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Costanzo F, Paccosi E, Proietti-De-Santis L, Egly JM. CS proteins and ubiquitination: orchestrating DNA repair with transcription and cell division. Trends Cell Biol 2024:S0962-8924(24)00116-8. [PMID: 38910038 DOI: 10.1016/j.tcb.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 06/25/2024]
Abstract
To face genotoxic stress, eukaryotic cells evolved extremely refined mechanisms. Defects in counteracting the threat imposed by DNA damage underlie the rare disease Cockayne syndrome (CS), which arises from mutations in the CSA and CSB genes. Although initially defined as DNA repair proteins, recent work shows that CSA and CSB act instead as master regulators of the integrated response to genomic stress by coordinating DNA repair with transcription and cell division. CSA and CSB exert this function through the ubiquitination of target proteins, which are effectors/regulators of these processes. This review describes how the ubiquitination of target substrates is a common denominator by which CSA and CSB participate in different aspects of cellular life and how their mutation gives rise to the complex disease CS.
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Affiliation(s)
- Federico Costanzo
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona 6500, Switzerland; Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Illkirch-Graffenstaden 67400, Strasbourg, France.
| | - Elena Paccosi
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo 01100, Italy
| | - Luca Proietti-De-Santis
- Unit of Molecular Genetics of Aging, Department of Ecology and Biology, University of Tuscia, Viterbo 01100, Italy
| | - Jean Marc Egly
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona 6500, Switzerland; Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Illkirch-Graffenstaden 67400, Strasbourg, France; College of Medicine, Centre for Genomics and Precision Medicine, National Taiwan University, Taipei City, Taiwan
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2
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R P, Rakshit S, Shanmugam G, George M, Sarkar K. Wiskott Aldrich syndrome protein (WASp)-deficient Th1 cells promote R-loop-driven transcriptional insufficiency and transcription-coupled nucleotide excision repair factor (TC-NER)-driven genome-instability in the pathogenesis of T cell acute lymphoblastic leukemia. Clin Immunol 2024; 263:110204. [PMID: 38582251 DOI: 10.1016/j.clim.2024.110204] [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: 01/25/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND T-ALL is an aggressive hematological tumor that develops as the result of a multi-step oncogenic process which causes expansion of hematopoietic progenitors that are primed for T cell development to undergo malignant transformation and growth. Even though first-line therapy has a significant response rate, 40% of adult patients and 20% of pediatric patients will relapse. Therefore, there is an unmet need for treatment for relapsed/refractory T-ALL to develop potential targeted therapies. METHODS Pediatric T-ALL patient derived T cells were grown under either nonskewingTh0 or Th1-skewing conditions to further process for ChIP-qPCR, RDIP-qPCR and other RT-PCR assays. Endogenous WASp was knocked out using CRISPR-Cas9 and was confirmed using flow cytometry and western blotting. LC-MS/MS was performed to find out proteomic dataset of WASp-interactors generated from Th1-skewed, human primary Th-cells. DNA-damage was assessed by immunofluorescence confocal-imaging and single-cell gel electrophoresis (comet assay). Overexpression of RNaseH1 was also done to restore normal Th1-transcription in WASp-deficient Th1-skewed cells. RESULTS We discovered that nuclear-WASp is required for suppressing R-loop production (RNA/DNA-hybrids) at Th1-network genes by ribonucleaseH2 (RNH2) and topoisomerase1. Nuclear-WASp is associated with the factors involved in preventing and dissolving R-loops in Th1 cells. In nuclear- WASp-reduced malignant Th1-cells, R-loops accumulate in vivo and are processed into DNA-breaks by transcription-coupled-nucleotide-excision repair (TC-NER). Several epigenetic modifications were also found to be involved at Th1 gene locus which are responsible for active/repressive marks of particular genes. By demonstrating WASp as a physiologic regulator of programmed versus unprogrammed R-loops, we suggest that the transcriptional role of WASp in vivo extends also to prevent transcription-linked DNA damage during malignancy and through modification of epigenetic dysregulations. CONCLUSION Our findings present a provocative possibility of resetting R-loops as a therapeutic intervention to correct both immune deficiency and malignancy in T-cell acute lymphoblastic leukemia patients and a novel role of WASp in the epigenetic regulation of T helper cell differentiation in T-ALL patients, anticipating WASp's requirement for the suppression of T-ALL progression.
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Affiliation(s)
- Pradeep R
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Melvin George
- Department of Clinical Pharmacology, SRM Medical College Hospital and Research Centre, Kattankulathur, Tamil Nadu 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India.
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3
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Afshari N, Koturbash I, Boerma M, Newhauser W, Kratz M, Willey J, Williams J, Chancellor J. A Review of Numerical Models of Radiation Injury and Repair Considering Subcellular Targets and the Extracellular Microenvironment. Int J Mol Sci 2024; 25:1015. [PMID: 38256089 PMCID: PMC10816679 DOI: 10.3390/ijms25021015] [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: 11/16/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Astronauts in space are subject to continuous exposure to ionizing radiation. There is concern about the acute and late-occurring adverse health effects that astronauts could incur following a protracted exposure to the space radiation environment. Therefore, it is vital to consider the current tools and models used to describe and study the organic consequences of ionizing radiation exposure. It is equally important to see where these models could be improved. Historically, radiobiological models focused on how radiation damages nuclear deoxyribonucleic acid (DNA) and the role DNA repair mechanisms play in resulting biological effects, building on the hypotheses of Crowther and Lea from the 1940s and 1960s, and they neglected other subcellular targets outside of nuclear DNA. The development of these models and the current state of knowledge about radiation effects impacting astronauts in orbit, as well as how the radiation environment and cellular microenvironment are incorporated into these radiobiological models, aid our understanding of the influence space travel may have on astronaut health. It is vital to consider the current tools and models used to describe the organic consequences of ionizing radiation exposure and identify where they can be further improved.
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Affiliation(s)
- Nousha Afshari
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
| | - Igor Koturbash
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Marjan Boerma
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Wayne Newhauser
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
| | - Maria Kratz
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Jeffrey Willey
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - Jacqueline Williams
- School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Jeffery Chancellor
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
- Department of Preventive Medicine and Population Health, University of Texas Medical Branch, Galveston, TX 77555, USA
- Outer Space Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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4
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Chatzinikolaou G, Stratigi K, Siametis A, Goulielmaki E, Akalestou-Clocher A, Tsamardinos I, Topalis P, Austin C, Bouwman BA, Crosetto N, Altmüller J, Garinis GA. XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes. SCIENCE ADVANCES 2023; 9:eadi2095. [PMID: 37939182 PMCID: PMC10631727 DOI: 10.1126/sciadv.adi2095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop-dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair-deficient syndromes associated with transcription-associated DNA damage.
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Affiliation(s)
- Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Tsamardinos
- Computer Science Department of University of Crete, Heraklion, Crete, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Caroline Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Britta A. M. Bouwman
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
| | - Nicola Crosetto
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157 Milan, Italy
| | - Janine Altmüller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Facility Genomics, Charitéplatz 1, 10117 Berlin, Germany
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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5
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Maritz C, Khaleghi R, Yancoskie MN, Diethelm S, Brülisauer S, Ferreira NS, Jiang Y, Sturla SJ, Naegeli H. ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair. Nat Commun 2023; 14:3892. [PMID: 37393406 PMCID: PMC10314917 DOI: 10.1038/s41467-023-39635-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 06/22/2023] [Indexed: 07/03/2023] Open
Abstract
To recognize DNA adducts, nucleotide excision repair (NER) deploys the XPC sensor, which detects damage-induced helical distortions, followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place in chromatin where DNA is tightly wrapped around histones. Here, we describe how the histone methyltransferase ASH1L, once activated by MRG15, helps XPC and TFIIH to navigate through chromatin and induce global-genome NER hotspots. Upon UV irradiation, ASH1L adds H3K4me3 all over the genome (except in active gene promoters), thus priming chromatin for XPC relocations from native to damaged DNA. The ASH1L-MRG15 complex further recruits the histone chaperone FACT to DNA lesions. In the absence of ASH1L, MRG15 or FACT, XPC is misplaced and persists on damaged DNA without being able to deliver the lesions to TFIIH. We conclude that ASH1L-MRG15 makes damage verifiable by the NER machinery through the sequential deposition of H3K4me3 and FACT.
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Affiliation(s)
- Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sonja Brülisauer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Natalia Santos Ferreira
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Yang Jiang
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland.
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6
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Yancoskie MN, Maritz C, van Eijk P, Reed SH, Naegeli H. To incise or not and where: SET-domain methyltransferases know. Trends Biochem Sci 2023; 48:321-330. [PMID: 36357311 DOI: 10.1016/j.tibs.2022.10.003] [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: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The concept of the histone code posits that histone modifications regulate gene functions once interpreted by epigenetic readers. A well-studied case is trimethylation of lysine 4 of histone H3 (H3K4me3), which is enriched at gene promoters. However, H3K4me3 marks are not needed for the expression of most genes, suggesting extra roles, such as influencing the 3D genome architecture. Here, we highlight an intriguing analogy between the H3K4me3-dependent induction of double-strand breaks in several recombination events and the impact of this same mark on DNA incisions for the repair of bulky lesions. We propose that Su(var)3-9, Enhancer-of-zeste and Trithorax (SET)-domain methyltransferases generate H3K4me3 to guide nucleases into chromatin spaces, the favorable accessibility of which ensures that DNA break intermediates are readily processed, thereby safeguarding genome stability.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland.
