DNA Repair最新文献

{"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}

{"title":"Ku80 is indispensable for repairing DNA double-strand breaks at highly methylated sites in human HCT116 cells","authors":"Mengtan Xing ,&nbsp;Yanhong Xiong ,&nbsp;Yong Zhang","doi":"10.1016/j.dnarep.2024.103627","DOIUrl":"10.1016/j.dnarep.2024.103627","url":null,"abstract":"<div><p><span>DNA<span><span> double-strand breaks (DSBs) are harmful to mammalian cells and a few of them can cause cell death. Accumulating DSBs in these cells to analyze their genomic distribution and their potential impact on </span>chromatin structure<span> is difficult. In this study, we used CRISPR to generate </span></span></span><span><em>Ku80</em></span>^<em>-/-</em><span> human cells and arrested the cells in G1 phase<span> to accumulate DSBs before conducting END-seq and Nanopore analysis. Our analysis revealed that DNA with high methylation level accumulates DSB hotspots in </span></span><em>Ku80</em>^<em>-/-</em> human cells. Furthermore, we identified chromosome structural variants (SVs) using Nanopore sequencing and observed a higher number of SVs in <em>Ku80</em>^<em>-/-</em> human cells. Based on our findings, we suggest that the high efficiency of <em>Ku80</em> knockout in human HCT116 cells makes it a promising model for characterizing SVs in the context of 3D chromatin structure and studying the alternative-end joining (Alt-EJ) DSB repair pathway.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103627"},"PeriodicalIF":3.8,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139375147","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":"DONSON: Slding in 2 the limelight","authors":"Grant S. Stewart","doi":"10.1016/j.dnarep.2023.103616","DOIUrl":"10.1016/j.dnarep.2023.103616","url":null,"abstract":"<div><p>For over a decade, it has been known that yeast Sld2, Dpb11, GINS and Polε form the pre-loading complex (pre-LC), which is recruited to a CDC45-bound MCM2–7 complex by the Sld3/Sld7 heterodimer in a phospho-dependent manner. Whilst functional orthologs of Dbp11 (TOPBP1), Sld3 (TICRR) and Sld7 (MTBP) have been identified in metazoans, controversy has surrounded the identity of the Sld2 ortholog. It was originally proposed that the RECQ helicase, RECQL4, which is mutated in Rothmund-Thomson syndrome, represented the closest vertebrate ortholog of Sld2 due to a small region of sequence homology at its N-Terminus. However, there is no clear evidence that RECQL4 is required for CMG loading. Recently, new findings suggest that the functional ortholog of Sld2 is actually DONSON, a replication fork stability factor mutated in a range of neurodevelopmental disorders characterised by microcephaly, short stature and limb abnormalities. These studies show that DONSON forms a complex with TOPBP1, GINS and Polε analogous to the pre-LC in yeast, which is required to position the GINS complex on the MCM complex and initiate DNA replication. Taken together with previously published functions for DONSON, these observations indicate that DONSON plays two roles in regulating DNA replication, one in promoting replication initiation and one in stabilising the fork during elongation. Combined, these findings may help to uncover why <em>DONSON</em> mutations are associated with such a wide range of clinical deficits.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103616"},"PeriodicalIF":3.8,"publicationDate":"2023-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786423001702/pdfft?md5=c2966d0d47839d24ad3047b6f06574c9&pid=1-s2.0-S1568786423001702-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139024061","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":"Biochemical analysis of H2O2-induced mutation spectra revealed that multiple damages were involved in the mutational process","authors":"Tomohiko Sugiyama ,&nbsp;Mahima R. Sanyal","doi":"10.1016/j.dnarep.2023.103617","DOIUrl":"10.1016/j.dnarep.2023.103617","url":null,"abstract":"<div><p>Reactive oxygen species (ROS) are a major threat to genomic integrity and believed to be one of the etiologies of cancers. Here we developed a cell-free system to analyze ROS-induced mutagenesis, in which DNA was exposed to H₂O₂ and then subjected to translesion DNA synthesis by various DNA polymerases. Then, frequencies of mutations on the DNA products were determined by using next-generation sequencing technology. The majority of observed mutations were either C&gt;A or G&gt;A, caused by dAMP insertion at G and C residues, respectively. These mutations showed similar spectra to COSMIC cancer mutational signature 18 and 36, which are proposed to be caused by ROS. The in vitro mutations can be produced by replicative DNA polymerases (yeast DNA polymerase δ and ε), suggesting that ordinary DNA replication is sufficient to produce them. Very little G&gt;A mutation was observed immediately after exposure to H₂O₂, but the frequency was increased during the 24 h <em>after</em> the ROS was removed, indicating that the initial oxidation product of cytosine needs to be maturated into a mutagenic lesion. Glycosylase-sensitivities of these mutations suggest that the C&gt;A were made on 8-oxoguanine or Fapy-guanine, and that G&gt;A were most likely made on 5-hydroxycytosine modification.</p></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103617"},"PeriodicalIF":3.8,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1568786423001714/pdfft?md5=00e86355fddb378636f4a48e12209041&pid=1-s2.0-S1568786423001714-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139022492","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":"Cutting Edge Perspectives in genome maintenance X","authors":"Penny Ann Jeggo","doi":"10.1016/j.dnarep.2023.103614","DOIUrl":"10.1016/j.dnarep.2023.103614","url":null,"abstract":"","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"134 ","pages":"Article 103614"},"PeriodicalIF":3.8,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138820611","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}