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Slyskova J, Muniesa-Vargas A, da Silva I, Drummond R, Park J, Häckes D, Poetsch I, Ribeiro-Silva C, Moretton A, Heffeter P, Schärer O, Vermeulen W, Lans H, Loizou J. Detection of oxaliplatin- and cisplatin-DNA lesions requires different global genome repair mechanisms that affect their clinical efficacy. NAR Cancer 2023; 5:zcad057. [PMID: 38058548 PMCID: PMC10696645 DOI: 10.1093/narcan/zcad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
The therapeutic efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection. Using a combination of genetic, transcriptomics and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.
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Affiliation(s)
- Jana Slyskova
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Israel Tojal da Silva
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Rodrigo Drummond
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Jiyeong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Isabella Poetsch
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- Research Cluster “Translational Cancer Therapy Research”, A-1090 Vienna, Austria
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Amandine Moretton
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Petra Heffeter
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- Research Cluster “Translational Cancer Therapy Research”, A-1090 Vienna, Austria
| | - 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
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Joanna I Loizou
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
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2
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Hameed J S F, Devarajan A, M S DP, Bhattacharyya A, Shirude MB, Dutta D, Karmakar P, Mukherjee A. PTEN-negative endometrial cancer cells protect their genome through enhanced DDB2 expression associated with augmented nucleotide excision repair. BMC Cancer 2023; 23:399. [PMID: 37142958 PMCID: PMC10157935 DOI: 10.1186/s12885-023-10892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Endometrial cancer (EC) arises from uterine endometrium tissue and is the most prevalent cancer of the female reproductive tract in developed countries. It has been predicted that the global prevalence of EC will increase in part because of its positive association with economic growth and lifestyle. The majority of EC presented with endometrioid histology and mutations in the tumor suppressor gene PTEN, resulting in its loss of function. PTEN negatively regulates the PI3K/Akt/mTOR axis of cell proliferation and thus serves as a tumorigenesis gatekeeper. Through its chromatin functions, PTEN is also implicated in genome maintenance procedures. However, our comprehension of how DNA repair occurs in the absence of PTEN function in EC is inadequate. METHODS We utilized The Cancer Genome Atlas (TCGA) data analysis to establish a correlation between PTEN and DNA damage response genes in EC, followed by a series of cellular and biochemical assays to elucidate a molecular mechanism utilizing the AN3CA cell line model for EC. RESULTS The TCGA analyses demonstrated an inverse correlation between the expression of the damage sensor protein of nucleotide excision repair (NER), DDB2, and PTEN in EC. The transcriptional activation of DDB2 is mediated by the recruitment of active RNA polymerase II to the DDB2 promoter in the PTEN-null EC cells, revealing a correlation between increased DDB2 expression and augmented NER activity in the absence of PTEN. CONCLUSION Our study indicated a causal relationship between NER and EC that may be exploited in disease management.
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Affiliation(s)
- Fathima Hameed J S
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Anjali Devarajan
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Devu Priya M S
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Ahel Bhattacharyya
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Mayur Balkrishna Shirude
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Debasree Dutta
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, 188, Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India
| | - Ananda Mukherjee
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India.
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3
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Grønbæk-Thygesen M, Kampmeyer C, Hofmann K, Hartmann-Petersen R. The moonlighting of RAD23 in DNA repair and protein degradation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194925. [PMID: 36863450 DOI: 10.1016/j.bbagrm.2023.194925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
A moonlighting protein is one, which carries out multiple, often wholly unrelated, functions. The RAD23 protein is a fascinating example of this, where the same polypeptide and the embedded domains function independently in both nucleotide excision repair (NER) and protein degradation via the ubiquitin-proteasome system (UPS). Hence, through direct binding to the central NER component XPC, RAD23 stabilizes XPC and contributes to DNA damage recognition. Conversely, RAD23 also interacts directly with the 26S proteasome and ubiquitylated substrates to mediate proteasomal substrate recognition. In this function, RAD23 activates the proteolytic activity of the proteasome and engages specifically in well-characterized degradation pathways through direct interactions with E3 ubiquitin-protein ligases and other UPS components. Here, we summarize the past 40 years of research into the roles of RAD23 in NER and the UPS.
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Affiliation(s)
- Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
| | - Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Germany
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
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4
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Kusakabe M, Kakumu E, Kurihara F, Tsuchida K, Maeda T, Tada H, Kusao K, Kato A, Yasuda T, Matsuda T, Nakao M, Yokoi M, Sakai W, Sugasawa K. Histone deacetylation regulates nucleotide excision repair through an interaction with the XPC protein. iScience 2022; 25:104040. [PMID: 35330687 PMCID: PMC8938288 DOI: 10.1016/j.isci.2022.104040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/07/2022] [Accepted: 03/04/2022] [Indexed: 12/05/2022] Open
Abstract
The XPC protein complex plays a central role in DNA lesion recognition for global genome nucleotide excision repair (GG-NER). Lesion recognition can be accomplished in either a UV-DDB-dependent or -independent manner; however, it is unclear how these sub-pathways are regulated in chromatin. Here, we show that histone deacetylases 1 and 2 facilitate UV-DDB-independent recruitment of XPC to DNA damage by inducing histone deacetylation. XPC localizes to hypoacetylated chromatin domains in a DNA damage-independent manner, mediated by its structurally disordered middle (M) region. The M region interacts directly with the N-terminal tail of histone H3, an interaction compromised by H3 acetylation. Although the M region is dispensable for in vitro NER, it promotes DNA damage removal by GG-NER in vivo, particularly in the absence of UV-DDB. We propose that histone deacetylation around DNA damage facilitates the recruitment of XPC through the M region, contributing to efficient lesion recognition and initiation of GG-NER. Histone deacetylation by HDAC1/2 promotes the DNA lesion recognition by XPC The HDAC1/2 activators, MTA proteins, also promote the recruitment of XPC XPC tends to localize in hypoacetylated chromatin independently of DNA damage Disordered middle region of XPC interacts with histone H3 tail and promotes GG-NER
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5
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Loureiro JB, Ribeiro R, Nazareth N, Ferreira T, Lopes EA, Gama A, Machuqueiro M, Alves MG, Marabini L, Oliveira PA, Santos MMM, Saraiva L. Mutant p53 reactivator SLMP53-2 hinders ultraviolet B radiation-induced skin carcinogenesis. Pharmacol Res 2022; 175:106026. [PMID: 34890775 DOI: 10.1016/j.phrs.2021.106026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023]
Abstract
The growing incidence of skin cancer (SC) has prompted the search for additional preventive strategies to counteract this global health concern. Mutant p53 (mutp53), particularly with ultraviolet radiation (UVR) signature, has emerged as a promising target for SC prevention based on its key role in skin carcinogenesis. Herein, the preventive activity of our previously disclosed mutp53 reactivator SLMP53-2 against UVR-induced SC was investigated. The pre-treatment of keratinocyte HaCaT cells with SLMP53-2, before UVB exposure, depleted mutp53 protein levels with restoration of wild-type-like p53 DNA-binding ability and subsequent transcriptional activity. SLMP53-2 increased cell survival by promoting G1-phase cell cycle arrest, while reducing UVB-induced apoptosis through inhibition of c-Jun N-terminal kinase (JNK) activity. SLMP53-2 also protected cells from reactive oxygen species and oxidative damage induced by UVB. Moreover, it enhanced DNA repair through upregulation of nucleotide excision repair pathway and depletion of UVB-induced DNA damage, as evidenced by a reduction of DNA in comet tails, γH2AX staining and cyclobutane pyrimidine dimers (CPD) levels. SLMP53-2 further suppressed UVB-induced inflammation by inhibiting the nuclear translocation and DNA-binding ability of NF-κB, and promoted the expression of key players involved in keratinocytes differentiation. Consistently, the topical application of SLMP53-2 in mice skin, prior to UVB irradiation, reduced cell death and DNA damage. It also decreased the expression of inflammatory-related proteins and promoted cell differentiation, in UVB-exposed mice skin. Notably, SLMP53-2 did not show signs of skin toxicity for cumulative topical use. Overall, these results support a promising protective activity of SLMP53-2 against UVB-induced SC.
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Affiliation(s)
- Joana B Loureiro
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-31b Porto, Portugal
| | - Rita Ribeiro
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-31b Porto, Portugal
| | - Nair Nazareth
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-31b Porto, Portugal
| | - Tiago Ferreira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Elizabeth A Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Marco G Alves
- Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | - Laura Marabini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Italy
| | - Paula A Oliveira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Maria M M Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Lucília Saraiva
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-31b Porto, Portugal.
