DNA Repair最新文献_第2页

Genetic analysis reveals a timing-dependent functional interplay between Polζ and Polη in translesion DNA synthesis upon UV damage 遗传分析揭示了在UV损伤下翻译DNA合成中Polζ和Polη之间的时间依赖功能相互作用。

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-24 DOI: 10.1016/j.dnarep.2025.103919

Mone Okuda, Minori Fujii, Ryotaro Kawasumi, Kouji Hirota

{"title":"Genetic analysis reveals a timing-dependent functional interplay between Polζ and Polη in translesion DNA synthesis upon UV damage","authors":"Mone Okuda, Minori Fujii, Ryotaro Kawasumi, Kouji Hirota","doi":"10.1016/j.dnarep.2025.103919","DOIUrl":"10.1016/j.dnarep.2025.103919","url":null,"abstract":"<div><div>Translesion DNA synthesis (TLS) plays a crucial role in restarting stalled replication at damaged templates. This process is facilitated by specialized DNA polymerases, such as Polη and Polζ, where Polη inserts nucleotides opposite the damaged template, and Polζ extends the primer following insertion. TLS occurring at the stalled replication fork is termed \"on-the-fly\" TLS, whereas TLS that fills gaps remaining after fork progression is referred to as \"post-replicative gap-filling\" TLS. However, the roles of Polη and Polζ in these two phases of TLS remain unclear. Here, we demonstrate the functional relationship between Polη and Polζ in these TLS pathways through genetic studies in human cells. We established <em>POLH</em><sup><em>−/−</em></sup>, <em>REV3L</em><sup><em>−/−</em></sup> (deficient in Polζ catalytic subunit, Rev3), and <em>POLH</em><sup><em>−/−</em></sup><em>/REV3L</em><sup><em>−/−</em></sup> cells from human TK6 cells and evaluated the sensitivity of these cell lines to ultraviolet (UV). We found that the loss of Polη in <em>REV3L</em><sup><em>−/−</em></sup> cells led to the synergistic increase of the UV sensitivity, accompanied by a marked rise in UV-induced chromosomal aberrations. However, such synergistic effects were not observed in the rate of replication fork stalling after UV damage in <em>POLH</em><sup><em>−/−</em></sup><em>/REV3L</em><sup><em>−/−</em></sup> cells. In marked contrast, the number of unrepaired gaps following UV irradiation was significantly increased in the double mutant. These findings suggest that Polη and Polζ function complementarily in promoting post-replicative gap-filling TLS while they act collaboratively in on-the-fly TLS. Our current genetic study in human cells revealed a previously unappreciated functional relationship between Polη and Polζ and showed the pivotal role of \"post-replicative gap-filling\" TLS in UV-tolerance.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103919"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145866906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cutting edge perspectives in genome maintenance XII 基因组维持的前沿观点。

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-24 DOI: 10.1016/j.dnarep.2025.103920

Penny Jeggo

引用次数: 0

A tale of two mechanisms: Clarification of the pathway for MBD4 catalyzed glycosidic bond cleavage using MD and QM/MM calculations 通过MD和QM/MM计算，阐明了MBD4催化糖苷键裂解的途径

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-19 DOI: 10.1016/j.dnarep.2025.103917

Dylan J. Nikkel, Stacey D. Wetmore

{"title":"A tale of two mechanisms: Clarification of the pathway for MBD4 catalyzed glycosidic bond cleavage using MD and QM/MM calculations","authors":"Dylan J. Nikkel, Stacey D. Wetmore","doi":"10.1016/j.dnarep.2025.103917","DOIUrl":"10.1016/j.dnarep.2025.103917","url":null,"abstract":"<div><div>DNA methylation to yield 5-methylcytosine (5mC) in CpG motifs plays a vital role in epigenetic regulation. However, deamination of 5mC results in canonical thymine (T) that requires methyl-CpG-binding domain protein 4 (MBD4) for repair. This important function has resulted in MBD4 being implicated in various human health disorders including MBD4-associated neoplasia syndrome and cancer resistance to 5-fluorouracil treatment. Nevertheless, the catalytic mechanism of MBD4 is poorly understood, with conflicting experimental observations resulting in multiple proposals. To provide atomic level structural details of the active site conformation and clarify the mechanistic pathway, this study uses a combination of adaptively biased molecular dynamics (abMD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations to map the MBD4 catalytic mechanism. Although our data indicate that the catalytic D560 residue is flexible in the active site, only one conformation facilitates 5mC excision. Despite some literature proposing the formation of a DNA−protein crosslinked intermediate, our modeling suggests catalysis is only viable through a deglycosylation mechanism that involves a water nucleophile attacking C1′ of T, with D560 activating the nucleophile and stabilizing the transition state and nucleobase departure facilitated by a network of hydrogen bonds. This proposal is fully consistent with experimental crystallographic, mutagenic, stereoscopic, and kinetic data, and aligns the MBD4 catalytic pathway with that characterized for several other monofunctional DNA glycosylases. By furthering our knowledge of MBD4 catalysis, this work will aid in the future development of treatments for MBD4-related genetic disorders and the rational design of transition state mimic inhibitors to enhance existing cancer therapies.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103917"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145837925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polymerase theta: Genome protection through regulated deployment 聚合酶theta：通过调控部署的基因组保护

