1
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Bai D, Cao Z, Attada N, Song J, Zhu C. Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability. Nat Methods 2025; 22:962-972. [PMID: 40128288 DOI: 10.1038/s41592-025-02632-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 02/18/2025] [Indexed: 03/26/2025]
Abstract
Maintenance of genome integrity is paramount to molecular programs in multicellular organisms. Throughout the lifespan, various endogenous and environmental factors pose persistent threats to the genome, which can result in DNA damage. Understanding the functional consequences of DNA damage requires investigating their preferred genomic distributions and influences on gene regulatory programs. However, such analysis is hindered by both the complex cell-type compositions within organs and the high background levels due to the stochasticity of damage formation. To address these challenges, we developed Paired-Damage-seq for joint analysis of oxidative and single-stranded DNA damage with gene expression in single cells. We applied this approach to cultured HeLa cells and the mouse brain as a proof of concept. Our results indicated the associations between damage formation and epigenetic changes. The distribution of oxidative DNA damage hotspots exhibits cell-type-specific patterns; this selective genome vulnerability, in turn, can predict cell types and dysregulated molecular programs that contribute to disease risks.
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Affiliation(s)
| | - Zhenkun Cao
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jinghui Song
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chenxu Zhu
- New York Genome Center, New York, NY, USA.
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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2
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Ji TT, Wang M, Guo X, Gang FY, Zhang S, Xiong J, Gu YH, Xie NB, Yuan BF. Glycosidase-Enabled Locus-Specific Detection of 8-Oxo-7,8-dihydroguanine in Genomes under Oxidative Stress. Anal Chem 2025; 97:8564-8573. [PMID: 40219948 DOI: 10.1021/acs.analchem.5c00632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2025]
Abstract
Oxidative DNA damage is closely linked to the onset of various age-related diseases. A significant oxidation product, 8-oxo-7,8-dihydroguanine (8OG), has been considered an important epigenetic-like marker in regulating gene expression. Accurately quantifying the locus-specific 8OG levels is crucial for understanding its functional roles in disease induction and gene regulation. In this study, we developed a glycosylase cleavage-mediated extension stalling (GCES) method for the locus-specific detection and quantification of 8OG in genomic DNA. This method utilizes the 8OG-DNA glycosylase Pab-AGOG, which induces single-strand breaks in DNA containing 8OG. The resulting cleavage is then assessed and quantified by using quantitative real-time PCR (qPCR). We successfully applied this strategy to evaluate locus-specific 8OG in synthesized DNA and genomic DNA from HEK293T, HeLa, and HepG2 cell lines under oxidative stress or triclosan treatment. The results demonstrate that the GCES method is accurate and suitable for the site-specific quantification of 8OG in both synthesized and genomic DNA from biological samples. We observed an increased level of 8OG in genomic DNA from biological samples treated with H2O2 or triclosan, indicating that both agents can elevate 8OG level in DNA. Overall, the GCES method provides a valuable, straightforward, and cost-effective tool for the quantitative detection of 8OG in DNA at base resolution, which facilitates the investigation of its functional roles as an epigenetic-like or DNA damage marker.
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Affiliation(s)
- Tong-Tong Ji
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, China
| | - Min Wang
- College of Chemical Engineering and Environmental Chemistry, Weifang University, Weifang 261061, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, China
| | - Fang-Yin Gang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Shan Zhang
- College of Chemistry and Molecular Sciences, Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, China
| | - Jun Xiong
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yao-Hua Gu
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Bi-Feng Yuan
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, China
- Hubei Provincial Center for Disease Control and Prevention & NHC Specialty Laboratory of Food Safety Risk Assessment and Standard Development, Wuhan 430079, China
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3
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Weaver TM, Ryan BJ, Thompson SH, Hussen AS, Spencer JJ, Xu Z, Schnicker NJ, Freudenthal BD. Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β. Nat Commun 2025; 16:2607. [PMID: 40097433 PMCID: PMC11914125 DOI: 10.1038/s41467-025-57915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 03/06/2025] [Indexed: 03/19/2025] Open
Abstract
Single-strand breaks (SSBs) are one of the most prevalent forms of DNA damage found in the chromatinized genome and are repaired by single-strand break repair (SSBR) or base excision repair (BER). DNA polymerase beta (Pol β) is the primary enzyme responsible for processing the 1-nt gap intermediate in chromatin during SSBR and BER. To date, the mechanism used by Pol β to process a 1-nt gap in the context of chromatin remains poorly understood. Here, we use biochemical assays and cryogenic electron microscopy (cryo-EM) to determine the kinetic and structural basis of gap-filling DNA synthesis in the nucleosome by Pol β. This work establishes that Pol β uses a global DNA sculpting mechanism for processing 1-nt gaps in the nucleosome during SSBR and BER, providing fundamental insight into DNA repair in chromatin.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Spencer H Thompson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Adil S Hussen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Jonah J Spencer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Zhen Xu
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS, 66160, USA.
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4
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Zewail-Foote M, del Mundo IMA, Klattenhoff AW, Vasquez KM. Oxidative damage within alternative DNA structures results in aberrant mutagenic processing. Nucleic Acids Res 2025; 53:gkaf066. [PMID: 39950343 PMCID: PMC11826088 DOI: 10.1093/nar/gkaf066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 01/21/2025] [Accepted: 01/25/2025] [Indexed: 02/17/2025] Open
Abstract
Genetic instability is a hallmark of cancer, and mutation hotspots in human cancer genomes co-localize with alternative DNA structure-forming sequences (e.g. H-DNA), implicating them in cancer etiology. H-DNA has been shown to stimulate genetic instability in mammals. Here, we demonstrate a new paradigm of genetic instability, where a cancer-associated H-DNA-forming sequence accumulates more oxidative lesions than B-DNA under conditions of oxidative stress (OS), often found in tumor microenvironments. We show that OS results in destabilization of the H-DNA structure and attenuates the fold increase in H-DNA-induced mutations over control B-DNA in mammalian cells. Furthermore, the mutation spectra revealed that the damaged H-DNA-containing region was processed differently compared to H-DNA in the absence of oxidative damage in mammalian cells. The oxidatively modified H-DNA elicits differential recruitment of DNA repair proteins from both the base excision repair and nucleotide excision repair mechanisms. Altogether, these results suggest a new model of genetic instability whereby H-DNA-forming regions are hotspots for DNA damage in oxidative microenvironments, resulting in its altered mutagenic processing. Our findings provide valuable insights into the role of OS in DNA structure-induced genetic instability and may establish H-DNA-forming sequences as promising genomic biomarkers and potential therapeutic targets for genetic diseases.
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Affiliation(s)
- Maha Zewail-Foote
- Department of Chemistry and Biochemistry, Southwestern University, 1001 E University Ave, Georgetown, TX 78626, United States
| | - Imee M A del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX 78723, United States
| | - Alex W Klattenhoff
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX 78723, United States
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX 78723, United States
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5
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Obermann T, Sakshaug T, Kanagaraj VV, Abentung A, Sousa MMLD, Hagen L, Sarno A, Bjørås M, Scheffler K. Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH. Redox Biol 2025; 79:103461. [PMID: 39662289 PMCID: PMC11697278 DOI: 10.1016/j.redox.2024.103461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/03/2024] [Accepted: 12/05/2024] [Indexed: 12/13/2024] Open
Abstract
8-oxo-7,8-dihydroguanine (OG) is one of the most abundant oxidative lesions in the genome and is associated with genome instability. Its mutagenic potential is counteracted by a concerted action of 8-oxoguanine DNA glycosylase (OGG1) and mutY homolog DNA glycosylase (MUTYH). It has been suggested that OG and its repair has epigenetic-like properties and mediates transcription, but genome-wide evidence of this interdependence is lacking. Here, we applied an improved OG-sequencing approach reducing artificial background oxidation and RNA-sequencing to correlate genome-wide distribution of OG with gene transcription in OGG1 and/or MUTYH-deficient cells. Our data identified moderate enrichment of OG in the genome that is mainly dependent on the genomic context and not affected by DNA glycosylase-initiated repair. Interestingly, no association was found between genomic OG deposition and gene expression changes upon loss of OGG1 and MUTYH. Regardless of DNA glycosylase activity, OG in promoter regions correlated with expression of genes related to metabolic processes and damage response pathways indicating that OG functions as a cellular stress sensor to regulate transcription. Our work provides novel insights into the mechanism underlying transcriptional regulation by OG and DNA glycosylases OGG1 and MUTYH and suggests that oxidative DNA damage accumulation and its repair utilize different pathways.