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6
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Apelt K, Lans H, Schärer OD, Luijsterburg MS. Nucleotide excision repair leaves a mark on chromatin: DNA damage detection in nucleosomes. Cell Mol Life Sci 2021; 78:7925-7942. [PMID: 34731255 PMCID: PMC8629891 DOI: 10.1007/s00018-021-03984-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) eliminates a broad spectrum of DNA lesions from genomic DNA. Genomic DNA is tightly wrapped around histones creating a barrier for DNA repair proteins to access DNA lesions buried in nucleosomal DNA. The DNA-damage sensors XPC and DDB2 recognize DNA lesions in nucleosomal DNA and initiate repair. The emerging view is that a tight interplay between XPC and DDB2 is regulated by post-translational modifications on the damage sensors themselves as well as on chromatin containing DNA lesions. The choreography between XPC and DDB2, their interconnection with post-translational modifications such as ubiquitylation, SUMOylation, methylation, poly(ADP-ribos)ylation, acetylation, and the functional links with chromatin remodelling activities regulate not only the initial recognition of DNA lesions in nucleosomes, but also the downstream recruitment and necessary displacement of GG-NER factors as repair progresses. In this review, we highlight how nucleotide excision repair leaves a mark on chromatin to enable DNA damage detection in nucleosomes.
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Affiliation(s)
- Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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7
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Van Houten B, Schnable B, Kumar N. Chaperones for dancing on chromatin: Role of post-translational modifications in dynamic damage detection hand-offs during nucleotide excision repair. Bioessays 2021; 43:e2100011. [PMID: 33620094 PMCID: PMC9756857 DOI: 10.1002/bies.202100011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
We highlight a recent study exploring the hand-off of UV damage to several key nucleotide excision repair (NER) proteins in the cascade: UV-DDB, XPC and TFIIH. The delicate dance of DNA repair proteins is choreographed by the dynamic hand-off of DNA damage from one recognition complex to another damage verification protein or set of proteins. These DNA transactions on chromatin are strictly chaperoned by post-translational modifications (PTM). This new study examines the role that ubiquitylation and subsequent DDB2 degradation has during this process. In total, this study suggests an intricate cellular timer mechanism that under normal conditions DDB2 helps recruit and ubiquitylate XPC, stabilizing XPC at damaged sites. If DDB2 persists at damaged sites too long, it is turned over by auto-ubiquitylation and removed from DNA by the action of VCP/p97 for degradation in the 26S proteosome.
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Affiliation(s)
- Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittani Schnable
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Namrata Kumar
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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8
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Fortuny A, Chansard A, Caron P, Chevallier O, Leroy O, Renaud O, Polo SE. Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance. Nat Commun 2021; 12:2428. [PMID: 33893291 PMCID: PMC8065061 DOI: 10.1038/s41467-021-22575-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
Heterochromatin is a critical chromatin compartment, whose integrity governs genome stability and cell fate transitions. How heterochromatin features, including higher-order chromatin folding and histone modifications associated with transcriptional silencing, are maintained following a genotoxic stress challenge is unknown. Here, we establish a system for targeting UV damage to pericentric heterochromatin in mammalian cells and for tracking the heterochromatin response to UV in real time. We uncover profound heterochromatin compaction changes during repair, orchestrated by the UV damage sensor DDB2, which stimulates linker histone displacement from chromatin. Despite massive heterochromatin unfolding, heterochromatin-specific histone modifications and transcriptional silencing are maintained. We unveil a central role for the methyltransferase SETDB1 in the maintenance of heterochromatic histone marks after UV. SETDB1 coordinates histone methylation with new histone deposition in damaged heterochromatin, thus protecting cells from genome instability. Our data shed light on fundamental molecular mechanisms safeguarding higher-order chromatin integrity following DNA damage.
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Affiliation(s)
- Anna Fortuny
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Audrey Chansard
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Pierre Caron
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Odile Chevallier
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Olivier Leroy
- Cell and Tissue Imaging Facility, UMR3215 PICT-IBiSA, Institut Curie, Paris, France
| | - Olivier Renaud
- Cell and Tissue Imaging Facility, UMR3215 PICT-IBiSA, Institut Curie, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France.
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9
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Robu M, Shah RG, Shah GM. Methods to Study Intracellular Movement and Localization of the Nucleotide Excision Repair Proteins at the DNA Lesions in Mammalian Cells. Front Cell Dev Biol 2020; 8:590242. [PMID: 33282869 PMCID: PMC7705073 DOI: 10.3389/fcell.2020.590242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA repair pathway that removes a wide variety of DNA lesions caused by different types of physical and chemical agents, such as ultraviolet radiation (UV), environmental carcinogen benzo[a]pyrene and anti-cancer drug carboplatin. The mammalian NER utilizes more than 30 proteins, in a multi-step process that begins with the lesion recognition within seconds of DNA damage to completion of repair after few hours to several days. The core proteins and their biochemical reactions are known from in vitro DNA repair assays using purified proteins, but challenge was to understand the dynamics of their rapid recruitment and departure from the lesion site and their coordination with other proteins and post-translational modifications to execute the sequential steps of repair. Here, we provide a brief overview of various techniques developed by different groups over last 20 years to overcome these challenges. However, more work is needed for a comprehensive knowledge of all aspects of mammalian NER. With this aim, here we provide detailed protocols of three simple yet innovative methods developed by many teams that range from local UVC irradiation to in situ extraction and sub-cellular fractionation that will permit study of endogenous as well as exogenous NER proteins in any cellular model. These methods do not require unique reagents or specialized instruments, and will allow many more laboratories to explore this repair pathway in different models. These techniques would reveal intracellular movement of these proteins to the DNA lesion site, their interactions with other proteins during repair and the effect of post-translational modifications on their functions. We also describe how these methods led us to identify hitherto unexpected role of poly(ADP-ribose) polymerase-1 (PARP1) in NER. Collectively these three simple techniques can provide an initial assessment of the functions of known and unknown proteins in the core or auxiliary events associated with mammalian NER. The results from these techniques could serve as a solid foundation and a justification for more detailed studies in NER using specialized reagents and more sophisticated tools. They can also be suitably modified to study other cellular processes beyond DNA repair.
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Affiliation(s)
- Mihaela Robu
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
| | - Rashmi G Shah
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
| | - Girish M Shah
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
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10
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Chen L, Bellone RR, Wang Y, Singer-Berk M, Sugasawa K, Ford JM, Artandi SE. A novel DDB2 mutation causes defective recognition of UV-induced DNA damages and prevalent equine squamous cell carcinoma. DNA Repair (Amst) 2020; 97:103022. [PMID: 33276309 DOI: 10.1016/j.dnarep.2020.103022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/22/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Squamous cell carcinoma (SCC) occurs frequently in the human Xeroderma Pigmentosum (XP) syndrome and is characterized by deficient UV-damage repair. SCC is the most common equine ocular cancer and the only associated genetic risk factor is a UV-damage repair protein. Specifically, a missense mutation in horse DDB2 (T338M) was strongly associated with both limbal SCC and third eyelid SCC in three breeds of horses (Halflinger, Belgian, and Rocky Mountain Horses) and was hypothesized to impair binding to UV-damaged DNA. Here, we investigate DDB2-T338M mutant's capacity to recognize UV lesions in vitro and in vivo, together with human XP mutants DDB2-R273H and -K244E. We show that the recombinant DDB2-T338M assembles with DDB1, but fails to show any detectable binding to DNA substrates with or without UV lesions, due to a potential structural disruption of the rigid DNA recognition β-loop. Consistently, we demonstrate that the cellular DDB2-T338M is defective in its recruitment to focally radiated DNA damages, and in its access to chromatin. Thus, we provide direct functional evidence indicating the DDB2-T338M recapitulates molecular defects of human XP mutants, and is the causal loss-of-function allele that gives rise to equine ocular SCCs. Our findings shed new light on the mechanism of DNA recognition by UV-DDB and on the initiation of ocular malignancy.
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Yan Wang
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moriel Singer-Berk
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - James M Ford
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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11
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Li S, Shi B, Liu X, An HX. Acetylation and Deacetylation of DNA Repair Proteins in Cancers. Front Oncol 2020; 10:573502. [PMID: 33194676 PMCID: PMC7642810 DOI: 10.3389/fonc.2020.573502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Hundreds of DNA repair proteins coordinate together to remove the diverse damages for ensuring the genomic integrity and stability. The repair system is an extensive network mainly encompassing cell cycle arrest, chromatin remodeling, various repair pathways, and new DNA fragment synthesis. Acetylation on DNA repair proteins is a dynamic epigenetic modification orchestrated by lysine acetyltransferases (HATs) and lysine deacetylases (HDACs), which dramatically affects the protein functions through multiple mechanisms, such as regulation of DNA binding ability, protein activity, post-translational modification (PTM) crosstalk, and protein–protein interaction. Accumulating evidence has indicated that the aberrant acetylation of DNA repair proteins contributes to the dysfunction of DNA repair ability, the pathogenesis and progress of cancer, as well as the chemosensitivity of cancer cells. In the present scenario, targeting epigenetic therapy is being considered as a promising method at par with the conventional cancer therapeutic strategies. This present article provides an overview of the recent progress in the functions and mechanisms of acetylation on DNA repair proteins involved in five major repair pathways, which warrants the possibility of regulating acetylation on repair proteins as a therapeutic target in cancers.