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7
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van den Heuvel D, Kim M, Wondergem AP, van der Meer PJ, Witkamp M, Lambregtse F, Kim HS, Kan F, Apelt K, Kragten A, González-Prieto R, Vertegaal ACO, Yeo JE, Kim BG, van Doorn R, Schärer OD, Luijsterburg MS. A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair. Proc Natl Acad Sci U S A 2023; 120:e2208860120. [PMID: 36893274 PMCID: PMC10089173 DOI: 10.1073/pnas.2208860120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Annelotte P. Wondergem
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Paula J. van der Meer
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Myrèse Witkamp
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Ferdy Lambregtse
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Folkert Kan
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine, University of Sevilla, 41092Seville, Spain
- Department of Cell Biology, University of Seville, 41012Seville, Spain
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZALeiden, The Netherlands
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Martijn S. Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
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8
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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9
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Sandoz J, Cigrang M, Zachayus A, Catez P, Donnio LM, Elly C, Nieminuszczy J, Berico P, Braun C, Alekseev S, Egly JM, Niedzwiedz W, Giglia-Mari G, Compe E, Coin F. Active mRNA degradation by EXD2 nuclease elicits recovery of transcription after genotoxic stress. Nat Commun 2023; 14:341. [PMID: 36670096 PMCID: PMC9859823 DOI: 10.1038/s41467-023-35922-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/06/2023] [Indexed: 01/22/2023] Open
Abstract
The transcriptional response to genotoxic stress involves gene expression arrest, followed by recovery of mRNA synthesis (RRS) after DNA repair. We find that the lack of the EXD2 nuclease impairs RRS and decreases cell survival after UV irradiation, without affecting DNA repair. Overexpression of wild-type, but not nuclease-dead EXD2, restores RRS and cell survival. We observe that UV irradiation triggers the relocation of EXD2 from mitochondria to the nucleus. There, EXD2 is recruited to chromatin where it transiently interacts with RNA Polymerase II (RNAPII) to promote the degradation of nascent mRNAs synthesized at the time of genotoxic attack. Reconstitution of the EXD2-RNAPII partnership on a transcribed DNA template in vitro shows that EXD2 primarily interacts with an elongation-blocked RNAPII and efficiently digests mRNA. Overall, our data highlight a crucial step in the transcriptional response to genotoxic attack in which EXD2 interacts with elongation-stalled RNAPII on chromatin to potentially degrade the associated nascent mRNA, allowing transcription restart after DNA repair.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Amélie Zachayus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Lise-Marie Donnio
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Clèmence Elly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Sergey Alekseev
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Giuseppina Giglia-Mari
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Strasbourg, France.
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10
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Takeuchi S, Fukumoto T, Takemori C, Saito N, Nishigori C, Sato M. Cell migration is impaired in XPA-deficient cells. FASEB Bioadv 2022; 5:53-61. [PMID: 36816512 PMCID: PMC9927838 DOI: 10.1096/fba.2022-00084] [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: 07/29/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a hereditary disorder characterized by photosensitivity, predisposition to skin cancers, and neurological abnormalities including microcephaly and progressive neurodegeneration. A lack of nucleotide excision repair (NER) in patients with XP can cause hypersensitivity to the sun, leading to skin cancer, whereas the etiology of the neuronal symptoms of XP remains ambiguous. There are various neurological disorders that perturb neuronal migration, causing mislocalization and disorganization of the cortical lamination. Here, we investigated the role of the XP group-A (Xpa) gene in directed cell migration. First, we adopted an in utero electroporation method to transduce shRNA vectors into the murine embryonic cerebral cortex for the in vivo knockdown of Xpa. Xpa-knockdown neurons in the embryonic cerebral cortex showed abnormal cell migration, cell cycle exit, and differentiation. The genotype-phenotype relationship between the lack of XPA and cell migration abnormalities was confirmed using both a scratch assay and time-lapse microscopy in XP-A patient-derived fibroblasts. Unlike healthy cells, these cells showed impairment in overall mobility and the direction of motility. Therefore, abnormal cell migration may explain neural tissue abnormalities in patients with XP-A.
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Affiliation(s)
- Seiji Takeuchi
- Division of Dermatology, Department of Internal RelatedKobe University Graduate School of MedicineKobeJapan,Division of Cell Biology and NeuroscienceDepartment of Morphological and Physiological Sciences, Faculty of Medical SciencesUniversity of FukuiFukuiJapan
| | - Takeshi Fukumoto
- Division of Dermatology, Department of Internal RelatedKobe University Graduate School of MedicineKobeJapan
| | - Chihiro Takemori
- Division of Dermatology, Department of Internal RelatedKobe University Graduate School of MedicineKobeJapan
| | - Naoaki Saito
- Laboratory of Molecular Pharmacology, Biosignal Research CenterKobe UniversityKobeJapan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal RelatedKobe University Graduate School of MedicineKobeJapan,Department of iPS cell applicationsGraduate School of Medicine, Kobe UniversityKobeJapan
| | - Makoto Sato
- Division of Cell Biology and NeuroscienceDepartment of Morphological and Physiological Sciences, Faculty of Medical SciencesUniversity of FukuiFukuiJapan,Department of Anatomy and NeuroscienceGraduate School of Medicine, Osaka UniversityOsakaJapan,United Graduate School of Child DevelopmentOsaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui (UGSCD)OsakaJapan
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11
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Bralić A, Tehseen M, Sobhy MA, Tsai CL, Alhudhali L, Yi G, Yu J, Yan C, Ivanov I, Tsutakawa SE, Tainer J, Hamdan S. A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. Nucleic Acids Res 2022; 51:1019-1033. [PMID: 36477609 PMCID: PMC9943652 DOI: 10.1093/nar/gkac1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022] Open
Abstract
Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.
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Affiliation(s)
- Amer Bralić
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed A Sobhy
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lubna Alhudhali
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gang Yi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jina Yu
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Correspondence may also be addressed to John A. Tainer. Tel: +1 713 563 7725; Fax: +1 713 794 3270;
| | - Samir M Hamdan
- To whom correspondence should be addressed. Tel: +96 628082384; Cell: +96 6544700031;
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12
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Compe E, Pangou E, Le May N, Elly C, Braun C, Hwang JH, Coin F, Sumara I, Choi KW, Egly JM. Phosphorylation of XPD drives its mitotic role independently of its DNA repair and transcription functions. SCIENCE ADVANCES 2022; 8:eabp9457. [PMID: 35977011 PMCID: PMC9385140 DOI: 10.1126/sciadv.abp9457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The helicase XPD is known as a key subunit of the DNA repair/transcription factor TFIIH. However, here, we report that XPD, independently to other TFIIH subunits, can localize with the motor kinesin Eg5 to mitotic spindles and the midbodies of human cells. The XPD/Eg5 partnership is promoted upon phosphorylation of Eg5/T926 by the kinase CDK1, and conversely, it is reduced once Eg5/S1033 is phosphorylated by NEK6, a mitotic kinase that also targets XPD at T425. The phosphorylation of XPD does not affect its DNA repair and transcription functions, but it is required for Eg5 localization, checkpoint activation, and chromosome segregation in mitosis. In XPD-mutated cells derived from a patient with xeroderma pigmentosum, the phosphomimetic form XPD/T425D or even the nonphosphorylatable form Eg5/S1033A specifically restores mitotic chromosome segregation errors. These results thus highlight the phospho-dependent mitotic function of XPD and reveal how mitotic defects might contribute to XPD-related disorders.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Evanthia Pangou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Cycle Cellulaire et Signalisation de l’Ubiquitine, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404, Strasbourg, France
| | - Nicolas Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Clémence Elly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Ji-Hyun Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Cycle Cellulaire et Signalisation de l’Ubiquitine, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404, Strasbourg, France
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
- College of Medicine, National Taiwan Institute, Taipei 10051, Taiwan
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13
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Ljungman M. Transcription and genome integrity. DNA Repair (Amst) 2022; 118:103373. [PMID: 35914488 DOI: 10.1016/j.dnarep.2022.103373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.
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Affiliation(s)
- Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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14
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Gopaul D, Denby Wilkes C, Goldar A, Giordanengo Aiach N, Barrault MB, Novikova E, Soutourina J. Genomic analysis of Rad26 and Rad1-Rad10 reveals differences in their dependence on Mediator and RNA polymerase II. Genome Res 2022; 32:gr.276371.121. [PMID: 35738899 PMCID: PMC9435749 DOI: 10.1101/gr.276371.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/16/2022] [Indexed: 02/03/2023]
Abstract
Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1-Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.
