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Zhao T, He X, Liang X, Kellum AH, Tang F, Yin J, Guo S, Wang Y, Gao Z, Wang Y. HMGB3 and SUB1 Bind to and Facilitate the Repair of N2-Alkylguanine Lesions in DNA. J Am Chem Soc 2024; 146:22553-22562. [PMID: 39101269 DOI: 10.1021/jacs.4c06680] [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: 08/06/2024]
Abstract
N2-Alkyl-2'-deoxyguanosine (N2-alkyl-dG) is a major type of minor-groove DNA lesions arising from endogenous metabolic processes and exogenous exposure to environmental contaminants. The N2-alkyl-dG lesions, if left unrepaired, can block DNA replication and transcription and induce mutations in these processes. Nevertheless, the repair pathways for N2-alkyl-dG lesions remain incompletely elucidated. By utilizing a photo-cross-linking coupled with mass spectrometry-based quantitative proteomic analysis, we identified a series of candidate N2-alkyl-dG-binding proteins. We found that two of these proteins, i.e., high-mobility group protein B3 (HMGB3) and SUB1, could bind directly to N2-nBu-dG-containing duplex DNA in vitro and promote the repair of this lesion in cultured human cells. In addition, HMGB3 and SUB1 protected cells against benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE). SUB1 exhibits preferential binding to both the cis and trans diastereomers of N2-BPDE-dG over unmodified dG. On the other hand, HMGB3 binds favorably to trans-N2-BPDE-dG; the protein, however, does not distinguish cis-N2-BPDE-dG from unmodified dG. Consistently, genetic ablation of HMGB3 conferred diminished repair of trans-N2-BPDE-dG, but not its cis counterpart, whereas loss of SUB1 conferred attenuated repair of both diastereomers. Together, we identified proteins involved in the cellular sensing and repair of minor-groove N2-alkyl-dG lesions and documented a unique role of HMGB3 in the stereospecific recognition and repair of N2-BPDE-dG.
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Affiliation(s)
- Ting Zhao
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Xiaomei He
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Xiaochen Liang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Andrew H Kellum
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Feng Tang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Su Guo
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Yinan Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Zi Gao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
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Torres MC, Rebok A, Sun D, Spratt TE. Activity of DNA polymerase κ across the genome in human fibroblasts. Proc Natl Acad Sci U S A 2024; 121:e2403130121. [PMID: 38950369 PMCID: PMC11252913 DOI: 10.1073/pnas.2403130121] [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: 03/04/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024] Open
Abstract
DNA polymerase κ (Polκ) is a specialized polymerase that has multiple cellular roles such as translesion DNA synthesis, replication of repetitive sequences, and nucleotide excision repair. We have developed a method for capturing DNA synthesized by Polκ utilizing a Polκ-specific substrate, N2-(4-ethynylbenzyl)-2'-deoxyguanosine (EBndG). After shearing of the DNA into 200 to 500 bp lengths, the EBndG-containing DNA was covalently bound to biotin using the Cu(I)-catalyzed alkyne-azide cycloaddition reaction and isolated with streptavidin beads. Isolated DNA was then ligated to adaptors, followed by PCR amplification and next-generation sequencing to generate genome-wide repair maps. We have termed this method polymerase κ sequencing. Here, we present the human genome maps for Polκ activity in an undamaged cell line. We found that Polκ activity was enhanced in GC-rich regions, euchromatin regions, the promoter of genes, and in DNA that is replicated early in the S phase.
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Affiliation(s)
- Mariela C. Torres
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA17033
| | - Abbey Rebok
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA17033
| | - Dongxiao Sun
- Department of Pharmacology, Pennsylvania State University, Hershey, PA17033
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA17033
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024:10.1038/s41576-024-00748-4. [PMID: 38918545 DOI: 10.1038/s41576-024-00748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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Cohen Y, Adar S. Novel insights into bulky DNA damage formation and nucleotide excision repair from high-resolution genomics. DNA Repair (Amst) 2023; 130:103549. [PMID: 37566959 DOI: 10.1016/j.dnarep.2023.103549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
DNA damages compromise cell function and fate. Cells of all organisms activate a global DNA damage response that includes a signaling stress response, activation of checkpoints, and recruitment of repair enzymes. Especially deleterious are bulky, helix-distorting damages that block transcription and replication. Due to their miscoding nature, these damages lead to mutations and cancer. In human cells, bulky DNA damages are repaired by nucleotide excision repair (NER). To date, the basic mechanism of NER in naked DNA is well defined. Still, there is a fundamental gap in our understanding of how repair is orchestrated despite the packaging of DNA in chromatin, and how it is coordinated with active transcription and replication. The last decade has brought forth huge advances in our ability to detect and assay bulky DNA damages and their repair at single nucleotide resolution across the human genome. Here we review recent findings on the effect of chromatin and DNA-binding proteins on the formation of bulky DNA damages, and novel insights on NER, provided by the recent application of genomic methods.
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Affiliation(s)
- Yuval Cohen
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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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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Huang A, Tang W. Smoking-Related DNA Alkylation Events Are Mapped at Single-Nucleotide Resolution. ACS CENTRAL SCIENCE 2023; 9:346-348. [PMID: 36968536 PMCID: PMC10037440 DOI: 10.1021/acscentsci.3c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Alvin
T. Huang
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637, United
States
| | - Weixin Tang
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637, United
States
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