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-16 DOI: 10.1016/j.dnarep.2025.103916

Chelsea M. Smith , Gaorav P. Gupta

{"title":"Polymerase theta: Genome protection through regulated deployment","authors":"Chelsea M. Smith , Gaorav P. Gupta","doi":"10.1016/j.dnarep.2025.103916","DOIUrl":"10.1016/j.dnarep.2025.103916","url":null,"abstract":"<div><div>DNA Polymerase theta (Polθ, gene name <em>POLQ</em>) is the central enzyme of theta-mediated end-joining (TMEJ), an intrinsically mutagenic DNA double-strand break (DSB) repair pathway. Polθ is broadly conserved across most metazoan and plant species, suggesting an essential yet incompletely understood role in genome maintenance. <em>POLQ</em>-deficient organisms are viable but often accumulate genomic aberrations, such as micronuclei and fragile site expression. In cancer, however, Polθ activity is often dysregulated, driving chromosomal rearrangements characteristic of TMEJ hyperactivity. The finding that some cancers are dependent on hyperactive TMEJ has positioned Polθ as a therapeutic target, particularly in tumors with homologous recombination deficiency. The dual nature of Polθ—as both a genome-preserving and genome-destabilizing factor—reflects the importance of damage context and multi-layered regulatory mechanisms that ensure its precise deployment in normal cells, while the loss of these regulatory controls may be prevalent in cancer. This review synthesizes current knowledge on the DNA damage contexts that require Polθ for repair and how Polθ activity is restricted to these contexts to prevent catastrophic genome rearrangements while also not interfering with error-free DNA repair.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103916"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145837926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Base excision repair and homologous recombination are required for prevention of a chronic DNA damage response in Saccharomyces cerevisiae 碱基切除修复和同源重组是预防酿酒酵母慢性DNA损伤反应所必需的。

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-16 DOI: 10.1016/j.dnarep.2025.103915

Yogesh Nepal , Sanjida Ahmed , Armand M. Berry , Anika Mahmood , Cory L. Holland , L. Kevin Lewis

{"title":"Base excision repair and homologous recombination are required for prevention of a chronic DNA damage response in Saccharomyces cerevisiae","authors":"Yogesh Nepal , Sanjida Ahmed , Armand M. Berry , Anika Mahmood , Cory L. Holland , L. Kevin Lewis","doi":"10.1016/j.dnarep.2025.103915","DOIUrl":"10.1016/j.dnarep.2025.103915","url":null,"abstract":"<div><div>The chromosomes within eukaryotic cells experience many types of damage that are generated naturally via endogenous processes. The specific pathways that are most critical for repair of such endogenously produced DNA lesions have not been identified. Previous work revealed that budding yeast mutants deficient in double-strand break repair exhibit a persistent DNA damage checkpoint response leading to chronically high levels of G<sub>2</sub> phase cells, even in the absence of exogenous damaging agents. In the current study yeast mutants deficient in each of the five major DNA repair pathways were tested separately for the high G<sub>2</sub> cell phenotype. Cells with reduced homologous recombination (HR) and base excision repair (BER), but not nucleotide excision repair, mismatch repair or nonhomologous end-joining, displayed high levels of large-budded G<sub>2</sub> cells. BER mutants exhibiting this phenotype included <em>apn1</em>, <em>apn2</em>, <em>ogg1</em>, <em>ung1</em>, <em>ntg1</em> and <em>ntg2</em> cells. The persistent stress response was abolished by inactivation of the checkpoint gene <em>RAD9</em>. Cell cycling aberrations were increased synergistically in severely BER-deficient <em>apn1 apn2</em> double mutants and strongly elevated in cells deficient in both HR and BER. <em>apn1 apn2 rad52</em> cells were inviable but could be partially rescued by inactivation of <em>UNG1</em>. Transcription of the damage-inducible <em>RNR3</em> (<em>DIN1</em>) gene was persistently activated in both BER and HR mutants. Like HR mutants, BER-deficient cells were larger in size and spent approximately three times longer in G<sub>2</sub> phase than wildtype cells. The results demonstrate that two pathways, HR and BER, are essential for repair of endogenously generated DNA lesions and prevention of a chronic cellular stress response.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103915"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient activity of uracil DNA glycosylase (UNG2) in proliferating cells requires binding to proliferating cell nuclear antigen (PCNA) and replication protein A (RPA) 尿嘧啶DNA糖基化酶（UNG2）在增殖细胞中的有效活性需要与增殖细胞核抗原（PCNA）和复制蛋白A （RPA）结合。

