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D'Souza A, Kim M, Chazin WJ, Schärer OD. Protein-protein interactions in the core nucleotide excision repair pathway. DNA Repair (Amst) 2024; 141:103728. [PMID: 39029374 DOI: 10.1016/j.dnarep.2024.103728] [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: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024]
Abstract
Nucleotide excision repair (NER) clears genomes of DNA adducts formed by UV light, environmental agents, and antitumor drugs. Gene mutations that lead to defects in the core NER reaction cause the skin cancer-prone disease xeroderma pigmentosum. In NER, DNA lesions are excised within an oligonucleotide of 25-30 residues via a complex, multi-step reaction that is regulated by protein-protein interactions. These interactions were first characterized in the 1990s using pull-down, co-IP and yeast two-hybrid assays. More recently, high-resolution structures and detailed functional studies have started to yield detailed pictures of the progression along the NER reaction coordinate. In this review, we highlight how the study of interactions among proteins by structural and/or functional studies have provided insights into the mechanisms by which the NER machinery recognizes and excises DNA lesions. Furthermore, we identify reported, but poorly characterized or unsubstantiated interactions in need of further validation.
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Affiliation(s)
- Areetha D'Souza
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, the Republic of Korea; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917, USA; Center for Structural Biology, Vandebilt University, Nashville, TN 37232-7917, USA
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, the Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917, USA; Center for Structural Biology, Vandebilt University, Nashville, TN 37232-7917, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232-7917, USA
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, the Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917, USA.
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2
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Gong W, Holmberg H, Lu C, Huang M, Li S. Interplay of the Tfb1 pleckstrin homology domain with Rad2 and Rad4 in transcription coupled and global genomic nucleotide excision repair. Nucleic Acids Res 2024; 52:6333-6346. [PMID: 38634797 PMCID: PMC11194066 DOI: 10.1093/nar/gkae286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Transcription-coupled repair (TCR) and global genomic repair (GGR) are two subpathways of nucleotide excision repair (NER). The TFIIH subunit Tfb1 contains a Pleckstrin homology domain (PHD), which was shown to interact with one PHD-binding segment (PB) of Rad4 and two PHD-binding segments (PB1 and PB2) of Rad2 in vitro. Whether and how the different Rad2 and Rad4 PBs interact with the same Tfb1 PHD, and whether and how they affect TCR and GGR within the cell remain mysterious. We found that Rad4 PB constitutively interacts with Tfb1 PHD, and the two proteins may function within one module for damage recognition in TCR and GGR. Rad2 PB1 protects Tfb1 from degradation and interacts with Tfb1 PHD at a basal level, presumably within transcription preinitiation complexes when NER is inactive. During a late step of NER, the interaction between Rad2 PB1 and Tfb1 PHD augments, enabling efficient TCR and GGR. Rather than interacting with Tfb1 PHD, Rad2 PB2 constrains the basal interaction between Rad2 PB1 and Tfb1 PHD, thereby weakening the protection of Tfb1 from degradation and enabling rapid augmentation of their interactions within TCR and GGR complexes. Our results shed new light on NER mechanisms.
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Affiliation(s)
- Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Hannah Holmberg
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Cheng Lu
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michelle Huang
- 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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Meng X, Ma J, Meng N, Yun T, Niu B. Case Report: SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder with genetic analysis. Front Oncol 2023; 13:1086266. [PMID: 37456262 PMCID: PMC10348478 DOI: 10.3389/fonc.2023.1086266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
SMARCA4 (BRG1)-deficient undifferentiated carcinoma is a rare and highly aggressive malignancy. It has been reported to occur in a multiple range of organs. However, to the best of our knowledge, SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder has not yet been reported. Here, we describe a case of SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder. Through comprehensive genetic analysis, we hypothesized that in addition to SMARCA4 (BRG1) deficiency, other genetic changes might also be involved in the tumorigenesis of undifferentiated gallbladder cancer in this patient, particularly somatic mutations in the CTNNB1, KRAS, PIK3CA, TP53, CREBBP, and FANCI genes. To the best of our knowledge, this is the first report of SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder with genetic analysis.
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Affiliation(s)
- Xiangpeng Meng
- Pancreatic Endocrinology Ward, Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Nan Meng
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
| | - Tianyu Yun
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
| | - Beifang Niu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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4
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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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Revisiting the Anti-Cancer Toxicity of Clinically Approved Platinating Derivatives. Int J Mol Sci 2022; 23:ijms232315410. [PMID: 36499737 PMCID: PMC9793759 DOI: 10.3390/ijms232315410] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Cisplatin (CDDP), carboplatin (CP), and oxaliplatin (OXP) are three platinating agents clinically approved worldwide for use against a variety of cancers. They are canonically known as DNA damage inducers; however, that is only one of their mechanisms of cytotoxicity. CDDP mediates its effects through DNA damage-induced transcription inhibition and apoptotic signalling. In addition, CDDP targets the endoplasmic reticulum (ER) to induce ER stress, the mitochondria via mitochondrial DNA damage leading to ROS production, and the plasma membrane and cytoskeletal components. CP acts in a similar fashion to CDDP by inducing DNA damage, mitochondrial damage, and ER stress. Additionally, CP is also able to upregulate micro-RNA activity, enhancing intrinsic apoptosis. OXP, on the other hand, at first induces damage to all the same targets as CDDP and CP, yet it is also capable of inducing immunogenic cell death via ER stress and can decrease ribosome biogenesis through its nucleolar effects. In this comprehensive review, we provide detailed mechanisms of action for the three platinating agents, going beyond their nuclear effects to include their cytoplasmic impact within cancer cells. In addition, we cover their current clinical use and limitations, including side effects and mechanisms of resistance.
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Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer. Cancers (Basel) 2022; 14:cancers14235967. [PMID: 36497448 PMCID: PMC9739414 DOI: 10.3390/cancers14235967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
The prevalence of hereditary cancer in children was estimated to be very low until recent studies suggested that at least 10% of pediatric cancer patients carry a germline mutation in a cancer predisposition gene. A significant proportion of pathogenic variants associated with an increased risk of hereditary cancer are variants affecting splicing. RNA splicing is an essential process involved in different cellular processes such as proliferation, survival, and differentiation, and alterations in this pathway have been implicated in many human cancers. Hereditary cancer genes are highly susceptible to splicing mutations, and among them there are several genes that may contribute to pediatric solid tumors when mutated in the germline. In this review, we have focused on the analysis of germline splicing-disrupting mutations found in pediatric solid tumors, as the discovery of pathogenic splice variants in pediatric cancer is a growing field for the development of personalized therapies. Therapies developed to correct aberrant splicing in cancer are also discussed as well as the options to improve the diagnostic yield based on the increase in the knowledge in splicing.