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Affiliation(s)
- Shiqin Li
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Bingbing Shi
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
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12
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Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair. Nat Commun 2020; 11:4868. [PMID: 32985517 PMCID: PMC7522231 DOI: 10.1038/s41467-020-18705-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
DNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds to UV-induced lesions directly and facilitates efficient recognition by XPC. We show that not only lesion-binding but also timely DDB2 dissociation is required for DNA damage handover to XPC and swift progression of the multistep repair reaction. DNA-binding-induced DDB2 ubiquitylation and ensuing degradation regulate its homeostasis to prevent excessive lesion (re)binding. Additionally, damage handover from DDB2 to XPC coincides with the arrival of the TFIIH complex, which further promotes DDB2 dissociation and formation of a stable XPC-TFIIH damage verification complex. Our results reveal a reciprocal coordination between DNA damage recognition and verification within NER and illustrate that timely repair factor dissociation is vital for correct spatiotemporal control of a multistep repair process.
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13
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Beecher M, Kumar N, Jang S, Rapić-Otrin V, Van Houten B. Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer. DNA Repair (Amst) 2020; 94:102860. [PMID: 32739133 DOI: 10.1016/j.dnarep.2020.102860] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023]
Abstract
UV-damaged DNA binding protein (UV-DDB) is a heterodimeric complex, composed of DDB1 and DDB2, and is involved in global genome nucleotide excision repair. Mutations in DDB2 are associated with xeroderma pigmentosum complementation group E. UV-DDB forms a ubiquitin E3 ligase complex with cullin-4A and RBX that helps to relax chromatin around UV-induced photoproducts through the ubiquitination of histone H2A. After providing a brief historical perspective on UV-DDB, we review our current knowledge of the structure and function of this intriguing repair protein. Finally, this article discusses emerging data suggesting that UV-DDB may have other non-canonical roles in base excision repair and the etiology of cancer.
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Affiliation(s)
- Maria Beecher
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Namrata Kumar
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sunbok Jang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vesna Rapić-Otrin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Bennett Van Houten
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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14
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Gsell C, Richly H, Coin F, Naegeli H. A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions. Nucleic Acids Res 2020; 48:1652-1668. [PMID: 31930303 PMCID: PMC7038933 DOI: 10.1093/nar/gkz1229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.
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Affiliation(s)
- Corina Gsell
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Holger Richly
- Boehringer Ingelheim Pharma, Department of Molecular Biology, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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15
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Rechkunova NI, Maltseva EA, Lavrik OI. Post-translational Modifications of Nucleotide Excision Repair Proteins and Their Role in the DNA Repair. BIOCHEMISTRY (MOSCOW) 2019; 84:1008-1020. [PMID: 31693460 DOI: 10.1134/s0006297919090037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleotide excision repair (NER) is one of the major DNA repair pathways aimed at maintaining genome stability. Correction of DNA damage by the NER system is a multistage process that proceeds with the formation of multiple DNA-protein and protein-protein intermediate complexes and requires precise coordination and regulation. NER proteins undergo post-translational modifications, such as ubiquitination, sumoylation, phosphorylation, acetylation, and poly(ADP-ribosyl)ation. These modifications affect the interaction of NER factors with DNA and other proteins and thus regulate either their recruitment into the complexes or dissociation from these complexes at certain stages of DNA repair, as well as modulate the functional activity of NER proteins and control the process of DNA repair in general. Here, we review the data on the post-translational modifications of NER factors and their effects on DNA repair. Protein poly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerase 1 and its impact on NER are discussed in detail, since such analysis has not been done before.
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Affiliation(s)
- N I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - E A Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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16
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Swope VB, Starner RJ, Rauck C, Abdel-Malek ZA. Endothelin-1 and α-melanocortin have redundant effects on global genome repair in UV-irradiated human melanocytes despite distinct signaling pathways. Pigment Cell Melanoma Res 2019; 33:293-304. [PMID: 31505093 DOI: 10.1111/pcmr.12823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 12/26/2022]
Abstract
Human melanocyte homeostasis is sustained by paracrine factors that reduce the genotoxic effects of ultraviolet radiation (UV), the major etiological factor for melanoma. The keratinocyte-derived endothelin-1 (End-1) and α-melanocyte-stimulating hormone (α-MSH) regulate human melanocyte function, proliferation and survival, and enhance repair of UV-induced DNA photoproducts by binding to the Gq - and Gi -protein-coupled endothelin B receptor (EDNRB), and the Gs -protein-coupled melanocortin 1 receptor (MC1R), respectively. We hereby report that End-1 and α-MSH regulate common effectors of the DNA damage response to UV, despite distinct signaling pathways. Both factors activate the two DNA damage sensors ataxia telangiectasia and Rad3-related and ataxia telangiectasia mutated, enhance DNA damage recognition by reducing soluble nuclear and chromatin-bound DNA damage binding protein 2, and increase total and chromatin-bound xeroderma pigmentosum (XP) C. Additionally, α-MSH and End-1 increase total levels and chromatin localization of the damage verification protein XPA, and the levels of γH2AX, which facilitates recruitment of DNA repair proteins to DNA lesions. Activation of EDNRB compensates for MC1R loss of function, thereby reducing the risk of malignant transformation of these vulnerable melanocytes. Therefore, MC1R and EDNRB signaling pathways represent redundant mechanisms that inhibit the genotoxic effects of UV and melanomagenesis.
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Affiliation(s)
- Viki B Swope
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
| | - Renny J Starner
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
| | - Corinne Rauck
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
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17
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Jang S, Kumar N, Beckwitt EC, Kong M, Fouquerel E, Rapić-Otrin V, Prasad R, Watkins SC, Khuu C, Majumdar C, David SS, Wilson SH, Bruchez MP, Opresko PL, Van Houten B. Damage sensor role of UV-DDB during base excision repair. Nat Struct Mol Biol 2019; 26:695-703. [PMID: 31332353 PMCID: PMC6684372 DOI: 10.1038/s41594-019-0261-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/28/2019] [Indexed: 12/22/2022]
Abstract
UV-DDB, a key protein in human global nucleotide excision repair (NER), binds avidly to abasic sites and 8-oxo-guanine (8-oxoG), suggesting a noncanonical role in base excision repair (BER). We investigated whether UV-DDB can stimulate BER for these two common forms of DNA damage, 8-oxoG and abasic sites, which are repaired by 8-oxoguanine glycosylase (OGG1) and apurinic/apyrimidinic endonuclease (APE1), respectively. UV-DDB increased both OGG1 and APE1 strand cleavage and stimulated subsequent DNA polymerase β-gap filling activity by 30-fold. Single-molecule real-time imaging revealed that UV-DDB forms transient complexes with OGG1 or APE1, facilitating their dissociation from DNA. Furthermore, UV-DDB moves to sites of 8-oxoG repair in cells, and UV-DDB depletion sensitizes cells to oxidative DNA damage. We propose that UV-DDB is a general sensor of DNA damage in both NER and BER pathways, facilitating damage recognition in the context of chromatin.
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Affiliation(s)
- Sunbok Jang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Namrata Kumar
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emily C Beckwitt
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Muwen Kong
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Graduate Program, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University and Sydney Kimmel Medical College, Philadelphia, PA, USA
| | - Vesna Rapić-Otrin
- Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rajendra Prasad
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cindy Khuu
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Graduate Group, University of California, Davis, Davis, CA, USA
| | - Chandrima Majumdar
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Graduate Group, University of California, Davis, Davis, CA, USA
| | - Samuel H Wilson
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Patricia L Opresko
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Graduate Program, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, PA, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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18
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Sugasawa K. Mechanism and regulation of DNA damage recognition in mammalian nucleotide excision repair. DNA Repair (Amst) 2019; 45:99-138. [DOI: 10.1016/bs.enz.2019.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Mandemaker IK, Geijer ME, Kik I, Bezstarosti K, Rijkers E, Raams A, Janssens RC, Lans H, Hoeijmakers JH, Demmers JA, Vermeulen W, Marteijn JA. DNA damage-induced replication stress results in PA200-proteasome-mediated degradation of acetylated histones. EMBO Rep 2018; 19:embr.201745566. [PMID: 30104204 PMCID: PMC6172457 DOI: 10.15252/embr.201745566] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation influences protein interactions and chromatin accessibility and plays an important role in the regulation of transcription, replication, and DNA repair. Conversely, DNA damage affects these crucial cellular processes and induces changes in histone acetylation. However, a comprehensive overview of the effects of DNA damage on the histone acetylation landscape is currently lacking. To quantify changes in histone acetylation, we developed an unbiased quantitative mass spectrometry analysis on affinity‐purified acetylated histone peptides, generated by differential parallel proteolysis. We identify a large number of histone acetylation sites and observe an overall reduction of acetylated histone residues in response to DNA damage, indicative of a histone‐wide loss of acetyl modifications. This decrease is mainly caused by DNA damage‐induced replication stress coupled to specific proteasome‐dependent loss of acetylated histones. Strikingly, this degradation of acetylated histones is independent of ubiquitylation but requires the PA200‐proteasome activator, a complex that specifically targets acetylated histones for degradation. The uncovered replication stress‐induced degradation of acetylated histones represents an important chromatin‐modifying response to cope with replication stress.
