1
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Herring P, Roedgaard M, Holst CM, Christensen H, Knudsen BR, Bjergbaek L, Andersen AH. A cellular system to study responses to a collision between the transcription complex and a protein-bound nick in the DNA template. FEBS Lett 2025. [PMID: 40309784 DOI: 10.1002/1873-3468.70053] [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: 01/13/2025] [Revised: 03/12/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025]
Abstract
We present a transcription-coupled Flp-nick system enabling a stable protein-bound nick mimicking a topoisomerase I-DNA cleavage complex. The nick is introduced at a single site within a controllable LacZ gene inserted into the Saccharomyces cerevisiae genome. This system allows unique single-site studies of a frequently occurring damage within a transcription unit in vivo. As proof of principle, we demonstrate RNA polymerase II accumulation at the damage site when MG132 inhibits the proteasome. Similarly, accumulation occurs when polymerase ubiquitination is abolished by deletion of the ubiquitinase ELC1 gene. This indicates that a topoisomerase I-DNA mimicking cleavage complex per se induces RNA polymerase II ubiquitination and degradation. These findings advance understanding of cellular responses to topoisomerase I-targeting drugs used in cancer chemotherapy.
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Affiliation(s)
- Petra Herring
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Morten Roedgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Camilla Myrup Holst
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Helene Christensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Lotte Bjergbaek
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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2
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Sun Y, Vermulst M. The hidden costs of imperfection: transcription errors in protein aggregation diseases. Curr Opin Genet Dev 2025; 93:102350. [PMID: 40300213 DOI: 10.1016/j.gde.2025.102350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/26/2025] [Accepted: 04/06/2025] [Indexed: 05/01/2025]
Abstract
At first glance, biological systems appear to operate with remarkable precision and order. Yet, closer examination reveals that this perfection is an illusion, biological processes are inherently prone to errors. Here, we describe recent evidence that indicates that errors that occur during transcription play an important role in neurological diseases. These errors, though transient, can have lasting consequences when they generate mutant proteins with amyloid or prion-like properties. Such proteins can seed aggregation cascades, converting wild-type counterparts into misfolded conformations, ultimately leading to toxic deposits seen in diseases like Alzheimer's and amyotrophic lateral sclerosis. These observations help to paint a fuller picture of the origins of neurodegenerative diseases in aging humans and suggest a unified mechanism by which they may arise.
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Affiliation(s)
- Yingwo Sun
- University of Southern California, School of Gerontology, Los Angeles 90089, United States
| | - Marc Vermulst
- University of Southern California, School of Gerontology, Los Angeles 90089, United States.
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3
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Zhong J, Liang L, Zhao N, Wang J, Shu P. Synergistic effects of retinol and retinyl palmitate in alleviating UVB-induced DNA damage and promoting the homologous recombination repair in keratinocytes. Front Pharmacol 2025; 16:1562244. [PMID: 40343007 PMCID: PMC12058701 DOI: 10.3389/fphar.2025.1562244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 04/11/2025] [Indexed: 05/11/2025] Open
Abstract
Background Ultraviolet B (UVB) rays are a type of ultraviolet radiation emitted by the sun, primarily responsible for skin photodamage. These rays mainly affect the epidermis, leading to direct damage to DNA and contributing to skin cancer development. Retinol and its derivatives are effective in combating skin aging and photodamage, but they often cause skin intolerance, limiting their use despite their potent effects. Therefore, investigating optimal compositions of retinoids is essential to enhance their efficacy against photodamage. Method In this study, we investigated the synergistic effects of retinol (ROL) and retinyl palmitate (RPalm) in alleviating UVB-induced DNA damage in human keratinocytes (HaCaT) and reconstructed human epidermis. The ROL+RPalm combination was applied after UVB exposure. We utilized bulk mRNA sequencing, comet assays, Western blotting, immunofluorescence, and flow cytometry to evaluate the level of DNA damage and repair. Result The application of the ROL+RPalm combination significantly reduced inflammation and apoptosis while promoting collagen synthesis compared to individual treatments with ROL or RPalm. Our findings indicated that the ROL+RPalm synergy primarily mediates DNA damage repair. Additionally, we elucidated that the molecular mechanism involves the activation of RARβ, which triggers the ATM-CHK2-p53 signaling pathway and increases the expression of homologous recombination (HR)-associated repair genes. Conclusion This combination of ROL and RPalm presents a potential therapeutic strategy for UVB-induced photodamage and emphasizes the synergistic effects in alleviating UVB-induced DNA damage.
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Affiliation(s)
| | | | | | | | - Peng Shu
- HBN Research Institute and Biological Laboratory, Shenzhen Hujia Technology Co., Ltd., Shenzhen, Guangdong, China
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4
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Mendes IC, Dos Reis Bertoldo W, Miranda-Junior AS, Assis AVD, Repolês BM, Ferreira WRR, Chame DF, Souza DDL, Pavani RS, Macedo AM, Franco GR, Serra E, Perdomo V, Menck CFM, da Silva Leandro G, Fragoso SP, Barbosa Elias MCQ, Machado CR. DNA lesions that block transcription induce the death of Trypanosoma cruzi via ATR activation, which is dependent on the presence of R-loops. DNA Repair (Amst) 2024; 141:103726. [PMID: 39096697 DOI: 10.1016/j.dnarep.2024.103726] [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: 11/23/2023] [Revised: 06/25/2024] [Accepted: 07/07/2024] [Indexed: 08/05/2024]
Abstract
Trypanosoma cruzi is the etiological agent of Chagas disease and a peculiar eukaryote with unique biological characteristics. DNA damage can block RNA polymerase, activating transcription-coupled nucleotide excision repair (TC-NER), a DNA repair pathway specialized in lesions that compromise transcription. If transcriptional stress is unresolved, arrested RNA polymerase can activate programmed cell death. Nonetheless, how this parasite modulates these processes is unknown. Here, we demonstrate that T. cruzi cell death after UV irradiation, a genotoxic agent that generates lesions resolved by TC-NER, depends on active transcription and is signaled mainly by an apoptotic-like pathway. Pre-treated parasites with α-amanitin, a selective RNA polymerase II inhibitor, become resistant to such cell death. Similarly, the gamma pre-irradiated cells are more resistant to UV when the transcription processes are absent. The Cockayne Syndrome B protein (CSB) recognizes blocked RNA polymerase and can initiate TC-NER. Curiously, CSB overexpression increases parasites' cell death shortly after UV exposure. On the other hand, at the same time after irradiation, the single-knockout CSB cells show resistance to the same treatment. UV-induced fast death is signalized by the exposition of phosphatidylserine to the outer layer of the membrane, indicating a cell death mainly by an apoptotic-like pathway. Furthermore, such death is suppressed in WT parasites pre-treated with inhibitors of ataxia telangiectasia and Rad3-related (ATR), a key DDR kinase. Signaling for UV radiation death may be related to R-loops since the overexpression of genes associated with the resolution of these structures suppress it. Together, results suggest that transcription blockage triggered by UV radiation activates an ATR-dependent apoptosis-like mechanism in T. cruzi, with the participation of CSB protein in this process.