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Affiliation(s)
- Diyavarshini Gopaul
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elizaveta Novikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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15
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Chandramouly G. Gadd45 in DNA Demethylation and DNA Repair. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1360:55-67. [PMID: 35505162 DOI: 10.1007/978-3-030-94804-7_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Growth arrest and DNA damage 45 (Gadd45) family genes, Gadd45A, Gadd45B, and GADD45 G are implicated as stress sensors that are rapidly induced upon genotoxic/physiological stress. They are involved in regulation of various cellular functions such as DNA repair, senescence, and cell cycle control. Gadd45 family of genes serve as tumor suppressors in response to different stimuli and defects in Gadd45 pathway can give rise to oncogenesis. More recently, Gadd45 has been shown to promote gene activation by demethylation and this function is important for transcriptional regulation and differentiation during development. Gadd45 serves as an adaptor for DNA repair factors to promote removal of 5-methylcytosine from DNA at gene specific loci. Therefore, Gadd45 serves as a powerful link between DNA repair and epigenetic gene regulation.
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Affiliation(s)
- Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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16
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Nasrallah NA, Wiese BM, Sears CR. Xeroderma Pigmentosum Complementation Group C (XPC): Emerging Roles in Non-Dermatologic Malignancies. Front Oncol 2022; 12:846965. [PMID: 35530314 PMCID: PMC9069926 DOI: 10.3389/fonc.2022.846965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Xeroderma pigmentosum complementation group C (XPC) is a DNA damage recognition protein essential for initiation of global-genomic nucleotide excision repair (GG-NER). Humans carrying germline mutations in the XPC gene exhibit strong susceptibility to skin cancer due to defective removal via GG-NER of genotoxic, solar UV-induced dipyrimidine photoproducts. However, XPC is increasingly recognized as important for protection against non-dermatologic cancers, not only through its role in GG-NER, but also by participating in other DNA repair pathways, in the DNA damage response and in transcriptional regulation. Additionally, XPC expression levels and polymorphisms likely impact development and may serve as predictive and therapeutic biomarkers in a number of these non-dermatologic cancers. Here we review the existing literature, focusing on the role of XPC in non-dermatologic cancer development, progression, and treatment response, and highlight possible future applications of XPC as a prognostic and therapeutic biomarker.
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Affiliation(s)
- Nawar Al Nasrallah
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Benjamin M. Wiese
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Catherine R. Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN, United States
- *Correspondence: Catherine R. Sears,
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17
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Kusakabe M, Kakumu E, Kurihara F, Tsuchida K, Maeda T, Tada H, Kusao K, Kato A, Yasuda T, Matsuda T, Nakao M, Yokoi M, Sakai W, Sugasawa K. Histone deacetylation regulates nucleotide excision repair through an interaction with the XPC protein. iScience 2022; 25:104040. [PMID: 35330687 PMCID: PMC8938288 DOI: 10.1016/j.isci.2022.104040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/07/2022] [Accepted: 03/04/2022] [Indexed: 12/05/2022] Open
Abstract
The XPC protein complex plays a central role in DNA lesion recognition for global genome nucleotide excision repair (GG-NER). Lesion recognition can be accomplished in either a UV-DDB-dependent or -independent manner; however, it is unclear how these sub-pathways are regulated in chromatin. Here, we show that histone deacetylases 1 and 2 facilitate UV-DDB-independent recruitment of XPC to DNA damage by inducing histone deacetylation. XPC localizes to hypoacetylated chromatin domains in a DNA damage-independent manner, mediated by its structurally disordered middle (M) region. The M region interacts directly with the N-terminal tail of histone H3, an interaction compromised by H3 acetylation. Although the M region is dispensable for in vitro NER, it promotes DNA damage removal by GG-NER in vivo, particularly in the absence of UV-DDB. We propose that histone deacetylation around DNA damage facilitates the recruitment of XPC through the M region, contributing to efficient lesion recognition and initiation of GG-NER. Histone deacetylation by HDAC1/2 promotes the DNA lesion recognition by XPC The HDAC1/2 activators, MTA proteins, also promote the recruitment of XPC XPC tends to localize in hypoacetylated chromatin independently of DNA damage Disordered middle region of XPC interacts with histone H3 tail and promotes GG-NER
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18
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Melis M, Tang XH, Trasino SE, Gudas LJ. Retinoids in the Pathogenesis and Treatment of Liver Diseases. Nutrients 2022; 14:1456. [PMID: 35406069 PMCID: PMC9002467 DOI: 10.3390/nu14071456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
Vitamin A (VA), all-trans-retinol (ROL), and its analogs are collectively called retinoids. Acting through the retinoic acid receptors RARα, RARβ, and RARγ, all-trans-retinoic acid, an active metabolite of VA, is a potent regulator of numerous biological pathways, including embryonic and somatic cellular differentiation, immune functions, and energy metabolism. The liver is the primary organ for retinoid storage and metabolism in humans. For reasons that remain incompletely understood, a body of evidence shows that reductions in liver retinoids, aberrant retinoid metabolism, and reductions in RAR signaling are implicated in numerous diseases of the liver, including hepatocellular carcinoma, non-alcohol-associated fatty liver diseases, and alcohol-associated liver diseases. Conversely, restoration of retinoid signaling, pharmacological treatments with natural and synthetic retinoids, and newer agonists for specific RARs show promising benefits for treatment of a number of these liver diseases. Here we provide a comprehensive review of the literature demonstrating a role for retinoids in limiting the pathogenesis of these diseases and in the treatment of liver diseases.
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Affiliation(s)
- Marta Melis
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA; (M.M.); (X.-H.T.)
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA; (M.M.); (X.-H.T.)
| | - Steven E. Trasino
- Nutrition Program, Hunter College, City University of New York, New York, NY 10065, USA;
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA; (M.M.); (X.-H.T.)
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19
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Costanzo F, Martínez Diez M, Santamaría Nuñez G, Díaz-Hernandéz JI, Genes Robles CM, Díez Pérez J, Compe E, Ricci R, Li TK, Coin F, Martínez Leal JF, Garrido-Martin EM, Egly JM. Promoters of ASCL1- and NEUROD1-dependent genes are specific targets of lurbinectedin in SCLC cells. EMBO Mol Med 2022; 14:e14841. [PMID: 35263037 PMCID: PMC8988166 DOI: 10.15252/emmm.202114841] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/22/2023] Open
Abstract
Small‐Cell Lung Cancer (SCLC) is an aggressive neuroendocrine malignancy with a poor prognosis. Here, we focus on the neuroendocrine SCLC subtypes, SCLC‐A and SCLC‐N, whose transcription addiction was driven by ASCL1 and NEUROD1 transcription factors which target E‐box motifs to activate up to 40% of total genes, the promoters of which are maintained in a steadily open chromatin environment according to ATAC and H3K27Ac signatures. This leverage is used by the marine agent lurbinectedin, which preferentially targets the CpG islands located downstream of the transcription start site, thus arresting elongating RNAPII and promoting its degradation. This abrogates the expression of ASCL1 and NEUROD1 and of their dependent genes, such as BCL2, INSM1, MYC, and AURKA, which are responsible for relevant SCLC tumorigenic properties such as inhibition of apoptosis and cell survival, as well as for a part of its neuroendocrine features. In summary, we show how the transcription addiction of these cells becomes their Achilles’s heel, and how this is effectively exploited by lurbinectedin as a novel SCLC therapeutic endeavor.
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Affiliation(s)
- Federico Costanzo
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,Cell Biology Department, Research and Development, Pharmamar SA, Colmenar Viejo, Spain
| | - Marta Martínez Diez
- Cell Biology Department, Research and Development, Pharmamar SA, Colmenar Viejo, Spain
| | - Gema Santamaría Nuñez
- Cell Biology Department, Research and Development, Pharmamar SA, Colmenar Viejo, Spain
| | | | - Carlos Mario Genes Robles
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France
| | - Javier Díez Pérez
- Cell Biology Department, Research and Development, Pharmamar SA, Colmenar Viejo, Spain
| | - Emmanuel Compe
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | - Romeo Ricci
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | - Tsai-Kun Li
- College of Medicine, Center for Genomics and Precision Medicine, National Taiwan University, Taipei city, Taiwan
| | - Frédéric Coin
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | | | | | - Jean Marc Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS/INSERM/University of Strasbourg, Equipe labellisée Ligue contre le Cancer, Strasbourg, France.,College of Medicine, Center for Genomics and Precision Medicine, National Taiwan University, Taipei city, Taiwan
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20
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Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
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21
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Zayoud K, Kraoua I, Chikhaoui A, Calmels N, Bouchoucha S, Obringer C, Crochemore C, Najjar D, Zarrouk S, Miladi N, Laugel V, Ricchetti M, Turki I, Yacoub-Youssef H. Identification and Characterization of a Novel Recurrent ERCC6 Variant in Patients with a Severe Form of Cockayne Syndrome B. Genes (Basel) 2021; 12:genes12121922. [PMID: 34946871 PMCID: PMC8701866 DOI: 10.3390/genes12121922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/06/2023] Open
Abstract
Cockayne syndrome (CS) is a rare disease caused by mutations in ERCC6/CSB or ERCC8/CSA. We report here the clinical, genetic, and functional analyses of three unrelated patients mutated in ERCC6/CSB with a severe phenotype. After clinical examination, two patients were investigated via next generation sequencing, targeting seventeen Nucleotide Excision Repair (NER) genes. All three patients harbored a novel, c.3156dup, homozygous mutation located in exon 18 of ERCC6/CSB that affects the C-terminal region of the protein. Sanger sequencing confirmed the mutation and the parental segregation in the three families, and Western blots showed a lack of the full-length protein. NER functional impairment was shown by reduced recovery of RNA synthesis with proficient unscheduled DNA synthesis after UV-C radiations in patient-derived fibroblasts. Despite sharing the same mutation, the clinical spectrum was heterogeneous among the three patients, and only two patients displayed clinical photosensitivity. This novel ERCC6 variant in Tunisian patients suggests a founder effect and has implications for setting-up prenatal diagnosis/genetic counselling in North Africa, where this disease is largely undiagnosed. This study reveals one of the rare cases of CS clinical heterogeneity despite the same mutation. Moreover, the occurrence of an identical homozygous mutation, which either results in clinical photosensitivity or does not, strongly suggests that this classic CS symptom relies on multiple factors.
