1
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 PMCID: PMC11088926 DOI: 10.1042/bst20230862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S. Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J. Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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2
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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3
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de Renty C, Pond KW, Yagle MK, Ellis NA. BLM Sumoylation Is Required for Replication Stability and Normal Fork Velocity During DNA Replication. Front Mol Biosci 2022; 9:875102. [PMID: 35847987 PMCID: PMC9284272 DOI: 10.3389/fmolb.2022.875102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
BLM is sumoylated in response to replication stress. We have studied the role of BLM sumoylation in physiologically normal and replication-stressed conditions by expressing in BLM-deficient cells a BLM with SUMO acceptor-site mutations, which we refer to as SUMO-mutant BLM cells. SUMO-mutant BLM cells exhibited multiple defects in both stressed and unstressed DNA replication conditions, including, in hydroxyurea-treated cells, reduced fork restart and increased fork collapse and, in untreated cells, slower fork velocity and increased fork instability as assayed by track-length asymmetry. We further showed by fluorescence recovery after photobleaching that SUMO-mutant BLM protein was less dynamic than normal BLM and comprised a higher immobile fraction at collapsed replication forks. BLM sumoylation has previously been linked to the recruitment of RAD51 to stressed forks in hydroxyurea-treated cells. An important unresolved question is whether the failure to efficiently recruit RAD51 is the explanation for replication stress in untreated SUMO-mutant BLM cells.
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Affiliation(s)
- Christelle de Renty
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Kelvin W. Pond
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Mary K. Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Nathan A. Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States
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4
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Joseph CR, Dusi S, Giannattasio M, Branzei D. Rad51-mediated replication of damaged templates relies on monoSUMOylated DDK kinase. Nat Commun 2022; 13:2480. [PMID: 35513396 PMCID: PMC9072374 DOI: 10.1038/s41467-022-30215-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage tolerance (DDT), activated by replication stress during genome replication, is mediated by translesion synthesis and homologous recombination (HR). Here we uncover that DDK kinase, essential for replication initiation, is critical for replication-associated recombination-mediated DDT. DDK relies on its multi-monoSUMOylation to facilitate HR-mediated DDT and optimal retention of Rad51 recombinase at replication damage sites. Impairment of DDK kinase activity, reduced monoSUMOylation and mutations in the putative SUMO Interacting Motifs (SIMs) of Rad51 impair replication-associated recombination and cause fork uncoupling with accumulation of large single-stranded DNA regions at fork branching points. Notably, genetic activation of salvage recombination rescues the uncoupled fork phenotype but not the recombination-dependent gap-filling defect of DDK mutants, revealing that the salvage recombination pathway operates preferentially proximal to fork junctions at stalled replication forks. Overall, we uncover that monoSUMOylated DDK acts with Rad51 in an axis that prevents replication fork uncoupling and mediates recombination-dependent gap-filling.
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Affiliation(s)
- Chinnu Rose Joseph
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Sabrina Dusi
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Michele Giannattasio
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
- Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-Oncologia, Via S. Sofia 9/1, 20122, Milano, Italy
| | - Dana Branzei
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy.
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5
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Kee Y, Lee JH, You HJ. RAD51 wrestles with SUMO. Mol Cell Oncol 2022; 9:2054263. [PMID: 35372672 PMCID: PMC8973377 DOI: 10.1080/23723556.2022.2054263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RAD51 loading onto chromatin is a key step during the homologous recombination (HR) repair. We recently reported a new mode of RAD51 regulation, which is mediated by TOPORS E3 SUMO ligase and RAD51 SUMOylation. ATM/ATR-induced phosphorylation of TOPORS is necessary for this event, revealing a new role of these master DNA damage response kinases in HR repair.