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Affiliation(s)
- Isabela Cecilia Mendes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Willian Dos Reis Bertoldo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Adalberto Sales Miranda-Junior
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Antônio Vinícius de Assis
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Bruno Marçal Repolês
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Wesley Roger Rodrigues Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Daniela Ferreira Chame
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Daniela De Laet Souza
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Raphael Souza Pavani
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, MG, São Paulo, SP 05503-900, Brazil
| | - Andrea Mara Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil
| | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Virginia Perdomo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Carlos Frederico Martins Menck
- Departamento de Microbiologia, Instituto de Ciências Biomédicas (ICB), Universidade de São Paulo (USP), São Paulo, SP 05508-900, Brazil
| | - Giovana da Silva Leandro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas (ICB), Universidade de São Paulo (USP), São Paulo, SP 05508-900, Brazil
| | | | | | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, MG 30161-970, Brazil.
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5
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Ahmed A, Kato N, Gautier J. Replication-Independent ICL Repair: From Chemotherapy to Cell Homeostasis. J Mol Biol 2024; 436:168618. [PMID: 38763228 PMCID: PMC11227339 DOI: 10.1016/j.jmb.2024.168618] [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: 03/18/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Interstrand crosslinks (ICLs) are a type of covalent lesion that can prevent transcription and replication by inhibiting DNA strand separation and instead trigger cell death. ICL inducing compounds are commonly used as chemotherapies due to their effectiveness in inhibiting cell proliferation. Naturally occurring crosslinking agents formed from metabolic processes can also pose a challenge to genome stability especially in slowly or non-dividing cells. Cells maintain a variety of ICL repair mechanisms to cope with this stressor within and outside the S phase of the cell cycle. Here, we discuss the mechanisms of various replication-independent ICL repair pathways and how crosslink repair efficiency is tied to aging and disease.
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Affiliation(s)
- Arooba Ahmed
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Niyo Kato
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA.
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6
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Nicholson MD, Anderson CJ, Odom DT, Aitken SJ, Taylor MS. DNA lesion bypass and the stochastic dynamics of transcription-coupled repair. Proc Natl Acad Sci U S A 2024; 121:e2403871121. [PMID: 38717857 PMCID: PMC11098089 DOI: 10.1073/pnas.2403871121] [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: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage.
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Affiliation(s)
- Michael D. Nicholson
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Craig J. Anderson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Duncan T. Odom
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center, Heidelberg69120, Germany
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
| | - Sarah J. Aitken
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Medical Research Council Toxicology Unit, University of Cambridge, CambridgeCB2 1QR, United Kingdom
- Department of Histopathology, Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
| | - Martin S. Taylor
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
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7
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Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nat Struct Mol Biol 2024; 31:190-202. [PMID: 38177677 PMCID: PMC10928753 DOI: 10.1038/s41594-023-01171-9] [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: 12/14/2021] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.
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Affiliation(s)
- Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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8
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Rajković M, Glavinić U, Bogunović D, Vejnović B, Davitkov D, Đelić N, Stanimirović Z. "Slow kill" treatment reduces DNA damage in leukocytes of dogs naturally infected with Dirofilaria immitis. Vet Parasitol 2023; 322:110008. [PMID: 37643566 DOI: 10.1016/j.vetpar.2023.110008] [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: 07/11/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023]
Abstract
Parasitic diseases are considered to be a cause of oxidative stress which leads to oxidative damage of various molecules including DNA. This can result in mutations, replication errors, and genome instability. Therefore, aim of this study was to measure DNA damage induced by Dirofilaria immitis in the single cells such as dogs' leukocytes using the comet assay. Also, we monitored the effects of antiparasitic treatment on mitigation of sensitivity to DNA damage in leukocytes treated with H2O2 using the in vivo and ex vivo comet assay. The whole blood samples from 34 dogs from Serbia were used, both males and females, from one to 13 years old, both pure and mixed-breeds. A rapid immunochromatographic test (Antigen Rapid Heartworm Ag 2.0 Test Kit, Bionote, Minnesota, USA) was used for the detection of D. immitis antigens. The modified Knott's test and PCR were used in the aim of detecting D. immitis microfilariae in dogs' blood, and evaluating the number of circulating microfilariae during the treatment. The genotoxicity evaluation showed that D. immitis infection resulted in DNA damage in naturally infected dogs, with the highest DNA damage occurring in the group of dogs with severe clinical signs. Treatment with ivermectin and doxycycline decreased DNA damage in leukocytes of dogs in all groups, as the intensity of infection decreased due to applied therapy. Ex vivo comet assay results showed that leukocytes exhibited decreased sensitivity to H2O2-induced DNA damage during treatment. The results of the modified Knott's test and PCR in our study showed that treatment with ivermectin and doxycycline was successful in decreasing the average number of microfilariae during the time and at the end eliminating them from the dogs' blood.
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Affiliation(s)
- Milan Rajković
- Department of Parasitology, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
| | - Uroš Glavinić
- Department of Biology, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
| | - Danica Bogunović
- Department of Parasitology, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
| | - Branislav Vejnović
- Department of Economics and Statistics, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia.
| | - Darko Davitkov
- Department of Equine, Small Animal, Poultry and Wild Animal Diseases, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
| | - Ninoslav Đelić
- Department of Biology, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
| | - Zoran Stanimirović
- Department of Biology, University of Belgrade - Faculty of Veterinary Medicine, Belgrade 11000, Serbia
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9
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Gong W, Li S. Rpb7 represses transcription-coupled nucleotide excision repair. J Biol Chem 2023; 299:104969. [PMID: 37380080 PMCID: PMC10382679 DOI: 10.1016/j.jbc.2023.104969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023] Open
Abstract
Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that is regulated by multiple facilitators, such as Rad26, and repressors, such as Rpb4 and Spt4/Spt5. How these factors interplay with each other and with core RNA polymerase II (RNAPII) remains largely unknown. In this study, we identified Rpb7, an essential RNAPII subunit, as another TCR repressor and characterized its repression of TCR in the AGP2, RPB2, and YEF3 genes, which are transcribed at low, moderate, and high rates, respectively. The Rpb7 region that interacts with the KOW3 domain of Spt5 represses TCR largely through the same common mechanism as Spt4/Spt5, as mutations in this region mildly enhance the derepression of TCR by spt4Δ only in the YEF3 gene but not in the AGP2 or RPB2 gene. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII repress TCR largely independently of Spt4/Spt5, as mutations in these regions synergistically enhance the derepression of TCR by spt4Δ in all the genes analyzed. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII may also play positive roles in other (non-NER) DNA damage repair and/or tolerance mechanisms, as mutations in these regions can cause UV sensitivity that cannot be attributed to derepression of TCR. Our study reveals a novel function of Rpb7 in TCR regulation and suggests that this RNAPII subunit may have broader roles in DNA damage response beyond its known function in transcription.
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Affiliation(s)
- Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA.
