DNA Repair最新文献

{"title":"How to write an ending: Telomere replication as a multistep process","authors":"Max E. Douglas","doi":"10.1016/j.dnarep.2024.103774","DOIUrl":"10.1016/j.dnarep.2024.103774","url":null,"abstract":"<div><div>Telomeres are protective nucleoprotein caps found at the natural ends of eukaryotic chromosomes and are crucial for the preservation of stable chromosomal structure. In cycling cells, telomeres are maintained by a multi-step process called telomere replication, which involves the eukaryotic replisome navigating a complex repetitive template tightly bound by specific proteins, before terminating at the chromosome end prior to a 5’ resection step that generates a protective 3’ overhang. In this review, we examine mechanistic aspects of the telomere replication process and consider how individual parts of this multistep event are integrated and coordinated with one-another.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103774"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483948","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}

{"title":"The flap endonuclease-1 mediated maturation of Okazaki fragments is critical for the cellular tolerance to remdesivir","authors":"Md Ratul Rahman,&nbsp;Ryotaro Kawasumi,&nbsp;Kouji Hirota","doi":"10.1016/j.dnarep.2024.103773","DOIUrl":"10.1016/j.dnarep.2024.103773","url":null,"abstract":"<div><div>Remdesivir is a 1’-cyano-modified adenine nucleotide analog used for the treatment of COVID-19. Recently, the anti-carcinogenic effect of remdesivir has been also identified in human cancers. However, the impact of this drug and the mechanisms underlying the cellular tolerance to remdesivir have not been elucidated. Here, we explored DNA repair pathways responsible for the cellular tolerance to remdesivir by monitoring the sensitivity of 24 mutant DT40 cells deficient in various DNA repair pathways. We found that cells deficient in FEN1 displayed the highest sensitivity against remdesivir. Since FEN1 contributes to base excision repair (BER), we measured the cellular sensitivity to remdesivir in mutants deficient in BER and found that other BER mutants such as <em>XRCC1</em>^{<em>−/−</em>} and <em>PARP1</em>^{<em>−/−</em>} cells are tolerant to remdesivir, indicating that FEN1 contributes to cellular tolerance to remdesivir through roles other than BER. We observed augmented DNA damage and acute cell cycle arrest at early S-phase after remdesivir treatment in <em>FEN1</em>^{<em>−/−</em>} cells. Moreover, the replication fork progression was significantly slowed by remdesivir in <em>FEN1</em>^{<em>−/−</em>} cells, indicating a direct involvement of FEN1 in replication fork progression when replication is challenged by remdesivir. Since FEN1 contributes to Okazaki fragment maturation (OFM), a process ligating Okazaki fragments generated during lagging strand synthesis, we analyzed the kinetics of the repair of single-strand breaks (SSBs) in nascent DNA. Strikingly, <em>FEN1</em>^{<em>−/−</em>} cells exhibited slowed kinetics in OFM, and remdesivir incorporation critically impaired this process in <em>FEN1</em>^{<em>−/−</em>} cells. These results indicate that remdesivir is preferentially incorporated in Okazaki fragments leading to the failure of Okazaki fragment maturation and FEN1 plays a critical role in suppressing remdesivir-mediated DNA damage through Okazaki fragment processing. Collectively, we revealed a previously unappreciated role of FEN1 in the cellular tolerance to remdesivir.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103773"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434414","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}

