatotoxicity

Yang, Z.-H., Zhang, B.-X., Ye, H.-F., Shi, L., Gong, R., Cai, Z., Chen, Q., Wu, L., Huang, J., Zhang, L., et al. (2026) · Vita · doi:10.15302/vita.2026.04.0029 · Cited by 2

ZNF512B safeguards genome integrity at regulatory regions to repress the SASP and inflammation

Sahu, S. K., Memczak, S., Thakurela, S., Lu, J., Gupta, P., Mutukula, N., Hirano, A., Zhang, Y., Hishida, T., Kurita, M., et al. (2026) · Cell stem cell · doi:10.1016/j.stem.2026.05.009 · Cited by 2

Genomic, epigenomic and transcriptomic regulation of cellular senescence

Salekeen, R., Kieu, T. L., Robbins, P. D., Niedernhofer, L. J., & Laux, L. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00982-y · Cited by 2

XPG gene polymorphisms and glioma susceptibility: a two-centre case–control study

Li, Y., Hu, W., Chen, K., Shi, Q., Lin, A., Chen, H., Zhuo, Z., & Zeng, L. (2021) · British Journal of Biomedical Science · doi:10.1080/09674845.2020.1870308 · Cited by 2

DNA replication, repair, and mutagenesis

Ha, C. E., & Bhagavan, N. V. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-88541-6.00029-6 · Cited by 2

Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma

Bai, Y., He, J., Ma, Y., He, L., Li, M., & Wu, Y. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1180722 · Cited by 2

Transcription as source of genetic heterogeneity in budding yeast

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Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

Huang, Z., Luo, S., Wang, Z., Zhang, Z., Jiang, B., Nie, Q. H., & Zhang, J. (2026) · eLife · doi:10.7554/elife.100623.4 · Cited by 2

Site-specific unnatural base excision via visible light

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CRISPR Technology - Recent Advances

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Maximizing the Efficacy of CRISPR/Cas Homology-Directed Repair Gene Targeting

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RNA polymerase II processing facilitates DNA repair and prevents DNA damage-induced neuronal and developmental failurePreprint

van der Woude, M., Thijssen, K. L., Sabatella, M., Marteijn, J. A. F., Vermeulen, W., & Lans, H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.21.644538 · Cited by 2

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damagePreprint

Huang, Z., Luo, S., Wang, Z., Zhang, Z., Jiang, B., Nie, Q. H., & Zhang, J. (2025) · eLife · doi:10.7554/elife.100623.2 · Cited by 2

The Pathogenic Role of the DNA Double-Stranded Breaks in Hereditary Cardiomyopathies

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Expression of long non-coding RNAs DINO and ROR in bone marrow stem cells under hyperglycemic conditions

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K63-linked ubiquitylation of S2P–RNAPII regulates transcription in a DNAPK inter-dependent manner in response to double-strand breaks

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Residual CSB activity explains mild UV-sensitive syndrome phenotype caused by CSB mutations

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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

Molecular Dynamic and Docking Simulation to Prevent Thymine Dimer as the Main Reason for Skin Cancer

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Enhanced glutathione levels confer resistance to apoptotic and ferroptotic programmed cell death in NEIL DNA glycosylase deficient HAP1 cells

Neurauter, C. G., Pannone, M., de Sousa, M. M. L., Wang, W., Kuśnierczyk, A., Luna, L., Sætrom, P., Scheffler, K., & Bjørås, M. (2024) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2024.01.037 · Cited by 1

Nephrotoxicity of Natural Products: Aristolochic Acid and Fungal Toxins

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Transcription: friend or foe of genome stability

Compe, E., & Orioli, D. (2025) · FEBS Letters · doi:10.1002/1873-3468.15091 · Cited by 1

IncRNA‐ZFAS1, an Emerging Gate‐Keeper in DNA Damage‐Dependent Transcriptional Regulation

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Active Hydrodynamic Theory of Euchromatin and Heterochromatin

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Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damagePreprint

Huang, Z., Luo, S., Wang, Z., Zhang, Z., Jiang, B., Nie, Q. H., & Zhang, J. (2024) · eLife · doi:10.7554/elife.100623.1 · Cited by 1

Defects in the DNA Damage Response of Patient-derived Endometriosis Stromal CellsPreprint

Cadle, K., Thomas, G., Schweiger, H. E., Menendez, J., Molinuevo, R., & Hinck, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.29.685406 · Cited by 1

The facilitates chromatin transcription (fact) complex as a novel target for the treatment of Neuroendocrine Prostate Cancer