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10
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Chung C, Verheijen BM, Navapanich Z, McGann EG, Shemtov S, Lai GJ, Arora P, Towheed A, Haroon S, Holczbauer A, Chang S, Manojlovic Z, Simpson S, Thomas KW, Kaplan C, van Hasselt P, Timmers M, Erie D, Chen L, Gout JF, Vermulst M. Evolutionary conservation of the fidelity of transcription. Nat Commun 2023; 14:1547. [PMID: 36941254 PMCID: PMC10027832 DOI: 10.1038/s41467-023-36525-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/03/2023] [Indexed: 03/23/2023] Open
Abstract
Accurate transcription is required for the faithful expression of genetic information. However, relatively little is known about the molecular mechanisms that control the fidelity of transcription, or the conservation of these mechanisms across the tree of life. To address these issues, we measured the error rate of transcription in five organisms of increasing complexity and found that the error rate of RNA polymerase II ranges from 2.9 × 10-6 ± 1.9 × 10-7/bp in yeast to 4.0 × 10-6 ± 5.2 × 10-7/bp in worms, 5.69 × 10-6 ± 8.2 × 10-7/bp in flies, 4.9 × 10-6 ± 3.6 × 10-7/bp in mouse cells and 4.7 × 10-6 ± 9.9 × 10-8/bp in human cells. These error rates were modified by various factors including aging, mutagen treatment and gene modifications. For example, the deletion or modification of several related genes increased the error rate substantially in both yeast and human cells. This research highlights the evolutionary conservation of factors that control the fidelity of transcription. Additionally, these experiments provide a reasonable estimate of the error rate of transcription in human cells and identify disease alleles in a subunit of RNA polymerase II that display error-prone transcription. Finally, we provide evidence suggesting that the error rate and spectrum of transcription co-evolved with our genetic code.
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Affiliation(s)
- Claire Chung
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bert M Verheijen
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Zoe Navapanich
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eric G McGann
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Sarah Shemtov
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Guan-Ju Lai
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Payal Arora
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Atif Towheed
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Suraiya Haroon
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Agnes Holczbauer
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Sharon Chang
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Simpson
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Kelley W Thomas
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Craig Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter van Hasselt
- Department of Metabolic Disease, University of Utrecht, Utrecht, the Netherlands
| | - Marc Timmers
- Department of Urology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dorothy Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Lin Chen
- Department of Molecular and Cellular Biology, University of Southern California, Los Angeles, CA, USA
| | - Jean-Franćois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Marc Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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11
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Effects of replication domains on genome-wide UV-induced DNA damage and repair. PLoS Genet 2022; 18:e1010426. [PMID: 36155646 PMCID: PMC9536635 DOI: 10.1371/journal.pgen.1010426] [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: 04/21/2022] [Revised: 10/06/2022] [Accepted: 09/12/2022] [Indexed: 11/19/2022] Open
Abstract
Nucleotide excision repair is the primary repair mechanism that removes UV-induced DNA lesions in placentals. Unrepaired UV-induced lesions could result in mutations during DNA replication. Although the mutagenesis of pyrimidine dimers is reasonably well understood, the direct effects of replication fork progression on nucleotide excision repair are yet to be clarified. Here, we applied Damage-seq and XR-seq techniques and generated replication maps in synchronized UV-treated HeLa cells. The results suggest that ongoing replication stimulates local repair in both early and late replication domains. Additionally, it was revealed that lesions on lagging strand templates are repaired slower in late replication domains, which is probably due to the imbalanced sequence context. Asymmetric relative repair is in line with the strand bias of melanoma mutations, suggesting a role of exogenous damage, repair, and replication in mutational strand asymmetry.
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12
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Mohamed AA, Vazquez Nunez R, Vos SM. Structural advances in transcription elongation. Curr Opin Struct Biol 2022; 75:102422. [PMID: 35816930 PMCID: PMC9398977 DOI: 10.1016/j.sbi.2022.102422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/22/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Transcription is the first step of gene expression and involves RNA polymerases. After transcription initiation, RNA polymerase enters elongation followed by transcription termination at the end of the gene. Only recently, structures of transcription elongation complexes bound to key transcription elongation factors have been determined in bacterial and eukaryotic systems. These structures have revealed numerous insights including the basis for transcriptional pausing, RNA polymerase interaction with large complexes such as the ribosome and the spliceosome, and the transition into productive elongation. Here, we review these structures and describe areas for future research.
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Affiliation(s)
- Abdallah A Mohamed
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/AMohamed_98
| | - Roberto Vazquez Nunez
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/rjareth
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA.
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13
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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14
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Kajitani GS, Quayle C, Garcia CCM, Fotoran WL, Dos Santos JFR, van der Horst GTJ, Hoeijmakers JHJ, Menck CFM. Photorepair of Either CPD or 6-4PP DNA Lesions in Basal Keratinocytes Attenuates Ultraviolet-Induced Skin Effects in Nucleotide Excision Repair Deficient Mice. Front Immunol 2022; 13:800606. [PMID: 35422806 PMCID: PMC9004445 DOI: 10.3389/fimmu.2022.800606] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ultraviolet (UV) radiation is one of the most genotoxic, universal agents present in the environment. UVB (280-315 nm) radiation directly damages DNA, producing cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs). These photolesions interfere with essential cellular processes by blocking transcription and replication polymerases, and may induce skin inflammation, hyperplasia and cell death eventually contributing to skin aging, effects mediated mainly by keratinocytes. Additionally, these lesions may also induce mutations and thereby cause skin cancer. Photolesions are repaired by the Nucleotide Excision Repair (NER) pathway, responsible for repairing bulky DNA lesions. Both types of photolesions can also be repaired by distinct (CPD- or 6-4PP-) photolyases, enzymes that specifically repair their respective photolesion by directly splitting each dimer through a light-dependent process termed photoreactivation. However, as photolyases are absent in placental mammals, these organisms depend solely on NER for the repair of DNA UV lesions. However, the individual contribution of each UV dimer in the skin effects, as well as the role of keratinocytes has remained elusive. In this study, we show that in NER-deficient mice, the transgenic expression and photorepair of CPD-photolyase in basal keratinocytes completely inhibited UVB-induced epidermal thickness and cell proliferation. On the other hand, photorepair by 6-4PP-photolyase in keratinocytes reduced but did not abrogate these UV-induced effects. The photolyase mediated removal of either CPDs or 6-4PPs from basal keratinocytes in the skin also reduced UVB-induced apoptosis, ICAM-1 expression, and myeloperoxidase activation. These findings indicate that, in NER-deficient rodents, both types of photolesions have causal roles in UVB-induced epidermal cell proliferation, hyperplasia, cell death and inflammation. Furthermore, these findings also support the notion that basal keratinocytes, instead of other skin cells, are the major cellular mediators of these UVB-induced effects.
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Affiliation(s)
- Gustavo S Kajitani
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Carolina Quayle
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Camila C M Garcia
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Wesley L Fotoran
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana F R Dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands.,University Hospital of Cologne, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Institute for Genome Stability in Aging and Disease, Cologne, Germany.,Princess Maxima Center for Pediatric Oncology, ONCODE Institute, Utrecht, Netherlands
| | - Carlos F M Menck
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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15
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Bellazzi F. The emergence of the postgenomic gene. EUROPEAN JOURNAL FOR PHILOSOPHY OF SCIENCE 2022; 12:17. [PMID: 35222747 PMCID: PMC8847258 DOI: 10.1007/s13194-022-00446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The identity and the existence of genes has been challenged by postgenomic discoveries. Specifically, the consideration of molecular and cellular phenomena in which genes are embedded has proved relevant for their understanding. In response to these challenges, I will argue that the complexity of genetic phenomena supports the weak emergence of genes from the DNA. In Section 2, I will expose what genes are taken to be in the postgenomic world. In Section 3, I will present the relevant account of emergence. I consider weak emergence as in Franklin and Knox (Studies for the History and Philosophy of Modern Physics, 64, 68-78, 2018), for which a phenomenon is emergent when it displays novelty and robustness. In Section 4, I will argue that genes are weakly emergent since they are novel, improving explanations, and robust in respect to some perturbations. Then, I will conclude in Section 5 that genes' emergence is a way to allow genes' flexibility and context dependency, without compromising their existence.