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Affiliation(s)
- Tobias Obermann
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Teri Sakshaug
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Vishnu Vignesh Kanagaraj
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Andreas Abentung
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, 7006, Trondheim, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491, Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway
| | - Katja Scheffler
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway; Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, 7006, Trondheim, Norway.
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6
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Detinis Zur T, Margalit S, Jeffet J, Grunwald A, Fishman S, Tulpová Z, Michaeli Y, Deek J, Ebenstein Y. Single-molecule toxicogenomics: Optical genome mapping of DNA-damage in nanochannel arrays. DNA Repair (Amst) 2025; 146:103808. [PMID: 39813882 DOI: 10.1016/j.dnarep.2025.103808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 11/19/2024] [Accepted: 01/08/2025] [Indexed: 01/18/2025]
Abstract
Quantitative genomic mapping of DNA damage may provide insights into the underlying mechanisms of damage and repair. Sequencing based approaches are bound to the limitations of PCR amplification bias and read length which hamper both the accurate quantitation of damage events and the ability to map them to structurally complex genomic regions. Optical Genome mapping in arrays of parallel nanochannels allows physical extension and genetic profiling of millions of long genomic DNA fragments, and has matured to clinical utility for characterization of complex structural aberrations in cancer genomes. Here we present a new mapping modality, Repair-Assisted Damage Detection - Optical Genome Mapping (RADD-OGM), a method for single-molecule level mapping of DNA damage on a genome-wide scale. Leveraging ultra-long reads to assemble the complex structure of a sarcoma cell-line genome, we mapped the genomic distribution of oxidative DNA damage, identifying regions more susceptible to DNA oxidation. We also investigated DNA repair by allowing cells to repair chemically induced DNA damage, pinpointing locations of concentrated repair activity, and highlighting variations in repair efficiency. Our results showcase the potential of the method for toxicogenomic studies, mapping the effect of DNA damaging agents such as drugs and radiation, as well as following specific DNA repair pathways by selective induction of DNA damage. The facile integration with optical genome mapping enables performing such analyses even in highly rearranged genomes such as those common in many cancers, a challenging task for sequencing-based approaches.
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Affiliation(s)
- Tahir Detinis Zur
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jonathan Jeffet
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Assaf Grunwald
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sivan Fishman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zuzana Tulpová
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Yael Michaeli
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jasline Deek
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel; Department of Biomedical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
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7
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Kubitschek J, Takhaveev V, Mingard C, Rochlitz M, Reinert P, Keller G, Kloter T, Fernández Cereijo R, Huber S, McKeague M, Sturla S. Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide. Nucleic Acids Res 2025; 53:gkae1320. [PMID: 39831306 PMCID: PMC11744188 DOI: 10.1093/nar/gkae1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 12/20/2024] [Accepted: 01/16/2025] [Indexed: 01/22/2025] Open
Abstract
Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. We analyzed O6-MeG formation and repair across sequence contexts and functional genomic regions in relation to MGMT expression in a glioblastoma-derived cell line. O6-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes. These data provide high resolution insight on how O6-MeG formation and repair are impacted by genome structure and nucleotide sequence. Further, O6-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.
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Affiliation(s)
- Jasmina Kubitschek
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Cécile Mingard
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Martha I Rochlitz
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Patricia B Reinert
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Giulia Keller
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Tom Kloter
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Raúl Fernández Cereijo
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Sabrina M Huber
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
- Department of Chemistry, Faculty of Science, McGill University, 801 Sherbrooke St. West, Montreal, QCH3A 0B8, Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, 3655 Prom. Sir William Osler, Montreal, QCH3G 1Y6, Canada
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
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8
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Delint-Ramirez I, Madabhushi R. DNA damage and its links to neuronal aging and degeneration. Neuron 2025; 113:7-28. [PMID: 39788088 PMCID: PMC11832075 DOI: 10.1016/j.neuron.2024.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 11/07/2024] [Accepted: 12/02/2024] [Indexed: 01/12/2025]
Abstract
DNA damage is a major risk factor for the decline of neuronal functions with age and in neurodegenerative diseases. While how DNA damage causes neurodegeneration is still being investigated, innovations over the past decade have provided significant insights into this issue. Breakthroughs in next-generation sequencing methods have begun to reveal the characteristics of neuronal DNA damage hotspots and the causes of DNA damage. Chromosome conformation capture-based approaches have shown that, while DNA damage and the ensuing cellular response alter chromatin topology, chromatin organization at damage sites also affects DNA repair outcomes in neurons. Additionally, neuronal activity results in the formation of programmed DNA breaks, which could burden DNA repair mechanisms and promote neuronal dysfunction. Finally, emerging evidence implicates DNA damage-induced inflammation as an important contributor to the age-related decline in neuronal functions. Together, these discoveries have ushered in a new understanding of the significance of genome maintenance for neuronal function.
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Affiliation(s)
- Ilse Delint-Ramirez
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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9
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Miller LG, Kim W, Schowe S, Taylor K, Han R, Jain V, Park R, Sherman M, Fang J, Ramirez H, Ellington A, Tamamis P, Resendiz MJE, Zhang YJ, Contreras L. Selective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation. Proc Natl Acad Sci U S A 2024; 121:e2317865121. [PMID: 39495922 PMCID: PMC11572968 DOI: 10.1073/pnas.2317865121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/15/2024] [Indexed: 11/06/2024] Open
Abstract
RNA oxidation, predominantly through the accumulation of 8-oxo-7,8-dihydroguanosine (8-oxo-rG), represents an important biomarker for cellular oxidative stress. Polynucleotide phosphorylase (PNPase) is a 3'-5' exoribonuclease that has been shown to preferentially recognize 8-oxo-rG-containing RNA and protect Escherichia coli cells from oxidative stress. However, the impact of 8-oxo-rG on PNPase-mediated RNA degradation has not been studied. Here, we show that the presence of 8-oxo-rG in RNA leads to catalytic stalling of E. coli PNPase through in vitro RNA degradation experiments and electrophoretic analysis. We also link this stalling to the active site of the enzyme through resolution of single-particle cryo-EM structures for PNPase in complex with singly or doubly oxidized RNA oligonucleotides. Following identification of Arg399 as a key residue in recognition of both single and sequential 8-oxo-rG nucleotides, we perform follow-up in vitro analysis to confirm the importance of this residue in 8-oxo-rG-specific PNPase stalling. Finally, we investigate the effects of mutations to active site residues implicated in 8-oxo-rG binding through E. coli cell growth experiments under H2O2-induced oxidative stress. Specifically, Arg399 mutations show significant effects on cell growth under oxidative stress. Overall, we demonstrate that 8-oxo-rG-specific stalling of PNPase is relevant to bacterial survival under oxidative stress and speculate that this enzyme might associate with other cellular factors to mediate this stress.