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-26 DOI: 10.1016/j.dnarep.2025.103918

Rashmi S. Kulkarni , Brian P. Weiser

{"title":"Efficient activity of uracil DNA glycosylase (UNG2) in proliferating cells requires binding to proliferating cell nuclear antigen (PCNA) and replication protein A (RPA)","authors":"Rashmi S. Kulkarni , Brian P. Weiser","doi":"10.1016/j.dnarep.2025.103918","DOIUrl":"10.1016/j.dnarep.2025.103918","url":null,"abstract":"<div><div>The compounds pemetrexed and 5-fluorodeoxyuridine (FdU) are widely used for cancer therapies and disrupt cell proliferation by inducing DNA damage and stressing DNA replication. The drugs disrupt pyrimidine nucleotide metabolism and promote the accumulation of uracil bases in genomic DNA, which are repaired by uracil DNA glycosylase (UNG2) and downstream base excision repair proteins. UNG2 interacts with Proliferating Cell Nuclear Antigen (PCNA) and Replication Protein A (RPA), which localize to the replication fork during DNA damage responses to orchestrate DNA repair. In this work, we tested whether UNG2 requires interaction with PCNA and RPA to repair DNA damage in a colorectal cancer model during treatment with pemetrexed or FdU. We genetically knocked out UNG2 in HT29 cells and engineered the cells to express UNG2 variants that cannot bind to PCNA or RPA. We found that eliminating UNG2 activity or disrupting its interaction with PCNA or RPA sensitized the cells to the DNA-damaging effects of pemetrexed and FdU. The ability of UNG2 to localize to stalled replication forks was impaired when the enzyme could not interact with PCNA or RPA. Finally, disrupting the interaction of UNG2 with PCNA or RPA sensitized the cells to the cytotoxicity of the drugs. We concluded that certain cancers may be sensitized to pemetrexed and FdU by directly inhibiting the enzymatic activity of UNG2, by depleting UNG2 levels in the cell, or by impairing UNG2 function by inhibiting its protein-protein interactions.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103918"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145866942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contents of previous 3 special issues in this series of perspectives 本系列专题前3期的内容

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-28 DOI: 10.1016/j.dnarep.2025.103921

Penny Jeggo

引用次数: 0

Stepwise DNA damage and repair mechanisms at replication forks in response to topoisomerase I inhibition 拓扑异构酶I抑制对复制叉的逐步DNA损伤和修复机制的影响

IF 2.7 3区生物学

DNA Repair Pub Date : 2026-01-01 Epub Date: 2025-12-11 DOI: 10.1016/j.dnarep.2025.103914

Sofie Østergård Bæk , Kristina Keuper , Giacomo Milletti , Alba Adelantado-Rubio , Michael Lisby , Jiri Bartek , Christoffel Dinant , Apolinar Maya-Mendoza

{"title":"Stepwise DNA damage and repair mechanisms at replication forks in response to topoisomerase I inhibition","authors":"Sofie Østergård Bæk , Kristina Keuper , Giacomo Milletti , Alba Adelantado-Rubio , Michael Lisby , Jiri Bartek , Christoffel Dinant , Apolinar Maya-Mendoza","doi":"10.1016/j.dnarep.2025.103914","DOIUrl":"10.1016/j.dnarep.2025.103914","url":null,"abstract":"<div><div>Camptothecin (CPT) and its derivative irinotecan inhibit DNA topoisomerase I (TOP1), inducing replication stress by stabilizing the TOP1 cleavage complex. This prevents DNA re-ligation, resulting in single-stranded breaks that, if unresolved, can cause DNA replication fork collapse and double-stranded breaks. Cells respond to TOP1 inhibitors through homologous recombination (HR) repair and fork protection, with RAD51 playing a central role. However, the full mechanisms of how cells react to TOP1 inhibitors are not fully understood. Here, we systematically investigated cellular responses to TOP1 inhibitors, assessing the effects on DNA damage repair (DDR), replication, and cell viability. Using state-of-the-art quantitative image-based cytometry and single-molecule analyses, we reveal a dose and time-dependent mechanistic switch in DDR pathways, which differentially affects DNA replication. While the replication forks arrest after minutes in the presence of CPT, unexpectedly, after two hours of CPT exposure, the fork speed is faster than in the controls. Furthermore, we explain some of the contrasting effects of the replication fork dynamics and DDR activation triggered by TOP1 inhibition. Finally, we identify cancer genetic vulnerabilities, such as HR deficiency, that may be exploitable with low-dose TOP1 inhibitors.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"157 ","pages":"Article 103914"},"PeriodicalIF":2.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145754011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How DNA secondary structures drive replication fork instability DNA二级结构如何驱动复制叉的不稳定性。