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TAUPELET F, DONNIO LM, MAGNANI C, MARI PO, GIGLIA-MARI G. A stable XPG protein is required for proper ribosome biogenesis: Insights on the phenotype of combinate Xeroderma Pigmentosum/Cockayne Syndrome patients. PLoS One 2022; 17:e0271246. [PMID: 35802638 PMCID: PMC9269744 DOI: 10.1371/journal.pone.0271246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
Nucleotide Excision Repair is one of the five DNA repair systems. More than 30 proteins are involved in this process, including the seven XP proteins. When mutated, the genes coding for these proteins are provoking the rare disease Xeroderma Pigmentosum, which causes cutaneous defects and a high prevalence of skin cancers in patients. The CSA and CSB proteins are also involved in Nucleotide Excision Repair, and their mutation leads to Cockayne Syndrome, another rare disease, causing dwarfism, neurodegeneration, and ultimately early death, but without high skin cancer incidence. Some mutations of ERCC5, the gene coding for XPG, may give rise to a combined Xeroderma Pigmentosum and Cockayne Syndrome. A defect in Nucleotide Excision Repair alone cannot explain all these phenotypes. XPG has been located in the nucleolus, where ribosome biogenesis happens. This energy-consuming process starts with the transcription of the ribosomal DNA in a long ribosomal RNA, the pre-rRNA 47S, by RNA Polymerase 1. 47S pre-rRNA undergoes several cleavages and modifications to form three mature products: the ribosomal RNAs 18S, 5.8S and 28S. In the cytoplasm, these three products will enter the ribosomes’ composition, the producers of protein in our cells. Our work aimed to observe ribosome biogenesis in presence of an unstable XPG protein. By working on Xeroderma Pigmentosum/Cockayne Syndrome cell lines, meaning in the absence of XPG, we uncovered that the binding of UBF, as well as the number of unresolved R-loops, is increased along the ribosomal DNA gene body and flanking regions. Furthermore, ribosomal RNA maturation is impaired, with increased use of alternative pathways of maturation as well as an increase of immature precursors. These defective processes may explain the neurodegeneration observed when the XPG protein is heavily truncated, as ribosomal homeostasis and R-loops resolution are critical for proper neuronal development.
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Affiliation(s)
- Florent TAUPELET
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Lise-Marie DONNIO
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Charlène MAGNANI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre-Olivier MARI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Giuseppina GIGLIA-MARI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail:
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8
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Low GKM, Ting APL, Fok EDZ, Gopalakrishnan K, Zeegers D, Khaw AK, Jayapal M, Martinez-Lopez W, Hande MP. Role of Xeroderma pigmentosum D (XPD) protein in genome maintenance in human cells under oxidative stress. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503444. [PMID: 35483790 DOI: 10.1016/j.mrgentox.2022.503444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Xeroderma pigmentosum D (XPD) protein plays a pivotal role in the nucleotide excision repair pathway. XPD unwinds the local area of the damaged DNA by virtue of constituting transcription factor II H (TFIIH) and is important not only for repair but also for basal transcription. Although cells deficient in XPD have shown to be defective in oxidative base-lesion repair, the effects of the oxidative assault on primary fibroblasts from patients suffering from Xeroderma Pigmentosum D have not been fully explored. Therefore, we sought to investigate the role of XPD in oxidative DNA damage-repair by treating primary fibroblasts derived from a patient suffering from Xeroderma Pigmentosum D, with hydrogen peroxide. Our results show dose-dependent increase in genotoxicity with minimal effect on cytotoxicity with H2O2 in XPD deficient cells compared to control cells. XPD deficient cells displayed increased susceptibility and reduced repair capacity when subjected to DNA damage induced by oxidative stress. XPD deficient fibroblasts exhibited increased telomeric loss after H2O2 treatment. In addition, we demonstrated that chronic oxidative stress induced accelerated premature senescence characteristics. Gene expression profiling revealed alterations in genes involved in transcription and nucleotide metabolisms, as well as in cellular and cell cycle processes in a more significant way than in other pathways. This study highlights the role of XPD in the repair of oxidative stress and telomere maintenance. Lack of functional XPD seems to increase the susceptibility of oxidative stress-induced genotoxicity while retaining cell viability posing as a potential cancer risk factor of Xeroderma Pigmentosum D patients.
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Affiliation(s)
- Grace Kah Mun Low
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Aloysius Poh Leong Ting
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Edwin Dan Zhihao Fok
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kalpana Gopalakrishnan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dimphy Zeegers
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Aik Kia Khaw
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Manikandan Jayapal
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wilner Martinez-Lopez
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; Associate Unit on Genomic Stability, Faculty of Medicine, University of the Republic (UdelaR), Montevideo, Uruguay; Vellore Institute of Technology, Vellore, India
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Vellore Institute of Technology, Vellore, India; Mangalore University, India.
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Haase J, Chen R, Parker WM, Bonner MK, Jenkins LM, Kelly AE. The TFIIH complex is required to establish and maintain mitotic chromosome structure. eLife 2022; 11:75475. [PMID: 35293859 PMCID: PMC8956287 DOI: 10.7554/elife.75475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is continuously required to establish and maintain a compacted chromosome structure in transcriptionally silent Xenopus egg extracts. Inhibiting the DNA-dependent ATPase activity of the TFIIH complex subunit XPB rapidly and reversibly induces a complete loss of chromosome structure and prevents the enrichment of condensins I and II, but not topoisomerase II, on chromatin. In addition, inhibiting TFIIH prevents condensation of both mouse and Xenopus nuclei in Xenopus egg extracts, which suggests an evolutionarily conserved mechanism of TFIIH action. Reducing nucleosome density through partial histone depletion restores chromosome structure and condensin enrichment in the absence of TFIIH activity. We propose that the TFIIH complex promotes mitotic chromosome condensation by dynamically altering the chromatin environment to facilitate condensin loading and condensin-dependent loop extrusion.