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Affiliation(s)
- Lucas G. Miller
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Shawn Schowe
- Department of Chemistry, University of Colorado Denver, Denver, CO80217
| | - Kathleen Taylor
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Vashita Jain
- Department of Chemistry, University of Colorado Denver, Denver, CO80217
| | - Raeyeon Park
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - Mark Sherman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
| | - Janssen Fang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
| | - Haydee Ramirez
- Department of Chemistry, University of Colorado Denver, Denver, CO80217
| | - Andrew Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX77840
| | | | - Y. Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX78712
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX78712
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10
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Weaver TM, Ryan BJ, Thompson SH, Hussen AS, Spencer JJ, Xu Z, Schnicker NJ, Freudenthal BD. Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.04.621902. [PMID: 39574623 PMCID: PMC11580861 DOI: 10.1101/2024.11.04.621902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2025]
Abstract
Single-strand breaks (SSBs) are one of the most prevalent forms of DNA damage found in the chromatinized genome and are repaired by direct single-strand break repair (SSBR) or base excision repair (BER). DNA polymerase beta (Pol β) is the primary enzyme responsible for processing the 1-nt gap intermediate in chromatin during SSBR and BER. However, the mechanism used by Pol β to process a 1-nt gap in the context of the nucleosome and chromatin remains poorly understood. Here, we use biochemical assays and cryogenic electron microscopy (cryo-EM) to determine the kinetic and structural basis of gap-filling DNA synthesis in the nucleosome by Pol β. Kinetic analysis identified that gap-filling DNA synthesis in the nucleosome by Pol β is position-dependent, where solvent exposed 1-nt gaps are processed more efficiently than histone-occluded 1-nt gaps. A series of cryo-EM structures of Pol β bound to a solvent-exposed 1-nt gap in the nucleosome reveal a global DNA sculpting mechanism for 1-nt gap recognition, which is mediated by sequential engagement of the Pol β lyase domain and polymerase domain. Finally, cryo-EM structures of Pol β bound to 1-nt gaps at two additional positions in the nucleosomal DNA define the structural basis for position-dependent nucleotide insertion in the nucleosome. This work establishes the mechanism used by Pol β for processing 1-nt gaps in the nucleosome during SSBR and BER, providing fundamental insight into DNA repair in chromatin.
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11
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Wang H, Tie W, Zhu W, Wang S, Zhang R, Duan J, Ye B, Zhu A, Li L. Recognition and Sequencing of Mutagenic DNA Adduct at Single-Base Resolution Through Unnatural Base Pair. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404622. [PMID: 39225557 PMCID: PMC11515917 DOI: 10.1002/advs.202404622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/06/2024] [Indexed: 09/04/2024]
Abstract
DNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging. In this paper, an unnatural-base-pair-promoting method for sequencing highly mutagenic ethenodeoxycytidine (εC) DNA lesions that occurred frequently is developed. First, a promising unnatural base pair of dεC-dNaM to recognize εC lesions is identified, and then a conversion PCR is developed to site-precise transfer dεC-dNaM to dTPT3-dNaM for convenient Sanger sequencing. The low sequence dependence of this method and its capacity for the enrichment of dεC in the abundance of as low as 1.6 × 10-6 nucleotides is also validated. Importantly, the current method can be smoothly applied for recognition, amplification, enrichment, and sequencing of the real biological samples in which εC lesions are generated in vitro or in vivo, thus offering the first sequencing methodology of εC lesions at single-base resolution. Owing to its simple operations and no destruction of inherent structures of DNA, the unnatural-base-pair strategy may provide a new platform to produce general tools for the sequencing of DNA lesions that are hardly sequenced by traditional strategies.
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Affiliation(s)
- Honglei Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Wenchao Tie
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Wuyuan Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Shuyuan Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Ruzhen Zhang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Jianlin Duan
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Bingyu Ye
- State Key Laboratory of Antiviral Drug and Pingyuan LabHenan Normal UniversityXinxiangHenan453007China
| | - Anlian Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Lingjun Li
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
- State Key Laboratory of Antiviral Drug and Pingyuan LabHenan Normal UniversityXinxiangHenan453007China
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringKey Laboratory of Green Chemical Media and ReactionsMinistry of EducationHenan Normal UniversityXinxiangHenan453007China
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12
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Cao M, Zhang X. DNA Adductomics: A Narrative Review of Its Development, Applications, and Future. Biomolecules 2024; 14:1173. [PMID: 39334939 PMCID: PMC11430648 DOI: 10.3390/biom14091173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/24/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
DNA adductomics is the global study of all DNA adducts and was first proposed in 2006 by the Matsuda group. Its development has been greatly credited to the advances in mass spectrometric techniques, particularly tandem and multiple-stage mass spectrometry. In fact, liquid chromatography-mass spectrometry (LC-MS)-based methods are virtually the sole technique with practicality for DNA adductomic studies to date. At present, DNA adductomics is primarily used as a tool to search for DNA adducts, known and unknown, providing evidence for exposure to exogenous genotoxins and/or for the molecular mechanisms of their genotoxicity. Some DNA adducts discovered in this way have the potential to predict cancer risks and/or to be associated with adverse health outcomes. DNA adductomics has been successfully used to identify and determine exogenous carcinogens that may contribute to the etiology of certain cancers, including bacterial genotoxins and an N-nitrosamine. Also using the DNA adductomic approach, multiple DNA adducts have been observed to show age dependence and may serve as aging biomarkers. These achievements highlight the capability and power of DNA adductomics in the studies of medicine, biological science, and environmental science. Nonetheless, DNA adductomics is still in its infancy, and great advances are expected in the future.
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Affiliation(s)
- Mengqiu Cao
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyu Zhang
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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13
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Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing unveils coordinated global transcription. Nature 2024; 631:216-223. [PMID: 38839954 PMCID: PMC11222150 DOI: 10.1038/s41586-024-07517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1,2. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations3. However, fundamental questions about the temporal regulation of transcription and enhancer-gene coordination remain unanswered, primarily because of the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq-a new single-cell nascent RNA sequencing assay that uses click chemistry-and unveil coordinated transcription throughout the genome. We demonstrate the episodic nature of transcription and the co-transcription of functionally related genes. scGRO-seq can estimate burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells and can leverage replication-dependent non-polyadenylated histone gene transcription to elucidate cell cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq enables the identification of networks of enhancers and genes. Our results suggest that the bursting of transcription at super-enhancers precedes bursting from associated genes. By imparting insights into the dynamic nature of global transcription and the origin and propagation of transcription signals, we demonstrate the ability of scGRO-seq to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
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Affiliation(s)
- Dig B Mahat
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathaniel D Tippens
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Sean K Waterton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiayu Fu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Sarah E Blatt
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Exact Sciences, Madison, WI, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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14
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Kong W, Zhao Y, Dai X, You C. Methodologies for the detection and sequencing of the epigenetic-like oxidative DNA modification, 8-oxo-7,8-dihydroguanine. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108516. [PMID: 39486616 DOI: 10.1016/j.mrrev.2024.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 10/26/2024] [Accepted: 10/27/2024] [Indexed: 11/04/2024]
Abstract
The human genome is constantly threatened by endogenous and environmental DNA damaging agents that can induce a variety of chemically modified DNA lesions including 8-oxo-7,8-dihydroguanine (OG). Increasing evidence has indicated that OG is not only a biomarker for oxidative DNA damage but also a novel epigenetic-like modification involved in regulation of gene expression in mammalian cells. Here we summarize the recent progress in OG research focusing on the following points: (i) the mechanism of OG production in organisms and its biological consequences in cells, (ii) the accurate identification of OG in low-abundance genomes and complex biological backgrounds, (iii) the development of OG sequencing methods. These studies will be helpful for further understanding of the molecular mechanisms of OG-induced mutagenesis and its potential roles in human development and diseases such as cancer.