{"title":"UVSSA facilitates transcription-coupled repair of DNA interstrand crosslinks","authors":"Rowyn C. Liebau ,&nbsp;Crystal Waters ,&nbsp;Arooba Ahmed ,&nbsp;Rajesh K. Soni ,&nbsp;Jean Gautier","doi":"10.1016/j.dnarep.2024.103771","DOIUrl":"10.1016/j.dnarep.2024.103771","url":null,"abstract":"<div><div>DNA interstrand crosslinks (ICLs) are covalent bonds between bases on opposing strands of the DNA helix which prevent DNA melting and subsequent DNA replication or RNA transcription. Here, we show that Ultraviolet Stimulated Scaffold Protein A (UVSSA) is critical for ICL repair in human cells, at least in part via the transcription coupled ICL repair (TC-ICR) pathway. Inactivation of UVSSA sensitizes human cells to ICL-inducing drugs, and delays ICL repair. UVSSA is required for replication-independent repair of a single ICL in a fluorescence-based reporter assay. UVSSA localizes to chromatin following ICL damage, and interacts with transcribing Pol II, CSA, CSB, and TFIIH. Specifically, UVSSA interaction with TFIIH is required for ICL repair and transcription inhibition blocks localization of transcription coupled repair factors to ICL damaged chromatin. Finally, UVSSA expression positively correlates with ICL-based chemotherapy resistance in human cancer cell lines. Our data strongly suggest that UVSSA is a novel ICL repair factor functioning in TC-ICR. These results provide further evidence that TC-ICR is a <em>bona fide</em> ICL repair mechanism that contributes to crosslinker drug resistance independently of replication-coupled ICL repair.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103771"},"PeriodicalIF":3.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396247","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}

{"title":"Remdesivir triphosphate is a valid substrate to initiate synthesis of DNA primers by human PrimPol","authors":"Marcos Jiménez-Juliana,&nbsp;María I. Martínez-Jiménez,&nbsp;Luis Blanco","doi":"10.1016/j.dnarep.2024.103772","DOIUrl":"10.1016/j.dnarep.2024.103772","url":null,"abstract":"<div><div>Remdesivir is a broad-spectrum antiviral drug which has been approved to treat COVID-19. Remdesivir is in fact a prodrug, which is metabolized <em>in vivo</em> into the active form remdesivir triphosphate (<em>RTP</em>), an analogue of adenosine triphosphate (<em>ATP</em>) with a cyano group substitution in the carbon 1’ of the ribose (1’-CN). <em>RTP</em> is a substrate for RNA synthesis and can be easily incorporated by viral RNA-dependent RNA polymerases (RdRp). Importantly, once remdesivir is incorporated (now monophosphate), it will act as a delayed chain terminator, thus blocking viral RNA synthesis. It has been reported that mitochondrial Polγ is also blocked <em>in vitro</em> by <em>RTP</em>, but the low impact <em>in vivo</em> on mitochondrial DNA replication stalling is likely due to repriming by the human DNA-directed DNA Primase/Polymerase (<em>Hs</em>PrimPol), which also operates in mitochondria. In this work, we have tested if <em>RTP</em> is a valid substrate for both DNA primase and DNA polymerase activities of <em>Hs</em>PrimPol, and its impact in the production of mature DNA primers. <em>RTP</em> resulted to be an invalid substrate for elongation, but it can be used to initiate primers at the 5´site, competing with <em>ATP</em>. Nevertheless, <em>RTP</em>-initiated primers are abortive, ocassionally reaching a maximal length of 4–5 nucleotides, and do not support elongation mediated by primer/template distortions. However, considering that the concentration of <em>ATP</em>, the natural substrate, is much higher than the intracellular concentration of <em>RTP</em>, it is unlikely that <em>Hs</em>PrimPol would use <em>RTP</em> for primer synthesis during a remdesivir treatment in real patients.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103772"},"PeriodicalIF":3.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396246","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}

