DNA Repair最新文献

{"title":"RNF4 prevents genomic instability caused by chronic DNA under-replication","authors":"Marissa K. Oram ,&nbsp;Ryan M. Baxley ,&nbsp;Emily M. Simon ,&nbsp;Kevin Lin ,&nbsp;Ya-Chu Chang ,&nbsp;Liangjun Wang ,&nbsp;Chad L. Myers ,&nbsp;Anja-Katrin Bielinsky","doi":"10.1016/j.dnarep.2024.103646","DOIUrl":"10.1016/j.dnarep.2024.103646","url":null,"abstract":"<div><p>Eukaryotic genome stability is maintained by a complex and diverse set of molecular processes. One class of enzymes that promotes proper DNA repair, replication and cell cycle progression comprises small ubiquitin-like modifier (SUMO)-targeted E3 ligases, or STUbLs. Previously, we reported a role for the budding yeast STUbL synthetically lethal with <em>sgs1</em> (Slx) 5/8 in preventing G₂/M-phase arrest in a minichromosome maintenance protein 10 (Mcm10)-deficient model of replication stress. Here, we extend these studies to human cells, examining the requirement for the human STUbL RING finger protein 4 (RNF4) in <em>MCM10</em> mutant cancer cells. We find that MCM10 and RNF4 independently promote origin firing but regulate DNA synthesis epistatically and, unlike in yeast, the negative genetic interaction between <em>RNF4</em> and <em>MCM10</em> causes cells to accumulate in G₁-phase. When MCM10 is deficient, RNF4 prevents excessive DNA under-replication at hard-to-replicate regions that results in large DNA copy number alterations and severely reduced viability. Overall, our findings highlight that STUbLs participate in species-specific mechanisms to maintain genome stability, and that human RNF4 is required for origin activation in the presence of chronic replication stress.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"135 ","pages":"Article 103646"},"PeriodicalIF":3.8,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000223/pdfft?md5=840a8eb7861dd76a0526afd8e8da8b68&pid=1-s2.0-S1568786424000223-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716754","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":"DNA polymerase λ Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining","authors":"Andrea M. Kaminski ,&nbsp;Kishore K. Chiruvella ,&nbsp;Dale A. Ramsden ,&nbsp;Katarzyna Bebenek ,&nbsp;Thomas A. Kunkel ,&nbsp;Lars C. Pedersen","doi":"10.1016/j.dnarep.2024.103645","DOIUrl":"10.1016/j.dnarep.2024.103645","url":null,"abstract":"<div><p>DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from a second DSB end. In this way, they promote the NHEJ ligation step and minimize the sequence loss normally associated with this pathway. The two polymerases differ in cognate substrate, as Polλ is preferred when synthesis must be primed from a base-paired DSB end, while Polμ is required when synthesis must be primed from an unpaired DSB end. We generated a Polλ variant (Polλ^KGET) that retained canonical Polλ activity on a paired end—albeit with reduced incorporation fidelity. We recently discovered that the variant had unexpectedly acquired the activity previously unique to Polμ—synthesis from an unpaired primer terminus. Though the sidechains of the Loop1 region make no contact with the DNA substrate, Polλ^KGET Loop1 amino acid sequence is surprisingly essential for its unique activity during NHEJ. Taken together, these results underscore that the Loop1 region plays distinct roles in different Family X polymerases.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"136 ","pages":"Article 103645"},"PeriodicalIF":3.8,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000211/pdfft?md5=0b4d32848371b45daa42695817419cb2&pid=1-s2.0-S1568786424000211-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139661270","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":"Variants in the first methionine of RAD51C are homologous recombination proficient due to an alternative start site","authors":"Hayley L. Rein ,&nbsp;Kara A. Bernstein","doi":"10.1016/j.dnarep.2024.103644","DOIUrl":"10.1016/j.dnarep.2024.103644","url":null,"abstract":"<div><p>In the 20+ years since the discovery of RAD51C, scientists have been perplexed as to how missense variants in this tumor suppressor gene impacts its function and pathogenicity. With a strong connection to breast and ovarian cancer, classifying these variants as pathogenic or benign aids in the diagnosis and treatment of patients with RAD51C variants. In particular, variants at translational starts sites are disruptive as they prevent protein expression. These variants are often classified as pathogenic, unless an alternative translational start is shown to produce a functional isoform to rescue protein expression. In this study, we