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Affiliation(s)
- Weiheng Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China; College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
| | - Yingqi Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiaoxia Dai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Changjun You
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Molecular Science and Biomedicine Laboratory, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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15
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Gao S, Oden P, Ryan B, Yang H, Freudenthal B, Greenberg M. Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β. Nucleic Acids Res 2024; 52:5392-5405. [PMID: 38634780 PMCID: PMC11109955 DOI: 10.1093/nar/gkae277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
N6-(2-deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
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Affiliation(s)
- Shijun Gao
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Peyton N Oden
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, KS City, KS 66160, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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16
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Fleming AM, Guerra Castañaza Jenkins BL, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. J Am Chem Soc 2024; 146. [PMID: 38602473 PMCID: PMC11046481 DOI: 10.1021/jacs.4c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Molecular details for the impact of DNA damage on folding of potential G-quadruplex sequences (PQSs) to noncanonical DNA structures involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, termed a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest the formation of G4 motifs and demonstrated a folding dependency on the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | | | - Bethany A. Buck
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
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17
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
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.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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18
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Sugiyama T, Sanyal MR. Biochemical analysis of H 2O 2-induced mutation spectra revealed that multiple damages were involved in the mutational process. DNA Repair (Amst) 2024; 134:103617. [PMID: 38154332 PMCID: PMC10842480 DOI: 10.1016/j.dnarep.2023.103617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
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>A or G>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>A mutation was observed immediately after exposure to H2O2, but the frequency was increased during the 24 h after 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>A were made on 8-oxoguanine or Fapy-guanine, and that G>A were most likely made on 5-hydroxycytosine modification.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA.
| | - Mahima R Sanyal
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
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19
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Xu Q, del Mundo IMA, Zewail-Foote M, Luke BT, Vasquez KM, Kowalski J. MoCoLo: a testing framework for motif co-localization. Brief Bioinform 2024; 25:bbae019. [PMID: 38521050 PMCID: PMC10960634 DOI: 10.1093/bib/bbae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 03/25/2024] Open
Abstract
Sequence-level data offers insights into biological processes through the interaction of two or more genomic features from the same or different molecular data types. Within motifs, this interaction is often explored via the co-occurrence of feature genomic tracks using fixed-segments or analytical tests that respectively require window size determination and risk of false positives from over-simplified models. Moreover, methods for robustly examining the co-localization of genomic features, and thereby understanding their spatial interaction, have been elusive. We present a new analytical method for examining feature interaction by introducing the notion of reciprocal co-occurrence, define statistics to estimate it and hypotheses to test for it. Our approach leverages conditional motif co-occurrence events between features to infer their co-localization. Using reverse conditional probabilities and introducing a novel simulation approach that retains motif properties (e.g. length, guanine-content), our method further accounts for potential confounders in testing. As a proof-of-concept, motif co-localization (MoCoLo) confirmed the co-occurrence of histone markers in a breast cancer cell line. As a novel analysis, MoCoLo identified significant co-localization of oxidative DNA damage within non-B DNA-forming regions that significantly differed between non-B DNA structures. Altogether, these findings demonstrate the potential utility of MoCoLo for testing spatial interactions between genomic features via their co-localization.
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Affiliation(s)
- Qi Xu
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Imee M A del Mundo
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Maha Zewail-Foote
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Brian T Luke
- Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21701, USA
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
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20
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Fleming AM, Jenkins BLGC, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576387. [PMID: 38293204 PMCID: PMC10827223 DOI: 10.1101/2024.01.20.576387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular details for DNA damage impact on the folding of potential G-quadruplex sequences (PQS) to non-canonical DNA structures that are involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, referred to as a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and the G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H-NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest formation of G4 motifs, and demonstrated a folding dependency with the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | | | - Bethany A Buck
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
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21
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Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM. Biochemical and Structural Characterization of Fapy•dG Replication by Human DNA Polymerase β. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575758. [PMID: 38293220 PMCID: PMC10827042 DOI: 10.1101/2024.01.15.575758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
N6-(2-deoxy-α,β-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
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22
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Dong JH, Zhang RH, Zhao LL, Xue CY, Pan HY, Zhong XY, Zhou YL, Zhang XX. Identification and Quantification of Locus-Specific 8-Oxo-7,8-dihydroguanine in DNA at Ultrahigh Resolution Based on G-Triplex-Assisted Rolling Circle Amplification. Anal Chem 2024; 96:437-445. [PMID: 38150621 DOI: 10.1021/acs.analchem.3c04498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Damage of reactive oxygen species to various molecules such as DNA has been related to many chronic and degenerative human diseases, aging, and even cancer. 8-Oxo-7,8-dihydroguanine (OG), the most significant oxidation product of guanine (G), has become a biomarker of oxidative stress as well as gene regulation. The positive effect of OG in activating transcription and the negative effect in inducing mutation are a double-edged sword; thus, site-specific quantification is helpful to quickly reveal the functional mechanism of OG at hotspots. Due to the possible biological effects of OG at extremely low abundance in the genome, the monitoring of OG is vulnerable to signal interference from a large amount of G. Herein, based on rolling circle amplification-induced G-triplex formation and Thioflavin T fluorescence enhancement, an ultrasensitive strategy for locus-specific OG quantification was constructed. Owing to the difference in the hydrogen-bonding pattern between OG and G, the nonspecific background signal of G sites was completely suppressed through enzymatic ligation of DNA probes and the triggered specificity of rolling circle amplification. After the signal amplification strategy was optimized, the high detection sensitivity of OG sites with an ultralow detection limit of 0.18 amol was achieved. Under the interference of G sites, as little as 0.05% of OG-containing DNA was first distinguished. This method was further used for qualitative and quantitative monitoring of locus-specific OG in genomic DNA under oxidative stress and identification of key OG sites with biological function.
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Affiliation(s)
- Jia-Hui Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Run-Hong Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ling-Li Zhao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100191, China
| | - Hui-Yu Pan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Ying Zhong
- Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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23
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Liang Y, Yuan Q, Zheng Q, Mei Z, Song Y, Yan H, Yang J, Wu S, Yuan J, Wu W. DNA Damage Atlas: an atlas of DNA damage and repair. Nucleic Acids Res 2024; 52:D1218-D1226. [PMID: 37831087 PMCID: PMC10767978 DOI: 10.1093/nar/gkad845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/06/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
DNA damage and its improper repair are the major source of genomic alterations responsible for many human diseases, particularly cancer. To aid researchers in understanding the underlying mechanisms of genome instability, a number of genome-wide profiling approaches have been developed to monitor DNA damage and repair events. The rapid accumulation of published datasets underscores the critical necessity of a comprehensive database to curate sequencing data on DNA damage and repair intermediates. Here, we present DNA Damage Atlas (DDA, http://www.bioinformaticspa.com/DDA/), the first large-scale repository of DNA damage and repair information. Currently, DDA comprises 6,030 samples from 262 datasets by 59 technologies, covering 16 species, 10 types of damage and 135 treatments. Data collected in DDA was processed through a standardized workflow, including quality checks, hotspots identification and a series of feature characterization for the hotspots. Notably, DDA encompasses analyses of highly repetitive regions, ribosomal DNA and telomere. DDA offers a user-friendly interface that facilitates browsing, searching, genome browser visualization, hotspots comparison and data downloading, enabling convenient and thorough exploration for datasets of interest. In summary, DDA will stand as a valuable resource for research in genome instability and its association with diseases.
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Affiliation(s)
- Yu Liang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qingqing Yuan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qijie Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Zilv Mei
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yawei Song
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Huan Yan
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiajie Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Shuheng Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Jiao Yuan
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Wei Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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24
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Xiao S, Fleming AM, Burrows CJ. Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0. Chem Commun (Camb) 2023; 59:8997-9000. [PMID: 37401666 PMCID: PMC10909242 DOI: 10.1039/d3cc02699j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Oxidative damage to DNA nucleotides has many cellular outcomes that could be aided by the development of sequencing methods. Herein, the previously reported click-code-seq method for sequencing a single damage type is redeveloped to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0).
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
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25
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Laughery MF, Plummer DA, Wilson HE, Vandenberg BN, Mitchell D, Mieczkowski PA, Roberts SA, Wyrick JJ. Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries. Genetics 2023; 224:iyad086. [PMID: 37170598 PMCID: PMC10324949 DOI: 10.1093/genetics/iyad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.