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Affiliation(s)
- Khouloud Zayoud
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, El Manar I, Tunis 1002, Tunisia; (K.Z.); (A.C.); (D.N.)
- Faculté des Sciences de Bizerte, Bizerte 7000, Tunisia
| | - Ichraf Kraoua
- LR18SP04 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis 1007, Tunisia; (I.K.); (I.T.)
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, El Manar I, Tunis 1002, Tunisia; (K.Z.); (A.C.); (D.N.)
| | - Nadège Calmels
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d’Alsace, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France;
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de génétique médicale d’Alsace, CRBS, 67000 Strasbourg, France; (C.O.); (V.L.)
| | - Sami Bouchoucha
- Service Orthopédie, Hôpital d’enfant Béchir Hamza, Tunis 1000, Tunisia;
| | - Cathy Obringer
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de génétique médicale d’Alsace, CRBS, 67000 Strasbourg, France; (C.O.); (V.L.)
| | - Clément Crochemore
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR 3738 CNRS, 25-28 rue du Dr. Roux, 75015 Paris, France; (C.C.); (M.R.)
| | - Dorra Najjar
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, El Manar I, Tunis 1002, Tunisia; (K.Z.); (A.C.); (D.N.)
| | - Sinda Zarrouk
- Genomics Platform, Institut Pasteur de Tunis (IPT), Tunis-Belvédère, Tunis 1002, Tunisia;
| | - Najoua Miladi
- Maghreb Medical Center, El Manar III, Tunis 9000, Tunisia;
| | - Vincent Laugel
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de génétique médicale d’Alsace, CRBS, 67000 Strasbourg, France; (C.O.); (V.L.)
| | - Miria Ricchetti
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR 3738 CNRS, 25-28 rue du Dr. Roux, 75015 Paris, France; (C.C.); (M.R.)
| | - Ilhem Turki
- LR18SP04 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis 1007, Tunisia; (I.K.); (I.T.)
| | - Houda Yacoub-Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, El Manar I, Tunis 1002, Tunisia; (K.Z.); (A.C.); (D.N.)
- Correspondence:
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22
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Quintero-Ruiz N, Corradi C, Moreno NC, de Souza TA, Pereira Castro L, Rocha CRR, Menck CFM. Mutagenicity Profile Induced by UVB Light in Human Xeroderma Pigmentosum Group C Cells †. Photochem Photobiol 2021; 98:713-731. [PMID: 34516658 DOI: 10.1111/php.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Nucleotide excision repair (NER) is one of the main pathways for genome protection against structural DNA damage caused by sunlight, which in turn is extensively related to skin cancer development. The mutation spectra induced by UVB were investigated by whole-exome sequencing of randomly selected clones of NER-proficient and XP-C-deficient human skin fibroblasts. As a model, a cell line unable to recognize and remove lesions (XP-C) was used and compared to the complemented isogenic control (COMP). As expected, a significant increase of mutagenesis was observed in irradiated XP-C cells, mainly C>T transitions, but also CC>TT and C>A base substitutions. Remarkably, the C>T mutations occur mainly at the second base of dipyrimidine sites in pyrimidine-rich sequence contexts, with 5'TC sequence the most mutated. Although T>N mutations were also significantly increased, they were not directly related to pyrimidine dimers. Moreover, the large-scale study of a single UVB irradiation on XP-C cells allowed recovering the typical mutation spectrum found in human skin cancer tumors. Eventually, the data may be used for comparison with the mutational profiles of skin tumors obtained from XP-C patients and may help to understand the mutational process in nonaffected individuals.
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Affiliation(s)
- Nathalia Quintero-Ruiz
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Corradi
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Natália Cestari Moreno
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Antonio de Souza
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Tau GC Bioinformatics, São Paulo, Brazil
| | - Ligia Pereira Castro
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Clarissa Ribeiro Reily Rocha
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Drug resistance and mutagenesis Laboratory, Departmento de Oncologia Clínica e Experimental, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos Frederico Martins Menck
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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23
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Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH. Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. DNA Repair (Amst) 2021; 107:103194. [PMID: 34428697 DOI: 10.1016/j.dnarep.2021.103194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/14/2023]
Abstract
Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Sagnik Chakraborty
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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24
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Guha S, Bhaumik SR. Transcription-coupled DNA double-strand break repair. DNA Repair (Amst) 2021; 109:103211. [PMID: 34883263 DOI: 10.1016/j.dnarep.2021.103211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/20/2022]
Abstract
The genomic DNA is constantly under attack by cellular and/or environmental factors. Fortunately, the cell is armed to safeguard its genome by various mechanisms such as nucleotide excision, base excision, mismatch and DNA double-strand break repairs. While these processes maintain the integrity of the genome throughout, DNA repair occurs preferentially faster at the transcriptionally active genes. Such transcription-coupled repair phenomenon plays important roles to maintain active genome integrity, failure of which would interfere with transcription, leading to an altered gene expression (and hence cellular pathologies/diseases). Among the various DNA damages, DNA double-strand breaks are quite toxic to the cells. If DNA double-strand break occurs at the active gene, it would interfere with transcription/gene expression, thus threatening cellular viability. Such DNA double-strand breaks are found to be repaired faster at the active gene in comparison to its inactive state or the inactive gene, thus supporting the existence of a new phenomenon of transcription-coupled DNA double-strand break repair. Here, we describe the advances of this repair process.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA.
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25
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Compe E, Egly JM. The Long Road to Understanding RNAPII Transcription Initiation and Related Syndromes. Annu Rev Biochem 2021; 90:193-219. [PMID: 34153211 DOI: 10.1146/annurev-biochem-090220-112253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In eukaryotes, transcription of protein-coding genes requires the assembly at core promoters of a large preinitiation machinery containing RNA polymerase II (RNAPII) and general transcription factors (GTFs). Transcription is potentiated by regulatory elements called enhancers, which are recognized by specific DNA-binding transcription factors that recruit cofactors and convey, following chromatin remodeling, the activating cues to the preinitiation complex. This review summarizes nearly five decades of work on transcription initiation by describing the sequential recruitment of diverse molecular players including the GTFs, the Mediator complex, and DNA repair factors that support RNAPII to enable RNA synthesis. The elucidation of the transcription initiation mechanism has greatly benefited from the study of altered transcription components associated with human diseases that could be considered transcription syndromes.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; ,
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; , .,College of Medicine, National Taiwan University, Taipei 10051, Taiwan
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26
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Transcriptional Stress Induces Chromatin Relocation of the Nucleotide Excision Repair Factor XPG. Int J Mol Sci 2021; 22:ijms22126589. [PMID: 34205418 PMCID: PMC8235791 DOI: 10.3390/ijms22126589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
Endonuclease XPG participates in nucleotide excision repair (NER), in basal transcription, and in the processing of RNA/DNA hybrids (R-loops): the malfunction of these processes may cause genome instability. Here, we investigate the chromatin association of XPG during basal transcription and after transcriptional stress. The inhibition of RNA polymerase II with 5,6-dichloro-l-β-D-ribofuranosyl benzimidazole (DRB), or actinomycin D (AD), and of topoisomerase I with camptothecin (CPT) resulted in an increase in chromatin-bound XPG, with concomitant relocation by forming nuclear clusters. The cotranscriptional activators p300 and CREB-binding protein (CREBBP), endowed with lysine acetyl transferase (KAT) activity, interact with and acetylate XPG. Depletion of both KATs by RNA interference, or chemical inhibition with C646, significantly reduced XPG acetylation. However, the loss of KAT activity also resulted in increased chromatin association and the relocation of XPG, indicating that these processes were induced by transcriptional stress and not by reduced acetylation. Transcription inhibitors, including C646, triggered the R-loop formation and phosphorylation of histone H2AX (γ-H2AX). Proximity ligation assay (PLA) showed that XPG colocalized with R-loops, indicating the recruitment of the protein to these structures. These results suggest that transcriptional stress-induced XPG relocation may represent recruitment to sites of R-loop processing.