utilized the ribosome profiling database GWIPS-VIZ to identify two active translational start sites in human RAD51C at methionine one and methionine ten. This second translational start at methionine ten is both conserved in 97 % of mammals and is the sole translational start in 80 % of mammals. Missense variants at either methionine have been identified in 47 individuals, preventing expression from one of these two start sites. Therefore, we stably expressed both wildtype isoforms, as well as the RAD51C M1 and M10 variants in a <em>RAD51C</em> CRISPR/Cas9 knockout U2OS cell and compared their homologous recombination function. Surprisingly, we find that expression of human RAD51C from either start site can equivalently rescue homologous recombination of <em>RAD51C</em> CRISPR/Cas9 knockout U2OS cells through a sister chromatid recombination assay. Similarly, each of our <em>RAD51C</em> CRISPR/Cas9 KO cells stably complemented with RAD51C missense variants at either M1 or M10 are homologous recombination proficient. Together, our data demonstrate that RAD51C has two translational start sites and that variants in either methionine result in homologous recombination proficiency. With this critical discovery, individuals with variants at M1 will be more accurately informed of their cancer risk upon reclassification of these variants.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"135 ","pages":"Article 103644"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139661480","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":"Microglial inflammation in genome instability: A neurodegenerative perspective","authors":"Nina L. Maliar ,&nbsp;Emily J. Talbot ,&nbsp;Abigail R. Edwards ,&nbsp;Svetlana V. Khoronenkova","doi":"10.1016/j.dnarep.2024.103634","DOIUrl":"10.1016/j.dnarep.2024.103634","url":null,"abstract":"<div><p>The maintenance of genome stability is crucial for cell homeostasis and tissue integrity. Numerous human neuropathologies display chronic inflammation in the central nervous system, set against a backdrop of genome instability, implying a close interplay between the DNA damage and immune responses in the context of neurological disease. Dissecting the molecular mechanisms of this crosstalk is essential for holistic understanding of neuroinflammatory pathways in genome instability disorders. Non-neuronal cell types, specifically microglia, are major drivers of neuroinflammation in the central nervous system with neuro-protective and -toxic capabilities. Here, we discuss how persistent DNA damage affects microglial homeostasis, zooming in on the cytosolic DNA sensing cGAS-STING pathway and the downstream inflammatory response, which can drive neurotoxic outcomes in the context of genome instability.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"135 ","pages":"Article 103634"},"PeriodicalIF":3.8,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000107/pdfft?md5=ee2eb4fcd9d8c407669b6e8f72591602&pid=1-s2.0-S1568786424000107-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555880","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":"Loss of alkyladenine DNA glycosylase alters gene expression in the developing mouse brain and leads to reduced anxiety and improved memory","authors":"Diana L. Bordin ,&nbsp;Kayla Grooms ,&nbsp;Nicola P. Montaldo ,&nbsp;Sarah L. Fordyce Martin ,&nbsp;Pål Sætrom ,&nbsp;Leona D. Samson ,&nbsp;Magnar Bjørås ,&nbsp;Barbara van Loon","doi":"10.1016/j.dnarep.2024.103632","DOIUrl":"10.1016/j.dnarep.2024.103632","url":null,"abstract":"<div><p>Neurodevelopment is a tightly coordinated process, during which the genome is exposed to spectra of endogenous agents at different stages of differentiation. Emerging evidence indicates that DNA damage is an important feature of developing brain, tightly linked to gene expression and neuronal activity. Some of the most frequent DNA damage includes changes to DNA bases, which are recognized by DNA glycosylases and repaired through base excision repair (BER) pathway. The only mammalian DNA glycosylase able to remove frequent alkylated DNA based is alkyladenine DNA glycosylase (Aag, aka Mpg). We recently demonstrated that, besides its role in DNA repair, AAG affects expression of neurodevelopmental genes in human cells. Aag was further proposed to act as reader of epigenetic marks, including 5-hydroxymethylcytosine (5hmC), in the mouse brain. Despite the potential Aag involvement in the key brain processes, the impact of Aag loss on developing brain remains unknown. Here, by using Aag knockout (<em>Aag</em>^<em>-/-</em>) mice, we show that Aag absence leads to reduced DNA break