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Affiliation(s)
- Imke K Mandemaker
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Iris Kik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erikjan Rijkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Hj Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,CECAD Forschungszentrum, Köln, Germany.,Princess Máxima Center for Pediatric Oncology, Bilthoven, The Netherlands
| | - Jeroen Aa Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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20
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Dutto I, Scalera C, Prosperi E. CREBBP and p300 lysine acetyl transferases in the DNA damage response. Cell Mol Life Sci 2018; 75:1325-1338. [PMID: 29170789 PMCID: PMC11105205 DOI: 10.1007/s00018-017-2717-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/21/2022]
Abstract
The CREB-binding protein (CREBBP, or in short CBP) and p300 are lysine (K) acetyl transferases (KAT) belonging to the KAT3 family of proteins known to modify histones, as well as non-histone proteins, thereby regulating chromatin accessibility and transcription. Previous studies have indicated a tumor suppressor function for these enzymes. Recently, they have been found to acetylate key factors involved in DNA replication, and in different DNA repair processes, such as base excision repair, nucleotide excision repair, and non-homologous end joining. The growing list of CBP/p300 substrates now includes factors involved in DNA damage signaling, and in other pathways of the DNA damage response (DDR). This review will focus on the role of CBP and p300 in the acetylation of DDR proteins, and will discuss how this post-translational modification influences their functions at different levels, including catalytic activity, DNA binding, nuclear localization, and protein turnover. In addition, we will exemplify how these functions may be necessary to efficiently coordinate the spatio-temporal response to DNA damage. CBP and p300 may contribute to genome stability by fine-tuning the functions of DNA damage signaling and DNA repair factors, thereby expanding their role as tumor suppressors.
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Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
- IRB, Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Claudia Scalera
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
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21
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ASH1L histone methyltransferase regulates the handoff between damage recognition factors in global-genome nucleotide excision repair. Nat Commun 2017; 8:1333. [PMID: 29109511 PMCID: PMC5673894 DOI: 10.1038/s41467-017-01080-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
Global-genome nucleotide excision repair (GG-NER) prevents ultraviolet (UV) light-induced skin cancer by removing mutagenic cyclobutane pyrimidine dimers (CPDs). These lesions are formed abundantly on DNA wrapped around histone octamers in nucleosomes, but a specialized damage sensor known as DDB2 ensures that they are accessed by the XPC initiator of GG-NER activity. We report that DDB2 promotes CPD excision by recruiting the histone methyltransferase ASH1L, which methylates lysine 4 of histone H3. In turn, methylated H3 facilitates the docking of the XPC complex to nucleosomal histone octamers. Consequently, DDB2, ASH1L and XPC proteins co-localize transiently on histone H3-methylated nucleosomes of UV-exposed cells. In the absence of ASH1L, the chromatin binding of XPC is impaired and its ability to recruit downstream GG-NER effectors diminished. Also, ASH1L depletion suppresses CPD excision and confers UV hypersensitivity. These findings show that ASH1L configures chromatin for the effective handoff between damage recognition factors during GG-NER activity.
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22
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Zhu Q, Wei S, Sharma N, Wani G, He J, Wani AA. Human CRL4 DDB2 ubiquitin ligase preferentially regulates post-repair chromatin restoration of H3K56Ac through recruitment of histone chaperon CAF-1. Oncotarget 2017; 8:104525-104542. [PMID: 29262658 PMCID: PMC5732824 DOI: 10.18632/oncotarget.21869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/30/2017] [Indexed: 11/25/2022] Open
Abstract
Acetylated histone H3 lysine 56 (H3K56Ac) diminishes in response to DNA damage but is restored following DNA repair. Here, we report that CRL4DDB2 ubiquitin ligase preferentially regulates post-repair chromatin restoration of H3K56Ac through recruitment of histone chaperon CAF-1. We show that H3K56Ac accumulates at DNA damage sites. The restoration of H3K56Ac but not H3K27Ac, H3K18Ac and H3K14Ac depends on CAF-1 function, whereas all these acetylations are mediated by CBP/p300. The CRL4DDB2 components, DDB1, DDB2 and CUL4A, are also required for maintaining the H3K56Ac and H3K9Ac level in chromatin, and for restoring H3K56Ac following induction of DNA photolesions and strand breaks. Depletion of CUL4A decreases the recruitment of CAF-1 p60 and p150 to ultraviolet radiation- and phleomycin-induced DNA damage. Neddylation inhibition renders CRL4DDB2 inactive, decreases H3K56Ac level, diminishes CAF-1 recruitment and prevents H3K56Ac restoration. Mutation in the PIP box of DDB2 compromises its capability to elevate the H3K56Ac level but does not affect XPC ubiquitination. These results demonstrated a function of CRL4DDB2 in differential regulation of histone acetylation in response to DNA damage, suggesting a novel role of CRL4DDB2 in repair-driven chromatin assembly.
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Affiliation(s)
- Qianzheng Zhu
- Department of Radiology, The Ohio State University, Columbus, 43210, OH
| | - Shengcai Wei
- Department of Radiology, The Ohio State University, Columbus, 43210, OH
| | - Nidhi Sharma
- Department of Radiology, The Ohio State University, Columbus, 43210, OH
| | - Gulzar Wani
- Department of Radiology, The Ohio State University, Columbus, 43210, OH
| | - Jinshan He
- Department of Radiology, The Ohio State University, Columbus, 43210, OH
| | - Altaf A Wani
- Department of Radiology, The Ohio State University, Columbus, 43210, OH.,Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, 43210, OH.,James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, 43210, OH
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23
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Rüthemann P, Balbo Pogliano C, Codilupi T, Garajovà Z, Naegeli H. Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair. EMBO J 2017; 36:3372-3386. [PMID: 29018037 DOI: 10.15252/embj.201695742] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 08/10/2017] [Accepted: 09/08/2017] [Indexed: 12/27/2022] Open
Abstract
Ultraviolet (UV) light induces mutagenic cyclobutane pyrimidine dimers (CPDs) in nucleosomal DNA that is tightly wrapped around histone octamers. How global-genome nucleotide excision repair (GG-NER) processes CPDs despite that this chromatin arrangement is poorly understood. An increased chromatin association of CHD1 (chromodomain helicase DNA-binding 1) upon UV irradiation indicated possible roles of this chromatin remodeler in the UV damage response. Immunoprecipitation of chromatin fragments revealed that CHD1 co-localizes in part with GG-NER factors. Chromatin fractionation showed that the UV-dependent recruitment of CHD1 occurs to UV lesions in histone-assembled nucleosomal DNA and that this CHD1 relocation requires the lesion sensor XPC (xeroderma pigmentosum group C). In situ immunofluorescence analyses further demonstrate that CHD1 facilitates substrate handover from XPC to the downstream TFIIH (transcription factor IIH). Consequently, CHD1 depletion slows down CPD excision and sensitizes cells to UV-induced cytotoxicity. The finding of a CHD1-driven lesion handover between sequentially acting GG-NER factors on nucleosomal histone octamers suggests that chromatin provides a recognition scaffold enabling the detection of a subset of CPDs.
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Affiliation(s)
- Peter Rüthemann
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Chiara Balbo Pogliano
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Tamara Codilupi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Zuzana Garajovà
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
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24
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Phosphorylated HBO1 at UV irradiated sites is essential for nucleotide excision repair. Nat Commun 2017; 8:16102. [PMID: 28719581 PMCID: PMC5520108 DOI: 10.1038/ncomms16102] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 05/30/2017] [Indexed: 12/22/2022] Open
Abstract
HBO1, a histone acetyl transferase, is a co-activator of DNA pre-replication complex formation. We recently reported that HBO1 is phosphorylated by ATM and/or ATR and binds to DDB2 after ultraviolet irradiation. Here, we show that phosphorylated HBO1 at cyclobutane pyrimidine dimer (CPD) sites mediates histone acetylation to facilitate recruitment of XPC at the damaged DNA sites. Furthermore, HBO1 facilitates accumulation of SNF2H and ACF1, an ATP-dependent chromatin remodelling complex, to CPD sites. Depletion of HBO1 inhibited repair of CPDs and sensitized cells to ultraviolet irradiation. However, depletion of HBO1 in cells derived from xeroderma pigmentosum patient complementation groups, XPE, XPC and XPA, did not lead to additional sensitivity towards ultraviolet irradiation. Our findings suggest that HBO1 acts in concert with SNF2H-ACF1 to make the chromosome structure more accessible to canonical nucleotide excision repair factors.