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Affiliation(s)
- Julian Haase
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Richard Chen
- Graduate School of Biomedical Sciences, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Wesley M Parker
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Mary Kate Bonner
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Lisa M Jenkins
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Alexander E Kelly
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
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Titov RA, Minina VI, Torgunakova AV, Buslaev VY, Voronina EN, Prosekov AY, Titov VA, Glushkov AN. Studying the Role of DNA Repair Gene Polymorphism in Formation of Predisposition to Lung Cancer Development in Women. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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van Toorn M, Turkyilmaz Y, Han S, Zhou D, Kim HS, Salas-Armenteros I, Kim M, Akita M, Wienholz F, Raams A, Ryu E, Kang S, Theil AF, Bezstarosti K, Tresini M, Giglia-Mari G, Demmers JA, Schärer OD, Choi JH, Vermeulen W, Marteijn JA. Active DNA damage eviction by HLTF stimulates nucleotide excision repair. Mol Cell 2022; 82:1343-1358.e8. [PMID: 35271816 PMCID: PMC9473497 DOI: 10.1016/j.molcel.2022.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/15/2021] [Accepted: 02/10/2022] [Indexed: 10/18/2022]
Abstract
Nucleotide excision repair (NER) counteracts the onset of cancer and aging by removing helix-distorting DNA lesions via a "cut-and-patch"-type reaction. The regulatory mechanisms that drive NER through its successive damage recognition, verification, incision, and gap restoration reaction steps remain elusive. Here, we show that the RAD5-related translocase HLTF facilitates repair through active eviction of incised damaged DNA together with associated repair proteins. Our data show a dual-incision-dependent recruitment of HLTF to the NER incision complex, which is mediated by HLTF's HIRAN domain that binds 3'-OH single-stranded DNA ends. HLTF's translocase motor subsequently promotes the dissociation of the stably damage-bound incision complex together with the incised oligonucleotide, allowing for an efficient PCNA loading and initiation of repair synthesis. Our findings uncover HLTF as an important NER factor that actively evicts DNA damage, thereby providing additional quality control by coordinating the transition between the excision and DNA synthesis steps to safeguard genome integrity.
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Affiliation(s)
- Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Yasemin Turkyilmaz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Sueji Han
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Irene Salas-Armenteros
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Masaki Akita
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Giuseppina Giglia-Mari
- Institut NeuroMyoGène (INMG), CNRS UMR 5310, INSERM U1217, Université de Lyon, Université Claude Bernard Lyon1, 16 rue Dubois, 69622 Villeurbanne Cedex, France
| | - Jeroen A Demmers
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands.
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12
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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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13
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Feltes BC. Revisiting the structural features of the xeroderma pigmentosum proteins: Focus on mutations and knowledge gaps. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108416. [PMID: 35690419 DOI: 10.1016/j.mrrev.2022.108416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The nucleotide excision repair pathway is a broadly studied DNA repair mechanism because impairments of its key players, the xeroderma pigmentosum proteins (XPA to XPG), are associated with multiple hereditary diseases. Due to the massive number of novel mutations reported for these proteins and new structural data published every year, proper categorization and discussion of relevant observations is needed to organize this extensive inflow of knowledge. This review aims to revisit the structural data of all XP proteins while updating it with the information developed in of the past six years. Discussions and interpretations of mutation outcomes, mechanisms of action, and knowledge gaps regarding their structures are provided, as well as new perspectives based on recent research.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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14
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DNA Repair in Haploid Context. Int J Mol Sci 2021; 22:ijms222212418. [PMID: 34830299 PMCID: PMC8620282 DOI: 10.3390/ijms222212418] [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: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 12/15/2022] Open
Abstract
DNA repair is a well-covered topic as alteration of genetic integrity underlies many pathological conditions and important transgenerational consequences. Surprisingly, the ploidy status is rarely considered although the presence of homologous chromosomes dramatically impacts the repair capacities of cells. This is especially important for the haploid gametes as they must transfer genetic information to the offspring. An understanding of the different mechanisms monitoring genetic integrity in this context is, therefore, essential as differences in repair pathways exist that differentiate the gamete’s role in transgenerational inheritance. Hence, the oocyte must have the most reliable repair capacity while sperm, produced in large numbers and from many differentiation steps, are expected to carry de novo variations. This review describes the main DNA repair pathways with a special emphasis on ploidy. Differences between Saccharomyces cerevisiae and Schizosaccharomyces pombe are especially useful to this aim as they can maintain a diploid and haploid life cycle respectively.
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15
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Gaul L, Svejstrup JQ. Transcription-coupled repair and the transcriptional response to UV-Irradiation. DNA Repair (Amst) 2021; 107:103208. [PMID: 34416541 DOI: 10.1016/j.dnarep.2021.103208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023]
Abstract
Lesions in genes that result in RNA polymerase II (RNAPII) stalling or arrest are particularly toxic as they are a focal point of genome instability and potently block further transcription of the affected gene. Thus, cells have evolved the transcription-coupled nucleotide excision repair (TC-NER) pathway to identify damage-stalled RNAPIIs, so that the lesion can be rapidly repaired and transcription can continue. However, despite the identification of several factors required for TC-NER, how RNAPII is remodelled, modified, removed, or whether this is even necessary for repair remains enigmatic, and theories are intensely contested. Recent studies have further detailed the cellular response to UV-induced ubiquitylation and degradation of RNAPII and its consequences for transcription and repair. These advances make it pertinent to revisit the TC-NER process in general and with specific discussion of the fate of RNAPII stalled at DNA lesions.
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Affiliation(s)
- Liam Gaul
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark.
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16
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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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17
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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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18
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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19
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Yang S, Liu JDH, Diem M, Wesseling S, Vervoort J, Oostenbrink C, Rietjens IMCM. Molecular Dynamics and In Vitro Quantification of Safrole DNA Adducts Reveal DNA Adduct Persistence Due to Limited DNA Distortion Resulting in Inefficient Repair. Chem Res Toxicol 2020; 33:2298-2309. [PMID: 32786539 DOI: 10.1021/acs.chemrestox.0c00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The formation and repair of N2-(trans-isosafrol-3'-yl)-2'-deoxyguanosine (S-3'-N2-dG) DNA adduct derived from the spice and herbal alkenylbenzene constituent safrole were investigated. DNA adduct formation and repair were studied in vitro and using molecular dynamics (MD) simulations. DNA adduct formation was quantified using liquid chromatography-mass spectrometry (LCMS) in wild type and NER (nucleotide excision repair) deficient CHO cells and also in HepaRG cells and primary rat hepatocytes after different periods of repair following exposure to safrole or 1'-hydroxysafrole (1'-OH safrole). The slower repair of the DNA adducts found in NER deficient cells compared to that in CHO wild type cells indicates a role for NER in repair of S-3'-N2-dG DNA adducts. However, DNA repair in liver cell models appeared to be limited, with over 90% of the adducts remaining even after 24 or 48 h recovery. In our further studies, MD simulations indicated that S-3'-N2-dG adduct formation causes only subtle changes in the DNA structure, potentially explaining inefficient activation of NER. Inefficiency of NER mediated repair of S-3'-N2-dG adducts points at persistence and potential bioaccumulation of safrole DNA adducts upon daily dietary exposure.