levels, evident in lowered number of γH2AX foci in postnatal day 5 (P5) hippocampi. This is accompanied by changes in 5hmC signal intensity in different hippocampal regions. Transcriptome analysis of hippocampi and prefrontal cortex, at different developmental stages, indicates that lack of Aag alters gene expression, primarily of genes involved in regulation of response to stress. Across all developmental stages tested aldehyde dehydrogenase 2 (<em>Aldh2</em>) emerged as one of the most prominent genes deregulated in Aag-dependent manner. In line with the changes in hippocampal DNA damage levels and the gene expression, adult <em>Aag</em>^<em>-/-</em> mice exhibit altered behavior, evident in decreased anxiety levels determined in the Elevated Zero Maze and increased alternations in the Elevated T Maze tests. Taken together these results suggests that Aag has functions in modulation of genome dynamics during brain development, important for animal behavior.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"135 ","pages":"Article 103632"},"PeriodicalIF":3.8,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000089/pdfft?md5=dfe89041e60b27b790f705d233362d1d&pid=1-s2.0-S1568786424000089-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555955","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":"Single-molecule analysis of purified proteins and nuclear extracts: Insights from 8-oxoguanine glycosylase 1","authors":"Matthew A. Schaich ,&nbsp;Tyler M. Weaver ,&nbsp;Vera Roginskaya ,&nbsp;Bret D. Freudenthal ,&nbsp;Bennett Van Houten","doi":"10.1016/j.dnarep.2024.103625","DOIUrl":"https://doi.org/10.1016/j.dnarep.2024.103625","url":null,"abstract":"<div><p><span>By observing one molecule at a time, single-molecule studies can offer detailed insights about biomolecular processes including on rates, off rates, and diffusivity<span><span> of molecules on strands of DNA. A recent technological advance (Single-molecule Analysis of DNA-binding proteins from Nuclear Extracts, SMADNE) has lowered the barrier to entry for single-molecule studies, and single-molecule dynamics can now be determined directly out of nuclear extracts, providing information in an intermediate environment between purified proteins in isolation and the heterogeneity of a nucleus. To compare and contrast the single-molecule </span>DNA binding dynamics in nuclear extracts versus purified proteins, combined </span></span>optical tweezers<span><span> and fluorescence microscopy<span> experiments were performed with purified GFP-tagged 8-oxoguanine glycosylase 1 (OGG1), purified GFP-OGG1 spiked into nuclear extracts, and nuclear extracts from human cells overexpressing GFP-OGG1. We observed differences in undamaged DNA binding during DNA damage search in each of the three conditions. Purified GFP-OGG1 engaged undamaged DNA for a weighted average lifetime of 5.7 s and 21% of these events underwent DNA diffusion after binding. However, unlike other glycosylases studied by SMADNE, OGG1 does not bind non-damaged DNA efficiently in nuclear extracts. In contrast, GFP-OGG1 binding dynamics on DNA substrates containing oxidative damage were relatively similar in all three conditions, with the weighted average binding lifetimes varying from 2.2 s in nuclear extracts to 7.8 s with purified GFP-OGG1 in isolation. Finally, we compared the purified protein and nuclear extract approaches for a catalytically dead OGG1 variant (GFP-OGG1-K249Q). This variant greatly increased the binding lifetime for oxidative DNA damage, with the weighted average lifetime for GFP-OGG1–249Q in nuclear extracts at 15.4 s vs 10.7 s for the purified protein. SMADNE will provide a new window of observation into the behavior of </span></span>nucleic acid binding proteins only accessible by biophysicists trained in protein purification and protein labeling.</span></p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103625"},"PeriodicalIF":3.8,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479960","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":"Super-resolution GSDIM microscopy unveils distinct nanoscale characteristics of DNA repair foci under diverse genotoxic stress","authors":"Haibin Qian ,&nbsp;Audrey Margaretha Plat ,&nbsp;Ard Jonker ,&nbsp;Ron A. Hoebe ,&nbsp;Przemek Krawczyk","doi":"10.1016/j.dnarep.2024.103626","DOIUrl":"https://doi.org/10.1016/j.dnarep.2024.103626","url":null,"abstract":"<div><p>DNA double-strand breaks initiate the DNA damage response (DDR), leading to the accumulation of repair proteins at break sites and the formation of the-so-called foci. Various microscopy methods, such as