Pub Date : 2025-02-01DOI: 10.1016/j.dnarep.2025.103809
Yixuan Gao , Lisa McPherson , Shanthi Adimoolam , Samyuktha Suresh , David L. Wilson , Ishani Das , Elizabeth R. Park , Christine S.C. Ng , Yong Woong Jun , James M. Ford , Eric T. Kool
A potentially promising approach to targeted cancer prevention in genetically at-risk populations is the pharmacological upregulation of DNA repair pathways. SMUG1 is a base excision repair enzyme that ameliorates adverse genotoxic and mutagenic effects of hydrolytic and oxidative damage to pyrimidines. Here we describe the discovery and initial cellular activity of a small-molecule activator of SMUG1. Screening of a kinase inhibitor library and iterative rounds of structure-activity relationship studies produced compound 40 (SU0547), which activates SMUG1 by as much as 350 ± 60 % in vitro at 100 nM, with an AC50 of 4.3 ± 1.1 µM. To investigate the effect of compound 40 on endogenous SMUG1, we performed in vitro cell-based experiments with 5-hydroxymethyl-2’-deoxyuridine (5-hmdU), a pyrimidine oxidation product that is selectively removed by SMUG1. In several human cell lines, compound 40 at 3–5 µM significantly reduces the cytotoxicity of 5-hmdU and decreases levels of double-strand breaks induced by the damaged nucleoside. We conclude that the SMUG1 activator compound 40 is a useful tool to study the mechanisms of 5-hmdU toxicity and the potentially beneficial effects of suppressing damage to pyrimidines in cellular DNA.
{"title":"Small-molecule activator of SMUG1 enhances repair of pyrimidine lesions in DNA","authors":"Yixuan Gao , Lisa McPherson , Shanthi Adimoolam , Samyuktha Suresh , David L. Wilson , Ishani Das , Elizabeth R. Park , Christine S.C. Ng , Yong Woong Jun , James M. Ford , Eric T. Kool","doi":"10.1016/j.dnarep.2025.103809","DOIUrl":"10.1016/j.dnarep.2025.103809","url":null,"abstract":"<div><div>A potentially promising approach to targeted cancer prevention in genetically at-risk populations is the pharmacological upregulation of DNA repair pathways. SMUG1 is a base excision repair enzyme that ameliorates adverse genotoxic and mutagenic effects of hydrolytic and oxidative damage to pyrimidines. Here we describe the discovery and initial cellular activity of a small-molecule activator of SMUG1. Screening of a kinase inhibitor library and iterative rounds of structure-activity relationship studies produced compound <strong>40</strong> (SU0547), which activates SMUG1 by as much as 350 ± 60 % <em>in vitro</em> at 100 nM, with an AC<sub>50</sub> of 4.3 ± 1.1 µM. To investigate the effect of compound <strong>40</strong> on endogenous SMUG1, we performed <em>in vitro</em> cell-based experiments with 5-hydroxymethyl-2’-deoxyuridine (5-hmdU), a pyrimidine oxidation product that is selectively removed by SMUG1. In several human cell lines, compound <strong>40</strong> at 3–5 µM significantly reduces the cytotoxicity of 5-hmdU and decreases levels of double-strand breaks induced by the damaged nucleoside. We conclude that the SMUG1 activator compound <strong>40</strong> is a useful tool to study the mechanisms of 5-hmdU toxicity and the potentially beneficial effects of suppressing damage to pyrimidines in cellular DNA.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"146 ","pages":"Article 103809"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070379","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}
Pub Date : 2025-02-01DOI: 10.1016/j.dnarep.2025.103814
Dillon E. King, William C. Copeland
Mitochondria contain their own small, circular genome that is present in high copy number. The mitochondrial genome (mtDNA) encodes essential subunits of the electron transport chain. Mutations in the mitochondrial genome are associated with a wide range of mitochondrial diseases and the maintenance and replication of mtDNA is crucial to cellular health. Despite the importance of maintaining mtDNA genomic integrity, fewer DNA repair pathways exist in the mitochondria than in the nucleus. However, mitochondria have numerous pathways that allow for the removal and degradation of DNA damage that may prevent accumulation of mutations. Here, we briefly review the DNA repair pathways present in the mitochondria, sources of mtDNA mutations, and discuss the passive role that mtDNA mutagenesis may play in cancer progression.