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Affiliation(s)
- Shuo Yang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jakob D H Liu
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Matthias Diem
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Sebastiaan Wesseling
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jacques Vervoort
- Division of Biochemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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20
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André KM, Sipos EH, Soutourina J. Mediator Roles Going Beyond Transcription. Trends Genet 2020; 37:224-234. [PMID: 32921511 DOI: 10.1016/j.tig.2020.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Dysfunctions of nuclear processes including transcription and DNA repair lead to severe human diseases. Gaining an understanding of how these processes operate in the crowded context of chromatin can be particularly challenging. Mediator is a large multiprotein complex conserved in eukaryotes with a key coactivator role in the regulation of RNA polymerase (Pol) II transcription. Despite intensive studies, the molecular mechanisms underlying Mediator function remain to be fully understood. Novel findings have provided insights into the relationship between Mediator and chromatin architecture, revealed its role in connecting transcription with DNA repair and proposed an emerging mechanism of phase separation involving Mediator condensates. Recent developments in the field suggest multiple functions of Mediator going beyond transcriptional processes per se that would explain its involvement in various human pathologies.
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Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eliet H Sipos
- 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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21
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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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22
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Peissert S, Sauer F, Grabarczyk DB, Braun C, Sander G, Poterszman A, Egly JM, Kuper J, Kisker C. In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair. Nat Commun 2020; 11:1667. [PMID: 32245994 PMCID: PMC7125077 DOI: 10.1038/s41467-020-15241-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
The XPD helicase is a central component of the general transcription factor TFIIH which plays major roles in transcription and nucleotide excision repair (NER). Here we present the high-resolution crystal structure of the Arch domain of XPD with its interaction partner MAT1, a central component of the CDK activating kinase complex. The analysis of the interface led to the identification of amino acid residues that are crucial for the MAT1-XPD interaction. More importantly, mutagenesis of the Arch domain revealed that these residues are essential for the regulation of (i) NER activity by either impairing XPD helicase activity or the interaction of XPD with XPG; (ii) the phosphorylation of the RNA polymerase II and RNA synthesis. Our results reveal how MAT1 shields these functionally important residues thereby providing insights into how XPD is regulated by MAT1 and defining the Arch domain as a major mechanistic player within the XPD scaffold. XPD is part of the TFIIH complex which plays major roles in transcription initiation and nucleotide excision repair (NER). Here the authors present a high-resolution crystal structure of the XPD-MAT1 interface and dissect the role of this interface in transcription and NER.
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Affiliation(s)
- Stefan Peissert
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Florian Sauer
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U., Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Gudrun Sander
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U., Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U., Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France. .,Université de Strasbourg, 67404, Illkirch, France.
| | - Jochen Kuper
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany.
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, 97080, Würzburg, Germany. .,Comprehensive Cancer Center Mainfranken, Würzburg, Germany.
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23
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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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24
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XPA: DNA Repair Protein of Significant Clinical Importance. Int J Mol Sci 2020; 21:ijms21062182. [PMID: 32235701 PMCID: PMC7139726 DOI: 10.3390/ijms21062182] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023] Open
Abstract
The nucleotide excision repair (NER) pathway is activated in response to a broad spectrum of DNA lesions, including bulky lesions induced by platinum-based chemotherapeutic agents. Expression levels of NER factors and resistance to chemotherapy has been examined with some suggestion that NER plays a role in tumour resistance; however, there is a great degree of variability in these studies. Nevertheless, recent clinical studies have suggested Xeroderma Pigmentosum group A (XPA) protein, a key regulator of the NER pathway that is essential for the repair of DNA damage induced by platinum-based chemotherapeutics, as a potential prognostic and predictive biomarker for response to treatment. XPA functions in damage verification step in NER, as well as a molecular scaffold to assemble other NER core factors around the DNA damage site, mediated by protein–protein interactions. In this review, we focus on the interacting partners and mechanisms of regulation of the XPA protein. We summarize clinical oncology data related to this DNA repair factor, particularly its relationship with treatment outcome, and examine the potential of XPA as a target for small molecule inhibitors.
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25
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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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26
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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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27
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Abstract
Nucleotide excision repair (NER) is a highly conserved mechanism to remove helix-distorting DNA lesions. A major substrate for NER is DNA damage caused by environmental genotoxins, most notably ultraviolet radiation. Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three human disorders caused by inherited defects in NER. The symptoms and severity of these diseases vary dramatically, ranging from profound developmental delay to cancer predisposition and accelerated ageing. All three syndromes include developmental abnormalities, indicating an important role for optimal transcription and for NER in protecting against spontaneous DNA damage during embryonic development. Here, we review the current knowledge on genes that function in NER that also affect embryonic development, in particular the development of a fully functional nervous system.
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Affiliation(s)
- Sofia J Araújo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.,Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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28
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Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H, Cramer P. Structural basis of TFIIH activation for nucleotide excision repair. Nat Commun 2019; 10:2885. [PMID: 31253769 PMCID: PMC6599211 DOI: 10.1038/s41467-019-10745-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 12/16/2022] Open
Abstract
Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a ‘plug’ element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway. The NER machinery contains the multisubunit transcription factor IIH (TFIIH) that opens the DNA repair bubble, scans for the lesion, and coordinates excision of the damaged site. Here the authors resolve the cryo-electron microscopy structure of the human core TFIIH-XPA-DNA complex and provide insights into its activation.