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16
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Brovarets’ OO, Muradova A, Hovorun DM. Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2026510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
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17
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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18
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Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
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Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
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19
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Tan Y, Guo S, Wu J, Du H, Li L, You C, Wang Y. DNA Polymerase η Promotes the Transcriptional Bypass of N2-Alkyl-2'-deoxyguanosine Adducts in Human Cells. J Am Chem Soc 2021; 143:16197-16205. [PMID: 34555898 DOI: 10.1021/jacs.1c07374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To cope with unrepaired DNA lesions, cells are equipped with DNA damage tolerance mechanisms, including translesion synthesis (TLS). While TLS polymerases are well documented in facilitating replication across damaged DNA templates, it remains unknown whether TLS polymerases participate in transcriptional bypass of DNA lesions in cells. Herein, we employed the competitive transcription and adduct bypass assay to examine the efficiencies and fidelities of transcription across N2-alkyl-2'-deoxyguanosine (N2-alkyl-dG, alkyl = methyl, ethyl, n-propyl, or n-butyl) lesions in HEK293T cells. We found that N2-alkyl-dG lesions strongly blocked transcription and elicited CC → AA tandem mutations in nascent transcripts, where adenosines were misincorporated opposite the lesions and their adjacent 5' nucleoside. Additionally, genetic ablation of Pol η, but not Pol κ, Pol ι, or Pol ζ, conferred marked diminutions in the transcriptional bypass efficiencies of the N2-alkyl-dG lesions, which is exacerbated by codepletion of Rev1 in Pol η-deficient background. We also observed that the repair of N2-nBu-dG was not pronouncedly affected by genetic depletion of Pol η or Rev1. Hence, our results provided insights into transcriptional perturbations induced by N2-alkyl-dG lesions and expanded the biological functions of TLS DNA polymerases.
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Affiliation(s)
- Ying Tan
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Su Guo
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Jun Wu
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Changjun You
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States.,Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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20
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Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat Chem Biol 2021; 17:906-914. [PMID: 34140682 PMCID: PMC8319059 DOI: 10.1038/s41589-021-00817-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3'-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.
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21
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Jia N, Guo C, Nakazawa Y, van den Heuvel D, Luijsterburg MS, Ogi T. Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders. DNA Repair (Amst) 2021; 106:103192. [PMID: 34358806 DOI: 10.1016/j.dnarep.2021.103192] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.
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Affiliation(s)
- Nan Jia
- Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
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22
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Fritsch C, Gout JF, Haroon S, Towheed A, Chung C, LaGosh J, McGann E, Zhang X, Song Y, Simpson S, Danthi PS, Benayoun BA, Wallace D, Thomas K, Lynch M, Vermulst M. Genome-wide surveillance of transcription errors in response to genotoxic stress. Proc Natl Acad Sci U S A 2021; 118:e2004077118. [PMID: 33443141 PMCID: PMC7817157 DOI: 10.1073/pnas.2004077118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutagenic compounds are a potent source of human disease. By inducing genetic instability, they can accelerate the evolution of human cancers or lead to the development of genetically inherited diseases. Here, we show that in addition to genetic mutations, mutagens are also a powerful source of transcription errors. These errors arise in dividing and nondividing cells alike, affect every class of transcripts inside cells, and, in certain cases, greatly exceed the number of mutations that arise in the genome. In addition, we reveal the kinetics of transcription errors in response to mutagen exposure and find that DNA repair is required to mitigate transcriptional mutagenesis after exposure. Together, these observations have far-reaching consequences for our understanding of mutagenesis in human aging and disease, and suggest that the impact of DNA damage on human physiology has been greatly underestimated.
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Affiliation(s)
- C Fritsch
- Department of Cellular and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - J-F Gout
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762
| | - S Haroon
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - A Towheed
- Touro College of Osteopathic Medicine, Middletown, NY 10940
| | - C Chung
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - J LaGosh
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - E McGann
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - X Zhang
- Bioinforx, Inc., Madison, WI 53719
| | - Y Song
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - S Simpson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - P S Danthi
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - B A Benayoun
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - D Wallace
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - K Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - M Lynch
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287;
| | - M Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA 90089;
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
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23
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Anagnostou M, Chung C, McGann E, Verheijen B, Kou Y, Chen L, Vermulst M. Transcription errors in aging and disease. TRANSLATIONAL MEDICINE OF AGING 2021. [DOI: 10.1016/j.tma.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Oh J, Xu J, Chong J, Wang D. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194659. [PMID: 33271312 DOI: 10.1016/j.bbagrm.2020.194659] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022]
Abstract
Transcription elongation by RNA polymerase II (Pol II) is constantly challenged by numerous types of obstacles that lead to transcriptional pausing or stalling. These obstacles include DNA lesions, DNA epigenetic modifications, DNA binding proteins, and non-B form DNA structures. In particular, lesion-induced prolonged transcriptional blockage or stalling leads to genome instability, cellular dysfunction, and cell death. Transcription-coupled nucleotide excision repair (TC-NER) pathway is the first line of defense that detects and repairs these transcription-blocking DNA lesions. In this review, we will first summarize the recent research progress toward understanding the molecular basis of transcriptional pausing and stalling by different kinds of obstacles. We will then discuss new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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25
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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26
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Formation and Recognition of UV-Induced DNA Damage within Genome Complexity. Int J Mol Sci 2020; 21:ijms21186689. [PMID: 32932704 PMCID: PMC7555853 DOI: 10.3390/ijms21186689] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
Ultraviolet (UV) light is a natural genotoxic agent leading to the formation of photolesions endangering the genomic integrity and thereby the survival of living organisms. To prevent the mutagenetic effect of UV, several specific DNA repair mechanisms are mobilized to accurately maintain genome integrity at photodamaged sites within the complexity of genome structures. However, a fundamental gap remains to be filled in the identification and characterization of factors at the nexus of UV-induced DNA damage, DNA repair, and epigenetics. This review brings together the impact of the epigenomic context on the susceptibility of genomic regions to form photodamage and focuses on the mechanisms of photolesions recognition through the different DNA repair pathways.