Pasilio, P. J. E. (2022) · Queensland University of Technology · doi:10.5204/thesis.eprints.229973

DNA Excision Repairs and Implication on Human HealthPreprint

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Dynamic Backtracking Regulates Lesion Bypass by RNAPIIPreprint

Moore, G., Han, Z., Xu, J., Oh, J., Wang, D., Svejstrup, J. Q., & Rueda, D. (2022) · Research Square · doi:10.21203/rs.3.rs-2285216/v1

Réparations de l'ADN

Robert, J. (2023) · Elsevier eBooks · doi:10.1016/b978-2-294-77967-1.00016-4

Splicing inhibition as a post-transcriptional stress

Vanzyl, E. J. (2023) · Carleton University's Institutional Repository (MacOdrum Library, Carleton University) · doi:10.22215/etd/2023-15484

Identification of DNA repair gene signature and potential molecular subtypes in hepatocellular carcinoma

Wang, Y. (2023) · Open Journal of Clinical and Medical Case Reports · doi:10.52768/2379-1039/1991

Targeting transcriptional addiction in cutaneous melanoma

Cigrang, M. (2023) · theses.fr (ABES) · doi:10.70675/32a61798z3cd7z4cd8za2acza750367acaf5

Dynamique des modifications d'histones en réponse aux dommages à l'ADN : impact sur la ségrégation des dommages au cours de la division cellulaire

Ferrand, J. (2021) · theses.fr (ABES) · doi:10.70675/e7c1674fz4e05z4082z822fz714f0e046518

Additional file 2 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

Tu, Q., Liu, X., Yao, X., Li, R., Liu, G., Jiang, H., Li, K., Chen, Q., Huang, X., Chang, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21129973

Additional file 5 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

Tu, Q., Liu, X., Yao, X., Li, R., Liu, G., Jiang, H., Li, K., Chen, Q., Huang, X., Chang, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21129976

Additional file 3 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

Tu, Q., Liu, X., Yao, X., Li, R., Liu, G., Jiang, H., Li, K., Chen, Q., Huang, X., Chang, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21129974

Additional file 4 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

Tu, Q., Liu, X., Yao, X., Li, R., Liu, G., Jiang, H., Li, K., Chen, Q., Huang, X., Chang, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21129975

Nucleotide excision repair. Methods of determination the efficiency functioning

Popov, A. A., Petruseva, I. O., Naumenko, N. V., & Lavrik, O. I. (2023) · Biochemistry (Moscow) · doi:10.31857/s0320972523110155

Tango6 regulates HSPC proliferation and definitive haematopoiesis via Ikzf1 and Cmyb in caudal haematopoietic tissue

Liu, S., Feng, Z. J., Su, M., Liu, C., Xi, Y., Chen, H., Luo, L., Tian, X., Zhao, F., & Li, L. (2024) · Development · doi:10.1242/dev.202903

Bypass of Blocking Lesions by RNAPII Impairs the Transcriptional DNA Damage ResponsePreprint

Bañuelos, C. P., Caeiro, L. D., Cingaram, P. R., Beckedorff, F., Morey, L., Cortes, D. B., Shiekhattar, R., & Verdún, R. E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.28.651040

A cellular system to study responses to a collision between the transcription complex and a protein‐bound nick in the DNA template

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POLR2H Serves as a Novel Prognostic Biomarker Correlated with Immune Infiltration in Prostate Cancer

Han, A., Shen, L., Zhang, J., & Li, W. (2025) · Biochemical Genetics · doi:10.1007/s10528-025-11150-y

LSH-mediated resolution of R-loops mitigates transcription-replication conflicts to preserve genomic stability in prostate cancer cellsPreprint

Ni, K., Zhang, Y., Zheng, K. C., Huang, J., Xiong, N., Liang, R., Chen, Y., Jin, H., Hai, Y., Wang, L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.04.657812

Optimizing the comet assay to measure DNA damage and repair

Zheng, C. (2025) · Research Publications (Maastricht University) · doi:10.26481/dis.20250422cz

Targeting the COP9 signalosome overcomes platinum resistance in ovarian cancer through two distinct genome stability mechanismsPreprint

Lomonosova, E., Loeb, M., Rodriguez, K., van Biljon, L. N., Brill, J. D., Schab, A. M., Minett, M., Barron, J., Bittner, M., Park, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.04.668450

Stress-Induced Nuclear Import Governs Transcription Recovery after DNA DamagePreprint