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Affiliation(s)
- Marian F Laughery
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Brittany N Vandenberg
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Debra Mitchell
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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26
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Stanio S, Bacurio JHT, Yang H, Greenberg MM, Basu AK. 8-Oxo-2'-deoxyguanosine Replication in Mutational Hot Spot Sequences of the p53 Gene in Human Cells Is Less Mutagenic than That of the Corresponding Formamidopyrimidine. Chem Res Toxicol 2023; 36:782-789. [PMID: 37093780 PMCID: PMC10192040 DOI: 10.1021/acs.chemrestox.3c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo) is a ubiquitous DNA damage formed by oxidation of 2'-deoxyguanosine. In this study, plasmid DNA containing 8-OxodGuo located in three mutational hot spots of human cancers, codons 248, 249, and 273 of the Tp53 tumor suppressor gene, was replicated in HEK 293T cells. 8-OxodGuo was only a weak block of replication, and the bypass was largely error-free. The mutations (1-5%) were primarily G → T transversions, and the mutation frequency was generally lower than that of the chemically related Fapy·dG. A unique 8-OxodGuo mutation spectrum was observed at each site, as reflected by replication in translesion synthesis (TLS) polymerase- or hPol λ-deficient cells. In codon 248 (CG*G) and 249 (AG*G), where G* denotes 8-OxodGuo, hPol η and hPol ζ carried out largely error-free bypass of the lesion, whereas hPol κ and hPol ι were involved mostly in error-prone TLS, resulting in G → T mutations. 8-OxodGuo bypass in codon 273 (CG*T) was unlike the other two sites, as hPol κ participated in the mostly error-free bypass of the lesion. Yet, in all three sites, including codon 273, simultaneous deficiency of hpol κ and hPol ι resulted in reduction of G → T transversions. This indicates a convincing role of these two TLS polymerases in error-prone bypass of 8-OxodGuo. Although the dominant mutation was G → T in each site, in codon 249, and to a lesser extent in codon 248, significant semi-targeted single-base deletions also occurred, which suggests that 8-OxodGuo can initiate slippage of a base near the lesion site. This study underscores the importance of sequence context in 8-OxodGuo mutagenesis in human cells. It also provides a more comprehensive comparison between 8-OxodGuo and the sister lesion, Fapy·dG. The greater mutagenicity of the latter in the same sequence contexts indicates that Fapy·dG is a biologically significant lesion and biomarker on par with 8-OxodGuo.
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Affiliation(s)
- Stephen Stanio
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | | | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ashis K. Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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27
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Selvam K, Sivapragasam S, Poon GMK, Wyrick JJ. Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing. Nat Commun 2023; 14:2702. [PMID: 37169747 PMCID: PMC10175485 DOI: 10.1038/s41467-023-38265-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Sequencing of melanomas has identified hundreds of recurrent mutations in both coding and non-coding DNA. These include a number of well-characterized oncogenic driver mutations, such as coding mutations in the BRAF and NRAS oncogenes, and non-coding mutations in the promoter of telomerase reverse transcriptase (TERT). However, the molecular etiology and significance of most of these mutations is unknown. Here, we use a new method known as CPD-capture-seq to map UV-induced cyclobutane pyrimidine dimers (CPDs) with high sequencing depth and single nucleotide resolution at sites of recurrent mutations in melanoma. Our data reveal that many previously identified drivers and other recurrent mutations in melanoma occur at CPD hotspots in UV-irradiated melanocytes, often associated with an overlapping binding site of an E26 transformation-specific (ETS) transcription factor. In contrast, recurrent mutations in the promoters of a number of known or suspected cancer genes are not associated with elevated CPD levels. Our data indicate that a subset of recurrent protein-coding mutations are also likely caused by ETS-induced CPD hotspots. This analysis indicates that ETS proteins profoundly shape the mutation landscape of melanoma and reveals a method for distinguishing potential driver mutations from passenger mutations whose recurrence is due to elevated UV damage.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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28
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Howpay Manage SA, Zhu J, Fleming AM, Burrows CJ. Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology. RSC Chem Biol 2023; 4:261-270. [PMID: 37034403 PMCID: PMC10074553 DOI: 10.1039/d2cb00233g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The DNA repair endonuclease APE1 is responsible for the cleavage of abasic sites (AP) in DNA as well as binding AP in promoter G-quadruplex (G4) folds in some genes to regulate transcription. The present studies focused on the topological properties of AP-bearing G4 folds and how they impact APE1 interaction. The human telomere sequence with a tetrahydrofuran model (F) of an AP was folded in K+- or Na+-containing buffers to adopt hybrid- or basket-folds, respectively. Endonuclease and binding assays were performed with APE1 and the G4 substrates, and the data were compared to prior work with parallel-stranded VEGF and NEIL3 promoter G4s to identify topological differences. The APE1-catalyzed endonuclease assays led to the conclusion that telomere G4 folds were slightly better substrates than the promoter G4s, but the yields were all low compared to duplex DNA. In the binding assays, G4 topological differences were observed in which APE1 bound telomere G4s with dissociation constants similar to single-stranded DNA, and promoter G4s were bound with nearly ten-fold lower values similar to duplex DNA. An in-cellulo assay with the telomere G4 in a model promoter bearing a lesion failed to regulate transcription. These data support a hypothesis that G4 topology in gene promoters is a critical feature that APE1 recognizes for gene regulation.
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Affiliation(s)
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
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29
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Pezone A, Olivieri F, Napoli MV, Procopio A, Avvedimento EV, Gabrielli A. Inflammation and DNA damage: cause, effect or both. Nat Rev Rheumatol 2023; 19:200-211. [PMID: 36750681 DOI: 10.1038/s41584-022-00905-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Inflammation is a biological response involving immune cells, blood vessels and mediators induced by endogenous and exogenous stimuli, such as pathogens, damaged cells or chemicals. Unresolved (chronic) inflammation is characterized by the secretion of cytokines that maintain inflammation and redox stress. Mitochondrial or nuclear redox imbalance induces DNA damage, which triggers the DNA damage response (DDR) that is orchestrated by ATM and ATR kinases, which modify gene expression and metabolism and, eventually, establish the senescent phenotype. DDR-mediated senescence is induced by the signalling proteins p53, p16 and p21, which arrest the cell cycle in G1 or G2 and promote cytokine secretion, producing the senescence-associated secretory phenotype. Senescence and inflammation phenotypes are intimately associated, but highly heterogeneous because they vary according to the cell type that is involved. The vicious cycle of inflammation, DNA damage and DDR-mediated senescence, along with the constitutive activation of the immune system, is the core of an evolutionarily conserved circuitry, which arrests the cell cycle to reduce the accumulation of mutations generated by DNA replication during redox stress caused by infection or inflammation. Evidence suggests that specific organ dysfunctions in apparently unrelated diseases of autoimmune, rheumatic, degenerative and vascular origins are caused by inflammation resulting from DNA damage-induced senescence.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Biologia, Università Federico II, Napoli, Italy.
| | - Fabiola Olivieri
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Maria Vittoria Napoli
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Antonio Procopio
- Dipartimento di Scienze Cliniche e Molecolari, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Clinica di Medicina di Laboratorio e di Precisione, IRCCS INRCA, Ancona, Italy
| | - Enrico Vittorio Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy.
| | - Armando Gabrielli
- Fondazione di Medicina Molecolare e Terapia Cellulare, Università Politecnica delle Marche, Ancona, Italy.