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25
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Kakumu E, Nakanishi S, Shiratori HM, Kato A, Kobayashi W, Machida S, Yasuda T, Adachi N, Saito N, Ikura T, Kurumizaka H, Kimura H, Yokoi M, Sakai W, Sugasawa K. Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3. Genes Cells 2017; 22:310-327. [PMID: 28233440 DOI: 10.1111/gtc.12479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 01/13/2017] [Indexed: 12/14/2022]
Abstract
In the mammalian global genome nucleotide excision repair pathway, two damage recognition factors, XPC and UV-DDB, play pivotal roles in the initiation of the repair reaction. However, the molecular mechanisms underlying regulation of the lesion recognition process in the context of chromatin structures remain to be understood. Here, we show evidence that damage recognition factors tend to associate with chromatin regions devoid of certain types of acetylated histones. Treatment of cells with histone deacetylase inhibitors retarded recruitment of XPC to sites of UV-induced DNA damage and the subsequent repair process. Biochemical studies showed novel multifaceted interactions of XPC with histone H3, which were profoundly impaired by deletion of the N-terminal tail of histone H3. In addition, histone H1 also interacted with XPC. Importantly, acetylation of histone H3 markedly attenuated the interaction with XPC in vitro, and local UV irradiation of cells decreased the level of H3K27ac in the damaged areas. Our results suggest that histone deacetylation plays a significant role in the process of DNA damage recognition for nucleotide excision repair and that the localization and functions of XPC can be regulated by acetylated states of histones.
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Affiliation(s)
- Erina Kakumu
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Seiya Nakanishi
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Hiromi M Shiratori
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Faculty of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Akari Kato
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Wataru Kobayashi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Shinichi Machida
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Takeshi Yasuda
- National Institute for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Naoko Adachi
- Division of Molecular Pharmacology, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Naoaki Saito
- Division of Molecular Pharmacology, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Tsuyoshi Ikura
- Department of Mutagenesis, Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Masayuki Yokoi
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Faculty of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Wataru Sakai
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Faculty of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Kaoru Sugasawa
- Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Department of Biology, Faculty of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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26
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Zhu Q, Wani AA. Nucleotide Excision Repair: Finely Tuned Molecular Orchestra of Early Pre-incision Events. Photochem Photobiol 2016; 93:166-177. [PMID: 27696486 DOI: 10.1111/php.12647] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022]
Abstract
Nucleotide excision repair (NER) eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause genomic instability. NER comprises two distinct subpathways: global genomic NER (GG-NER) operating throughout the genome, and transcription-coupled NER (TC-NER) preferentially removing DNA lesions from transcribing DNA strands of transcriptionally active genes. Several NER factors undergo post-translational modifications, including ubiquitination, occurring swiftly and reversibly at DNA lesion sites. Accumulating evidence indicates that ubiquitination not only orchestrates the spatio-temporal recruitment of key protein factors to DNA lesion sites but also the productive assembly of NER pre-incision complex. This review will be restricted to the latest conceptual understanding of ubiquitin-mediated regulation of initial damage sensors of NER, that is DDB, XPC, RNAPII and CSB. We project hypothetical NER models in which ubiquitin-specific segregase, valosin-containing protein (VCP)/p97, plays an essential role in timely extraction of the congregated DNA damage sensors to functionally facilitate the DNA lesion elimination from the genome.
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Affiliation(s)
- Qianzheng Zhu
- Department of Radiology, The Ohio State University, Columbus, OH
| | - Altaf A Wani
- Department of Radiology, The Ohio State University, Columbus, OH.,Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH.,James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH
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27
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Publisher’s Note. DNA Repair (Amst) 2016. [DOI: 10.1016/j.dnarep.2016.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Abstract
Nucleotide excision repair (NER) protects genome stability by eliminating DNA helix distorting lesions, such as those induced by UV radiation. The addition and removal of ubiquitin, namely, ubiquitination and deubiquitination, have recently been demonstrated as general mechanisms to regulate protein functions. Accumulating evidence shows that several NER factors are subjected to extensive regulation by ubiquitination and deubiquitination. Thus, the balance between E3 ligases and deubiquitinating enzyme activities can dynamically alter the ubiquitin landscape at DNA damage sites, thereby regulating NER efficiency. Current knowledge about XPC ubiquitination by different ubiquitin E3 ligases highlights the importance of ubiquitin linkage types in regulating XPC binding and release from damaged DNA. Here, we discuss the emerging roles of deubiquitinating enzymes and their ubiquitin linkage specificities in NER.
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29
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Sugasawa K. Molecular mechanisms of DNA damage recognition for mammalian nucleotide excision repair. DNA Repair (Amst) 2016; 44:110-117. [PMID: 27264556 DOI: 10.1016/j.dnarep.2016.05.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
For faithful DNA repair, it is crucial for cells to locate lesions precisely within the vast genome. In the mammalian global genomic nucleotide excision repair (NER) pathway, this difficult task is accomplished through multiple steps, in which the xeroderma pigmentosum group C (XPC) protein complex plays a central role. XPC senses the presence of oscillating 'normal' bases in the DNA duplex, and its binding properties contribute to the extremely broad substrate specificity of NER. Unlike XPC, which acts as a versatile sensor of DNA helical distortion, the UV-damaged DNA-binding protein (UV-DDB) is more specialized, recognizing UV-induced photolesions and facilitating recruitment of XPC. Recent single-molecule analyses and structural studies have advanced our understanding of how UV-DDB finds its targets, particularly in the context of chromatin. After XPC binds DNA, it is necessary to verify the presence of damage in order to avoid potentially deleterious incisions at damage-free sites. Accumulating evidence suggests that XPA and the helicase activity of transcription factor IIH (TFIIH) cooperate to verify abnormalities in DNA chemistry. This chapter reviews recent findings about the mechanisms underlying the efficiency, versatility, and accuracy of NER.
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Affiliation(s)
- Kaoru Sugasawa
- Biosignal Research Center, Kobe University, Kobe, Hyogo 657-8501, Japan.
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30
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Rüthemann P, Balbo Pogliano C, Naegeli H. Global-genome Nucleotide Excision Repair Controlled by Ubiquitin/Sumo Modifiers. Front Genet 2016; 7:68. [PMID: 27200078 PMCID: PMC4848295 DOI: 10.3389/fgene.2016.00068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/12/2016] [Indexed: 11/13/2022] Open
Abstract
Global-genome nucleotide excision repair (GG-NER) prevents genome instability by excising a wide range of different DNA base adducts and crosslinks induced by chemical carcinogens, ultraviolet (UV) light or intracellular side products of metabolism. As a versatile damage sensor, xeroderma pigmentosum group C (XPC) protein initiates this generic defense reaction by locating the damage and recruiting the subunits of a large lesion demarcation complex that, in turn, triggers the excision of aberrant DNA by endonucleases. In the very special case of a DNA repair response to UV radiation, the function of this XPC initiator is tightly controlled by the dual action of cullin-type CRL4(DDB2) and sumo-targeted RNF111 ubiquitin ligases. This twofold protein ubiquitination system promotes GG-NER reactions by spatially and temporally regulating the interaction of XPC protein with damaged DNA across the nucleosome landscape of chromatin. In the absence of either CRL4(DDB2) or RNF111, the DNA excision repair of UV lesions is inefficient, indicating that these two ubiquitin ligases play a critical role in mitigating the adverse biological effects of UV light in the exposed skin.
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Affiliation(s)
- Peter Rüthemann
- Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
| | - Chiara Balbo Pogliano
- Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
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31
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Puumalainen MR, Rüthemann P, Min JH, Naegeli H. Xeroderma pigmentosum group C sensor: unprecedented recognition strategy and tight spatiotemporal regulation. Cell Mol Life Sci 2016; 73:547-66. [PMID: 26521083 PMCID: PMC4713717 DOI: 10.1007/s00018-015-2075-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 12/14/2022]
Abstract
The cellular defense system known as global-genome nucleotide excision repair (GG-NER) safeguards genome stability by eliminating a plethora of structurally unrelated DNA adducts inflicted by chemical carcinogens, ultraviolet (UV) radiation or endogenous metabolic by-products. Xeroderma pigmentosum group C (XPC) protein provides the promiscuous damage sensor that initiates this versatile NER reaction through the sequential recruitment of DNA helicases and endonucleases, which in turn recognize and excise insulting base adducts. As a DNA damage sensor, XPC protein is very unique in that it (a) displays an extremely wide substrate range, (b) localizes DNA lesions by an entirely indirect readout strategy, (c) recruits not only NER factors but also multiple repair players, (d) interacts avidly with undamaged DNA, (e) also interrogates nucleosome-wrapped DNA irrespective of chromatin compaction and (f) additionally functions beyond repair as a co-activator of RNA polymerase II-mediated transcription. Many recent reports highlighted the complexity of a post-translational circuit that uses polypeptide modifiers to regulate the spatiotemporal activity of this multiuse sensor during the UV damage response in human skin. A newly emerging concept is that stringent regulation of the diverse XPC functions is needed to prioritize DNA repair while avoiding the futile processing of undamaged genes or silent genomic sequences.