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Affiliation(s)
- Younghoon Kee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jung-Hee Lee
- Department of Cellular and Molecular Medicine, Chosun University School of medicine, Gwangju, Republic of Korea
| | - Ho Jin You
- Department of Cellular and Molecular Medicine, Chosun University School of medicine, Gwangju, Republic of Korea
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6
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Cappadocia L, Kochańczyk T, Lima CD. DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA. EMBO J 2021; 40:e103787. [PMID: 34585421 PMCID: PMC8591536 DOI: 10.15252/embj.2019103787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Repair of DNA double‐stranded breaks by homologous recombination (HR) is dependent on DNA end resection and on post‐translational modification of repair factors. In budding yeast, single‐stranded DNA is coated by replication protein A (RPA) following DNA end resection, and DNA–RPA complexes are then SUMO‐modified by the E3 ligase Siz2 to promote repair. Here, we show using enzymatic assays that DNA duplexes containing 3' single‐stranded DNA overhangs increase the rate of RPA SUMO modification by Siz2. The SAP domain of Siz2 binds DNA duplexes and makes a key contribution to this process as highlighted by models and a crystal structure of Siz2 and by assays performed using protein mutants. Enzymatic assays performed using DNA that can accommodate multiple RPA proteins suggest a model in which the SUMO‐RPA signal is amplified by successive rounds of Siz2‐dependent SUMO modification of RPA and dissociation of SUMO‐RPA at the junction between single‐ and double‐stranded DNA. Our results provide insights on how DNA architecture scaffolds a substrate and E3 ligase to promote SUMO modification in the context of DNA repair.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.,Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada
| | - Tomasz Kochańczyk
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.,Howard Hughes Medical Institute, Sloan Kettering Institute, New York, NY, USA
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7
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Zhao R, Chenoweth DM, Zhang H. Chemical Dimerization-Induced Protein Condensates on Telomeres. J Vis Exp 2021. [PMID: 33900288 DOI: 10.3791/62173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Chromatin-associated condensates are implicated in many nuclear processes, but the underlying mechanisms remain elusive. This protocol describes a chemically-induced protein dimerization system to create condensates on telomeres. The chemical dimerizer consists of two linked ligands that can each bind to a protein: Halo ligand to Halo-enzyme and trimethoprim (TMP) to E. coli dihydrofolate reductase (eDHFR), respectively. Fusion of Halo enzyme to a telomere protein anchors dimerizers to telomeres through covalent Halo ligand-enzyme binding. Binding of TMP to eDHFR recruits eDHFR-fused phase separating proteins to telomeres and induces condensate formation. Because TMP-eDHFR interaction is non-covalent, condensation can be reversed by using excess free TMP to compete with the dimerizer for eDHFR binding. An example of inducing promyelocytic leukemia (PML) nuclear body formation on telomeres and determining condensate growth, dissolution, localization and composition is shown. This method can be easily adapted to induce condensates at other genomic locations by fusing Halo to a protein that directly binds to the local chromatin or to dCas9 that is targeted to the genomic locus with a guide RNA. By offering the temporal resolution required for single cell live imaging while maintaining phase separation in a population of cells for biochemical assays, this method is suitable for probing both the formation and function of chromatin-associated condensates.
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Affiliation(s)
- Rongwei Zhao
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University
| | - David M Chenoweth
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania
| | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University;
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8
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Sun Y, Saha LK, Saha S, Jo U, Pommier Y. Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways. DNA Repair (Amst) 2020; 94:102926. [DOI: 10.1016/j.dnarep.2020.102926] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
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9
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Zhang H, Schaub JM, Finkelstein IJ. RADX condenses single-stranded DNA to antagonize RAD51 loading. Nucleic Acids Res 2020; 48:7834-7843. [PMID: 32621611 PMCID: PMC7430644 DOI: 10.1093/nar/gkaa559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
RADX is a mammalian single-stranded DNA-binding protein that stabilizes telomeres and stalled replication forks. Cellular biology studies have shown that the balance between RADX and Replication Protein A (RPA) is critical for DNA replication integrity. RADX is also a negative regulator of RAD51-mediated homologous recombination at stalled forks. However, the mechanism of RADX acting on DNA and its interactions with RPA and RAD51 are enigmatic. Using single-molecule imaging of the key proteins in vitro, we reveal that RADX condenses ssDNA filaments, even when the ssDNA is coated with RPA at physiological protein ratios. RADX compacts RPA-coated ssDNA filaments via higher-order assemblies that can capture ssDNA in trans. Furthermore, RADX blocks RPA displacement by RAD51 and prevents RAD51 loading on ssDNA. Our results indicate that RADX is an ssDNA condensation protein that inhibits RAD51 filament formation and may antagonize other ssDNA-binding proteins on RPA-coated ssDNA.