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30
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Mingard C, Battey JND, Takhaveev V, Blatter K, Hürlimann V, Sierro N, Ivanov NV, Sturla SJ. Dissection of Cancer Mutational Signatures with Individual Components of Cigarette Smoking. Chem Res Toxicol 2023; 36:714-723. [PMID: 36976926 PMCID: PMC10114081 DOI: 10.1021/acs.chemrestox.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Tobacco smoke delivers a complex mixture of hazardous and potentially hazardous chemicals. Some of these may induce the formation of DNA mutations, which increases the risk of various cancers that display characteristic patterns of accumulated mutations arising from the causative exposures. Tracking the contributions of individual mutagens to mutational signatures present in human cancers can help understand cancer etiology and advance disease prevention strategies. To characterize the potential contributions of individual constituents of tobacco smoke to tobacco exposure-associated mutational signatures, we first assessed the toxic potential of 13 tobacco-relevant compounds by determining their impact on the viability of a human bronchial lung epithelial cell line (BEAS-2B). Experimentally derived high-resolution mutational profiles were characterized for the seven most potent compounds by sequencing the genomes of clonally expanded mutants that arose after exposure to the individual chemicals. Analogous to the classification of mutagenic processes on the basis of signatures from human cancers, we extracted mutational signatures from the mutant clones. We confirmed the formation of previously characterized benzo[a]pyrene mutational signatures. Furthermore, we discovered three novel mutational signatures. The mutational signatures arising from benzo[a]pyrene and norharmane were similar to human lung cancer signatures attributed to tobacco smoking. However, the signatures arising from N-methyl-N'-nitro-N-nitrosoguanidine and 4-(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone were not directly related to known tobacco-linked mutational signatures from human cancers. This new data set expands the scope of the in vitro mutational signature catalog and advances understanding of how environmental agents mutate DNA.
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Affiliation(s)
- Cécile Mingard
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - James N D Battey
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Katharina Blatter
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Vera Hürlimann
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
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31
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Jiang Y, Mingard C, Huber SM, Takhaveev V, McKeague M, Kizaki S, Schneider M, Ziegler N, Hürlimann V, Hoeng J, Sierro N, Ivanov NV, Sturla SJ. Quantification and Mapping of Alkylation in the Human Genome Reveal Single Nucleotide Resolution Precursors of Mutational Signatures. ACS CENTRAL SCIENCE 2023; 9:362-372. [PMID: 36968528 PMCID: PMC10037492 DOI: 10.1021/acscentsci.2c01100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Indexed: 06/18/2023]
Abstract
Chemical modifications to DNA bases, including DNA adducts arising from reactions with electrophilic chemicals, are well-known to impact cell growth, miscode during replication, and influence disease etiology. However, knowledge of how genomic sequences and structures influence the accumulation of alkylated DNA bases is not broadly characterized with high resolution, nor have these patterns been linked with overall quantities of modified bases in the genome. For benzo(a) pyrene (BaP), a ubiquitous environmental carcinogen, we developed a single-nucleotide resolution damage sequencing method to map in a human lung cell line the main mutagenic adduct arising from BaP. Furthermore, we combined this analysis with quantitative mass spectrometry to evaluate the dose-response profile of adduct formation. By comparing damage abundance with DNase hypersensitive sites, transcription levels, and other genome annotation data, we found that although overall adduct levels rose with increasing chemical exposure concentration, genomic distribution patterns consistently correlated with chromatin state and transcriptional status. Moreover, due to the single nucleotide resolution characteristics of this DNA damage map, we could determine preferred DNA triad sequence contexts for alkylation accumulation, revealing a characteristic DNA damage signature. This new BaP damage signature had a profile highly similar to mutational signatures identified previously in lung cancer genomes from smokers. Thus, these data provide insight on how genomic features shape the accumulation of alkylation products in the genome and predictive strategies for linking single-nucleotide resolution in vitro damage maps with human cancer mutations.
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Affiliation(s)
- Yang Jiang
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Cécile Mingard
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Sabrina M. Huber
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Vakil Takhaveev
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Maureen McKeague
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
- Pharmacology
and Therapeutics, Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Seiichiro Kizaki
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Mirjam Schneider
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Nathalie Ziegler
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Vera Hürlimann
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Julia Hoeng
- Philip
Morris Products SA, Quai
Jeanrenaud 3, Neuchatel 2000, Switzerland
| | - Nicolas Sierro
- Philip
Morris Products SA, Quai
Jeanrenaud 3, Neuchatel 2000, Switzerland
| | - Nikolai V. Ivanov
- Philip
Morris Products SA, Quai
Jeanrenaud 3, Neuchatel 2000, Switzerland
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
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32
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Zhou X, Gao S, Yue M, Zhu S, Liu Q, Zhao XE. Recent advances in analytical methods of oxidative stress biomarkers induced by environmental pollutant exposure. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116978] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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33
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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34
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Hahm JY, Park J, Jang ES, Chi SW. 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification. Exp Mol Med 2022; 54:1626-1642. [PMID: 36266447 PMCID: PMC9636213 DOI: 10.1038/s12276-022-00822-z] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.
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Affiliation(s)
- Ja Young Hahm
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Jongyeun Park
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Eun-Sook Jang
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Sung Wook Chi
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02481 Republic of Korea
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35
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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36
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Li CC, Liu WX, Jiang S, Liu M, Luo X, Zhang CY. Construction of Bioluminescent Sensors for Label-Free, Template-Free, Separation-Free, and Sequence-Independent Detection of both Clustered and Isolated Damage in Genomic DNA. Anal Chem 2022; 94:14716-14724. [PMID: 36223141 DOI: 10.1021/acs.analchem.2c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage induced by endogenous/exogenous factors may cause various diseases, and the genomic DNA damage has become an important biomarker for clinical diagnosis and risk assessment, but it remains a great challenge to accurately quantify both clustered and isolated damage because of their random locations, large diversity, and low abundance. Herein, we demonstrate the development of bioluminescent sensors for label-free, template-free, separation-free, and sequence-independent detection of both clustered and isolated damage in genomic DNA based on the base-excision repair (BER) pathway and terminal transferase (TdT)-initiated template-free isothermal cyclic amplification. The damaged bases are cleaved by DNA glycosylase to generate a new 3'-OH terminus, and subsequently, TdT catalyzes the repeated incorporation of dTTPs into the 3'-OH terminus to produce poly-T structures which can hybridize with the signal probe to form a poly-T sequence/signal probe duplex. Under the lambda exonuclease hydrolysis, a large number of adenosine monophosphate (AMP) molecules are produced to generate a high bioluminescence signal through the cyclic interconversion of AMP-adenosine triphosphate (ATP)-AMP in the presence of luciferin and firefly luciferase. Moreover, the introduction of APE1-induced cyclic cleavage signal amplification can greatly improve the detection sensitivity. The proposed strategy can detect both clustered and isolated damage in genomic DNA with extremely high sensitivity and excellent specificity, and it can even distinguish 0.001% DNA damage in the mixture. Importantly, it can detect the cellular DNA damage with a detection limit of 0.011 ng and further extend to measure various DNA damage with the integration of appropriate DNA repair enzymes.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wan-Xin Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Zichuan Experimental Middle School, Zibo 255100, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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37
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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38
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Yu T, Slone J, Liu W, Barnes R, Opresko PL, Wark L, Mai S, Horvath S, Huang T. Premature aging is associated with higher levels of 8-oxoguanine and increased DNA damage in the Polg mutator mouse. Aging Cell 2022; 21:e13669. [PMID: 35993394 PMCID: PMC9470903 DOI: 10.1111/acel.13669] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 01/24/2023] Open
Abstract
Mitochondrial dysfunction plays an important role in the aging process. However, the mechanism by which this dysfunction causes aging is not fully understood. The accumulation of mutations in the mitochondrial genome (or "mtDNA") has been proposed as a contributor. One compelling piece of evidence in support of this hypothesis comes from the PolgD257A/D257A mutator mouse (Polgmut/mut ). These mice express an error-prone mitochondrial DNA polymerase that results in the accumulation of mtDNA mutations, accelerated aging, and premature death. In this paper, we have used the Polgmut/mut model to investigate whether the age-related biological effects observed in these mice are triggered by oxidative damage to the DNA that compromises the integrity of the genome. Our results show that mutator mouse has significantly higher levels of 8-oxoguanine (8-oxoGua) that are correlated with increased nuclear DNA (nDNA) strand breakage and oxidative nDNA damage, shorter average telomere length, and reduced mtDNA integrity. Based on these results, we propose a model whereby the increased level of reactive oxygen species (ROS) associated with the accumulation of mtDNA mutations in Polgmut/mut mice results in higher levels of 8-oxoGua, which in turn lead to compromised DNA integrity and accelerated aging via increased DNA fragmentation and telomere shortening. These results suggest that mitochondrial play a central role in aging and may guide future research to develop potential therapeutics for mitigating aging process.