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Affiliation(s)
- Marjo-Riitta Puumalainen
- Institute of Pharmacology and Toxicology, University of Zürich-Vetsuisse, 8057, Zurich, Switzerland
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Peter Rüthemann
- Institute of Pharmacology and Toxicology, University of Zürich-Vetsuisse, 8057, Zurich, Switzerland
| | - Jun-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zürich-Vetsuisse, 8057, Zurich, Switzerland.
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32
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Abstract
XPC has long been considered instrumental in DNA damage recognition during global genome nucleotide excision repair (GG-NER). While this recognition is crucial for organismal health and survival, as XPC's recognition of lesions stimulates global genomic repair, more recent lines of research have uncovered many new non-canonical pathways in which XPC plays a role, such as base excision repair (BER), chromatin remodeling, cell signaling, proteolytic degradation, and cellular viability. Since the first discovery of its yeast homolog, Rad4, the involvement of XPC in cellular regulation has expanded considerably. Indeed, our understanding appears to barely scratch the surface of the incredible potential influence of XPC on maintaining proper cellular function. Here, we first review the canonical role of XPC in lesion recognition and then explore the new world of XPC function.
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33
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SUMO and ubiquitin-dependent XPC exchange drives nucleotide excision repair. Nat Commun 2015; 6:7499. [PMID: 26151477 PMCID: PMC4501428 DOI: 10.1038/ncomms8499] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/15/2015] [Indexed: 02/07/2023] Open
Abstract
XPC recognizes UV-induced DNA lesions and initiates their removal by nucleotide excision repair (NER). Damage recognition in NER is tightly controlled by ubiquitin and SUMO modifications. Recent studies have shown that the SUMO-targeted ubiquitin ligase RNF111 promotes K63-linked ubiquitylation of SUMOylated XPC after DNA damage. However, the exact regulatory function of these modifications in vivo remains elusive. Here we show that RNF111 is required for efficient repair of ultraviolet-induced DNA lesions. RNF111-mediated ubiquitylation promotes the release of XPC from damaged DNA after NER initiation, and is needed for stable incorporation of the NER endonucleases XPG and ERCC1/XPF. Our data suggest that RNF111, together with the CRL4(DDB2) ubiquitin ligase complex, is responsible for sequential XPC ubiquitylation, which regulates the recruitment and release of XPC and is crucial for efficient progression of the NER reaction, thereby providing an extra layer of quality control of NER.
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34
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DDB2 is involved in ubiquitination and degradation of PAQR3 and regulates tumorigenesis of gastric cancer cells. Biochem J 2015. [PMID: 26205499 DOI: 10.1042/bj20150253] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DDB2 (damage-specific DNA-binding protein 2) is the product of the xeroderma pigmentosum group E gene which is involved in the initiation of nucleotide excision repair via an ubiquitin ligase complex together with DDB1 and CUL4A (cullin 4A). PAQR3 (progestin and adipoQ receptor family member III) is a newly discovered tumour suppressor that is implicated in the development of many types of human cancers. In the present paper, we report that DDB2 is involved in ubiquitination and degradation of PAQR3. DDB2 is able to interact with PAQR3 in vivo and in vitro. Both overexpression and knockdown experiments reveal that the protein expression level, protein stability and polyubiquitination of PAQR3 are changed by DDB2. Negative regulation of EGF (epidermal growth factor)- and insulin-induced signalling by PAQR3 is also altered by DDB2. At the molecular level, Lys(61) of PAQR3 is targeted by DDB2 for ubiquitination. The cell proliferation rate and migration of gastric cancer cells are inhibited by DDB2 knockdown and such effects are abrogated by PAQR3 knockdown, indicating that the effect of DDB2 on the cancer cells is mediated by PAQR3. Collectively, our studies not only pinpoint that DDB2 is a post-translational regulator of PAQR3, but also indicate that DDB2 may play an active role in tumorigenesis via regulating PAQR3.
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35
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Alekseev S, Coin F. Orchestral maneuvers at the damaged sites in nucleotide excision repair. Cell Mol Life Sci 2015; 72:2177-86. [PMID: 25681868 PMCID: PMC11113351 DOI: 10.1007/s00018-015-1859-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
To safeguard the genome from the accumulation of deleterious effects arising from DNA lesions, cells developed several DNA repair mechanisms that remove specific types of damage from the genome. Among them, Nucleotide Excision Repair (NER) is unique in its ability to remove a very broad spectrum of lesions, the most important of which include UV-induced damage, bulky chemical adducts and some forms of oxidative damage. Two sub-pathways exist in NER; Transcription-Coupled Repair (TC-NER) removes lesion localized exclusively in transcribed genes while Global Genome Repair (GG-NER) removes lesions elsewhere. In TC- or GG-NER, more than 30 proteins detect, open, incise and resynthesize DNA. Intriguingly, half of them are involved in the detection of DNA damage, implying that this is a crucial repair step requiring a high level of regulation. We review here the complex damage recognition step of GG-NER with a focus on post-translational modifications that help the comings and goings of several protein complexes on the same short damaged DNA locus.
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Affiliation(s)
- Sergey Alekseev
- Department of Functional Genomics and Cancer, IGBMC, Equipe Labellisée Ligue 2014, CNRS/INSERM/University of Strasbourg, BP 163, 67404 Illkirch Cedex, C. U. Strasbourg, France
| | - Frédéric Coin
- Department of Functional Genomics and Cancer, IGBMC, Equipe Labellisée Ligue 2014, CNRS/INSERM/University of Strasbourg, BP 163, 67404 Illkirch Cedex, C. U. Strasbourg, France
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36
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Matsumoto S, Fischer ES, Yasuda T, Dohmae N, Iwai S, Mori T, Nishi R, Yoshino KI, Sakai W, Hanaoka F, Thomä NH, Sugasawa K. Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein. Nucleic Acids Res 2015; 43:1700-13. [PMID: 25628365 PMCID: PMC4330392 DOI: 10.1093/nar/gkv038] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In mammalian nucleotide excision repair, the DDB1-DDB2 complex recognizes UV-induced DNA photolesions and facilitates recruitment of the XPC complex. Upon binding to damaged DNA, the Cullin 4 ubiquitin ligase associated with DDB1-DDB2 is activated and ubiquitinates DDB2 and XPC. The structurally disordered N-terminal tail of DDB2 contains seven lysines identified as major sites for ubiquitination that target the protein for proteasomal degradation; however, the precise biological functions of these modifications remained unknown. By exogenous expression of mutant DDB2 proteins in normal human fibroblasts, here we show that the N-terminal tail of DDB2 is involved in regulation of cellular responses to UV. By striking contrast with behaviors of exogenous DDB2, the endogenous DDB2 protein was stabilized even after UV irradiation as a function of the XPC expression level. Furthermore, XPC competitively suppressed ubiquitination of DDB2 in vitro, and this effect was significantly promoted by centrin-2, which augments the DNA damage-recognition activity of XPC. Based on these findings, we propose that in cells exposed to UV, DDB2 is protected by XPC from ubiquitination and degradation in a stochastic manner; thus XPC allows DDB2 to initiate multiple rounds of repair events, thereby contributing to the persistence of cellular DNA repair capacity.
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Affiliation(s)
- Syota Matsumoto
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Eric S Fischer
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Takeshi Yasuda
- National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Wako 351-0198, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
| | - Toshio Mori
- Advanced Medical Research Center, Nara Medical University, Kashihara 634-8521, Japan
| | - Ryotaro Nishi
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan
| | - Ken-ichi Yoshino
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan
| | - Wataru Sakai
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Kaoru Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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37
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Shah P, He YY. Molecular regulation of UV-induced DNA repair. Photochem Photobiol 2015; 91:254-64. [PMID: 25534312 DOI: 10.1111/php.12406] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/09/2014] [Indexed: 12/21/2022]
Abstract
Ultraviolet (UV) radiation from sunlight is a major etiologic factor for skin cancer, the most prevalent cancer in the United States, as well as premature skin aging. In particular, UVB radiation causes formation of specific DNA damage photoproducts between pyrimidine bases. These DNA damage photoproducts are repaired by a process called nucleotide excision repair, also known as UV-induced DNA repair. When left unrepaired, UVB-induced DNA damage leads to accumulation of mutations, predisposing people to carcinogenesis as well as to premature aging. Genetic loss of nucleotide excision repair leads to severe disorders, namely, xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS), which are associated with predisposition to skin carcinogenesis at a young age as well as developmental and neurological conditions. Regulation of nucleotide excision repair is an attractive avenue to preventing or reversing these detrimental consequences of impaired nucleotide excision repair. Here, we review recent studies on molecular mechanisms regulating nucleotide excision repair by extracellular cues and intracellular signaling pathways, with a special focus on the molecular regulation of individual repair factors.