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27
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Barve A, Galande AA, Ghaskadbi SS, Ghaskadbi S. DNA Repair Repertoire of the Enigmatic Hydra. Front Genet 2021; 12:670695. [PMID: 33995496 PMCID: PMC8117345 DOI: 10.3389/fgene.2021.670695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since its discovery by Abraham Trembley in 1744, hydra has been a popular research organism. Features like spectacular regeneration capacity, peculiar tissue dynamics, continuous pattern formation, unique evolutionary position, and an apparent lack of organismal senescence make hydra an intriguing animal to study. While a large body of work has taken place, particularly in the domain of evolutionary developmental biology of hydra, in recent years, the focus has shifted to molecular mechanisms underlying various phenomena. DNA repair is a fundamental cellular process that helps to maintain integrity of the genome through multiple repair pathways found across taxa, from archaea to higher animals. DNA repair capacity and senescence are known to be closely associated, with mutations in several repair pathways leading to premature ageing phenotypes. Analysis of DNA repair in an animal like hydra could offer clues into several aspects including hydra’s purported lack of organismal ageing, evolution of DNA repair systems in metazoa, and alternative functions of repair proteins. We review here the different DNA repair mechanisms known so far in hydra. Hydra genes from various DNA repair pathways show very high similarity with their vertebrate orthologues, indicating conservation at the level of sequence, structure, and function. Notably, most hydra repair genes are more similar to deuterostome counterparts than to common model invertebrates, hinting at ancient evolutionary origins of repair pathways and further highlighting the relevance of organisms like hydra as model systems. It appears that hydra has the full repertoire of DNA repair pathways, which are employed in stress as well as normal physiological conditions and may have a link with its observed lack of senescence. The close correspondence of hydra repair genes with higher vertebrates further demonstrates the need for deeper studies of various repair components, their interconnections, and functions in this early metazoan.
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Affiliation(s)
- Apurva Barve
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India.,Centre of Excellence in Science and Mathematics Education, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Alisha A Galande
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India
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28
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Rizza ERH, DiGiovanna JJ, Khan SG, Tamura D, Jeskey JD, Kraemer KH. Xeroderma Pigmentosum: A Model for Human Premature Aging. J Invest Dermatol 2021; 141:976-984. [PMID: 33436302 DOI: 10.1016/j.jid.2020.11.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022]
Abstract
Aging results from intrinsic changes (chronologic) and damage from external exposures (extrinsic) on the human body. The skin is ideal to visually differentiate their unique features. Inherited diseases of DNA repair, such as xeroderma pigmentosum (XP), provide an excellent model for human aging due to the accelerated accumulation of DNA damage. Poikiloderma, atypical lentigines, and skin cancers, the primary cutaneous features of XP, occur in the general population but at a much older age. Patients with XP also exhibit ocular changes secondary to premature photoaging, including ocular surface tumors and pterygium. Internal manifestations of premature aging, including peripheral neuropathy, progressive sensorineural hearing loss, and neurodegeneration, are reported in 25% of patients with XP. Internal malignancies, such as lung cancer, CNS tumors, and leukemia and/or lymphoma, occur at a younger age in patients with XP, as do thyroid nodules. Premature ovarian failure is overrepresented among females with XP, occurring 20 years earlier than in the general population. Taken together, these clinical findings highlight the importance of DNA repair in maintaining genomic integrity. XP is a unique model of human premature aging, which is revealing new insights into aging mechanisms.
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Affiliation(s)
- Elizabeth R H Rizza
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sikandar G Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jack D Jeskey
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Medical Research Scholar Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
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29
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Zhang X, Heng Y, Kooistra SM, van Weering HRJ, Brummer ML, Gerrits E, Wesseling EM, Brouwer N, Nijboer TW, Dubbelaar ML, Boddeke EWGM, Eggen BJL. Intrinsic DNA damage repair deficiency results in progressive microglia loss and replacement. Glia 2020; 69:729-745. [PMID: 33068332 PMCID: PMC7821301 DOI: 10.1002/glia.23925] [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: 06/05/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022]
Abstract
The DNA excision repair protein Ercc1 is important for nucleotide excision, double strand DNA break, and interstrand DNA crosslink repair. In constitutive Ercc1‐knockout mice, microglia display increased phagocytosis, proliferation and an enhanced responsiveness to lipopolysaccharide (LPS)‐induced peripheral inflammation. However, the intrinsic effects of Ercc1‐deficiency on microglia are unclear. In this study, Ercc1 was specifically deleted from Cx3cr1‐expressing cells and changes in microglia morphology and immune responses at different times after deletion were determined. Microglia numbers were reduced with approximately 50% at 2–12 months after Ercc1 deletion. Larger and more ramified microglia were observed following Ercc1 deletion both in vivo and in organotypic hippocampal slice cultures. Ercc1‐deficient microglia were progressively lost, and during this period, microglia proliferation was transiently increased. Ercc1‐deficient microglia were gradually replaced by nondeficient microglia carrying a functional Ercc1 allele. In contrast to constitutive Ercc1‐deficient mice, microglia‐specific deletion of Ercc1 did not induce microglia activation or increase their responsiveness to a systemic LPS challenge. Gene expression analysis suggested that Ercc1 deletion in microglia induced a transient aging signature, which was different from a priming or disease‐associated microglia gene expression profile.
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Affiliation(s)
- Xiaoming Zhang
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Heng
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Susanne M Kooistra
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hilmar R J van Weering
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maaike L Brummer
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Emma Gerrits
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Evelyn M Wesseling
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nieske Brouwer
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tjalling W Nijboer
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marissa L Dubbelaar
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik W G M Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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30
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Xu J, Wang W, Xu L, Chen JY, Chong J, Oh J, Leschziner AE, Fu XD, Wang D. Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers. Proc Natl Acad Sci U S A 2020; 117:25486-25493. [PMID: 32989164 PMCID: PMC7568279 DOI: 10.1073/pnas.2013379117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
While loss-of-function mutations in Cockayne syndrome group B protein (CSB) cause neurological diseases, this unique member of the SWI2/SNF2 family of chromatin remodelers has been broadly implicated in transcription elongation and transcription-coupled DNA damage repair, yet its mechanism remains largely elusive. Here, we use a reconstituted in vitro transcription system with purified polymerase II (Pol II) and Rad26, a yeast ortholog of CSB, to study the role of CSB in transcription elongation through nucleosome barriers. We show that CSB forms a stable complex with Pol II and acts as an ATP-dependent processivity factor that helps Pol II across a nucleosome barrier. This noncanonical mechanism is distinct from the canonical modes of chromatin remodelers that directly engage and remodel nucleosomes or transcription elongation factors that facilitate Pol II nucleosome bypass without hydrolyzing ATP. We propose a model where CSB facilitates gene expression by helping Pol II bypass chromatin obstacles while maintaining their structures.
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Affiliation(s)
- Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Wei Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Liang Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - 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, University of California San Diego, La Jolla, CA 92093
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Wang S, Meyer DH, Schumacher B. H3K4me2 regulates the recovery of protein biosynthesis and homeostasis following DNA damage. Nat Struct Mol Biol 2020; 27:1165-1177. [DOI: 10.1038/s41594-020-00513-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/02/2020] [Indexed: 01/08/2023]
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Gul S, Khan A, Raza A, Khan I, Ehtisham S. Association of XPD Lys751Gln gene polymorphism with susceptibility and clinical outcome of colorectal cancer in Pakistani population: a case-control pharmacogenetic study. Genes Genomics 2020; 42:1389-1398. [PMID: 33025549 DOI: 10.1007/s13258-020-01004-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/19/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND XPD Lys751Gln polymorphism may modulate inter-individual variation in repair capacity of DNA, which may enhance a person's susceptibility to develop colorectal cancer (CRC). The analysis of XPD Lys751Gln polymorphism may provide important information for identifying high-risk individuals and for selecting the most appropriate treatment for poor prognostic CRC patients. OBJECTIVE The overall objective was to find out the association of XPD Lys751Gln gene polymorphism with the risk of having a colorectal cancer and the ultimate clinical outcomes. In this study a total of 300 subjects (CRC and Controls), were genotyped for XPD Lys751Gln. METHODS Using PCR-RFLP methods, the association of XPD Lys751Gln gene polymorphism with the risk of having a colorectal cancer was studied. In addition to overall risk assessment, genotyping results were also investigated with respect to the lifestyle risk factors, patients treated with oxaliplatin-based chemotherapy and clinicopathological characteristics. RESULTS The overall correlation between the XPD Lys751Gln genetic variation and the CRC risk was observed to be significant with both the homozygous variant genotype Gln/Gln as well as heterozygous genotype Lys/Gln being associated with the increased risk of CRC. Additional stratified analyses revealed that XPD Lys751Gln variants remarkably increased risk of CRC in males and younger individuals (≤ 50 years), Naswar users (8.09-fold) and high intake of red meat. CONCLUSIONS Our findings suggest that the relationship between the XPD Lys751Gln variants and lifestyle factors modulates the risk for CRC in Pakistani population.