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Affiliation(s)
- Tenghui Yu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Human Aging Research Institute, School of Life ScienceNanchang UniversityNanchangChina,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Jesse Slone
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Wensheng Liu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA
| | - Ryan Barnes
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Patricia L. Opresko
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Landon Wark
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Steve Horvath
- Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Taosheng Huang
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
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39
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Biechele-Speziale DJ, Sutton TB, Delaney S. Obstacles and opportunities for base excision repair in chromatin. DNA Repair (Amst) 2022; 116:103345. [PMID: 35689883 PMCID: PMC9253077 DOI: 10.1016/j.dnarep.2022.103345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/01/2023]
Abstract
Most eukaryotic DNA is packaged into chromatin, which is made up of tandemly repeating nucleosomes. This packaging of DNA poses a significant barrier to the various enzymes that must act on DNA, including DNA damage response enzymes that interact intimately with DNA to prevent mutations and cell death. To regulate access to certain DNA regions, chromatin remodeling, variant histone exchange, and histone post-translational modifications have been shown to assist several DNA repair pathways including nucleotide excision repair, single strand break repair, and double strand break repair. While these chromatin-level responses have been directly linked to various DNA repair pathways, how they modulate the base excision repair (BER) pathway remains elusive. This review highlights recent findings that demonstrate how BER is regulated by the packaging of DNA into nucleosome core particles (NCPs) and higher orders of chromatin structures. We also summarize the available data that indicate BER may be enabled by chromatin modifications and remodeling.
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Affiliation(s)
| | | | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, USA.
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40
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Danforth JM, Provencher L, Goodarzi AA. Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage. Front Cell Dev Biol 2022; 10:910440. [PMID: 35912116 PMCID: PMC9326100 DOI: 10.3389/fcell.2022.910440] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.
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41
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Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles. DNA Repair (Amst) 2022; 116:103355. [PMID: 35717761 PMCID: PMC9262417 DOI: 10.1016/j.dnarep.2022.103355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.
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42
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Welch G, Tsai LH. Mechanisms of DNA damage-mediated neurotoxicity in neurodegenerative disease. EMBO Rep 2022; 23:e54217. [PMID: 35499251 PMCID: PMC9171412 DOI: 10.15252/embr.202154217] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/18/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Neurons are highly susceptible to DNA damage accumulation due to their large energy requirements, elevated transcriptional activity, and long lifespan. While newer research has shown that DNA breaks and mutations may facilitate neuron diversity during development and neuronal function throughout life, a wealth of evidence indicates deficient DNA damage repair underlies many neurological disorders, especially age-associated neurodegenerative diseases. Recently, efforts to clarify the molecular link between DNA damage and neurodegeneration have improved our understanding of how the genomic location of DNA damage and defunct repair proteins impact neuron health. Additionally, work establishing a role for senescence in the aging and diseased brain reveals DNA damage may play a central role in neuroinflammation associated with neurodegenerative disease.
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Affiliation(s)
- Gwyneth Welch
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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43
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Jin SG, Meng Y, Johnson J, Szabó PE, Pfeifer GP. Concordance of hydrogen peroxide-induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors. SCIENCE ADVANCES 2022; 8:eabn3815. [PMID: 35658030 PMCID: PMC9166614 DOI: 10.1126/sciadv.abn3815] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Oxidative DNA damage has been linked to inflammation, cancer, and aging. Here, we have mapped two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by potassium permanganate, at a single-base resolution. 8-Oxo-guanine occurs strictly dependent on the G/C sequence context and shows a pronounced peak at transcription start sites (TSSs). We determined the trinucleotide sequence pattern of guanine oxidation. This pattern shows high similarity to the cancer-associated single-base substitution signatures SBS18 and SBS36. SBS36 is found in colorectal cancers that carry mutations in MUTYH, encoding a repair enzyme that operates on 8-oxo-guanine mispairs. SBS18 is common in inflammation-associated upper gastrointestinal tract tumors including esophageal and gastric adenocarcinomas. Oxidized thymines induced by permanganate occur with a distinct dinucleotide specificity, 5'T-A/C, and are depleted at the TSS. Our data suggest that two cancer mutational signatures, SBS18 and SBS36, are caused by reactive oxygen species.
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Affiliation(s)
- Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Yingying Meng
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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44
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Dong JH, Xue CY, Zhong XY, Zhou YL, Zhang XX. Ultrasensitive and Single-Base Resolution Quantification of 8-Oxo-7,8-dihydroguanine in DNA by Extension and Ligation-Based qPCR. Anal Chem 2022; 94:8066-8074. [PMID: 35613360 DOI: 10.1021/acs.analchem.2c01679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxidative DNA damage is tightly linked to the development of multiple age-related diseases. The prominent oxidation product is 8-oxo-7,8-dihydroguanine (OG), which has been proved to be an important epigenetic-like biomarker. Quantification of the locus-specific OG frequency includes quantitative and locating information, which is of great significance for exploring the functional roles of OG in disease induction and gene regulation. Herein, an ultrasensitive quantification of OG at single-base resolution was established using real-time fluorescence quantitative polymerase chain reaction as an amplification tool. Based on the coding property of Bsu DNA polymerase that incorporates adenine on the opposite site of OG and the selectivity of the ligase for perfectly matched sequences, the difference between OG and G on the sequence could be enlarged. Well-performed Taq DNA ligase was selected out, and as low as 46.2 zmol of target DNA with an OG site and an OG frequency of 5% could be detected. G contents on a specific site were also detectable based on the similar principle, thus the OG frequency of this locus could be accurately determined by a standard addition method. This strategy was successfully applied to the evaluation of locus-specific OG in both model DNA and genomic DNA from human cervical carcinoma cell lines under multiple oxidative stress, showing the potential for functional research and dynamic monitoring of critical OG sites.
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Affiliation(s)
- Jia-Hui Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chen-Yu Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Ying Zhong
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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45
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Sun J, Antczak NM, Gahlon HL, Sturla SJ. Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases. Chem Sci 2022; 13:4295-4302. [PMID: 35509469 PMCID: PMC9007065 DOI: 10.1039/d1sc05648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.
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Affiliation(s)
- Jingjing Sun
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Biological Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Nicole M Antczak
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Chemistry, Skidmore College 815 North Broadway Saratoga Springs NY 12866 USA
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
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46
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Scala G, Gorini F, Ambrosio S, Chiariello AM, Nicodemi M, Lania L, Majello B, Amente S. 8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops. Nucleic Acids Res 2022; 50:3292-3306. [PMID: 35234932 PMCID: PMC8989568 DOI: 10.1093/nar/gkac143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of the DNA oxidization process, has been proposed to have an epigenetic function in gene regulation and has been associated with genome instability. NGS-based methodologies are contributing to the characterization of the 8-oxodG function in the genome. However, the 8-oxodG epigenetic role at a genomic level and the mechanisms controlling the genomic 8-oxodG accumulation/maintenance have not yet been fully characterized. In this study, we report the identification and characterization of a set of enhancer regions accumulating 8-oxodG in human epithelial cells. We found that these oxidized enhancers are mainly super-enhancers and are associated with bidirectional-transcribed enhancer RNAs and DNA Damage Response activation. Moreover, using ChIA-PET and HiC data, we identified specific CTCF-mediated chromatin loops in which the oxidized enhancer and promoter regions physically associate. Oxidized enhancers and their associated chromatin loops accumulate endogenous double-strand breaks which are in turn repaired by NHEJ pathway through a transcription-dependent mechanism. Our work suggests that 8-oxodG accumulation in enhancers-promoters pairs occurs in a transcription-dependent manner and provides novel mechanistic insights on the intrinsic fragility of chromatin loops containing oxidized enhancers-promoters interactions.