{"title":"Enhancing quantitative imaging to study DNA damage response: A guide to automated liquid handling and imaging","authors":"Calvin Shun Yu Lo ,&nbsp;Nitika Taneja ,&nbsp;Arnab Ray Chaudhuri","doi":"10.1016/j.dnarep.2024.103769","DOIUrl":"10.1016/j.dnarep.2024.103769","url":null,"abstract":"<div><div>Laboratory automation and quantitative high-content imaging are pivotal in advancing diverse scientific fields. These innovative techniques alleviate the burden of manual labour, facilitating large-scale experiments characterized by exceptional reproducibility. Nonetheless, the seamless integration of such systems continues to pose a constant challenge in many laboratories. Here, we present a meticulously designed workflow that automates the immunofluorescence staining process, coupled with quantitative high-content imaging to study DNA damage signalling as an example. This is achieved by using an automatic liquid handling system for sample preparation. Additionally, we also offer practical recommendations aimed at ensuring the reproducibility and scalability of experimental outcomes. We illustrate the high level of efficiency and reproducibility achieved through the implementation of the liquid handling system but also addresses the associated challenges. Furthermore, we extend the discussion into critical aspects such as microscope selection, optimal objective choices, and considerations for high-content image acquisition. Our study streamlines the image analysis process, offering valuable recommendations for efficient computing resources and the integration of cutting-edge deep learning techniques. Emphasizing the paramount importance of robust data management systems aligned with the FAIR data principles, we provide practical insights into suitable storage options and effective data visualization techniques. Together, our work serves as a comprehensive guide for life science laboratories seeking to elevate their high-content quantitative imaging capabilities through the seamless integration of advanced laboratory automation.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"144 ","pages":"Article 103769"},"PeriodicalIF":3.0,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434415","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}

{"title":"LncRNA LINC01664 promotes cancer resistance through facilitating homologous recombination-mediated DNA repair","authors":"Jie Du ,&nbsp;Fuqiang Chen ,&nbsp;Zihan Chen ,&nbsp;Wenna Zhao ,&nbsp;Jianyu Wang ,&nbsp;Meijuan Zhou","doi":"10.1016/j.dnarep.2024.103770","DOIUrl":"10.1016/j.dnarep.2024.103770","url":null,"abstract":"<div><div>The intracellular responses to DNA double-strand breaks (DSB) repair are crucial for genomic stability and play an essential role in cancer resistance. In addition to canonical DSB repair proteins, long non-coding RNAs (lncRNAs) have been found to be involved in this sophisticated network. In the present study, we performed a loss-of-function screen for a customized siRNA Premix Library to identify lncRNAs that participate in homologous recombination (HR) process. Among the candidates, we identified LINC01664 as a novel lncRNA required for HR repair. Furthermore, LINC01664 knockdown significantly increased the sensitivity of cancer cells to DNA damage agents such as ionizing radiation and genotoxic drugs. Mechanistically, LINC01664 interacted with Sirt1 promoter and then activated Sirt1 transcription, which contributed to HR-mediated DNA damage repair. In summary, our findings revealed a new mechanism of LINC01664 in DNA damage repair, providing evidence for a potential therapeutic strategy for eliminating the treatment bottlenecks caused by cancer resistance to chemotherapy and radiotherapy.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103770"},"PeriodicalIF":3.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome","authors":"Sarah A. Marks ,&nbsp;Zhi-Xiong Zhou ,&nbsp;Scott A. Lujan ,&nbsp;Adam B. Burkholder ,&nbsp;Thomas A. Kunkel","doi":"10.1016/j.dnarep.2024.103768","DOIUrl":"10.1016/j.dnarep.2024.103768","url":null,"abstract":"<div><div>We show that the rates of single base substitutions, additions, and deletions across the nuclear genome are strongly increased in a strain harboring a mutator variant of DNA polymerase α combined with a mutation that inactivates the 3´-5´ exonuclease activity of DNA polymerase δ. Moreover, tetrad dissections attempting to produce a haploid triple mutant lacking Msh6, which is essential for DNA mismatch repair (MMR) of base•base mismatches made during replication, result in tiny colonies that grow very slowly and appear to be aneuploid and/or defective in oxidative metabolism. These observations are consistent with the hypothesis that during initiation of nuclear DNA replication, single-base mismatches made by naturally exonuclease-deficient DNA polymerase α are extrinsically proofread by DNA polymerase δ, such that in the absence of this proofreading, the mutation rate is strongly elevated. Several implications of these data are discussed, including that the mutational signature of defective extrinsic proofreading in yeast could appear in human tumors.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"143 ","pages":"Article 103768"},"PeriodicalIF":3.0,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323313","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}