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Affiliation(s)
- Hongshan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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10
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Zhang H, Zhao R, Tones J, Liu M, Dilley RL, Chenoweth DM, Greenberg RA, Lampson MA. Nuclear body phase separation drives telomere clustering in ALT cancer cells. Mol Biol Cell 2020; 31:2048-2056. [PMID: 32579423 PMCID: PMC7543070 DOI: 10.1091/mbc.e19-10-0589] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates in response to telomere DNA damage, suggesting two potential functions: condensation to enrich DNA repair factors and coalescence to cluster telomeres. To test these models, we developed a chemically induced dimerization approach to induce de novo APB condensation in live cells without DNA damage. We show that telomere-binding protein sumoylation nucleates APB condensation via interactions between small ubiquitin-like modifier (SUMO) and SUMO interaction motif (SIM), and that APB coalescence drives telomere clustering. The induced APBs lack DNA repair factors, indicating that APB functions in promoting telomere clustering can be uncoupled from enriching DNA repair factors. Indeed, telomere clustering relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering independent of sumoylation. Our findings introduce a chemical dimerization approach to manipulate phase separation and demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how chromatin condensates promote cellular functions.
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Affiliation(s)
- Huaiying Zhang
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104.,Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Rongwei Zhao
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Jason Tones
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Michel Liu
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert L Dilley
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - David M Chenoweth
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine
| | - Roger A Greenberg
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael A Lampson
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
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11
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Tang HL, Xu L, Chen XQ. [Bortezomib interferes with DNA repair and exerts synergistic anti-multiple myeloma activity with doxorubicin]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:417-421. [PMID: 32536140 PMCID: PMC7342068 DOI: 10.3760/cma.j.issn.0253-2727.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/30/2022]
Affiliation(s)
- H L Tang
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
| | - L Xu
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
| | - X Q Chen
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
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12
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[Bortezomib interferes with DNA repair and exerts synergistic anti-multiple myeloma activity with doxorubicin]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41. [PMID: 32536140 PMCID: PMC7342068 DOI: 10.3760/cma.j.issn.0253-2727.2020.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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14
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Garvin AJ. Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response. Biochem Soc Trans 2019; 47:1881-1893. [PMID: 31769469 PMCID: PMC6925521 DOI: 10.1042/bst20190534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein-protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.
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Affiliation(s)
- Alexander J. Garvin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, U.K
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15
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Abstract
The homologous recombination (HR) machinery plays multiple roles in genome maintenance. Best studied in the context of DNA double-stranded break (DSB) repair, recombination enzymes can cleave, pair, and unwind DNA molecules, and collaborate with regulatory proteins to execute multiple DNA processing steps before generating specific repair products. HR proteins also help to cope with problems arising from DNA replication, modulating impaired replication forks or filling DNA gaps. Given these important roles, it is not surprising that each HR step is subject to complex regulation to adjust repair efficiency and outcomes as well as to limit toxic intermediates. Recent studies have revealed intricate regulation of all steps of HR by the protein modifier SUMO, which has been increasingly recognized for its broad influence in nuclear functions. This review aims to connect established roles of SUMO with its newly identified effects on recombinational repair and stimulate further thought on many unanswered questions.
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Affiliation(s)
- Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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16
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PIAS1 is not suitable as a urothelial carcinoma biomarker protein and pharmacological target. PLoS One 2019; 14:e0224085. [PMID: 31639157 PMCID: PMC6804980 DOI: 10.1371/journal.pone.0224085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/05/2019] [Indexed: 11/19/2022] Open
Abstract
Urothelial cancer (UC) is one of the most common cancers in Europe and is also one of the costliest to treat. When first line therapies show initial success, around 50% of cancers relapse and proceed to metastasis. In this study we assessed the Protein inhibitor of activated signal transducers and activators of transcription (PIAS)1 as a potential therapeutic target in urothelial cancer. PIAS1 is a key regulator of STAT1 signalling and may be implicated in carcinogenesis. In contrast to other cancer types PIAS1 protein expression is not significantly different in malignant areas of UC specimens compared to non-malignant tissue. In addition, we found that down-regulation and overexpression of PIAS1 had no effect on the viability or colony forming ability of tested cell lines. Whilst other studies of PIAS1 suggest an important biological role in cancer, this study shows that PIAS1 has no influence on reducing the cytotoxic effects of Cisplatin or cell recovery after DNA damage induced by irradiation. Taken together, these in vitro data demonstrate that PIAS1 is not a promising therapeutic target in UC cancer as previously shown in different entities such as prostate cancer (PCa).