{"title":"DNA repair pathways in the mitochondria","authors":"Dillon E. King, William C. Copeland","doi":"10.1016/j.dnarep.2025.103814","DOIUrl":"10.1016/j.dnarep.2025.103814","url":null,"abstract":"<div><div>Mitochondria contain their own small, circular genome that is present in high copy number. The mitochondrial genome (mtDNA) encodes essential subunits of the electron transport chain. Mutations in the mitochondrial genome are associated with a wide range of mitochondrial diseases and the maintenance and replication of mtDNA is crucial to cellular health. Despite the importance of maintaining mtDNA genomic integrity, fewer DNA repair pathways exist in the mitochondria than in the nucleus. However, mitochondria have numerous pathways that allow for the removal and degradation of DNA damage that may prevent accumulation of mutations. Here, we briefly review the DNA repair pathways present in the mitochondria, sources of mtDNA mutations, and discuss the passive role that mtDNA mutagenesis may play in cancer progression.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"146 ","pages":"Article 103814"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143140725","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}
Pub Date : 2025-02-01DOI: 10.1016/j.dnarep.2025.103812
Artem P. Gureev, Veronika V. Nesterova, Irina S. Sadovnikova
Mitochondrial DNA (mtDNA) is often more susceptible to damage compared to nuclear DNA. This is due to its localization in the mitochondrial matrix, where a large portion of reactive oxygen species are produced. Mitochondria do not have histones and mtDNA is only slightly protected by histone-like proteins and is believed to have less efficient repair mechanisms. In this review, we discuss the long-range PCR method, which allows for the effective detection of mtDNA damage. The method is based on the assumption that various types of DNA lesions can interfere the progress of DNA polymerase, resulting in reduced amplification efficiency. It can be used to estimate the number of additional (above background) lesions in mtDNA. The review outlines the evolution of the methodology, its variations, applications in a wide range of model organisms, the advantages of the method and its limitations, as well as ways to overcome these limitations. Over the past two decades, the use of long-range PCR has allowed the study of mtDNA repair mechanisms, the characteristics of mitochondrial genome damage in various neurodegenerative diseases, aging, ischemic and oncological processes, as well as in anticancer therapy. The assessment of mtDNA damage has also been proposed for use in environmental biomonitoring. This review provides a critical evaluation of the various variations of this method, summarizes the accumulated data, and discusses the role of mtDNA damage in different organs at the organismal level.
{"title":"Long-range PCR as a tool for evaluating mitochondrial DNA damage: Principles, benefits, and limitations of the technique","authors":"Artem P. Gureev, Veronika V. Nesterova, Irina S. Sadovnikova","doi":"10.1016/j.dnarep.2025.103812","DOIUrl":"10.1016/j.dnarep.2025.103812","url":null,"abstract":"<div><div>Mitochondrial DNA (mtDNA) is often more susceptible to damage compared to nuclear DNA. This is due to its localization in the mitochondrial matrix, where a large portion of reactive oxygen species are produced. Mitochondria do not have histones and mtDNA is only slightly protected by histone-like proteins and is believed to have less efficient repair mechanisms. In this review, we discuss the long-range PCR method, which allows for the effective detection of mtDNA damage. The method is based on the assumption that various types of DNA lesions can interfere the progress of DNA polymerase, resulting in reduced amplification efficiency. It can be used to estimate the number of additional (above background) lesions in mtDNA. The review outlines the evolution of the methodology, its variations, applications in a wide range of model organisms, the advantages of the method and its limitations, as well as ways to overcome these limitations. Over the past two decades, the use of long-range PCR has allowed the study of mtDNA repair mechanisms, the characteristics of mitochondrial genome damage in various neurodegenerative diseases, aging, ischemic and oncological processes, as well as in anticancer therapy. The assessment of mtDNA damage has also been proposed for use in environmental biomonitoring. This review provides a critical evaluation of the various variations of this method, summarizes the accumulated data, and discusses the role of mtDNA damage in different organs at the organismal level.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"146 ","pages":"Article 103812"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030488","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}