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Affiliation(s)
- Sumera Gul
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan
| | - Abad Khan
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan.
| | - Abida Raza
- National Institute of Laser and Optronics, Pakistan Atomic Energy Commission, Islamabad, 44000, Pakistan
| | - Ismail Khan
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan
| | - Shumaila Ehtisham
- Department of Statistics, Islamia College Peshawar, Peshawar, 25120, Pakistan
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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Manickavinayaham S, Velez-Cruz R, Biswas AK, Chen J, Guo R, Johnson DG. The E2F1 transcription factor and RB tumor suppressor moonlight as DNA repair factors. Cell Cycle 2020; 19:2260-2269. [PMID: 32787501 PMCID: PMC7513849 DOI: 10.1080/15384101.2020.1801190] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023] Open
Abstract
The E2F1 transcription factor and RB tumor suppressor are best known for their roles in regulating the expression of genes important for cell cycle progression but, they also have transcription-independent functions that facilitate DNA repair at sites of damage. Depending on the type of DNA damage, E2F1 can recruit either the GCN5 or p300/CBP histone acetyltransferases to deposit different histone acetylation marks in flanking chromatin. At DNA double-strand breaks, E2F1 also recruits RB and the BRG1 ATPase to remodel chromatin and promote loading of the MRE11-RAD50-NBS1 complex. Knock-in mouse models demonstrate important roles for E2F1 post-translational modifications in regulating DNA repair and physiological responses to DNA damage. This review highlights how E2F1 moonlights in DNA repair, thus revealing E2F1 as a versatile protein that recruits many of the same chromatin-modifying enzymes to sites of DNA damage to promote repair that it recruits to gene promoters to regulate transcription.
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Affiliation(s)
- Swarnalatha Manickavinayaham
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Renier Velez-Cruz
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, USA
| | - Anup K. Biswas
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Jie Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David G. Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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XPA deficiency affects the ubiquitin-proteasome system function. DNA Repair (Amst) 2020; 94:102937. [PMID: 32693352 DOI: 10.1016/j.dnarep.2020.102937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/25/2020] [Accepted: 07/13/2020] [Indexed: 01/02/2023]
Abstract
Xeroderma pigmentosum complementation group A (XPA), is defective in xeroderma pigmentosum patients, causing pre-disposition to skin cancer and neurological abnormalities, which is not well understood. Here, we analyzed the XPA-deficient cells transcriptional profile under oxidative stress. The imbalance in of ubiquitin-proteasome system (UPS) gene expression was observed in XPA-deficient cells and the involvement of nuclear factor erythroid 2-related factor-2 (NFE2L2) was indicated. Co-immunoprecipitation assays showed the interaction between XPA, apurinic-apyrimidinic endonuclease 1 (APE1) and NFE2L2 proteins. Decreased NFE2L2 protein expression and proteasome activity was also observed in XPA-deficient cells. The data suggest the involvement of the growth arrest and DNA-damage-inducible beta (GADD45β) in NFE2L2 functions. Similar results were obtained in xpa-1 (RNAi) Caenorhabditis elegans suggesting the conservation of XPA and NFE2L2 interactions. In conclusion, stress response activation occurs in XPA-deficient cells under oxidative stress; however, these cells fail to activate the UPS cytoprotective response, which may contribute to XPA patient's phenotypes.
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36
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Mori MP, Souza-Pinto NCD. PPRC1, but not PGC-1α, levels directly correlate with expression of mitochondrial proteins in human dermal fibroblasts. Genet Mol Biol 2020; 43:e20190083. [PMID: 32639509 PMCID: PMC7341727 DOI: 10.1590/1678-4685-gmb-2019-0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/15/2020] [Indexed: 11/22/2022] Open
Abstract
The XPC protein, which is mutated in xeroderma pigmentosum (XP) complementation group C (XP-C), is a lesion recognition factor in NER, but it has also been shown to interact with and stimulate DNA glycosylases, to act as transcriptional co-activator and on energy metabolism adaptation. We have previously demonstrated that XP-C cells show increased mitochondrial H2O2 production with a shift between respiratory complexes I and II, leading to sensitivity to mitochondrial stress. Here we report a marked decrease in expression of the transcriptional co-activator PGC-1α, a master regulator of mitochondrial biogenesis, in XP-C cells. A transcriptional role for XPC in PGC-1α expression was discarded, as XPC knockdown did not downregulate PGC-1α expression and XPC-corrected cells still showed lower PGC-1α expression. DNA methylation alone did not explain PGC-1α silencing. In four different XP-C cell lines tested, reduction of PGC-1α expression was detected in three, all of them carrying the c.1643_1644delTG mutation (ΔTG) in XPC. Indeed, all cell lines carrying XPC ΔTG mutation, whether homozygous or heterozygous, presented decreased PGC-1α expression. However, this alteration in gene expression was not exclusive to XPC ΔTG cell lines, for other non-related cell lines also showed altered PGC-1α expression. Moreover, PGC1-α expression did not correlate with expression levels of TFAM and SDHA, known PGC-1α target-genes. In turn, PPRC1, another member of the PGC family of transcription co-activators controlling mitochondrial biogenesis, displayed a good correlation between its expression in 10 cell lines and TFAM and SDHA. Nonetheless, PGC-1α knockdown led to a slight decrease of its target-gene protein level, TFAM, and subsequently of a mtDNA-encoded gene, MT-CO2. These results indicate that PGC-1α and PPRC1 cooperate as regulators of mitochondrial biogenesis and maintenance in fibroblasts.
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Affiliation(s)
- Mateus Prates Mori
- Universidade de São Paulo, Departamento de Bioquímica, Instituto de Química, São Paulo, SP, Brazil
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37
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Vessoni AT, Guerra CCC, Kajitani GS, Nascimento LLS, Garcia CCM. Cockayne Syndrome: The many challenges and approaches to understand a multifaceted disease. Genet Mol Biol 2020; 43:e20190085. [PMID: 32453336 PMCID: PMC7250278 DOI: 10.1590/1678-4685-gmb-2019-0085] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
The striking and complex phenotype of Cockayne syndrome (CS) patients combines progeria-like features with developmental deficits. Since the establishment of the in vitro culture of skin fibroblasts derived from patients with CS in the 1970s, significant progress has been made in the understanding of the genetic alterations associated with the disease and their impact on molecular, cellular, and organismal functions. In this review, we provide a historic perspective on the research into CS by revisiting seminal papers in this field. We highlighted the great contributions of several researchers in the last decades, ranging from the cloning and characterization of CS genes to the molecular dissection of their roles in DNA repair, transcription, redox processes and metabolism control. We also provide a detailed description of all pathological mutations in genes ERCC6 and ERCC8 reported to date and their impact on CS-related proteins. Finally, we review the contributions (and limitations) of many genetic animal models to the study of CS and how cutting-edge technologies, such as cell reprogramming and state-of-the-art genome editing, are helping us to address unanswered questions.
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Affiliation(s)
| | - Camila Chaves Coelho Guerra
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
| | - Gustavo Satoru Kajitani
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, São Paulo,SP, Brazil
| | - Livia Luz Souza Nascimento
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, São Paulo,SP, Brazil
| | - Camila Carrião Machado Garcia
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
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38
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Mulderrig L, Garaycoechea JI. XPF-ERCC1 protects liver, kidney and blood homeostasis outside the canonical excision repair pathways. PLoS Genet 2020; 16:e1008555. [PMID: 32271760 PMCID: PMC7144963 DOI: 10.1371/journal.pgen.1008555] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/05/2019] [Indexed: 01/02/2023] Open
Abstract
Loss of the XPF-ERCC1 endonuclease causes a dramatic phenotype that results in progeroid features associated with liver, kidney and bone marrow dysfunction. As this nuclease is involved in multiple DNA repair transactions, it is plausible that this severe phenotype results from the simultaneous inactivation of both branches of nucleotide excision repair (GG- and TC-NER) and Fanconi anaemia (FA) inter-strand crosslink (ICL) repair. Here we use genetics in human cells and mice to investigate the interaction between the canonical NER and ICL repair pathways and, subsequently, how their joint inactivation phenotypically overlaps with XPF-ERCC1 deficiency. We find that cells lacking TC-NER are sensitive to crosslinking agents and that there is a genetic interaction between NER and FA in the repair of certain endogenous crosslinking agents. However, joint inactivation of GG-NER, TC-NER and FA crosslink repair cannot account for the hypersensitivity of XPF-deficient cells to classical crosslinking agents nor is it sufficient to explain the extreme phenotype of Ercc1-/- mice. These analyses indicate that XPF-ERCC1 has important functions outside of its central role in NER and FA crosslink repair which are required to prevent endogenous DNA damage. Failure to resolve such damage leads to loss of tissue homeostasis in mice and humans.