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Affiliation(s)
- Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
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38
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van Cuijk L, Vermeulen W, Marteijn JA. Ubiquitin at work: The ubiquitous regulation of the damage recognition step of NER. Exp Cell Res 2014; 329:101-9. [DOI: 10.1016/j.yexcr.2014.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/14/2014] [Indexed: 12/28/2022]
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39
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Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol 2014; 15:465-81. [PMID: 24954209 DOI: 10.1038/nrm3822] [Citation(s) in RCA: 776] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleotide excision repair (NER) eliminates various structurally unrelated DNA lesions by a multiwise 'cut and patch'-type reaction. The global genome NER (GG-NER) subpathway prevents mutagenesis by probing the genome for helix-distorting lesions, whereas transcription-coupled NER (TC-NER) removes transcription-blocking lesions to permit unperturbed gene expression, thereby preventing cell death. Consequently, defects in GG-NER result in cancer predisposition, whereas defects in TC-NER cause a variety of diseases ranging from ultraviolet radiation-sensitive syndrome to severe premature ageing conditions such as Cockayne syndrome. Recent studies have uncovered new aspects of DNA-damage detection by NER, how NER is regulated by extensive post-translational modifications, and the dynamic chromatin interactions that control its efficiency. Based on these findings, a mechanistic model is proposed that explains the complex genotype-phenotype correlations of transcription-coupled repair disorders.
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Abstract
Nucleotide excision repair (NER) is a key component of the DNA damage response (DDR) and it is essential to safeguard genome integrity against genotoxic insults. The regulation of NER is primarily mediated by protein post-translational modifications (PTMs). The NER machinery removes a wide spectrum of DNA helix distorting lesions, including those induced by solar radiation, through two sub-pathways: global genome nucleotide excision repair (GG-NER) and transcription coupled nucleotide excision repair (TC-NER). Severe clinical consequences associated with inherited NER defects, including premature ageing, neurodegeneration and extreme cancer-susceptibility, underscore the biological relevance of NER. In the last two decades most of the core NER machinery has been elaborately described, shifting attention to molecular mechanisms that either facilitate NER in the context of chromatin or promote the timely and accurate interplay between NER factors and various post-translational modifications. In this review, we summarize and discuss the latest findings in NER. In particular, we focus on emerging factors and novel molecular mechanisms by which NER is regulated.
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Chromatin retention of DNA damage sensors DDB2 and XPC through loss of p97 segregase causes genotoxicity. Nat Commun 2014; 5:3695. [PMID: 24770583 PMCID: PMC4007632 DOI: 10.1038/ncomms4695] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 03/19/2014] [Indexed: 01/12/2023] Open
Abstract
DNA damage recognition subunits like DDB2 and XPC protect the human skin from ultraviolet (UV) light-induced genome instability and cancer, as demonstrated by the devastating inherited syndrome xeroderma pigmentosum. Here, we show that the beneficial DNA repair response triggered by these two genome caretakers critically depends on a dynamic spatiotemporal regulation of their homeostasis. The prolonged retention of DDB2 and XPC in chromatin, due to a failure to readily remove both recognition subunits by the ubiquitin-dependent p97/VCP/Cdc48 segregase complex, leads to impaired DNA excision repair of UV lesions. Surprisingly, the ensuing chromosomal aberrations in p97-deficient cells are alleviated by a concomitant down regulation of DDB2 or XPC. Also, genome instability resulting from an excess of DDB2 persisting in UV-irradiated cells is prevented by concurrent p97 over-expression. Our findings demonstrate that DNA damage sensors and repair initiators acquire unexpected genotoxic properties if not controlled by timely extraction from chromatin.
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Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates. Proc Natl Acad Sci U S A 2014; 111:E1862-71. [PMID: 24760829 DOI: 10.1073/pnas.1323856111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How human DNA repair proteins survey the genome for UV-induced photoproducts remains a poorly understood aspect of the initial damage recognition step in nucleotide excision repair (NER). To understand this process, we performed single-molecule experiments, which revealed that the human UV-damaged DNA-binding protein (UV-DDB) performs a 3D search mechanism and displays a remarkable heterogeneity in the kinetics of damage recognition. Our results indicate that UV-DDB examines sites on DNA in discrete steps before forming long-lived, nonmotile UV-DDB dimers (DDB1-DDB2)2 at sites of damage. Analysis of the rates of dissociation for the transient binding molecules on both undamaged and damaged DNA show multiple dwell times over three orders of magnitude: 0.3-0.8, 8.1, and 113-126 s. These intermediate states are believed to represent discrete UV-DDB conformers on the trajectory to stable damage detection. DNA damage promoted the formation of highly stable dimers lasting for at least 15 min. The xeroderma pigmentosum group E (XP-E) causing K244E mutant of DDB2 found in patient XP82TO, supported UV-DDB dimerization but was found to slide on DNA and failed to stably engage lesions. These findings provide molecular insight into the loss of damage discrimination observed in this XP-E patient. This study proposes that UV-DDB recognizes lesions via multiple kinetic intermediates, through a conformational proofreading mechanism.
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Tsuge M, Masuda Y, Kaneoka H, Kidani S, Miyake K, Iijima S. SUMOylation of damaged DNA-binding protein DDB2. Biochem Biophys Res Commun 2013; 438:26-31. [PMID: 23860269 DOI: 10.1016/j.bbrc.2013.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
Abstract
Damaged DNA-binding protein (DDB) is a heterodimer composed of two subunits, p127 and p48, which have been designated DDB1 and DDB2, respectively. DDB2 recognizes and binds to UV-damaged DNA during nucleotide excision repair. Here, we demonstrated that DDB2 was SUMOylated in a UV-dependent manner, and its major SUMO E3 ligase was PIASy as determined by RNA interference-mediated knockdown. The UV-induced physical interaction between DDB2 and PIASy supported this notion. PIASy knockdown reduced the removal of cyclobutane pyrimidine dimers (CPDs) from total genomic DNA, but did not affect that of 6-4 pyrimidine pyrimidone photoproducts (6-4PPs). Thus, DDB2 plays an indispensable role in CPD repair, but not in 6-4PP repair, which is consistent with the observation that DDB2 was SUMOylated by PIASy. These results suggest that the SUMOylation of DDB2 facilitates CPD repair.
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Affiliation(s)
- Maasa Tsuge
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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Hannah J, Zhou PB. The CUL4A ubiquitin ligase is a potential therapeutic target in skin cancer and other malignancies. CHINESE JOURNAL OF CANCER 2013; 32:478-82. [PMID: 23845142 PMCID: PMC3845565 DOI: 10.5732/cjc.012.10279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cullin 4A (CUL4A) is an E3 ubiquitin ligase that directly affects DNA repair and cell cycle progression by targeting substrates including damage-specific DNA-binding protein 2 (DDB2), xeroderma pigmentosum complementation group C (XPC), chromatin licensing and DNA replication factor 1 (Cdt1), and p21. Recent work from our laboratory has shown that Cul4a-deficient mice have greatly reduced rates of ultraviolet-induced skin carcinomas. On a cellular level, Cul4a-deficient cells have great capacity for DNA repair and demonstrate a slow rate of proliferation due primarily to increased expression of DDB2 and p21, respectively. This suggests that CUL4A promotes tumorigenesis (as well as accumulation of skin damage and subsequent premature aging) by limiting DNA repair activity and expediting S phase entry. In addition, CUL4A has been found to be up-regulated via gene amplification or overexpression in breast cancers, hepatocellular carcinomas, squamous cell carcinomas, adrenocortical carcinomas, childhood medulloblastomas, and malignant pleural mesotheliomas. Because of its oncogenic activity in skin cancer and up-regulation in other malignancies, CUL4A has arisen as a potential candidate for targeted therapeutic approaches. In this review, we outline the established functions of CUL4A and discuss the E3 ligase's emergence as a potential driver of tumorigenesis.