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Affiliation(s)
- Goran Kokic
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Dimitry Tegunov
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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29
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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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30
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Chikhaoui A, Elouej S, Nabouli I, Jones M, Lagarde A, Ben Rekaya M, Messaoud O, Hamdi Y, Zghal M, Delague V, Levy N, De Sandre-Giovannoli A, Abdelhak S, Yacoub-Youssef H. Identification of a ERCC5 c.2333T>C (L778P) Variant in Two Tunisian Siblings With Mild Xeroderma Pigmentosum Phenotype. Front Genet 2019; 10:111. [PMID: 30838033 PMCID: PMC6383105 DOI: 10.3389/fgene.2019.00111] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/30/2019] [Indexed: 11/22/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder due to a defect in the nucleotide excision repair (NER) DNA repair pathway, characterized by severe sunburn development of freckles, premature skin aging, and susceptibility to develop cancers at an average age of eight. XP is an example of accelerated photo-aging. It is a genetically and clinically heterogeneous disease. Eight complementation groups have been described worldwide. In Tunisia, five groups have been already identified. In this work, we investigated the genetic etiology in a family with an atypically mild XP phenotype. Two Tunisian siblings born from first-degree consanguineous parents underwent clinical examination in the dermatology department of the Charles Nicolle Hospital on the basis of acute sunburn reaction and mild neurological disorders. Blood samples were collected from two affected siblings after written informed consent. As all mutations reported in Tunisia have been excluded using Sanger sequencing, we carried out mutational analysis through a targeted panel of gene sequencing using the Agilent HaloPlex target enrichment system. Our clinical study shows, in both patients, the presence of achromic macula in sun exposed area with dermatological feature suggestive of Xeroderma pigmentosum disease. No developmental and neurological disorders were observed except mild intellectual disability. Genetic investigation shows that both patients were carriers of an homozygous T to C transition at the nucleotide position c.2333, causing the leucine to proline amino acid change at the position 778 (p.Leu778Pro) of the ERCC5 gene, and resulting in an XP-G phenotype. The same variation was previously reported at the heterozygous state in a patient cell line in Europe, for which no clinical data were available and was suggested to confer an XP/CS phenotype based on functional tests. This study contributes to further characterization of the mutation spectrum of XP in consanguineous Tunisian families and is potentially helpful for early diagnosis. It also indicates that the genotype-phenotype correlation is not always coherent for patients with mild clinical features. These data therefore suggest that targeted NGS is a highly informative diagnostic strategy, which can be used for XP molecular etiology determination.
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Affiliation(s)
- Asma Chikhaoui
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Sahar Elouej
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.,Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
| | - Imen Nabouli
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Meriem Jones
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.,Service de Dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | - Arnaud Lagarde
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
| | - Meriem Ben Rekaya
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mohamed Zghal
- Service de Dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | | | - Nicolas Levy
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France.,Département de Génétique Médicale, AP-HM, Hôpital la Timone, Marseille, France
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France.,Département de Génétique Médicale, AP-HM, Hôpital la Timone, Marseille, France
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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31
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Kolesnikova O, Radu L, Poterszman A. TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 115:21-67. [PMID: 30798933 DOI: 10.1016/bs.apcsb.2019.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factor IIH (TFIIH) is a multiprotein complex involved in both eukaryotic transcription and DNA repair, revealing a tight connection between these two processes. Composed of 10 subunits, it can be resolved into a 7-subunits core complex with the XPB translocase and the XPD helicase, and the 3-subunits kinase complex CAK, which also exists as a free complex with a distinct function. Initially identified as basal transcription factor, TFIIH also participates in transcription regulation and plays a key role in nucleotide excision repair (NER) for opening DNA at damaged sites, lesion verification and recruitment of additional repair factors. Our understanding of TFIIH function in eukaryotic cells has greatly benefited from studies of the genetic rare diseases xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD), that are not only characterized by cancer and aging predispositions but also by neurological and developmental defects. Although much remains unknown about TFIIH function, significant progresses have been done regarding the structure of the complex, the functions of its catalytic subunits and the multiple roles of the regulatory core-TFIIH subunits. This review provides a non-exhaustive survey of key discoveries on the structure and function of this pivotal factor, which can be considered as a promising target for therapeutic strategies.
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Affiliation(s)
- Olga Kolesnikova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. 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
| | - Laura Radu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. 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
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. 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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32
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Sabatella M, Theil AF, Ribeiro-Silva C, Slyskova J, Thijssen K, Voskamp C, Lans H, Vermeulen W. Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features. Nucleic Acids Res 2018; 46:9563-9577. [PMID: 30165384 PMCID: PMC6182131 DOI: 10.1093/nar/gky774] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 12/28/2022] Open
Abstract
The structure-specific ERCC1-XPF endonuclease plays a key role in DNA damage excision by nucleotide excision repair (NER) and interstrand crosslink repair. Mutations in this complex can either cause xeroderma pigmentosum (XP) or XP combined with Cockayne syndrome (XPCS-complex) or Fanconi anemia. However, most patients carry compound heterozygous mutations, which confounds the dissection of the phenotypic consequences for each of the identified XPF alleles. Here, we analyzed the functional impact of individual pathogenic XPF alleles on NER. We show that XP-causing mutations diminish XPF recruitment to DNA damage and only mildly affect global genome NER. In contrast, an XPCS-complex-specific mutation causes persistent recruitment of XPF and the upstream core NER machinery to DNA damage and severely impairs both global genome and transcription-coupled NER. Remarkably, persistence of NER factors at DNA damage appears to be a common feature of XPCS-complex cells, suggesting that this could be a determining factor contributing to the development of additional developmental and/or neurodegenerative features in XP patients.
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Affiliation(s)
- Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Karen Thijssen
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Chantal Voskamp
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
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33
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Ricotti R, Nardo T, Striano P, Stefanini M, Orioli D, Botta E. Phenotypic variability in xeroderma pigmentosum group G: An uncommon case with severe prenatal-onset Cockayne syndrome features. Clin Genet 2018; 94:386-388. [DOI: 10.1111/cge.13364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/30/2018] [Accepted: 04/06/2018] [Indexed: 11/27/2022]
Affiliation(s)
- R. Ricotti
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche; Pavia Italy
| | - T. Nardo
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche; Pavia Italy
| | - P. Striano
- Pediatric Neurology and Muscular Diseases Unit; “G. Gaslini” Institute; Genoa Italy
| | - M. Stefanini
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche; Pavia Italy
| | - D. Orioli
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche; Pavia Italy
| | - E. Botta
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche; Pavia Italy
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34
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Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. DNA Repair (Amst) 2018; 71:33-42. [PMID: 30174301 DOI: 10.1016/j.dnarep.2018.08.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) is the main pathway for the removal of bulky lesions from DNA and is characterized by an extraordinarily wide substrate specificity. Remarkably, the efficiency of lesion removal varies dramatically and certain lesions escape repair altogether and are therefore associated with high levels of mutagenicity. Central to the multistep mechanism of damage recognition in NER is the sensing of lesion-induced thermodynamic and structural alterations of DNA by the XPC-RAD23B protein and the verification of the damage by the transcription/repair factor TFIIH. Additional factors contribute to the process: UV-DDB, for the recognition of certain UV-induced lesions in particular in the context of chromatin, while the XPA protein is believed to have a role in damage verification and NER complex assembly. Here we consider the molecular mechanisms that determine repair efficiency in GG-NER based on recent structural, computational, biochemical, cellular and single molecule studies of XPC-RAD23B and its yeast ortholog Rad4. We discuss how the actions of XPC-RAD23B are integrated with those of other NER proteins and, based on recent high-resolution structures of TFIIH, present a structural model of how XPC-RAD23B and TFIIH cooperate in damage recognition and verification.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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35
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Xu M, Liu Y, Li D, Wang X, Liang S, Zhang G, Yang X. Chinese C allele carriers of the ERCC5 rs1047768 polymorphism are more sensitive to platinum-based chemotherapy: a meta-analysis. Oncotarget 2018; 9:1248-1256. [PMID: 29416691 PMCID: PMC5787435 DOI: 10.18632/oncotarget.18981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
It is suspected that ERCC5 rs1047768 and rs17655 polymorphisms influence the response to platinum-based chemotherapy. This meta-analysis was performed to summarize the scattered evidence regarding the association between these two polymorphisms and sensitivity to platinum-based treatment. Thirteen studies were included after a comprehensive literature search. The pooled odds ratios and 95% confidence intervals suggested that the C allele of the ERCC5 rs1047768 polymorphism is associated with elevated sensitivity to platinating agents, especially for Chinese patients. However, no difference among rs17655 genotypes could be detected.