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Affiliation(s)
- Giovanni Scala
- Department of Biology, University of Naples ‘Federico II’, Naples, Italy
| | - Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples ‘Federico II’, Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples ‘Federico II’, Naples, Italy
| | - Andrea M Chiariello
- Department of Physics, University of Naples Federico II, and INFN, Naples, Italy
| | - Mario Nicodemi
- Department of Physics, University of Naples Federico II, and INFN, Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples ‘Federico II’, Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples ‘Federico II’, Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples ‘Federico II’, Naples, Italy
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47
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Teng X, Dai Y, Li J. Methodological advances of bioanalysis and biochemical targeting of intracellular G-quadruplexes. EXPLORATION (BEIJING, CHINA) 2022; 2:20210214. [PMID: 37323879 PMCID: PMC10191030 DOI: 10.1002/exp.20210214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 06/17/2023]
Abstract
G-quadruplexes (G4s) are a kind of non-canonical nucleic acid secondary structures, which involve in various biological processes in living cells. The relationships between G4s and human diseases, such as tumors, neurodegenerative diseases, and viral infections, have attracted great attention in the last decade. G4s are considered as a promising new target for disease treatment. For instance, G4 ligands are reported to be potentially effective in SARS-COV-2 treatment. However, because of the lack of analytical methods with high performance for the identification of intracellular G4s, the detailed mechanisms of the biofunctions of G4s remain elusive. Meanwhile, through demonstrating the principles of how the G4s systematically modulate the cellular processes with advanced detection methods, biochemical targeting of G4s in living cells can be realized by chemical and biological tools and becomes useful in biomedicine. This review highlights recent methodological advances about intracellular G4s and provides an outlook on the improvement of the bioanalysis and biochemical targeting tools of G4s.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
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48
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Niu Y, Zhu Q, Zong C. Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA). Bio Protoc 2022; 12:e4357. [PMID: 35434195 PMCID: PMC8983167 DOI: 10.21769/bioprotoc.4357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 10/19/2021] [Accepted: 02/01/2022] [Indexed: 02/08/2024] Open
Abstract
Spontaneous DNA damage frequently occurs on the human genome, and it could alter gene expression by inducing mutagenesis or epigenetic changes. Therefore, it is highly desired to profile DNA damage distribution on the human genome and identify the genes that are prone to DNA damage. Here, we present a novel single-cell whole-genome amplification method which employs linear-copying followed by a split-amplification scheme, to efficiently remove amplification errors and achieve accurate detection of DNA damage in individual cells. In comparison to previous methods that measure DNA damage, our method uses a next-generation sequencing platform to detect misincorporated bases derived from spontaneous DNA damage with single-cell resolution.
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Affiliation(s)
- Yichi Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Genetics & Genomics Program, Baylor College of Medicine, TX, USA
| | - Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Genetics & Genomics Program, Baylor College of Medicine, TX, USA
- Cancer and Cell Biology Program, Baylor College of Medicine, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, TX, USA
- McNair Medical Institute, Baylor College of Medicine, TX, USA
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49
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Hong X, Wang L, Zhang K, Liu J, Liu JP. Molecular Mechanisms of Alveolar Epithelial Stem Cell Senescence and Senescence-Associated Differentiation Disorders in Pulmonary Fibrosis. Cells 2022; 11:877. [PMID: 35269498 PMCID: PMC8909789 DOI: 10.3390/cells11050877] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Pulmonary senescence is accelerated by unresolved DNA damage response, underpinning susceptibility to pulmonary fibrosis. Recently it was reported that the SARS-Cov-2 viral infection induces acute pulmonary epithelial senescence followed by fibrosis, although the mechanism remains unclear. Here, we examine roles of alveolar epithelial stem cell senescence and senescence-associated differentiation disorders in pulmonary fibrosis, exploring the mechanisms mediating and preventing pulmonary fibrogenic crisis. Notably, the TGF-β signalling pathway mediates alveolar epithelial stem cell senescence by mechanisms involving suppression of the telomerase reverse transcriptase gene in pulmonary fibrosis. Alternatively, telomere uncapping caused by stress-induced telomeric shelterin protein TPP1 degradation mediates DNA damage response, pulmonary senescence and fibrosis. However, targeted intervention of cellular senescence disrupts pulmonary remodelling and fibrosis by clearing senescent cells using senolytics or preventing senescence using telomere dysfunction inhibitor (TELODIN). Studies indicate that the development of senescence-associated differentiation disorders is reprogrammable and reversible by inhibiting stem cell replicative senescence in pulmonary fibrosis, providing a framework for targeted intervention of the molecular mechanisms of alveolar stem cell senescence and pulmonary fibrosis. Abbreviations: DPS, developmental programmed senescence; IPF, idiopathic pulmonary fibrosis; OIS, oncogene-induced replicative senescence; SADD, senescence-associated differentiation disorder; SALI, senescence-associated low-grade inflammation; SIPS, stress-induced premature senescence; TERC, telomerase RNA component; TERT, telomerase reverse transcriptase; TIFs, telomere dysfunction-induced foci; TIS, therapy-induced senescence; VIS, virus-induced senescence.
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Affiliation(s)
- Xiaojing Hong
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou 311121, China; (X.H.); (L.W.); (K.Z.); (J.L.)
| | - Lihui Wang
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou 311121, China; (X.H.); (L.W.); (K.Z.); (J.L.)
| | - Kexiong Zhang
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou 311121, China; (X.H.); (L.W.); (K.Z.); (J.L.)
| | - Jun Liu
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou 311121, China; (X.H.); (L.W.); (K.Z.); (J.L.)
| | - Jun-Ping Liu
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou 311121, China; (X.H.); (L.W.); (K.Z.); (J.L.)
- Department of Immunology and Pathology, Monash University Faculty of Medicine, Prahran, VIC 3181, Australia
- Hudson Institute of Medical Research, Monash University Department of Molecular and Translational Science, Clayton, VIC 3168, Australia
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50
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Boysen G, Nookaew I. Current and Future Methodology for Quantitation and Site-Specific Mapping the Location of DNA Adducts. TOXICS 2022; 10:toxics10020045. [PMID: 35202232 PMCID: PMC8876591 DOI: 10.3390/toxics10020045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023]
Abstract
Formation of DNA adducts is a key event for a genotoxic mode of action, and their presence is often used as a surrogate for mutation and increased cancer risk. Interest in DNA adducts are twofold: first, to demonstrate exposure, and second, to link DNA adduct location to subsequent mutations or altered gene regulation. Methods have been established to quantitate DNA adducts with high chemical specificity and to visualize the location of DNA adducts, and elegant bio-analytical methods have been devised utilizing enzymes, various chemistries, and molecular biology methods. Traditionally, these highly specific methods cannot be combined, and the results are incomparable. Initially developed for single-molecule DNA sequencing, nanopore-type technologies are expected to enable simultaneous quantitation and location of DNA adducts across the genome. Herein, we briefly summarize the current methodologies for state-of-the-art quantitation of DNA adduct levels and mapping of DNA adducts and describe novel single-molecule DNA sequencing technologies to achieve both measures. Emerging technologies are expected to soon provide a comprehensive picture of the exposome and identify gene regions susceptible to DNA adduct formation.
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Affiliation(s)
- Gunnar Boysen
- Department Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence:
| | - Intawat Nookaew
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Department Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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