Pub Date : 2025-01-01DOI: 10.1016/j.dnarep.2024.103801
Michelle C. Chirinos-Arias , Claudia P. Spampinato
The MSH7 protein is a binding partner of MSH2 forming the MutSγ complex. This complex contributes to the plant mismatch repair (MMR) system by recognizing DNA base-base mismatches. Here, we evaluated the impact of MSH7 on genetic diversity of the tenth generation (G10) of wild type and MSH7 deficient Arabidopsis thaliana plants before and after two days exposure to 100 mM NaCl. Genetic diversity was assessed using inter simple sequence repeats (ISSR) and high-resolution melting (HRM) analyses. ISSR analyses revealed a 6.7 % or 5.8 % average polymorphism in the G10 of wild type before and after a short-term salt stress, respectively, and a 64.4 % or 72.1 % average polymorphism in the G10 of msh7 mutant plants before and after salt treatment, respectively. Interestingly, several ISSR markers showed different polymorphism patterns after salt stress compared with the control before treatment. We next compared the percentage of the G10 of wild type and msh7 seedlings with polymorphic bands. Statistically significant differences between genotypes but not due to the salt treatment were observed. In addition, co-amplification at lower temperature-PCR followed by HRM analysis was performed. Of the five assayed HRM loci, two loci allowed the discrimination of fragment alleles between genotypes and two loci, between conditions. We conclude that MSH7 deficient A. thaliana mutants accumulated mutations over 10 generations, and that two days of salt stress caused a further increase in new mutations, thus enhancing genetic diversity that may favor new traits associated with stress tolerance, fitness, and adaptation.
MSH7蛋白是MSH2的结合伙伴，形成MutSγ复合物。该复合体通过识别DNA碱基错配来促进植物错配修复（MMR）系统。本研究评估了MSH7对野生型和MSH7缺失型拟南芥第10代（G10）植株在100 mM NaCl处理前后遗传多样性的影响。遗传多样性采用简单序列重复序列（ISSR）和高分辨率融化分析（HRM）进行评估。ISSR分析显示，短期盐胁迫前后野生型G10的平均多态性分别为6.7 %和5.8 %，盐胁迫前后msh7突变体植株G10的平均多态性分别为64.4 %和72.1 %。有趣的是，与处理前的对照相比，盐胁迫后的几个ISSR标记表现出不同的多态性模式。接下来，我们比较了野生型和msh7幼苗G10中多态带的百分比。基因型间差异有统计学意义，但与盐处理无关。此外，低温共扩增- pcr后进行HRM分析。在5个检测的HRM位点中，2个位点允许基因型之间的片段等位基因区分，2个位点允许条件之间的片段等位基因区分。我们得出结论，缺乏MSH7的拟南芥突变体在10代内积累了突变，并且两天的盐胁迫导致新突变进一步增加，从而增强了遗传多样性，可能有利于与耐受性、适应性和适应性相关的新性状。
{"title":"Spontaneous and salt stress-induced molecular instability in the progeny of MSH7 deficient Arabidopsis thaliana plants","authors":"Michelle C. Chirinos-Arias , Claudia P. Spampinato","doi":"10.1016/j.dnarep.2024.103801","DOIUrl":"10.1016/j.dnarep.2024.103801","url":null,"abstract":"<div><div>The MSH7 protein is a binding partner of MSH2 forming the MutSγ complex. This complex contributes to the plant mismatch repair (MMR) system by recognizing DNA base-base mismatches. Here, we evaluated the impact of MSH7 on genetic diversity of the tenth generation (G<sub>10</sub>) of wild type and MSH7 deficient <em>Arabidopsis thaliana</em> plants before and after two days exposure to 100 mM NaCl. Genetic diversity was assessed using inter simple sequence repeats (ISSR) and high-resolution melting (HRM) analyses. ISSR analyses revealed a 6.7 % or 5.8 % average polymorphism in the G<sub>10</sub> of wild type before and after a short-term salt stress, respectively, and a 64.4 % or 72.1 % average polymorphism in the G<sub>10</sub> of <em>msh7</em> mutant plants before and after salt treatment, respectively. Interestingly, several ISSR markers showed different polymorphism patterns after salt stress compared with the control before treatment. We next compared the percentage of the G<sub>10</sub> of wild type and <em>msh7</em> seedlings with polymorphic bands. Statistically significant differences between genotypes but not due to the salt treatment were observed. In addition, co-amplification at lower temperature-PCR followed by HRM analysis was performed. Of the five assayed HRM loci, two loci allowed the discrimination of fragment alleles between genotypes and two loci, between conditions. We conclude that MSH7 deficient <em>A. thaliana</em> mutants accumulated mutations over 10 generations, and that two days of salt stress caused a further increase in new mutations, thus enhancing genetic diversity that may favor new traits associated with stress tolerance, fitness, and adaptation.