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27
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Agapov A, Ignatov A, Turtola M, Belogurov G, Esyunina D, Kulbachinskiy A. Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase. J Biol Chem 2020; 295:9583-9595. [PMID: 32439804 DOI: 10.1074/jbc.ra119.011844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 05/20/2020] [Indexed: 11/06/2022] Open
Abstract
DNA lesions can severely compromise transcription and block RNA synthesis by RNA polymerase (RNAP), leading to subsequent recruitment of DNA repair factors to the stalled transcription complex. Recent structural studies have uncovered molecular interactions of several DNA lesions within the transcription elongation complex. However, little is known about the role of key elements of the RNAP active site in translesion transcription. Here, using recombinantly expressed proteins, in vitro transcription, kinetic analyses, and in vivo cell viability assays, we report that point amino acid substitutions in the trigger loop, a flexible element of the active site involved in nucleotide addition, can stimulate translesion RNA synthesis by Escherichia coli RNAP without altering the fidelity of nucleotide incorporation. We show that these substitutions also decrease transcriptional pausing and strongly affect the nucleotide addition cycle of RNAP by increasing the rate of nucleotide addition but also decreasing the rate of translocation. The secondary channel factors DksA and GreA modulated translesion transcription by RNAP, depending on changes in the trigger loop structure. We observed that although the mutant RNAPs stimulate translesion synthesis, their expression is toxic in vivo, especially under stress conditions. We conclude that the efficiency of translesion transcription can be significantly modulated by mutations affecting the conformational dynamics of the active site of RNAP, with potential effects on cellular stress responses and survival.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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28
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Saha LK, Wakasugi M, Akter S, Prasad R, Wilson SH, Shimizu N, Sasanuma H, Huang SYN, Agama K, Pommier Y, Matsunaga T, Hirota K, Iwai S, Nakazawa Y, Ogi T, Takeda S. Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Proc Natl Acad Sci U S A 2020; 117:14412-14420. [PMID: 32513688 PMCID: PMC7321995 DOI: 10.1073/pnas.1920165117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-destabilizing adducts including ultraviolet (UV) lesions, cyclobutane pyrimidine dimers (CPDs), and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). In comparison with CPDs, 6-4PPs have greater cytotoxicity and more strongly destabilizing properties of the DNA helix. It is generally believed that NER is the only DNA repair pathway that removes the UV lesions as evidenced by the previous data since no repair of UV lesions was detected in NER-deficient skin fibroblasts. Topoisomerase I (TOP1) constantly creates transient single-strand breaks (SSBs) releasing the torsional stress in genomic duplex DNA. Stalled TOP1-SSB complexes can form near DNA lesions including abasic sites and ribonucleotides embedded in chromosomal DNA. Here we show that base excision repair (BER) increases cellular tolerance to UV independently of NER in cancer cells. UV lesions irreversibly trap stable TOP1-SSB complexes near the UV damage in NER-deficient cells, and the resulting SSBs activate BER. Biochemical experiments show that 6-4PPs efficiently induce stable TOP1-SSB complexes, and the long-patch repair synthesis of BER removes 6-4PPs downstream of the SSB. Furthermore, NER-deficient cancer cell lines remove 6-4PPs within 24 h, but not CPDs, and the removal correlates with TOP1 expression. NER-deficient skin fibroblasts weakly express TOP1 and show no detectable repair of 6-4PPs. Remarkably, the ectopic expression of TOP1 in these fibroblasts led them to completely repair 6-4PPs within 24 h. In conclusion, we reveal a DNA repair pathway initiated by TOP1, which significantly contributes to cellular tolerance to UV-induced lesions particularly in malignant cancer cells overexpressing TOP1.
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Affiliation(s)
- Liton Kumar Saha
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Salma Akter
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Naoto Shimizu
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Kouji Hirota
- Department of Chemistry, Tokyo Metropolitan University, 192-0397 Tokyo, Japan
| | - Shigenori Iwai
- Biological Chemistry Group, Graduate School of Engineering Science, Osaka University, 565-0871 Osaka, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan;
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29
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RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-π and CH-π interactions. Proc Natl Acad Sci U S A 2020; 117:9338-9348. [PMID: 32284409 DOI: 10.1073/pnas.1919904117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Oxidation of guanine generates several types of DNA lesions, such as 8-oxoguanine (8OG), 5-guanidinohydantoin (Gh), and spiroiminodihydantoin (Sp). These guanine-derived oxidative DNA lesions interfere with both replication and transcription. However, the molecular mechanism of transcription processing of Gh and Sp remains unknown. In this study, by combining biochemical and structural analysis, we revealed distinct transcriptional processing of these chemically related oxidized lesions: 8OG allows both error-free and error-prone bypass, whereas Gh or Sp causes strong stalling and only allows slow error-prone incorporation of purines. Our structural studies provide snapshots of how polymerase II (Pol II) is stalled by a nonbulky Gh lesion in a stepwise manner, including the initial lesion encounter, ATP binding, ATP incorporation, jammed translocation, and arrested states. We show that while Gh can form hydrogen bonds with adenosine monophosphate (AMP) during incorporation, this base pair hydrogen bonding is not sufficient to hold an ATP substrate in the addition site and is not stable during Pol II translocation after the chemistry step. Intriguingly, we reveal a unique structural reconfiguration of the Gh lesion in which the hydantoin ring rotates ∼90° and is perpendicular to the upstream base pair planes. The perpendicular hydantoin ring of Gh is stabilized by noncanonical lone pair-π and CH-π interactions, as well as hydrogen bonds. As a result, the Gh lesion, as a functional mimic of a 1,2-intrastrand crosslink, occupies canonical -1 and +1 template positions and compromises the loading of the downstream template base. Furthermore, we suggest Gh and Sp lesions are potential targets of transcription-coupled repair.
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30
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Lans H, Hoeijmakers JHJ, Vermeulen W, Marteijn JA. The DNA damage response to transcription stress. Nat Rev Mol Cell Biol 2019; 20:766-784. [DOI: 10.1038/s41580-019-0169-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/30/2022]
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31
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Agapov A, Esyunina D, Kulbachinskiy A. Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase. RNA Biol 2019; 16:1711-1720. [PMID: 31416390 DOI: 10.1080/15476286.2019.1656027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deinococcus radiodurans is a highly stress resistant bacterium that encodes universal as well as lineage-specific factors involved in DNA transcription and repair. However, the effects of DNA lesions on RNA synthesis by D. radiodurans RNA polymerase (RNAP) have never been studied. We investigated the ability of this RNAP to transcribe damaged DNA templates and demonstrated that various lesions significantly affect the efficiency and fidelity of RNA synthesis. DNA modifications that disrupt correct base-pairing can strongly inhibit transcription and increase nucleotide misincorporation by D. radiodurans RNAP. The universal transcription factor GreA and Deinococcus-specific factor Gfh1 stimulate RNAP stalling at various DNA lesions, depending on the type of the lesion and the presence of Mn2+ ions, abundant divalent cations in D. radiodurans. Furthermore, Gfh1 stimulates the action of the Mfd translocase, which removes transcription elongation complexes paused at the sites of DNA lesions. Thus, Gre-family factors in D. radiodurans might have evolved to increase the efficiency of DNA damage recognition by the transcription and repair machineries in this bacterium.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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32
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Haijes HA, Koster MJE, Rehmann H, Li D, Hakonarson H, Cappuccio G, Hancarova M, Lehalle D, Reardon W, Schaefer GB, Lehman A, van de Laar IMBH, Tesselaar CD, Turner C, Goldenberg A, Patrier S, Thevenon J, Pinelli M, Brunetti-Pierri N, Prchalová D, Havlovicová M, Vlckova M, Sedláček Z, Lopez E, Ragoussis V, Pagnamenta AT, Kini U, Vos HR, van Es RM, van Schaik RFMA, van Essen TAJ, Kibaek M, Taylor JC, Sullivan J, Shashi V, Petrovski S, Fagerberg C, Martin DM, van Gassen KLI, Pfundt R, Falk MJ, McCormick EM, Timmers HTM, van Hasselt PM. De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. Am J Hum Genet 2019; 105:283-301. [PMID: 31353023 PMCID: PMC6699192 DOI: 10.1016/j.ajhg.2019.06.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/30/2019] [Indexed: 11/26/2022] Open
Abstract
The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.