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Affiliation(s)
- Meizhen Xu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yina Liu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Dan Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,School of Life Science and Technology, Tongji University, Shanghai, China.,Present address: Jiayin BioTechnology Co., Ltd., Shanghai, China
| | | | | | - Gaochuan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xiaoqin Yang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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36
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Okuda M, Nakazawa Y, Guo C, Ogi T, Nishimura Y. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways. Nucleic Acids Res 2017; 45:13043-13055. [PMID: 29069470 PMCID: PMC5727438 DOI: 10.1093/nar/gkx970] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/03/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA Polymerase II detects a lesion on the transcribed strand and recruits TFIIH by an unknown mechanism. Here, we found that the TCR initiation factor UVSSA forms a stable complex with the PH domain of p62 via a short acidic string in the central region of UVSSA, and determined the complex structure by NMR. The acidic string of UVSSA binds strongly to the basic groove of the PH domain by inserting Phe408 and Val411 into two pockets, highly resembling the interaction mechanism of XPC with p62. Mutational binding analysis validated the structure and identified residues crucial for binding. TCR activity was markedly diminished in UVSSA-deficient cells expressing UVSSA mutated at Phe408 or Val411. Thus, a common TFIIH recruitment mechanism is shared by UVSSA in TCR and XPC in GGR.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuka Nakazawa
- Department of Genome Repair, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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37
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Garcia-Moreno H, Fassihi H, Sarkany RPE, Phukan J, Warner T, Lehmann AR, Giunti P. Xeroderma pigmentosum is a definite cause of Huntington's disease-like syndrome. Ann Clin Transl Neurol 2017; 5:102-108. [PMID: 29376097 PMCID: PMC5771320 DOI: 10.1002/acn3.511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022] Open
Abstract
Xeroderma pigmentosum is characterized by cutaneous, ophthalmological, and neurological features. Although it is typical of childhood, late presentations can mimic different neurodegenerative conditions. We report two families presenting as Huntington's disease‐like syndromes. The first case (group G) presented with neuropsychiatric features, cognitive decline and chorea. Typical lentigines were only noticed after the neurological disease started. The second case (group B) presented adult‐onset chorea and neuropsychiatric symptoms after an aggressive ocular melanoma. Xeroderma pigmentosum can manifest as a Huntington's Disease‐like syndrome. Classic dermatological and oncological features have to be investigated in choreic patients with negative genetic tests for Huntington's disease‐like phenotypes.
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Affiliation(s)
- Hector Garcia-Moreno
- Ataxia Centre Department of Molecular Neuroscience University College London Institute of Neurology London WC1N 3BG United Kingdom
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service St John's Institute of Dermatology Guy's and St Thomas' Foundation Trust London SE1 7EH United Kingdom
| | - Robert P E Sarkany
- National Xeroderma Pigmentosum Service St John's Institute of Dermatology Guy's and St Thomas' Foundation Trust London SE1 7EH United Kingdom
| | - Julie Phukan
- Neurology Department Royal Free Hospital London NW3 2QG United Kingdom
| | - Thomas Warner
- Reta Lila Weston Institute of Neurological Studies University College London, Institute of Neurology 1 Wakefield Street London WC1N 1PJ United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre University of Sussex Falmer, Brighton BN1 9RQ United Kingdom
| | - Paola Giunti
- Ataxia Centre Department of Molecular Neuroscience University College London Institute of Neurology London WC1N 3BG United Kingdom.,National Xeroderma Pigmentosum Service St John's Institute of Dermatology Guy's and St Thomas' Foundation Trust London SE1 7EH United Kingdom
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Mori T, Yousefzadeh MJ, Faridounnia M, Chong JX, Hisama FM, Hudgins L, Mercado G, Wade EA, Barghouthy AS, Lee L, Martin GM, Nickerson DA, Bamshad MJ, Niedernhofer LJ, Oshima J. ERCC4 variants identified in a cohort of patients with segmental progeroid syndromes. Hum Mutat 2017; 39:255-265. [PMID: 29105242 DOI: 10.1002/humu.23367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/26/2017] [Accepted: 10/29/2017] [Indexed: 12/30/2022]
Abstract
Pathogenic variants in genes, which encode DNA repair and damage response proteins, result in a number of genomic instability syndromes with features of accelerated aging. ERCC4 (XPF) encodes a protein that forms a complex with ERCC1 and is required for the 5' incision during nucleotide excision repair. ERCC4 is also FANCQ, illustrating a critical role in interstrand crosslink repair. Pathogenic variants in this gene cause xeroderma pigmentosum, XFE progeroid syndrome, Cockayne syndrome (CS), and Fanconi anemia. We performed massive parallel sequencing for 42 unsolved cases submitted to the International Registry of Werner Syndrome. Two cases, each carrying two novel heterozygous ERCC4 variants, were identified. The first case was a compound heterozygote for: c.2395C > T (p.Arg799Trp) and c.388+1164_792+795del (p.Gly130Aspfs*18). Further molecular and cellular studies indicated that the ERCC4 variants in this patient are responsible for a phenotype consistent with a variant of CS. The second case was heterozygous for two variants in cis: c.[1488A > T; c.2579C > A] (p.[Gln496His; Ala860Asp]). While the second case also had several phenotypic features of accelerated aging, we were unable to provide biological evidence supporting the pathogenic roles of the associated ERCC4 variants. Precise genetic causes and disease mechanism of the second case remains to be determined.