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103801"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866851","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}
Pub Date : 2025-01-01DOI: 10.1016/j.dnarep.2024.103802
Ralph Scully , Dominik Glodzik , Francesca Menghi , Edison T. Liu , Cheng-Zhong Zhang
Tandem duplications (TD) are among the most frequent type of structural variant (SV) in the cancer genome. They are characterized by a single breakpoint junction that defines the boundaries and the size of the duplicated segment. Cancer-associated TDs often increase oncogene copy number or disrupt tumor suppressor gene function, and thus have important roles in tumor evolution. TDs in cancer genomes fall into three classes, defined by the size of duplications, and are associated with distinct genetic drivers. In this review, we survey key features of cancer-related TDs and consider possible underlying mechanisms in relation to stressed DNA replication and the 3D organization of the S phase genome.
{"title":"Mechanisms of tandem duplication in the cancer genome","authors":"Ralph Scully , Dominik Glodzik , Francesca Menghi , Edison T. Liu , Cheng-Zhong Zhang","doi":"10.1016/j.dnarep.2024.103802","DOIUrl":"10.1016/j.dnarep.2024.103802","url":null,"abstract":"<div><div>Tandem duplications (TD) are among the most frequent type of structural variant (SV) in the cancer genome. They are characterized by a single breakpoint junction that defines the boundaries and the size of the duplicated segment. Cancer-associated TDs often increase oncogene copy number or disrupt tumor suppressor gene function, and thus have important roles in tumor evolution. TDs in cancer genomes fall into three classes, defined by the size of duplications, and are associated with distinct genetic drivers. In this review, we survey key features of cancer-related TDs and consider possible underlying mechanisms in relation to stressed DNA replication and the 3D organization of the S phase genome.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103802"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916516","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}
Pub Date : 2025-01-01DOI: 10.1016/j.dnarep.2024.103792
Sam S.H. Chu, Guangxin Xing, Vikash K. Jha , Hong Ling
Rad51 filaments are Rad51-coated single-stranded DNA and essential in homologous recombination (HR). The yeast Shu complex (Shu) is a conserved regulator of homologous recombination, working through its modulation on Rad51 filaments to direct HR-associated DNA damage response. However, the biochemical properties of Shu remain unclear, which hinders molecular insights into Shu’s role in HR and the DNA damage response. In this work, we biochemically characterized Shu and analyzed its molecular actions on single-stranded DNA and Rad51 filaments. First, we revealed that Shu preferentially binds fork-shaped DNA with 20nt ssDNA components. Then, we identified and validated, through site-specific mutagenesis, that Shu is an ATPase and hydrolyzes ATP in a DNA-dependent manner. Furthermore, we showed that Shu interacts with ssDNA and Rad51 filaments and alters the properties of ssDNA and the filaments with a 5′-3′ polarity. The alterations depend on the ATP hydrolysis of Shu, suggesting that the ATPase activity of Shu is important in regulating its functions. The preference of Shu for acting on the 5′ end of Rad51 filaments aligns with the observation that Shu promotes lesion bypass at the lagging strand of a replication fork. Our work on Shu, a prototype modulator of Rad51 filaments in eukaryotes, provides a general molecular mechanism for Rad51-mediated error-free DNA lesion bypass.