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Affiliation(s)
- Hanneke A Haijes
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Maria J E Koster
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Holger Rehmann
- Expertise Center for Structural Biology, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Dong Li
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Daphne Lehalle
- Department of Genetics, Centre Hospitalier Universitaire de Dijon, 21000 Dijon, France
| | - Willie Reardon
- Department of Clinical and Medical Genetics, Our Lady's Hospital for Sick Children, D12 N512 Dublin, Ireland
| | - G Bradley Schaefer
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, AR 72223, USA
| | - Anna Lehman
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus Medical University Center Rotterdam, 3000 CA Rotterdam, the Netherlands
| | - Coranne D Tesselaar
- Department of Pediatrics, Amphia Hospital Breda, 4818 CK Breda, the Netherlands
| | - Clesson Turner
- Department of Clinical Genetics and Pediatrics, Walter Reed National Military Medical Center, Bethesda, Maryland, MD 20814, USA
| | - Alice Goldenberg
- Department of Genetics, Rouen University Hospital, Centre de Référence Anomalies du Développement, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
| | - Sophie Patrier
- Department of Pathology, Rouen University Hospital, Centre de Référence Anomalies du Développement, 76000 Rouen, France
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalier Universitaire de Grenoble, 38700 Grenoble, France
| | - Michele Pinelli
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Vlckova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Zdeněk Sedláček
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Elena Lopez
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Vassilis Ragoussis
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Alistair T Pagnamenta
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Usha Kini
- Department of Genomic Medicine, Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, OX3 7LE Oxford, UK
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Richard F M A van Schaik
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Ton A J van Essen
- Department of Clinical Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Maria Kibaek
- H.C. Andersen Children Hospital, Odense University Hospital, 5000 Odense, Denmark
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Slave Petrovski
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, CB4 0WG Cambridge, United Kingdom; Department of Medicine, the University of Melbourne, VIC 3010 Melbourne, Australia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, MI 48109, USA
| | - Koen L I van Gassen
- Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center Nijmegen, 6525 HR Nijmegen, the Netherlands
| | - Marni J Falk
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Department of Urology, University Medical Center Freiburg, University of Freiburg, 79110 Freiburg, Germany
| | - Peter M van Hasselt
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands.
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33
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Oh J, Xu J, Chong J, Wang D. Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest. Methods 2019; 159-160:29-34. [PMID: 30797902 DOI: 10.1016/j.ymeth.2019.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types of obstacles by its active site. A major class of obstacles is DNA lesions. While some DNA lesions can cause transient transcriptional pausing, which can be bypassed by Pol II itself or with the help from other elongation factors, bulky DNA damage can cause prolonged transcriptional pausing and arrest, which signals for transcription coupled repair. Using biochemical and structural biology approaches, the outcomes of many different types of DNA lesions, DNA modifications, and DNA binding molecules to transcription were studied. In this mini review, we will describe the in vitro transcription assays with Pol II to investigate the impacts of various DNA lesions on transcriptional outcomes and the crystallization method of lesion-arrested Pol II complex. These methods can provide a general platform for the structural and biochemical analysis of Pol II transcriptional pausing and bypass mechanisms.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States.
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34
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Selvam K, Ding B, Sharma R, Li S. Evidence that Moderate Eviction of Spt5 and Promotion of Error-Free Transcriptional Bypass by Rad26 Facilitates Transcription Coupled Nucleotide Excision Repair. J Mol Biol 2019; 431:1322-1338. [PMID: 30790631 DOI: 10.1016/j.jmb.2019.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/12/2019] [Accepted: 02/11/2019] [Indexed: 11/18/2022]
Abstract
Transcription coupled repair (TC-NER) is a subpathway of nucleotide excision repair triggered by stalling of RNA polymerase at DNA lesions. It has been suspected that transcriptional misincorporations of certain nucleotides opposite lesions that result in irreversible transcription stalling might be important for TC-NER. However, the spectra of nucleotide misincorporations opposite UV photoproducts and how they are implicated in transcriptional stalling and TC-NER in the cell remain unknown. Rad26, a low abundant yeast protein, and its human homolog CSB have been proposed to facilitate TC-NER in part by positioning and stabilizing stalling of RNA polymerase II (RNAPII) at DNA lesions. Here, we found that substantial AMPs but no other nucleotides are transcriptionally misincoporated and extended opposite UV photoproducts and adjacent bases in Saccharomyces cerevisiae. Rad26 does not significantly affect either the misincorporation or extension of AMPs. At normally low or moderately increased levels, Rad26 promotes error-free transcriptional bypass and TC-NER of UV photoproducts. However, Rad26 completely loses these functions when it is overexpressed to ~1/3 the level of RNAPII molecules. Also, Rad26 does not directly displace RNAPII but constitutively evicts Spt5, a key transcription elongation factor and TC-NER repressor, from the chromatin. Our results indicate that transcriptional nucleotide misincorporation is not implicated in TC-NER, and moderate eviction of Spt5 and promotion of error-free transcriptional bypass of DNA lesions by Rad26 facilitates TC-NER.
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Affiliation(s)
- Kathiresan Selvam
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Baojin Ding
- Department of Biology, University of Louisiana at Lafayette, 410 E. St. Mary Blvd, Lafayette, LA 70503, USA
| | - Rahul Sharma
- National Hansen's Disease Program, Laboratory Research Branch at Louisiana State University, 3519E School of Veterinary Medicine, Baton Rouge, LA 70803, USA
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA.
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35
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Konovalov KA, Pardo-Avila F, Tse CKM, Oh J, Wang D, Huang X. 8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II. J Biol Chem 2019; 294:4924-4933. [PMID: 30718278 DOI: 10.1074/jbc.ra118.007333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/29/2019] [Indexed: 01/05/2023] Open
Abstract
RNA polymerase II (Pol II) has an intrinsic fidelity control mechanism to maintain faithful genetic information transfer during transcription. 8-Oxo-guanine (8OG), a commonly occurring damaged guanine base, promotes misincorporation of adenine into the RNA strand. Recent structural work has shown that adenine can pair with the syn conformation of 8OG directly upstream of the Pol II active site. However, it remains unknown how 8OG is accommodated in the active site as a template base for the incoming ATP. Here, we used molecular dynamics (MD) simulations to investigate two consecutive steps that may contribute to the adenine misincorporation by Pol II. First, the mismatch is located in the active site, contributing to initial incorporation of adenine. Second, the mismatch is in the adjacent upstream position, contributing to extension from the mismatched bp. These results are supported by an in vitro transcription assay, confirming that 8OG can induce adenine misincorporation. Our simulations further suggest that 8OG forms a stable bp with the mismatched adenine in both the active site and the adjacent upstream position. This stability predominantly originates from hydrogen bonding between the mismatched adenine and 8OG in a noncanonical syn conformation. Interestingly, we also found that an unstable bp present directly upstream of the active site, such as adenine paired with 8OG in the canonical anti conformation, largely disrupts the stability of the active site. Our findings have uncovered two main factors contributing to how 8OG induces transcriptional errors and escapes Pol II transcriptional fidelity control checkpoints.