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Affiliation(s)
- Jeffrey Hannah
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College and Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
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Melanson BD, Cabrita MA, Bose R, Hamill JD, Pan E, Brochu C, Marcellus KA, Zhao TT, Holcik M, McKay BC. A novel cis-acting element from the 3'UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression. Nucleic Acids Res 2013; 41:5692-703. [PMID: 23605047 PMCID: PMC3675493 DOI: 10.1093/nar/gkt279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The DNA damage-binding protein 2 (DDB2) is an adapter protein that can direct a modular Cul4-DDB1-RING E3 Ligase complex to sites of ultraviolet light-induced DNA damage to ubiquitinate substrates during nucleotide excision repair. The DDB2 transcript is ultraviolet-inducible; therefore, its regulation is likely important for its function. Curiously, the DDB2 mRNA is reportedly short-lived, but the transcript does not contain any previously characterized cis-acting determinants of mRNA stability in its 3' untranslated region (3'UTR). Here, we used a tetracycline regulated d2EGFP reporter construct containing specific 3'UTR sequences from DDB2 to identify novel cis-acting elements that regulate mRNA stability. Synthetic 3'UTRs corresponding to sequences as short as 25 nucleotides from the central region of the 3'UTR of DDB2 were sufficient to accelerate decay of the heterologous reporter mRNA. Conversely, these same 3'UTRs led to more rapid induction of the reporter mRNA, export of the message to the cytoplasm and the subsequent accumulation of the encoded reporter protein, indicating that this newly identified cis-acting element affects transcriptional and post-transciptional processes. These results provide clear evidence that nuclear and cytoplasmic processing of the DDB2 mRNA is inextricably linked.
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Affiliation(s)
- Brian D Melanson
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada, K1H 8L6
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Li T, Wang Z, Zhao Y, He W, An L, Liu S, Liu Y, Wang H, Hang H. Checkpoint protein Rad9 plays an important role in nucleotide excision repair. DNA Repair (Amst) 2013; 12:284-92. [PMID: 23433811 DOI: 10.1016/j.dnarep.2013.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 01/11/2013] [Accepted: 01/17/2013] [Indexed: 11/27/2022]
Abstract
Rad9, an evolutionarily conserved checkpoint gene with multiple functions for preserving genomic integrity, has been shown to play important roles in homologous recombination repair, base excision repair and mismatch repair. However, whether Rad9 has an impact on nucleotide excision repair remains unknown. Here we demonstrated that Rad9 was involved in nucleotide excision repair and loss of Rad9 led to defective removal of the UV-derived photoproduct 6-4PP (6,4 pyrimidine-pyrimidone) and the BPDE (anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide)-DNA adducts in mammalian cells. We also demonstrated that Rad9 could co-localize with XPC in response to local UV irradiation. However, our data showed that Rad9 was not required for the photoproducts recognition step of nucleotide excision repair. Further investigation revealed that reduction of Rad9 reduced the UV-induced transcription of the genes of the nucleotide excision repair factors DDB2, XPC, DDB1 and XPB and DDB2 protein levels in human cells. Interestingly, knockdown of one subunit of DNA damage recognition complex, hHR23B impaired Rad9-loading onto UV-damaged chromatin. Based on these results, we suggest that Rad9 plays an important role in nucleotide excision repair through mechanisms including maintaining DDB2 protein level in human cells.
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Affiliation(s)
- Tiepeng Li
- Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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47
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Wang QE, Han C, Zhao R, Wani G, Zhu Q, Gong L, Battu A, Racoma I, Sharma N, Wani AA. p38 MAPK- and Akt-mediated p300 phosphorylation regulates its degradation to facilitate nucleotide excision repair. Nucleic Acids Res 2012; 41:1722-33. [PMID: 23275565 PMCID: PMC3561975 DOI: 10.1093/nar/gks1312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Besides the primary histone acetyltransferase (HAT)-mediated chromatin remodeling function, co-transcriptional factor, p300, is also known to play a distinct role in DNA repair. However, the exact mechanism of p300 function in DNA repair has remained unclear and difficult to discern due to the phosphorylation and degradation of p300 in response to DNA damage. Here, we have demonstrated that p300 is only degraded in the presence of specific DNA lesions, which are the substrates of nucleotide excision repair (NER) pathway. In contrast, DNA double-strand breaks fail to degrade p300. Degradation is initiated by phosphorylation of p300 at serine 1834, which is catalyzed by the cooperative action of p38 mitogen-activated protein kinases and Akt kinases. In depth, functional analysis revealed that (i) p300 and CBP act redundantly in repairing ultraviolet (UV) lesions, (ii) the phosphorylation of p300 at S1834 is critical for efficient removal of UV-induced cyclobutane pyrimidine dimers and (iii) p300 is recruited to DNA damage sites located within heterochromatin. Taken together, we conclude that phosphorylated p300 initially acetylates histones to relax heterochromatin to allow damage recognition factors access to damage DNA. Thereupon, p300 is promptly degraded to allow the sequential recruitment of downstream repair proteins for successful execution of NER.
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Affiliation(s)
- Qi-En Wang
- Department of Radiology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA.
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Zhang L, Lubin A, Chen H, Sun Z, Gong F. The deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability. Cell Cycle 2012; 11:4378-84. [PMID: 23159851 PMCID: PMC3552920 DOI: 10.4161/cc.22688] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Damage-specific DNA-binding protein 2 (DDB2) was first isolated as a subunit of the UV-DDB heterodimeric complex that is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). DDB2 is required for efficient repair of CPDs in chromatin and is a component of the CRL4DDB2 E3 ligase that targets XPC, histones and DDB2 itself for ubiquitination. In this study, a yeast two-hybrid screening of a human cDNA library was performed to identify potential DDB2 cellular partners. We identified a deubiquitinating enzyme, USP24, as a likely DDB2-interacting partner. Interaction between DDB2 and USP24 was confirmed by co-precipitation. Importantly, knockdown of USP24 in two human cell lines decreased the steady-state levels of DDB2, indicating that USP24-mediated DDB2 deubiquitination prevents DDB2 degradation. In addition, we demonstrated that USP24 can cleave an ubiquitinated form of DDB2 in vitro. Taken together, our results suggest that the ubiquitin-specific protease USP24 is a novel regulator of DDB2 stability.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL USA
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49
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Abstract
CDT2 targets proteins involved in replication licensing (CDT1), cell cycle control (p21), and chromatin modification (SET8) for destruction by the CUL4-based E3 ligase (CRL4). CRL4(CDT2) recruits these substrates through interactions with chromatin-bound PCNA and ubiquitinates them exclusively on chromatin. Rereplication and G(2) cell cycle arrest are observed in CDT2-depleted cells. The rereplication phenotype has been attributed to an inability to destroy CDT1, but the molecular target important for G(2) cell cycle arrest in CDT2-depleted cells has not been identified. Here we identify CHK1 as a novel CRL4(CDT2) substrate and demonstrate that CHK1 activity is required for maintaining G(2) arrest in CDT2-depleted cells. We demonstrate that CRL4(CDT2) targets the activated form of CHK1 for destruction in the nucleoplasm rather than on chromatin and that this occurs in a PCNA-independent manner. Although both CRL1 and CRL4 ubiquitinate CHK1, we report that they bind CHK1 in distinct cellular compartments. Our study provides insight into how elevated CDT2 expression levels may provide tumors with a proliferative advantage.
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50
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Pines A, Vrouwe MG, Marteijn JA, Typas D, Luijsterburg MS, Cansoy M, Hensbergen P, Deelder A, de Groot A, Matsumoto S, Sugasawa K, Thoma N, Vermeulen W, Vrieling H, Mullenders L. PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1. ACTA ACUST UNITED AC 2012; 199:235-49. [PMID: 23045548 PMCID: PMC3471223 DOI: 10.1083/jcb.201112132] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PARP1-mediated poly(ADP-ribosyl)ation of DDB2 prolongs its occupation on UV-damaged chromatin and promotes the recruitment of the chromatin remodeler ALC1. The WD40-repeat protein DDB2 is essential for efficient recognition and subsequent removal of ultraviolet (UV)-induced DNA lesions by nucleotide excision repair (NER). However, how DDB2 promotes NER in chromatin is poorly understood. Here, we identify poly(ADP-ribose) polymerase 1 (PARP1) as a novel DDB2-associated factor. We demonstrate that DDB2 facilitated poly(ADP-ribosyl)ation of UV-damaged chromatin through the activity of PARP1, resulting in the recruitment of the chromatin-remodeling enzyme ALC1. Depletion of ALC1 rendered cells sensitive to UV and impaired repair of UV-induced DNA lesions. Additionally, DDB2 itself was targeted by poly(ADP-ribosyl)ation, resulting in increased protein stability and a prolonged chromatin retention time. Our in vitro and in vivo data support a model in which poly(ADP-ribosyl)ation of DDB2 suppresses DDB2 ubiquitylation and outline a molecular mechanism for PARP1-mediated regulation of NER through DDB2 stabilization and recruitment of the chromatin remodeler ALC1.
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Affiliation(s)
- Alex Pines
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, Netherlands
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