{"title":"The Shu complex is an ATPase that regulates Rad51 filaments during homologous recombination in the DNA damage response","authors":"Sam S.H. Chu, Guangxin Xing, Vikash K. Jha , Hong Ling","doi":"10.1016/j.dnarep.2024.103792","DOIUrl":"10.1016/j.dnarep.2024.103792","url":null,"abstract":"<div><div>Rad51 filaments are Rad51-coated single-stranded DNA and essential in homologous recombination (HR). The yeast Shu complex (Shu) is a conserved regulator of homologous recombination, working through its modulation on Rad51 filaments to direct HR-associated DNA damage response. However, the biochemical properties of Shu remain unclear, which hinders molecular insights into Shu’s role in HR and the DNA damage response. In this work, we biochemically characterized Shu and analyzed its molecular actions on single-stranded DNA and Rad51 filaments. First, we revealed that Shu preferentially binds fork-shaped DNA with 20nt ssDNA components. Then, we identified and validated, through site-specific mutagenesis, that Shu is an ATPase and hydrolyzes ATP in a DNA-dependent manner. Furthermore, we showed that Shu interacts with ssDNA and Rad51 filaments and alters the properties of ssDNA and the filaments with a 5′-3′ polarity. The alterations depend on the ATP hydrolysis of Shu, suggesting that the ATPase activity of Shu is important in regulating its functions. The preference of Shu for acting on the 5′ end of Rad51 filaments aligns with the observation that Shu promotes lesion bypass at the lagging strand of a replication fork. Our work on Shu, a prototype modulator of Rad51 filaments in eukaryotes, provides a general molecular mechanism for Rad51-mediated error-free DNA lesion bypass.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103792"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796722","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}
DNA double-strand breaks (DSBs) trigger the recruitment of repair protein and promote signal transduction through posttranslational modifications such as phosphorylation. After DSB induction, ataxia telangiectasia mutated (ATM) phosphorylates H2AX on chromatin surrounds the mega-base pairs proximal to the DSBs. Advanced super-resolution microscopic technology has demonstrated the formation of γH2AX nano foci as a unit of nano domain comprised of multiple nucleosomes. The formation of γH2AX nano foci could be potentially affected by pre-existing chromatin structure prior to DSB induction; however, it remains unclear whether chromatin status around DSBs influences the formation of γH2AX nano foci. In this study, to investigate γH2AX nano foci formation in the context of chromatin relaxation, γH2AX nano foci were examined following the depletion of MeCP2, which is a factor promoting chromatin condensation. Remarkably, by using super-resolution imaging analysis, we found that the volume of γH2AX nano foci cluster in MeCP2-depleted cells was significantly greater than that in control cells, both 5 and 30 min after ionizing radiation (IR). Corresponding to the increased volume size, the number of γH2AX nano foci per cluster was greater than that in control cells, while the distance of each nano focus within foci clusters remained unchanged. These findings suggest that relaxed chromatin condition by MeCP2 depletion facilitates faster and more extensive γH2AX nano foci formation after IR. Collectively, our super-resolution analysis suggests that the chromatin status surrounding DSBs influences the expansion of γH2AX nano foci formation, thus, potentially influencing the DSB repair and signaling.