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Affiliation(s)
- Lee Mulderrig
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, United Kingdom
| | - Juan I. Garaycoechea
- Hubrecht Institute–KNAW, University Medical Center Utrecht, Uppsalalaan, CT Utrecht, Netherlands
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39
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Gonçalves-Maia M, Gache Y, Basante M, Cosson E, Salavagione E, Muller M, Bernerd F, Avril MF, Schaub S, Sarasin A, Braud VM, Magnaldo T. NK Cell and Fibroblast-Mediated Regulation of Skin Squamous Cell Carcinoma Invasion by CLEC2A Is Compromised in Xeroderma Pigmentosum. J Invest Dermatol 2020; 140:1723-1732. [PMID: 32061658 DOI: 10.1016/j.jid.2020.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/12/2020] [Accepted: 01/21/2020] [Indexed: 12/24/2022]
Abstract
The ability of cancer cells to invade and disseminate can be affected by components of the surrounding microenvironment. To identify dermal components that regulate the growth of epidermal carcinomas, we studied the genetic disease called xeroderma pigmentosum that bears mutations in genes involved in the nucleotide excision repair of DNA. Patients with xeroderma pigmentosum are more prone to develop cutaneous tumors than the general population and their dermal fibroblasts display the features of dermal cancer-associated fibroblasts, which promote the invasion of keratinocytes. Here, we report that 3-dimensional dermal cultures of fibroblasts from healthy donors but not from patients with xeroderma pigmentosum complementation group C express CLEC2A, which is the ligand of the activating NK cell receptor NKp65. A similar loss of CLEC2A was observed in sporadic dermal cancer-associated fibroblasts and upon the culture of fibroblasts with cutaneous squamous cell carcinoma-conditioned medium. Using an innovative 3-dimensional organotypic skin culture model that contain NK cells in addition to fibroblasts and squamous cell carcinoma cells, we unveiled a key role of CLEC2A that orchestrates a crosstalk between fibroblasts and NK cells, thereby leading to the control of squamous cell carcinoma invasion. These findings indicate that CLEC2A-expressing dermal fibroblasts play a major role in immune surveillance of the skin.
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Affiliation(s)
- Maria Gonçalves-Maia
- Université Côte d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging, Nice, U1081, UMR7284, Nice, France
| | - Yannick Gache
- Université Côte d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging, Nice, U1081, UMR7284, Nice, France
| | - Miguel Basante
- Université Côte d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging, Nice, U1081, UMR7284, Nice, France; Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Estelle Cosson
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Valbonne, Sophia Antipolis, France
| | - Emie Salavagione
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Valbonne, Sophia Antipolis, France
| | - Margot Muller
- Université Côte d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging, Nice, U1081, UMR7284, Nice, France
| | | | - Marie Françoise Avril
- Assistance Publique-Hôpitaux de Paris, Department of Dermatology, Hospital Cochin, University Paris Descartes, Paris, France
| | - Sébastien Schaub
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Alain Sarasin
- Université Paris-Sud, Institut Gustave Roussy, UMR8200, CNRS, F-94805, Villejuif, France
| | - Véronique M Braud
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, Valbonne, Sophia Antipolis, France
| | - Thierry Magnaldo
- Université Côte d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging, Nice, U1081, UMR7284, Nice, France.
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40
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Defective transcription of ATF3 responsive genes, a marker for Cockayne Syndrome. Sci Rep 2020; 10:1105. [PMID: 31980658 PMCID: PMC6981198 DOI: 10.1038/s41598-020-57999-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Cockayne syndrome (CS) is a rare genetic disorder caused by mutations (dysfunction) in CSA and CSB. CS patients exhibit mild photosensitivity and severe neurological problems. Currently, CS diagnosis is based on the inefficiency of CS cells to recover RNA synthesis upon genotoxic (UV) stress. Indeed, upon genotoxic stress, ATF3, an immediate early gene is activated to repress up to 5000 genes encompassing its responsive element for a short period of time. On the contrary in CS cells, CSA and CSB dysfunction impairs the degradation of the chromatin-bound ATF3, leading to a permanent transcriptional arrest as observed by immunofluorescence and ChIP followed by RT-PCR. We analysed ChIP-seq of Pol II and ATF3 promoter occupation analysis and RNA sequencing-based gene expression profiling in CS cells, as well as performed immunofluorescence study of ATF3 protein stability and quantitative RT-PCR screening in 64 patient cell lines. We show that the analysis of few amount (as for example CDK5RAP2, NIPBL and NRG1) of ATF3 dependent genes, could serve as prominent molecular markers to discriminate between CS and non-CS patient’s cells. Such assay can significantly simplify the timing and the complexity of the CS diagnostic procedure in comparison to the currently available methods.
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41
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Georges A, Gopaul D, Denby Wilkes C, Giordanengo Aiach N, Novikova E, Barrault MB, Alibert O, Soutourina J. Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin. Nucleic Acids Res 2019; 47:8988-9004. [PMID: 31299084 PMCID: PMC6753472 DOI: 10.1093/nar/gkz598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.
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Affiliation(s)
- Adrien Georges
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Diyavarshini Gopaul
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Giordanengo Aiach
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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42
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Apostolou Z, Chatzinikolaou G, Stratigi K, Garinis GA. Nucleotide Excision Repair and Transcription-Associated Genome Instability. Bioessays 2019; 41:e1800201. [PMID: 30919497 DOI: 10.1002/bies.201800201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Transcription is a potential threat to genome integrity, and transcription-associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Here, these findings are critically discussed and a working model that explains the puzzling clinical heterogeneity of NER syndromes highlighting the relevance of physiological, transcription-associated DNA damage to mammalian development and disease is proposed.
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Affiliation(s)
- Zivkos Apostolou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
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43
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Selvam K, Rahman SA, Li S. Histone H4 H75E mutation attenuates global genomic and Rad26-independent transcription-coupled nucleotide excision repair. Nucleic Acids Res 2019; 47:7392-7401. [PMID: 31114907 PMCID: PMC6698655 DOI: 10.1093/nar/gkz453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023] Open
Abstract
Nucleotide excision repair (NER) consists of global genomic NER (GG-NER) and transcription coupled NER (TC-NER) subpathways. In eukaryotic cells, genomic DNA is wrapped around histone octamers (an H3–H4 tetramer and two H2A–H2B dimers) to form nucleosomes, which are well known to profoundly inhibit the access of NER proteins. Through unbiased screening of histone H4 residues in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain, we identified 24 mutations that enhance or decrease UV sensitivity of Saccharomyces cerevisiae cells. The histone H4 H75E mutation, which is largely embedded in the nucleosome and interacts with histone H2B, significantly attenuates GG-NER and Rad26-independent TC-NER but does not affect TC-NER in the presence of Rad26. All the other histone H4 mutations, except for T73F and T73Y that mildly attenuate GG-NER, do not substantially affect GG-NER or TC-NER. The attenuation of GG-NER and Rad26-independent TC-NER by the H4H75E mutation is not due to decreased chromatin accessibility, impaired methylation of histone H3 K79 that is at the center of the LRS domain, or lowered expression of NER proteins. Instead, the attenuation is at least in part due to impaired recruitment of Rad4, the key lesion recognition and verification protein, to chromatin following induction of DNA lesions.
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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
| | - Sheikh Arafatur Rahman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, 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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44
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Crochemore C, Fernández-Molina C, Montagne B, Salles A, Ricchetti M. CSB promoter downregulation via histone H3 hypoacetylation is an early determinant of replicative senescence. Nat Commun 2019; 10:5576. [PMID: 31811121 PMCID: PMC6898346 DOI: 10.1038/s41467-019-13314-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023] Open
Abstract
Cellular senescence has causative links with ageing and age-related diseases, however, it remains unclear if progeroid factors cause senescence in normal cells. Here, we show that depletion of CSB, a protein mutated in progeroid Cockayne syndrome (CS), is the earliest known trigger of p21-dependent replicative senescence. CSB depletion promotes overexpression of the HTRA3 protease resulting in mitochondrial impairments, which are causally linked to CS pathological phenotypes. The CSB promoter is downregulated by histone H3 hypoacetylation during DNA damage-response. Mechanistically, CSB binds to the p21 promoter thereby downregulating its transcription and blocking replicative senescence in a p53-independent manner. This activity of CSB is independent of its role in the repair of UV-induced DNA damage. HTRA3 accumulation and senescence are partially rescued upon reduction of oxidative/nitrosative stress. These findings establish a CSB/p21 axis that acts as a barrier to replicative senescence, and link a progeroid factor with the process of regular ageing in human. Senescence of metabolically active cells is a process linked to ageing. Here the authors reveal that CSB is required to block replicative senescence, and epigenetic control of CSB downregulation triggers proliferative arrest in a p21-dependent manner.