wide-field, confocal, electron, and super-resolution microscopy, have been used to study these structures. However, the impact of different DNA-damaging agents on their (nano)structure remains unclear. Utilising GSDIM super-resolution microscopy, here we investigated the distribution of fluorescently tagged DDR proteins (53BP1, RNF168, MDC1) and γH2AX in U2OS cells treated with γ-irradiation, etoposide, cisplatin, or hydroxyurea. Our results revealed that both foci structure and their nanoscale ultrastructure, including foci size, nanocluster characteristics, fluorophore density and localisation, can be significantly altered by different inducing agents, even ones with similar mechanisms. Furthermore, distinct behaviours of DDR proteins were observed under the same treatment. These findings have implications for cancer treatment strategies involving these agents and provide insights into the nanoscale organisation of the DDR.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103626"},"PeriodicalIF":3.8,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000028/pdfft?md5=2ddabf3319ce7509625805c5a17233eb&pid=1-s2.0-S1568786424000028-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139473544","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":"Corrigendum to “Over-expression of miR-100 is responsible for the low-expression of ATM in the human glioma cell line: M059J” [DNA Repair 9 (2010) 1170-1175]","authors":"Wooi Loon Ng ,&nbsp;Dan Yan ,&nbsp;Xiangming Zhang ,&nbsp;Yin-Yuan Mo ,&nbsp;Ya Wang","doi":"10.1016/j.dnarep.2024.103631","DOIUrl":"https://doi.org/10.1016/j.dnarep.2024.103631","url":null,"abstract":"","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103631"},"PeriodicalIF":3.8,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000077/pdfft?md5=a81ddb7e080fa21f04762c7a28330eed&pid=1-s2.0-S1568786424000077-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139434129","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":"Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools","authors":"Arwa A. Abugable ,&nbsp;Sarah Antar ,&nbsp;Sherif F. El-Khamisy","doi":"10.1016/j.dnarep.2024.103629","DOIUrl":"10.1016/j.dnarep.2024.103629","url":null,"abstract":"<div><p>Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"135 ","pages":"Article 103629"},"PeriodicalIF":3.8,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786424000053/pdfft?md5=7bd73d969afccba3f01a54434887ef4b&pid=1-s2.0-S1568786424000053-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139460826","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":"Catalytic activity of OGG1 is impaired by Zinc deficiency","authors":"Priyanka Sharma ,&nbsp;Carmen P. Wong ,&nbsp;Emily Ho ,&nbsp;Harini Sampath","doi":"10.1016/j.dnarep.2024.103628","DOIUrl":"10.1016/j.dnarep.2024.103628","url":null,"abstract":"<div><p><span><span>Oxidative stress-induced DNA base modifications, if unrepaired, can increase </span>mutagenesis<span><span> and genomic instability<span>, ultimately leading to cell death. Cells predominantly use the base excision repair<span> (BER) pathway to repair oxidatively-induced non-helix distorting lesions. BER is initiated by DNA glycosylases, such as 8-oxoguanine DNA glycosylase (OGG1), which repairs oxidatively modified </span></span></span>guanine bases, including 7,8-dihydro-8-oxoguanine (8-oxoG) and ring-opened formamidopyrimidine lesions, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). The OGG1 protein contains a C2H2 zinc (Zn) finger DNA binding domain. However, the impact of dietary </span></span>Zn deficiency<span> on OGG1 catalytic activity has not been extensively studied. Zn is a common nutrient of concern with increasing age, and the prevalence of oxidative DNA damage is also concurrently increased during aging. Thus, understanding the potential regulation of OGG1 activity by Zn is clinically relevant. The present study investigates the impact of a range of Zn statuses, varying from severe Zn deficiency to exogenous Zn-supplementation, in the context of young and aged animals to determine the impact of dietary Zn-status on OGG1 activity and oxidative DNA damage in mice. Our findings suggest that nutritional Zn deficiency impairs OGG1 activity and function, without altering gene expression, and that aging further exacerbates these effects. These results have important implications for nutritional management of Zn during aging to mitigate age-associated DNA damage.</span></p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103628"},"PeriodicalIF":3.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139411989","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}