{"title":"MeCP2 deficiency leads to the γH2AX nano foci expansion after ionizing radiation","authors":"Hikaru Okumura , Ryota Hayashi , Daiki Unami , Mayu Isono , Motohiro Yamauchi , Kensuke Otsuka , Yu Kato , Takahiro Oike , Yuki Uchihara , Atsushi Shibata","doi":"10.1016/j.dnarep.2024.103790","DOIUrl":"10.1016/j.dnarep.2024.103790","url":null,"abstract":"<div><div>DNA double-strand breaks (DSBs) trigger the recruitment of repair protein and promote signal transduction through posttranslational modifications such as phosphorylation. After DSB induction, ataxia telangiectasia mutated (ATM) phosphorylates H2AX on chromatin surrounds the mega-base pairs proximal to the DSBs. Advanced super-resolution microscopic technology has demonstrated the formation of γH2AX nano foci as a unit of nano domain comprised of multiple nucleosomes. The formation of γH2AX nano foci could be potentially affected by pre-existing chromatin structure prior to DSB induction; however, it remains unclear whether chromatin status around DSBs influences the formation of γH2AX nano foci. In this study, to investigate γH2AX nano foci formation in the context of chromatin relaxation, γH2AX nano foci were examined following the depletion of MeCP2, which is a factor promoting chromatin condensation. Remarkably, by using super-resolution imaging analysis, we found that the volume of γH2AX nano foci cluster in MeCP2-depleted cells was significantly greater than that in control cells, both 5 and 30 min after ionizing radiation (IR). Corresponding to the increased volume size, the number of γH2AX nano foci per cluster was greater than that in control cells, while the distance of each nano focus within foci clusters remained unchanged. These findings suggest that relaxed chromatin condition by MeCP2 depletion facilitates faster and more extensive γH2AX nano foci formation after IR. Collectively, our super-resolution analysis suggests that the chromatin status surrounding DSBs influences the expansion of γH2AX nano foci formation, thus, potentially influencing the DSB repair and signaling.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103790"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796703","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}
Pub Date : 2025-01-01DOI: 10.1016/j.dnarep.2024.103800
Christopher Parker , Adam C. Chambers , Dustin J. Flanagan , Jasmine Wing Yu Ho , Tracey J. Collard , Greg Ngo , Duncan M. Baird , Penny Timms , Rhys G. Morgan , Owen J. Sansom , Ann C. Williams
{"title":"Corrigendum to “BCL-3 loss sensitises colorectal cancer cells to DNA damage by targeting homologous recombination” [DNA Repair 115 (2022) 103331]","authors":"Christopher Parker , Adam C. Chambers , Dustin J. Flanagan , Jasmine Wing Yu Ho , Tracey J. Collard , Greg Ngo , Duncan M. Baird , Penny Timms , Rhys G. Morgan , Owen J. Sansom , Ann C. Williams","doi":"10.1016/j.dnarep.2024.103800","DOIUrl":"10.1016/j.dnarep.2024.103800","url":null,"abstract":"","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103800"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808892","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}
Most giant viruses including Mimiviridae family build large viral factories within the host cytoplasms. These giant viruses are presumed to possess specific genes that enable the rapid and massive replication of their large double-stranded DNA genomes within viral factories. It has been revealed that a functionally uncharacterized protein, MutS7, is expressed during the operational phase of the viral factory. MutS7 contains an N-terminal mismatched DNA-binding domain, which is similar to the mismatched DNA-recognizing protein MutS1, and a unique C-terminal HNH endonuclease domain absent in other MutS family proteins. MutS7 gene of the genus Mimivirus of the family Mimiviridae is encoded in the locus that is responsible for resistance against infection of a virophage. In the present study, we characterized the MutS7 HNH domain of Mimivirus shirakomae. The HNH domain preferentially bound to branched DNA structures containing single-stranded regions, especially the displacement-loop structure, which is a primary intermediate in homologous/homeologous recombination, rather than to linear DNAs and branched DNAs lacking single-stranded regions. However, the HNH domain exhibited no endonuclease activity. The site-directed mutagenesis analysis revealed that the Cys4-type zinc finger of the HNH domain was not essential, but was important for the DNA binding. Given that giant virus MutS7 contains a mismatch-binding domain in addition to the HNH domain, we propose that giant virus MutS7 may suppress homeologous recombination in the viral factory.