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Affiliation(s)
- Kirill A Konovalov
- From the HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, and
| | - Fátima Pardo-Avila
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, and
| | - Carmen Ka Man Tse
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, and
| | - Juntaek Oh
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093
| | - Dong Wang
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093
| | - Xuhui Huang
- From the HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China, .,Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, and
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36
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Pupov D, Ignatov A, Agapov A, Kulbachinskiy A. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase. Biochem Biophys Res Commun 2019; 510:122-127. [PMID: 30665719 DOI: 10.1016/j.bbrc.2019.01.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/12/2019] [Indexed: 01/08/2023]
Abstract
DNA lesions can severely compromise genome stability and lead to cell death if unrepaired. RNA polymerase (RNAP) is known to serve as a sensor of DNA damage and to attract DNA repair factors to the damaged template sites. Here, we systematically investigated the ability of Escherichia coli RNAP to transcribe DNA templates containing various types of DNA lesions, and analyzed their effects on transcription fidelity. We showed that transcription is strongly inhibited on templates containing cyclobutane thymine dimers, 1,N6-ethenoadenine and abasic sites, while 8-oxoguanine and thymine glycol have mild effects on transcription efficiency. Similarly to many polymerases, E. coli RNAP follows the "A" rule during nucleotide insertion opposite abasic sites and bulky lesions, and can also incorporate and efficiently extend an adenine nucleotide opposite 8-oxoguanine. Mutations in RNAP regions around the templating nucleotide decrease the efficiency of translesion synthesis, likely by altering the RNAP-template contacts in the active site. Thus, DNA lesions can lead to distinct outcomes in transcription, depending on the severity of the damage and contacts of the damaged template with the active site of RNAP.
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Affiliation(s)
- Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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Portman JR, Strick TR. Transcription-Coupled Repair and Complex Biology. J Mol Biol 2018; 430:4496-4512. [DOI: 10.1016/j.jmb.2018.04.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/24/2022]
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Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernández-Tornero C. Structural basis of RNA polymerase I stalling at UV light-induced DNA damage. Proc Natl Acad Sci U S A 2018; 115:8972-8977. [PMID: 30127008 PMCID: PMC6130403 DOI: 10.1073/pnas.1802626115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase I (Pol I) transcribes ribosomal DNA (rDNA) to produce the ribosomal RNA (rRNA) precursor, which accounts for up to 60% of the total transcriptional activity in growing cells. Pol I monitors rDNA integrity and influences cell survival, but little is known about how this enzyme processes UV-induced lesions. We report the electron cryomicroscopy structure of Pol I in an elongation complex containing a cyclobutane pyrimidine dimer (CPD) at a resolution of 3.6 Å. The structure shows that the lesion induces an early translocation intermediate exhibiting unique features. The bridge helix residue Arg1015 plays a major role in CPD-induced Pol I stalling, as confirmed by mutational analysis. These results, together with biochemical data presented here, reveal the molecular mechanism of Pol I stalling by CPD lesions, which is distinct from Pol II arrest by CPD lesions. Our findings open the avenue to unravel the molecular mechanisms underlying cell endurance to lesions on rDNA.
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Affiliation(s)
- Marta Sanz-Murillo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain
| | - Jun Xu
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0625
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093-0625
| | | | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain
| | - David Gil-Carton
- Structural Biology Unit, Cooperative Center for Research in Biosciences (CIC bioGUNE), 48160 Derio, Spain
| | - María Moreno-Morcillo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC, 28049 Madrid, Spain
| | - Dong Wang
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0625;
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093-0625
| | - Carlos Fernández-Tornero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain;
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Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2018; 71:43-55. [PMID: 30174298 DOI: 10.1016/j.dnarep.2018.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic transcription-coupled nucleotide excision repair (TC-NER) is a pathway that removes DNA lesions capable of blocking RNA polymerase II (Pol II) transcription from the template strand. This process is initiated by lesion-arrested Pol II and the recruitment of Cockayne Syndrome B protein (CSB). In this review, we will focus on the lesion recognition steps of eukaryotic TC-NER and summarize the recent research progress toward understanding the structural basis of Pol II-mediated lesion recognition and Pol II-CSB interactions. We will discuss the roles of CSB in both TC-NER initiation and transcription elongation. Finally, we propose an updated model of tripartite lesion recognition and verification for TC-NER in which CSB ensures Pol II-mediated recognition of DNA lesions for TC-NER.
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Burns JA, Chowdhury MA, Cartularo L, Berens C, Scicchitano DA. Genetic instability associated with loop or stem-loop structures within transcription units can be independent of nucleotide excision repair. Nucleic Acids Res 2018; 46:3498-3516. [PMID: 29474673 PMCID: PMC5909459 DOI: 10.1093/nar/gky110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/04/2018] [Accepted: 02/14/2018] [Indexed: 12/31/2022] Open
Abstract
Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem-loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them.
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Affiliation(s)
- John A Burns
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Laura Cartularo
- Department of Biology, New York University, New York, NY 10003, USA
| | - Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Löffler-Institut, Jena, Germany
| | - David A Scicchitano
- Department of Biology, New York University, New York, NY 10003, USA
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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42
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Wang W, Walmacq C, Chong J, Kashlev M, Wang D. Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc Natl Acad Sci U S A 2018; 115:E2538-E2545. [PMID: 29487211 PMCID: PMC5856558 DOI: 10.1073/pnas.1722050115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Abasic sites are among the most abundant DNA lesions and interfere with DNA replication and transcription, but the mechanism of their action on transcription remains unknown. Here we applied a combined structural and biochemical approach for a comprehensive investigation of how RNA polymerase II (Pol II) processes an abasic site, leading to slow bypass of lesion. Encounter of Pol II with an abasic site involves two consecutive slow steps: insertion of adenine opposite a noninstructive abasic site (the A-rule), followed by extension of the 3'-rAMP with the next cognate nucleotide. Further studies provided structural insights into the A-rule: ATP is slowly incorporated into RNA in the absence of template guidance. Our structure revealed that ATP is bound to the Pol II active site, whereas the abasic site is located at an intermediate state above the Bridge Helix, a conserved structural motif that is cirtical for Pol II activity. The next extension step occurs in a template-dependent manner where a cognate substrate is incorporated, despite at a much slower rate compared with nondamaged template. During the extension step, neither the cognate substrate nor the template base is located at the canonical position, providing a structural explanation as to why this step is as slow as the insertion step. Taken together, our studies provide a comprehensive understanding of Pol II stalling and bypass of the abasic site in the DNA template.