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Affiliation(s)
- Takayasu Mori
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Maryam Faridounnia
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Erin A Wade
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Amira S Barghouthy
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Lin Lee
- Department of Pathology, University of Washington, Seattle, Washington
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Department of Genome Sciences, University of Washington, Seattle, Washington.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington
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- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Laura J Niedernhofer
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, Washington.,Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
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Fujii N. Potential Strategies to Target Protein-Protein Interactions in the DNA Damage Response and Repair Pathways. J Med Chem 2017; 60:9932-9959. [PMID: 28654754 DOI: 10.1021/acs.jmedchem.7b00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, on the basis of functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent.
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Affiliation(s)
- Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
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40
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Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD. Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst) 2017; 57:76-90. [PMID: 28704716 PMCID: PMC5731452 DOI: 10.1016/j.dnarep.2017.06.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 11/25/2022]
Abstract
Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the ∼14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum.
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Affiliation(s)
- Mandira Manandhar
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA; MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, TX, USA
| | - Megan G Lowery
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA
| | - Karen S Boulware
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA
| | - Kevin H Lin
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA
| | - Yue Lu
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX, 78957, USA; MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, TX, USA.
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41
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42
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Xiang T, Kang X, Gong Z, Bai W, Chen C, Zhang W. XPG genetic polymorphisms and clinical outcome of patients with advanced non-small cell lung cancer under platinum-based treatment: a meta-analysis of 12 studies. Cancer Chemother Pharmacol 2017; 79:791-800. [PMID: 28314991 DOI: 10.1007/s00280-017-3280-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/07/2017] [Indexed: 01/10/2023]
Abstract
PURPOSE A number of studies on the relationship between xeroderma pigmentosum group G (XPG) polymorphisms and clinical outcomes in non-small cell cancer (NSCLC) have led to inconclusive results. This meta-analysis evaluates the predictive value of XPG polymorphisms on the treatment response rate and overall survival of patients with NSCLC. METHODS To measure the correlative strength of the relationship between XPG polymorphisms and outcomes of patients with NSCLC, we searched electronic databases, including PubMed and China National Knowledge Infrastructure, to retrieve studies up to August 2016. We also employed pooled odds ratios (ORs) and hazard ratios (HRs) corresponding to 95% confidence intervals (95% CIs). RESULTS Twelve studies involving 2877 patients with NSCLC were included: 8 studies involving 1473 patients examined the correlation between XPG polymorphisms and tumor response rate and 7 studies involving 2329 patients reported on the correlation of XPG polymorphisms with overall survival. None of the XPG His1104Asp(C>G)/His46His(C>T) polymorphisms exhibited a correlation with treatment response rate or overall survival. However, in a further stratified analysis by ethnicity, carriers of the 1104G allele were associated with good response among Asians in the homozygote model (GG vs. CC: OR = 1.57, 95% CI: 1.05-2.34, P = 0.027). Meanwhile, further stratified by ethnicity, His46His polymorphism was not associated with RR and OS in any genetic models. CONCLUSIONS No strong evidence was found to support the use of XPG polymorphisms as tumor response and prognostic factors of patients with NSCLC receiving a platinum-based treatment regimen, which is attributed to marginal association. Studies with large-scale and multiple ethnicities need to be conducted to verify the conclusion.
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Affiliation(s)
- Tianxin Xiang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiuhua Kang
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenghua Gong
- Shenzhen Peking University and Hong Kong University of Science and Technology Medical Center, FuTian District, Shenzhen, China
| | - Wei Bai
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chuanhui Chen
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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43
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Yang Y, Yao X, Luo Y, Zhao L, Zhou B, Tu M, Zhao R. Identification of a novel mutation confirms phenotypic variability of mutant XPG truncations. Int J Dermatol 2017; 56:e149-e151. [PMID: 28251620 DOI: 10.1111/ijd.13554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/29/2016] [Accepted: 12/14/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Yongjia Yang
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Xu Yao
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Yongqi Luo
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China.,The Department of dermatology, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Liu Zhao
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Bin Zhou
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China.,The Department of dermatology, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Ming Tu
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
| | - Rui Zhao
- The Lab. of Genetics and Metabolism, Hunan Children's Research Institute (HCRI), Hunan Children's Hospital, The Paediatric Academy of University of South China, Changsha, China
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44
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Dutto I, Cazzalini O, Stivala LA, Prosperi E. An improved method for the detection of nucleotide excision repair factors at local UV DNA damage sites. DNA Repair (Amst) 2017; 51:79-84. [PMID: 28185850 DOI: 10.1016/j.dnarep.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/12/2017] [Indexed: 12/19/2022]
Abstract
Among different DNA repair processes that cells use to face with DNA damage, nucleotide excision repair (NER) is particularly important for the removal of a high variety of lesions, including those generated by some antitumor drugs. A number of factors participating in NER, such as the TFIIH complex and the endonuclease XPG are also involved in basal processes, e.g. transcription. For this reason, localization of these factors at DNA damage sites may be difficult. Here we have applied a mild digestion of chromatin with DNase I to improve the in situ extraction necessary to detect chromatin-bound proteins by immunofluorescence. We have compared this method with different extraction protocols and investigated its application on different cell types, and with different antibodies. Our results show that a short DNase I treatment before the immunoreaction, enhances the fluorescence signal of NER proteins, such as XPG, DDB2 and XPC. In addition, our findings indicate that the antibody choice is a critical factor for accurate localization of DNA repair proteins at DNA damage sites. In conclusion, a mild DNA digestion with DNase I improves the immunofluorescence detection of the recruitment of NER factors at local DNA damage sites by enhancing accessibility to the antibodies, independently of the cell type.
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Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ornella Cazzalini
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia generale, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Lucia Anna Stivala
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia generale, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100 Pavia, Italy.
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45
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Nucleotide Excision Repair: From Neurodegeneration to Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:17-39. [PMID: 28840550 DOI: 10.1007/978-3-319-60733-7_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA damage poses a constant threat to genome integrity taking a variety of shapes and arising by normal cellular metabolism or environmental insults. Human syndromes, characterized by increased cancer pre-disposition or early onset of age-related pathology and developmental abnormalities, often result from defective DNA damage responses and compromised genome integrity. Over the last decades intensive research worldwide has made important contributions to our understanding of the molecular mechanisms underlying genomic instability and has substantiated the importance of DNA repair in cancer prevention in the general population. In this chapter, we discuss Nucleotide Excision Repair pathway, the causative role of its components in disease-related pathology and recent technological achievements that decipher mutational landscapes and may facilitate pathological classification and personalized therapy.