{"title":"The HNH endonuclease domain of the giant virus MutS7 specifically binds to branched DNA structures with single-stranded regions","authors":"Satoshi Yoshioka , Hirochika Kurazono , Koki Ohshita , Kenji Fukui , Masaharu Takemura , Shin-Ichiro Kato , Kouhei Ohnishi , Takato Yano , Taisuke Wakamatsu","doi":"10.1016/j.dnarep.2024.103804","DOIUrl":"10.1016/j.dnarep.2024.103804","url":null,"abstract":"<div><div>Most giant viruses including <em>Mimiviridae</em> family build large viral factories within the host cytoplasms. These giant viruses are presumed to possess specific genes that enable the rapid and massive replication of their large double-stranded DNA genomes within viral factories. It has been revealed that a functionally uncharacterized protein, MutS7, is expressed during the operational phase of the viral factory. MutS7 contains an N-terminal mismatched DNA-binding domain, which is similar to the mismatched DNA-recognizing protein MutS1, and a unique C-terminal HNH endonuclease domain absent in other MutS family proteins. MutS7 gene of the genus <em>Mimivirus</em> of the family <em>Mimiviridae</em> is encoded in the locus that is responsible for resistance against infection of a virophage. In the present study, we characterized the MutS7 HNH domain of <em>Mimivirus shirakomae.</em> The HNH domain preferentially bound to branched DNA structures containing single-stranded regions, especially the displacement-loop structure, which is a primary intermediate in homologous/homeologous recombination, rather than to linear DNAs and branched DNAs lacking single-stranded regions. However, the HNH domain exhibited no endonuclease activity. The site-directed mutagenesis analysis revealed that the Cys4-type zinc finger of the HNH domain was not essential, but was important for the DNA binding. Given that giant virus MutS7 contains a mismatch-binding domain in addition to the HNH domain, we propose that giant virus MutS7 may suppress homeologous recombination in the viral factory.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103804"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916525","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}
Pub Date : 2024-11-26DOI: 10.1016/j.dnarep.2024.103791
Hannah Trost , Felicia Wednesday Lopezcolorado , Arianna Merkell , Jeremy M. Stark
Repeat-mediated deletions (RMDs) are a type of deletion rearrangement that utilizes two repetitive elements to bridge a DNA double-strand break (DSB) that leads to loss of the intervening sequence and one of the repeats. Sequence divergence between repeats causes RMD suppression and indeed this divergence must be resolved in the RMD products. The mismatch repair factor, MLH1, was shown to be critical for both RMD suppression and a polarity of sequence divergence resolution in RMDs. Here, we sought to study the interrelationship between these two aspects of RMD regulation (i.e., RMD suppression and polar divergence resolution), by examining several mutants of MLH1 and its binding partner PMS2. To begin with, we show that PMS2 is also critical for both RMD suppression and polar resolution of sequence divergence in RMD products. Then, with six mutants of the MLH1-PMS2 heterodimer, we found several different patterns: three mutants showed defects in both functions, one mutant showed loss of RMD suppression but not polar divergence resolution, whereas another mutant showed the opposite, and finally one mutant showed loss of RMD suppression but had a complex effect on polar divergence resolution. These findings indicate that RMD suppression vs. polar resolution of sequence divergence are distinct functions of MLH1-PMS2.
{"title":"Functions of PMS2 and MLH1 important for regulation of divergent repeat-mediated deletions","authors":"Hannah Trost , Felicia Wednesday Lopezcolorado , Arianna Merkell , Jeremy M. Stark","doi":"10.1016/j.dnarep.2024.103791","DOIUrl":"10.1016/j.dnarep.2024.103791","url":null,"abstract":"<div><div>Repeat-mediated deletions (RMDs) are a type of deletion rearrangement that utilizes two repetitive elements to bridge a DNA double-strand break (DSB) that leads to loss of the intervening sequence and one of the repeats. Sequence divergence between repeats causes RMD suppression and indeed this divergence must be resolved in the RMD products. The mismatch repair factor, MLH1, was shown to be critical for both RMD suppression and a polarity of sequence divergence resolution in RMDs. Here, we sought to study the interrelationship between these two aspects of RMD regulation (i.e., RMD suppression and polar divergence resolution), by examining several mutants of MLH1 and its binding partner PMS2. To begin with, we show that PMS2 is also critical for both RMD suppression and polar resolution of sequence divergence in RMD products. Then, with six mutants of the MLH1-PMS2 heterodimer, we found several different patterns: three mutants showed defects in both functions, one mutant showed loss of RMD suppression but not polar divergence resolution, whereas another mutant showed the opposite, and finally one mutant showed loss of RMD suppression but had a complex effect on polar divergence resolution. These findings indicate that RMD suppression vs. polar resolution of sequence divergence are distinct functions of MLH1-PMS2.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"145 ","pages":"Article 103791"},"PeriodicalIF":3.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142743342","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号