Coin, F., Sandoz, J., Catez, P., Hannus, A., Brion, A., Donnio, L., Mari, P., Concordet, J., & Bergamin, E. (2025) · Research Square · doi:10.21203/rs.3.rs-7241921/v1

A nuclear trafficking checkpoint licenses resolution of RNA–DNA hybrids at stalled RNAPII to maintain genome stability under genotoxic stressPreprint

Sandoz, J., Capelli, C., Catez, P., Hannus, A., Brion, A., Donnio, L., Mari, P., Concordet, J., Bergamin, E., Compe, E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.13.670051

Consistent asymmetry in DNA damage artefacts across target regions in exome sequencing data

Medina, T. D., Bennett, D., & Seoighe, C. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf120

Exercise-induced DNA damage response and memory formation in micePreprint

Ricciardi, N. R., McCartan, R., Paz, J. L., Cao, H., Borja, C., Cherry, A., Baranov, A., Locklear, C. E., Wójcikowska, O., Zeier, Z. R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.26.678909

Mechanisms of Dysmyelination in Niemann-Pick Type C Disease

Kunkel, T. J. (2023) · Deep Blue (University of Michigan) · doi:10.7302/8224

Subtleties of the synergistic inhibition of Microcystis aeruginosa by L-lysine and a flow-through copper ionization cell: Insights from physiology and transcriptomics

Zhang, Y., Gao, Y., Hong, Y., Liang, M., & Xie, X. (2025) · Algal Research · doi:10.1016/j.algal.2025.104467

Additional file 2 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000769

Additional file 1 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M. C., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000766

From Jumping Genes to Domesticated Elements: The Human PGBD Family as a Model for DNA Transposon Evolution

Radscheit, K. (2023) · doi:10.17169/refubium-42598

Genetic basis of cardiometabolic disease in the Lyon Hypertensive rat

Clark, K. C. (2022) · Iowa Research Online (The University of Iowa) · doi:10.25820/etd.006742

Additional file 1 of RNA N6-methyladenosine reader IGF2BP3 regulates cell cycle and angiogenesis in colon cancer

Yang, Z., Wang, T., Wu, D., Min, Z., Tan, J., & Yu, B. (2020) · Figshare · doi:10.6084/m9.figshare.13024446

Additional file 3 of RNA N6-methyladenosine reader IGF2BP3 regulates cell cycle and angiogenesis in colon cancer

Yang, Z., Wang, T., Wu, D., Min, Z., Tan, J., & Yu, B. (2020) · Figshare · doi:10.6084/m9.figshare.13024452

Investigations of the UV-induced DNA damage response in human cells and zebrafish embryos

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Additional file 2 of Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism

Kupkova, K., Shetty, S. J., Haque, R., Petri, W. A., & Auble, D. (2021) · Figshare · doi:10.6084/m9.figshare.16683131

Additional file 3 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M. C., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000772

Additional file 1 of In vivo 5-ethynyluridine (EU) labelling detects reduced transcription in Purkinje cell degeneration mouse mutants, but can itself induce neurodegeneration

van’t Sant, L. J., White, J. J., Hoeijmakers, J. H. J., Vermeij, W. P., & Jaarsma, D. (2021) · Figshare · doi:10.6084/m9.figshare.14643022

Additional file 5 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M. C., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000778

Additional file 1 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

Tu, Q., Liu, X., Yao, X., Li, R., Liu, G., Jiang, H., Li, K., Chen, Q., Huang, X., Chang, Q., et al. (2022) · Figshare · doi:10.6084/m9.figshare.21129972

Additional file 4 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M. C., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000775

Additional file 2 of RNA N6-methyladenosine reader IGF2BP3 regulates cell cycle and angiogenesis in colon cancer

Yang, Z., Wang, T., Wu, D., Min, Z., Tan, J., & Yu, B. (2020) · Figshare · doi:10.6084/m9.figshare.13024449

Additional file 6 of Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

Chandrasekaran, V., Andersson, K., Erlandsson, M., Li, S., Olsson, T. N., Garcia-Bonete, M.-J., Malmhäll-Bah, E., Johansson, P., Katona, G., & Bokarewa, M. I. (2024) · Figshare · doi:10.6084/m9.figshare.27000781

eLife Assessment: Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

Gómez-Schiavon, M. (2026) · eLife · doi:10.7554/elife.100623.3.sa2

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

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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

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Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation

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Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches

Duan, M., Speer, R. M., Ulibarri, J., Liu, K. J., & Mao, P. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103126 · Cited by 54