{"title":"Transcription reprogramming and endogenous DNA damage","authors":"Lei Li","doi":"10.1016/j.dnarep.2024.103754","DOIUrl":"10.1016/j.dnarep.2024.103754","url":null,"abstract":"<div><p>Transcription reprogramming is essential to carry out a variety of cell dynamics such as differentiation and stress response. During reprogramming of transcription, a number of adverse effects occur and potentially compromise genomic stability. Formaldehyde as an obligatory byproduct is generated in the nucleus via oxidative protein demethylation at regulatory regions, leading to the formation of DNA crosslinking damage. Elevated levels of transcription activities can result in the accumulation of unscheduled R-loop. DNA strand breaks can form if processed 5-methylcytosines are exercised by DNA glycosylase during imprint reversal. When cellular differentiation involves a large number of genes undergoing transcription reprogramming, these endogenous DNA lesions and damage-prone structures may pose a significant threat to genome stability. In this review, we discuss how DNA damage is formed during cellular differentiation, cellular mechanisms for their removal, and diseases associated with transcription reprogramming.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"142 ","pages":"Article 103754"},"PeriodicalIF":3.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130232","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}

{"title":"Structure, function and evolution of the HerA subfamily proteins","authors":"Yiyang Sun ,&nbsp;Kaiying Cheng","doi":"10.1016/j.dnarep.2024.103760","DOIUrl":"10.1016/j.dnarep.2024.103760","url":null,"abstract":"<div><p>HerA is an ATP-dependent translocase that is widely distributed in archaea and some bacteria. It belongs to the HerA/FtsK translocase bacterial family, which is a subdivision of the RecA family. Currently, it is identified that HerA participates in the repair of DNA double-strand breaks (DSBs) or confers anti-phage defense by assembling other proteins into large complexes. In recent years, there has been a growing understanding of the bioinformatics, biochemistry, structure, and function of HerA subfamily members in both archaea and bacteria. This comprehensive review compares the structural disparities among diverse HerAs and elucidates their respective roles in specific life processes.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"142 ","pages":"Article 103760"},"PeriodicalIF":3.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142137402","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}

{"title":"Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2","authors":"Dominic Johnson ,&nbsp;Rachal M. Allison ,&nbsp;Elda Cannavo ,&nbsp;Petr Cejka ,&nbsp;Jon A. Harper ,&nbsp;Matthew J. Neale","doi":"10.1016/j.dnarep.2024.103757","DOIUrl":"10.1016/j.dnarep.2024.103757","url":null,"abstract":"<div><p>Meiotic recombination is initiated by DNA double-strand breaks (DSBs) created by Spo11, a type-II topoisomerase-like protein that becomes covalently linked to DSB ends. Whilst Spo11 oligos—the products of nucleolytic removal by Mre11—have been detected in several organisms, the lifetime of the covalent Spo11-DSB precursor has not been determined and may be subject to alternative processing. Here, we explore the activity of human Tyrosyl DNA Phosphodiesterase, TDP2—a protein known to repair DNA ends arising from abortive topoisomerase activity—on Spo11 DSBs isolated from <em>S. cerevisiae</em> cells. We demonstrate that TDP2 can remove Spo11 peptides from ssDNA oligos and dsDNA ends even in the presence of competitor genomic DNA. Interestingly, TDP2-processed DSB ends are refractory to resection by Exo1, suggesting that ssDNA generated by Mre11 may be essential <em>in vivo</em> to facilitate HR at Spo11 DSBs even if TDP2 were active. Moreover, although TDP2 can remove Spo11 peptides <em>in vitro</em>, TDP2 expression in meiotic cells was unable to remove Spo11 <em>in vivo</em>—contrasting its ability to aid repair of topoisomerase-induced DNA lesions. These results suggest that Spo11-DNA, but not topoisomerase-DNA cleavage complexes, are inaccessible to the TDP2 enzyme, perhaps due to occlusion by higher-order protein complexes at sites of meiotic recombination.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"142 ","pages":"Article 103757"},"PeriodicalIF":3.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142137403","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}