IF 2.7 3区生物学

DNA Repair Pub Date : 2025-12-01 Epub Date: 2025-12-05 DOI: 10.1016/j.dnarep.2025.103913

Aditya Sethi , María Fernández-Casañas , Billie Delpino , Gideon Coster

{"title":"How DNA secondary structures drive replication fork instability","authors":"Aditya Sethi , María Fernández-Casañas , Billie Delpino , Gideon Coster","doi":"10.1016/j.dnarep.2025.103913","DOIUrl":"10.1016/j.dnarep.2025.103913","url":null,"abstract":"<div><div>DNA secondary structures, such as hairpins, cruciforms, triplexes, G-quadruplexes and iMotifs, are common, dynamic features that replication forks routinely encounter. However, how these structures destabilise the replication fork remains unclear. Here, we propose a framework describing the immediate consequences of replication forks encountering DNA secondary structures. This review considers outcomes according to the affected strand (leading or lagging) and the timing of structure formation, linking strand geometry and folding dynamics to replisome behaviour. Stable, pre-formed structures on the leading strand template either impede, or are bypassed by, the CMG (CDC45-MCM-GINS) helicase, frequently leaving single-stranded DNA (ssDNA) gaps. Leading strand structures inhibit DNA polymerase ε (Pol ε), induce fork uncoupling, again producing post-replicative ssDNA gaps which can channel into fork reversal or PrimPol-dependent repriming. Lagging strand template structures inhibit DNA polymerase δ (Pol δ) and structures on 5′ flaps impair Okazaki fragment maturation (OFM); both impediments yield ssDNA nicks or gaps. In each case, replication protein A (RPA) availability and the replication checkpoint define a tolerance window and coordinate hand-offs to accessory helicases, Pol δ strand displacement synthesis, and translesion synthesis (TLS). Immediate double-strand breaks (DSBs) are unlikely as an immediate consequence. Instead, we propose strand-specific ssDNA gaps predominate and may later be converted into DSBs during late S/G2 processing, mitosis, or the next S phase. This review integrates mechanisms to connect structure dynamics with fork responses and downstream ssDNA gaps and breaks, providing possible models of structure-induced genome instability.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"156 ","pages":"Article 103913"},"PeriodicalIF":2.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145727788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent advances in understanding the molecular mechanisms of SLX4 recruitment in the replication stress response SLX4在复制应激反应中募集的分子机制研究进展

IF 2.7 3区生物学

DNA Repair Pub Date : 2025-12-01 Epub Date: 2025-11-19 DOI: 10.1016/j.dnarep.2025.103911

Takuma Okano , Minoru Takata , Masatoshi Fujita , Yoko Katsuki

{"title":"Recent advances in understanding the molecular mechanisms of SLX4 recruitment in the replication stress response","authors":"Takuma Okano , Minoru Takata , Masatoshi Fujita , Yoko Katsuki","doi":"10.1016/j.dnarep.2025.103911","DOIUrl":"10.1016/j.dnarep.2025.103911","url":null,"abstract":"<div><div>Although DNA replication is tightly regulated, various impediments can stall DNA replication forks. SLX4 is a scaffold protein that responds to different types of replication stress. While the yeast Slx4 interacts mainly with structure-specific endonucleases, mammalian SLX4 collaborates with not only such nucleases but also a telomere-binding factor, a DNA helicase, and DNA repair proteins to resolve a variety of DNA intermediates arising from replication stress, thereby maintaining genome stability. Since SLX4 was identified as a causative gene for Fanconi anemia in humans, with UBZ4 domain–deleting mutation observed in a few patients, the UBZ4 domains have been highlighted as a key determinant for its recruitment to stalled forks, which has attracted considerable attention. While several studies have advanced our understanding of how SLX4 is recruited under distinct replication stresses, the precise details and context-specific regulation remain incompletely understood. In this review, we summarize what is currently known about SLX4, including its interactions with partner proteins and its roles under different types of replication stress. We also discuss the molecular basis of its recruitment to stalled forks, with particular emphasis on recent advances in understanding the contributions of the ubiquitin-binding zinc finger type 4 (UBZ4) domains and the SUMO-interacting motif (SIM) in the DNA replication stress response.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"156 ","pages":"Article 103911"},"PeriodicalIF":2.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145672993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0