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46
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Zurita M, Cruz-Becerra G. TFIIH: New Discoveries Regarding its Mechanisms and Impact on Cancer Treatment. J Cancer 2016; 7:2258-2265. [PMID: 27994662 PMCID: PMC5166535 DOI: 10.7150/jca.16966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/30/2016] [Indexed: 12/16/2022] Open
Abstract
The deregulation of gene expression is a characteristic of cancer cells, and malignant cells require very high levels of transcription to maintain their cancerous phenotype and survive. Therefore, components of the basal transcription machinery may be considered as targets to preferentially kill cancerous cells. TFIIH is a multisubunit basal transcription factor that also functions in nucleotide excision repair. The recent discoveries of some small molecules that interfere with TFIIH and that preferentially kill cancer cells have increased researchers' interest to elucidate the complex mechanisms by which TFIIH operates. In this review, we summarize the knowledge generated during the 25 years of TFIIH research, highlighting the recent advances in TFIIH structural and mechanistic analyses that suggest the potential of TFIIH as a target for cancer treatment.
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Affiliation(s)
- Mario Zurita
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
| | - Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
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Larionov AV, Sinitsky MY, Druzhinin VG, Volobaev VP, Minina VI, Asanov MA, Meyer AV, Tolochko TA, Kalyuzhnaya EE. DNA excision repair and double-strand break repair gene polymorphisms and the level of chromosome aberration in children with long-term exposure to radon. Int J Radiat Biol 2016; 92:466-74. [DOI: 10.1080/09553002.2016.1186303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aleksey V. Larionov
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
| | - Maxim Y. Sinitsky
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
- Federal State Budget Scientific Institution, The Federal Research Center of Coal and Coal Chemistry of Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russian Federation
- Laboratory of Genome Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russian Federation
| | - Vladimir G. Druzhinin
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
- Federal State Budget Scientific Institution, The Federal Research Center of Coal and Coal Chemistry of Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russian Federation
| | - Valentin P. Volobaev
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
| | - Varvara I. Minina
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
- Federal State Budget Scientific Institution, The Federal Research Center of Coal and Coal Chemistry of Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russian Federation
| | - Maxim A. Asanov
- Federal State Budget Scientific Institution, The Federal Research Center of Coal and Coal Chemistry of Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russian Federation
| | - Alina V. Meyer
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
| | - Tatiana A. Tolochko
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
| | - Ekaterina E. Kalyuzhnaya
- Department of Genetics, Biology Faculty, Kemerovo State University, Kemerovo, Russian Federation
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48
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Compe E, Egly JM. Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond. Annu Rev Biochem 2016; 85:265-90. [DOI: 10.1146/annurev-biochem-060815-014857] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université de Strasbourg, 67404 Illkirch Cedex, Commune Urbaine Strasbourg, France; ,
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université de Strasbourg, 67404 Illkirch Cedex, Commune Urbaine Strasbourg, France; ,
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49
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Li W, Selvam K, Rahman SA, Li S. Sen1, the yeast homolog of human senataxin, plays a more direct role than Rad26 in transcription coupled DNA repair. Nucleic Acids Res 2016; 44:6794-802. [PMID: 27179024 PMCID: PMC5001595 DOI: 10.1093/nar/gkw428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/05/2016] [Indexed: 11/13/2022] Open
Abstract
Rad26, a DNA dependent ATPase that is homologous to human CSB, has been well known to play an important role in transcription coupled DNA repair (TCR) in the yeast Saccharomyces cerevisiae Sen1, a DNA/RNA helicase that is essential for yeast cell viability and homologous to human senataxin, has been known to be required for transcriptional termination of short noncoding RNA genes and for a fail-safe transcriptional termination mechanism of protein-coding genes. Sen1 has also been shown to protect the yeast genome from transcription-associated recombination by resolving RNA:DNA hybrids naturally formed during transcription. Here, we show that the N-terminal non-essential region of Sen1 plays an important role in TCR, whereas the C-terminal nonessential region and the helicase activity of Sen1 are largely dispensable for the repair. Unlike Rad26, which becomes completely dispensable for TCR in cells lacking the TCR repressor Spt4, Sen1 is still required for efficient TCR in the absence of Spt4. Also unlike Rad26, which is important for repair at many but not all damaged sites in the transcribed strand of a gene, Sen1 is required for efficient repair at essentially all the damaged sites. Our results indicate that Sen1 plays a more direct role than Rad26 in TCR.
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Affiliation(s)
- Wentao Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kathiresan Selvam
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sheikh A 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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50
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Avila AI, Illing A, Becker F, Maerz LD, Morita Y, Philipp M, Burkhalter MD. Xpg limits the expansion of haematopoietic stem and progenitor cells after ionising radiation. Nucleic Acids Res 2016; 44:6252-61. [PMID: 27137888 PMCID: PMC5291257 DOI: 10.1093/nar/gkw376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/25/2016] [Indexed: 12/17/2022] Open
Abstract
Reduced capacity of genome maintenance represents a problem for any organism, potentially causing premature death, carcinogenesis, or accelerated ageing. Strikingly though, loss of certain genome stability factors can be beneficial, especially for the maintenance of tissue stem cells of the intestine and the haematopoietic system. We therefore screened for genome stability factors negatively impacting maintenance of haematopoietic stem cells (HSC) in the context of ionising radiation (IR). We found that in vivo knock down of Xeroderma pigmentosum, complementation group G (Xpg) causes elevation of HSC numbers after IR treatment, while numbers of haematopoietic progenitors are elevated to a lesser extent. IR rapidly induces Xpg both on mRNA and on protein level. Prevention of this induction does not influence activation of the checkpoint cascade, yet attenuates late checkpoint steps such as induction of p21 and Noxa. This causes a leaky cell cycle arrest and lower levels of apoptosis, both contributing to increased colony formation and transformation rates. Xpg thus helps to adequately induce DNA damage responses after IR, thereby keeping the expansion of damaged cells under control. This represents a new function of Xpg in the response to IR, in addition to its well-characterized role in nucleotide excision repair.
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Affiliation(s)
- Alush I Avila
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Anett Illing
- Department of Internal Medicine I, Ulm University, 89081 Ulm, Germany
| | - Friedrich Becker
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Lars D Maerz
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Yohei Morita
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Melanie Philipp
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Martin D Burkhalter
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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