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17
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Shi L, Sun J, Kinomura A, Fukuto A, Horikoshi Y, Tashiro S. Matrin3 promotes homologous recombinational repair by regulation of RAD51. J Biochem 2019; 166:343-351. [PMID: 31119278 DOI: 10.1093/jb/mvz041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023] Open
Abstract
Matrin3 is a highly conserved inner nuclear matrix protein involved in multiple stages of RNA metabolism. Although Matrin3 may also play a role in DNA repair, its precise roles have remained unclear. In this study, we showed that the depletion of Matrin3 led to decreased homologous recombination (HR) efficiency and increased radiation sensitivity of cells. Matrin3-depleted cells showed impaired DNA damage-dependent focus formation of RAD51, a key protein in HR. These findings suggest that Matrin3 promotes HR by regulating RAD51.
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Affiliation(s)
- Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine
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18
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Garvin AJ, Walker AK, Densham RM, Chauhan AS, Stone HR, Mackay HL, Jamshad M, Starowicz K, Daza-Martin M, Ronson GE, Lanz AJ, Beesley JF, Morris JR. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms. Genes Dev 2019; 33:333-347. [PMID: 30796017 PMCID: PMC6411010 DOI: 10.1101/gad.321125.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022]
Abstract
SUMOylation (small ubiquitin-like modifier) in the DNA double-strand break (DSB) response regulates recruitment, activity, and clearance of repair factors. However, our understanding of a role for deSUMOylation in this process is limited. Here we identify different mechanistic roles for deSUMOylation in homologous recombination (HR) and nonhomologous end joining (NHEJ) through the investigation of the deSUMOylase SENP2. We found that regulated deSUMOylation of MDC1 prevents excessive SUMOylation and its RNF4-VCP mediated clearance from DSBs, thereby promoting NHEJ. In contrast, we show that HR is differentially sensitive to SUMO availability and SENP2 activity is needed to provide SUMO. SENP2 is amplified as part of the chromosome 3q amplification in many cancers. Increased SENP2 expression prolongs MDC1 focus retention and increases NHEJ and radioresistance. Collectively, our data reveal that deSUMOylation differentially primes cells for responding to DSBs and demonstrates the ability of SENP2 to tune DSB repair responses.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexandra K Walker
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ruth M Densham
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Anoop Singh Chauhan
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen R Stone
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Hannah L Mackay
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Daza-Martin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - George E Ronson
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James F Beesley
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Joanna R Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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19
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Chang SM, Jain V, Chen TL, Patel AS, Pidugu HB, Lin YW, Wu MH, Huang JR, Wu HC, Shah A, Su TL, Lee TC. Design and Synthesis of 1,2-Bis(hydroxymethyl)pyrrolo[2,1-a]phthalazine Hybrids as Potent Anticancer Agents that Inhibit Angiogenesis and Induce DNA Interstrand Cross-links. J Med Chem 2019; 62:2404-2418. [DOI: 10.1021/acs.jmedchem.8b01689] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Anamik Shah
- Center of Excellence in Drug Discovery, Saurashtra University, Rajkot 360005, India
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20
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Zhang Z, Huo H, Liao K, Wang Z, Gong Z, Li Y, Liu C, Hu G. RPA1 downregulation enhances nasopharyngeal cancer radiosensitivity via blocking RAD51 to the DNA damage site. Exp Cell Res 2018; 371:330-341. [PMID: 30144445 DOI: 10.1016/j.yexcr.2018.08.