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Affiliation(s)
- Wei Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Celine Walmacq
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Mikhail Kashlev
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093
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43
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Paredes JA, Ezerskyte M, Bottai M, Dreij K. Transcriptional mutagenesis reduces splicing fidelity in mammalian cells. Nucleic Acids Res 2017; 45:6520-6529. [PMID: 28460122 PMCID: PMC5499639 DOI: 10.1093/nar/gkx339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/18/2017] [Indexed: 12/11/2022] Open
Abstract
Splicing fidelity is essential to the maintenance of cellular functions and viability, and mutations or natural variations in pre-mRNA sequences and consequent alteration of splicing have been implicated in the etiology and progression of numerous diseases. The extent to which transcriptional errors or lesion-induced transcriptional mutagenesis (TM) influences splicing fidelity is not currently known. To investigate this, we employed site-specific DNA lesions on the transcribed strand of a minigene splicing reporter in normal mammalian cells. These were the common mutagenic lesions O6-methylguanine (O6-meG) and 8-oxoguanine (8-oxoG). The minigene splicing reporters were derived from lamin A (LMNA) and proteolipid protein 1 (PLP1), both with known links to human diseases that result from deregulated splicing. In cells with active DNA repair, 1–4% misincorporation occurred opposite the lesions, which increased to 20–40% when repair was compromised. Furthermore, our results reveal that TM at a splice site significantly reduces in vivo splicing fidelity, thereby changing the relative expression of alternative splicing forms in mammalian cells. These findings suggest that splicing defects caused by transcriptional errors can potentially lead to phenotypic cellular changes and increased susceptibility to the development of disease.
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Affiliation(s)
- João A Paredes
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Monika Ezerskyte
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Matteo Bottai
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kristian Dreij
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
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44
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Appling FD, Lucius AL, Schneider DA. Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity. Biophys Chem 2017; 230:84-88. [PMID: 28893424 DOI: 10.1016/j.bpc.2017.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022]
Abstract
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates. We found that 5' modifications had no discernable effect on the kinetics of nucleotide addition; however, we observed clear, but modest, effects on the rate of backtracking and/or dinucleotide cleavage. These data suggest that the 5'-end may influence RNA polymerase translocation, consistent with previous prokaryotic studies, and these findings may have implications on kinetic barriers that confront RNA polymerases during the transition from initiation to elongation.
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Affiliation(s)
- Francis D Appling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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45
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Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E7082-E7091. [PMID: 28784758 DOI: 10.1073/pnas.1708748114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O2-, N3-, and O4-ethylthymidine (O2-, N3-, and O4-EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O2-EtdT and N3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O2-EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O4-EtdT lesion. For the N3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove-sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.
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46
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Fujii N. Potential Strategies to Target Protein-Protein Interactions in the DNA Damage Response and Repair Pathways. J Med Chem 2017; 60:9932-9959. [PMID: 28654754 DOI: 10.1021/acs.jmedchem.7b00358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, on the basis of functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent.
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Affiliation(s)
- Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
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47
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Winton CE, Gilmore BL, Tanner JR, Varano AC, Sheng Z, Kelly DF. Tunable substrates improve imaging of viruses and cancer proteins. MICROSCOPY TODAY 2017; 25:22-27. [PMID: 29056883 PMCID: PMC5648339 DOI: 10.1017/s1551929517000657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recent breakthroughs in cryo-electron microscopy imaging technology provide an unprecedented view of biology at the nanoscale. To complement these technical advances, here we demonstrate the use of tunable substrates to streamline the isolation of biological entities from human cells. We have tested the capacity of tunable microchip devices using a variety of samples including virus assemblies and the breast cancer susceptibility protein (BRCA1) produced in cancer cells. Overall, microchip applications may shed light on ill-defined clinical issues related to molecular disease mechanisms.
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Affiliation(s)
- Carly E. Winton
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Brian L. Gilmore
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Justin R. Tanner
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - A. Cameron Varano
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zhi Sheng
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
| | - Deborah F. Kelly
- Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA 24016, USA
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Abstract
Transcription-coupled DNA repair (TCR) acts on lesions in the transcribed strand of active genes. Helix distorting adducts and other forms of DNA damage often interfere with the progression of the transcription apparatus. Prolonged stalling of RNA polymerase can promote genome instability and also induce cell cycle arrest and apoptosis. These generally unfavorable events are counteracted by RNA polymerase-mediated recruitment of specific proteins to the sites of DNA damage to perform TCR and eventually restore transcription. In this perspective we discuss the decision-making process to employ TCR and we elucidate the intricate biochemical pathways leading to TCR in E. coli and human cells.
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Affiliation(s)
- Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
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49
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Kolbanovskiy M, Chowdhury MA, Nadkarni A, Broyde S, Geacintov NE, Scicchitano DA, Shafirovich V. The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro. Biochemistry 2017; 56:3008-3018. [PMID: 28514164 DOI: 10.1021/acs.biochem.7b00295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The most common, oxidatively generated lesion in cellular DNA is 8-oxo-7,8-dihydroguanine, which can be oxidized further to yield highly mutagenic spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in DNA. In human cell-free extracts, both lesions can be excised by base excision repair and global genomic nucleotide excision repair. However, it is not known if these lesions can be removed by transcription-coupled DNA repair (TCR), a pathway that clears lesions from DNA that impede RNA synthesis. To determine if Sp or Gh impedes transcription, which could make each a viable substrate for TCR, either an Sp or a Gh lesion was positioned on the transcribed strand of DNA under the control of a promoter that supports transcription by human RNA polymerase II. These constructs were incubated in HeLa nuclear extracts that contained active RNA polymerase II, and the resulting transcripts were resolved by denaturing polyacrylamide gel electrophoresis. The structurally rigid Sp strongly blocks transcription elongation, permitting 1.6 ± 0.5% nominal lesion bypass. In contrast, the conformationally flexible Gh poses less of a block to human RNAPII, allowing 9 ± 2% bypass. Furthermore, fractional lesion bypass for Sp and Gh is minimally affected by glycosylase activity found in the HeLa nuclear extract. These data specifically suggest that both Sp and Gh may well be susceptible to TCR because each poses a significant block to human RNA polymerase II progression. A more general principle is also proposed: Conformational flexibility may be an important structural feature of DNA lesions that enhances their transcriptional bypass.
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Affiliation(s)
- Marina Kolbanovskiy
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Moinuddin A Chowdhury
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Aditi Nadkarni
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Suse Broyde
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - Nicholas E Geacintov
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
| | - David A Scicchitano
- Department of Biology, New York University , 100 Washington Square East, New York, New York 10003-5180, United States.,Division of Science, New York University Abu Dhabi , P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Vladimir Shafirovich
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003-5180, United States
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50
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Menoni H, Di Mascio P, Cadet J, Dimitrov S, Angelov D. Chromatin associated mechanisms in base excision repair - nucleosome remodeling and DNA transcription, two key players. Free Radic Biol Med 2017; 107:159-169. [PMID: 28011149 DOI: 10.1016/j.freeradbiomed.2016.12.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin?
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Affiliation(s)
- Hervé Menoni
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France.
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000 São Paulo, SP, Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stefan Dimitrov
- Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
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