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Affiliation(s)
- Clément Crochemore
- Institut Pasteur, Stem Cells and Development, Department of Developmental and Stem Cell Biology, 75015, Paris, France.,CNRS UMR 3738, Team Stability of Nuclear and Mitochondrial DNA, 75015, Paris, France
| | - Cristina Fernández-Molina
- Institut Pasteur, Stem Cells and Development, Department of Developmental and Stem Cell Biology, 75015, Paris, France.,CNRS UMR 3738, Team Stability of Nuclear and Mitochondrial DNA, 75015, Paris, France.,Sorbonne Universités, UPMC, University of Paris 06, IFD-ED 515, Paris, France
| | - Benjamin Montagne
- Institut Pasteur, Stem Cells and Development, Department of Developmental and Stem Cell Biology, 75015, Paris, France.,CNRS UMR 3738, Team Stability of Nuclear and Mitochondrial DNA, 75015, Paris, France
| | - Audrey Salles
- Institut Pasteur, UTechS Photonic BioImaging PBI (Imagopole), Centre de Recherche et de Ressources Technologiques C2RT, Paris, France
| | - Miria Ricchetti
- Institut Pasteur, Stem Cells and Development, Department of Developmental and Stem Cell Biology, 75015, Paris, France. .,CNRS UMR 3738, Team Stability of Nuclear and Mitochondrial DNA, 75015, Paris, France.
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45
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Zebian A, Shaito A, Mazurier F, Rezvani HR, Zibara K. XPC beyond nucleotide excision repair and skin cancers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 782:108286. [DOI: 10.1016/j.mrrev.2019.108286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/23/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022]
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46
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Taghbalout A, Du M, Jillette N, Rosikiewicz W, Rath A, Heinen CD, Li S, Cheng AW. Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nat Commun 2019; 10:4296. [PMID: 31541098 PMCID: PMC6754513 DOI: 10.1038/s41467-019-12339-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
Here we develop a methylation editing toolbox, Casilio-ME, that enables not only RNA-guided methylcytosine editing by targeting TET1 to genomic sites, but also by co-delivering TET1 and protein factors that couple methylcytosine oxidation to DNA repair activities, and/or promote TET1 to achieve enhanced activation of methylation-silenced genes. Delivery of TET1 activity by Casilio-ME1 robustly alters the CpG methylation landscape of promoter regions and activates methylation-silenced genes. We augment Casilio-ME1 to simultaneously deliver the TET1-catalytic domain and GADD45A (Casilio-ME2) or NEIL2 (Casilio-ME3) to streamline removal of oxidized cytosine intermediates to enhance activation of targeted genes. Using two-in-one effectors or modular effectors, Casilio-ME2 and Casilio-ME3 remarkably boost gene activation and methylcytosine demethylation of targeted loci. We expand the toolbox to enable a stable and expression-inducible system for broader application of the Casilio-ME platforms. This work establishes a platform for editing DNA methylation to enable research investigations interrogating DNA methylomes.
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Affiliation(s)
- Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Menghan Du
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Nathaniel Jillette
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Abhijit Rath
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Christopher D Heinen
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Albert W Cheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health, 400 Farmington Avenue, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, UConn Health Science Center, 400 Farmington Avenue, Farmington, CT, 06030, USA.
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47
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Semer M, Bidon B, Larnicol A, Caliskan G, Catez P, Egly JM, Coin F, Le May N. DNA repair complex licenses acetylation of H2A.Z.1 by KAT2A during transcription. Nat Chem Biol 2019; 15:992-1000. [PMID: 31527837 DOI: 10.1038/s41589-019-0354-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/24/2019] [Indexed: 12/11/2022]
Abstract
Post-translational modifications of histone variant H2A.Z accompany gene transactivation, but its modifying enzymes still remain elusive. Here, we reveal a hitherto unknown function of human KAT2A (GCN5) as a histone acetyltransferase (HAT) of H2A.Z at the promoters of a set of transactivated genes. Expression of these genes also depends on the DNA repair complex XPC-RAD23-CEN2. We established that XPC-RAD23-CEN2 interacts both with H2A.Z and KAT2A to drive the recruitment of the HAT at promoters and license H2A.Z acetylation. KAT2A selectively acetylates H2A.Z.1 versus H2A.Z.2 in vitro on several well-defined lysines and we unveiled that alanine-14 in H2A.Z.2 is responsible for inhibiting the activity of KAT2A. Notably, the use of a nonacetylable H2A.Z.1 mutant shows that H2A.Z.1ac recruits the epigenetic reader BRD2 to promote RNA polymerase II recruitment. Our studies identify KAT2A as an H2A.Z.1 HAT in mammals and implicate XPC-RAD23-CEN2 as a transcriptional co-activator licensing the reshaping of the promoter epigenetic landscape.
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Affiliation(s)
- M Semer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - B Bidon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - A Larnicol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - G Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Department of Pharmaceutical Biotechnology, Faculty of pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - P Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - J M Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - F Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
| | - N Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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48
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TFIIE orchestrates the recruitment of the TFIIH kinase module at promoter before release during transcription. Nat Commun 2019; 10:2084. [PMID: 31064989 PMCID: PMC6504876 DOI: 10.1038/s41467-019-10131-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022] Open
Abstract
In eukaryotes, the general transcription factors TFIIE and TFIIH assemble at the transcription start site with RNA Polymerase II. However, the mechanism by which these transcription factors incorporate the preinitiation complex and coordinate their action during RNA polymerase II transcription remains elusive. Here we show that the TFIIEα and TFIIEβ subunits anchor the TFIIH kinase module (CAK) within the preinitiation complex. In addition, we show that while RNA polymerase II phosphorylation and DNA opening occur, CAK and TFIIEα are released from the promoter. This dissociation is impeded by either ATP-γS or CDK7 inhibitor THZ1, but still occurs when XPB activity is abrogated. Finally, we show that the Core-TFIIH and TFIIEβ are subsequently removed, while elongation factors such as DSIF are recruited. Remarkably, these early transcriptional events are affected by TFIIE and TFIIH mutations associated with the developmental disorder, trichothiodystrophy. The general transcription factors TFIIE and TFIIH assemble at the transcription start site with RNA Polymerase II. Here the authors provide evidence that the TFIIEα and TFIIEβ subunits anchor the TFIIH kinase module within the preinitiation complex before their release during transcription.
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49
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Ferri D, Orioli D, Botta E. Heterogeneity and overlaps in nucleotide excision repair disorders. Clin Genet 2019; 97:12-24. [PMID: 30919937 DOI: 10.1111/cge.13545] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/27/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
Abstract
Nucleotide excision repair (NER) is an essential DNA repair pathway devoted to the removal of bulky lesions such as photoproducts induced by the ultraviolet (UV) component of solar radiation. Deficiencies in NER typically result in a group of heterogeneous distinct disorders ranging from the mild UV sensitive syndrome to the cancer-prone xeroderma pigmentosum and the neurodevelopmental/progeroid conditions trichothiodystrophy, Cockayne syndrome and cerebro-oculo-facio-skeletal-syndrome. A complicated genetic scenario underlines these disorders with the same gene linked to different clinical entities as well as different genes associated with the same disease. Overlap syndromes with combined hallmark features of different NER disorders can occur and sporadic presentations showing extra features of the hematological disorder Fanconi Anemia or neurological manifestations mimicking Hungtinton disease-like syndromes have been described. Here, we discuss the multiple functions of the five major pleiotropic NER genes (ERCC3/XPB, ERCC2/XPD, ERCC5/XPG, ERCC1 and ERCC4/XPF) and their relevance in phenotypic complexity. We provide an update of mutational spectra and examine genotype-phenotype relationships. Finally, the molecular defects that could explain the puzzling overlap syndromes are discussed.
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Affiliation(s)
- Debora Ferri
- Istituto di Genetica Molecolare (IGM), Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Donata Orioli
- Istituto di Genetica Molecolare (IGM), Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Elena Botta
- Istituto di Genetica Molecolare (IGM), Consiglio Nazionale delle Ricerche, Pavia, Italy
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50
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Aberrations in DNA repair pathways in cancer and therapeutic significances. Semin Cancer Biol 2019; 58:29-46. [PMID: 30922960 DOI: 10.1016/j.semcancer.2019.02.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 01/16/2023]
Abstract
Cancer cells show various types of mutations and aberrant expression in genes involved in DNA repair responses. These alterations induce genome instability and promote carcinogenesis steps and cancer progression processes. These defects in DNA repair have also been considered as suitable targets for cancer therapies. A most effective target so far clinically demonstrated is "homologous recombination repair defect", such as BRCA1/2 mutations, shown to cause synthetic lethality with inhibitors of poly(ADP-ribose) polymerase (PARP), which in turn is involved in DNA repair as well as multiple physiological processes. Different approaches targeting genomic instability, including immune therapy targeting mismatch-repair deficiency, have also recently been demonstrated to be promising strategies. In these DNA repair targeting-strategies, common issues could be how to optimize treatment and suppress/conquer the development of drug resistance. In this article, we review the extending framework of DNA repair response pathways and the potential impact of exploiting those defects on cancer treatments, including chemotherapy, radiation therapy and immune therapy.
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