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/01/2018] [Accepted: 08/21/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND/AIM Nasopharyngeal cancer (NPC) has a high local recurrence rate due to its resistance to ionizing radiation (IR). Replication protein A1 (RPA1) is one of the main elements in the homologous repair (HR) pathway, which is closely associated with the repair of DNA double strand breaks (DDBs). Studies on the relationship between RPA1 and the radiosensitivity of NPC are substantially limited. It was hypothesized that RPA1 plays a crucial role in predicting the radiosensitivity of NPC. METHODS The protein expression of RPA1 in 182 patients with NPC in the complete response (CR) and non-complete response (nCR) groups was evaluated using immunohistochemistry. Then, univariate and multivariate analysis were performed using SPSS software vision 22 to determine the relationship between the expression of RPA1 and the clinicopathological features. In addition, the mRNA expression of RPA1 was tested in 24 fresh samples using qRT-PCR. RPA1 was silenced in CNE-2R cell lines combined with IR to measure the radiosensitivity, proliferation, DNA damage repair and cell cycle of CNE-2R cells. Xenograft models in nude mice were used to determine the effect of RPA1 on tumor growth after IR. Immunoblotting and immunofluorescence staining were performed to identify proteins that interacted with RPA1. All statistical tests were two-sided. RESULTS RPA1 protein was overexpressed in NPC patients with nCR (65.31%), and was an independent predictor of radiosensitivity (HR: 3.755, 95% CI: 1.990-7.085), in addition to Epstein-Barr virus (EBV; HR: 3.984; 95% CI: 1.524-10.410). The silencing of RPA1 increased the radiosensitivity of CNE-2R cells, blocked the repair of DNA, impaired cell proliferation, and contributed to G2/M cell cycle arrest. Furthermore, the xenograft models in nude mice revealed that silencing RPA1 combined with irradiation significantly retarded the growth of tumors. Moreover, the knockdown of RPA1 decreased Rad51 collection to the damage site and prolonged the time of DNA repair. CONCLUSION RPA1 protein is frequently overexpressed in NPC patients with nCR. The silencing of RPA1 enhanced the radiosensitivity of CNE-2R cells. These present findings reveal that RPA1 is a potential biomarker for predicting the radiosensitivity in NPC.
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Affiliation(s)
- Zixin Zhang
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Radiotherapy, the General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Haifeng Huo
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Kui Liao
- Department of Oncology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhihai Wang
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhitao Gong
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yanshi Li
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Chuan Liu
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Guohua Hu
- Department of Otorhinolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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21
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DNA damage and tissue repair: What we can learn from planaria. Semin Cell Dev Biol 2018; 87:145-159. [PMID: 29727725 DOI: 10.1016/j.semcdb.2018.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/22/2018] [Accepted: 04/30/2018] [Indexed: 12/21/2022]
Abstract
Faithful renewal of aging and damaged tissues is central to organismal lifespan. Stem cells (SCs) generate the cellular progeny that replenish adult tissues across the body but this task becomes increasingly compromised over time. The age related decline in SC-mediated tissue maintenance is a multifactorial event that commonly affects genome integrity. The presence of DNA damage in SCs that are under continuous demand to divide poses a great risk for age-related disorders such as cancer. However, performing analysis of SCs with genomic instability and the DNA damage response during tissue renewal present significant challenges. Here we introduce an alternative experimental system based on the planaria flatworm Schmidtea mediterranea to address at the organismal level studies intersecting SC-mediated tissue renewal in the presence of genomic instability. Planaria have abundant SCs (neoblasts) that maintain high rates of cellular turnover and a variety of molecular tools have been developed to induce DNA damage and dissect how neoblasts respond to this stressor. S. mediterranea displays high evolutionary conservation of DNA repair mechanisms and signaling pathways regulating adult SCs. We describe genetically induced-DNA damage models and highlight body-wide signals affecting cellular decisions such as survival, proliferation, and death in the presence of genomic instability. We also discuss transcriptomic changes in the DNA damage response during injury repair and propose DNA repair as key component of tissue regeneration. Additional studies using planaria will provide insights about mechanisms regulating survival and growth of cells with DNA damage during tissue renewal and regeneration.
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22
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Thiruvalluvan M, Barghouth PG, Tsur A, Broday L, Oviedo NJ. SUMOylation controls stem cell proliferation and regional cell death through Hedgehog signaling in planarians. Cell Mol Life Sci 2018; 75:1285-1301. [PMID: 29098326 PMCID: PMC7083543 DOI: 10.1007/s00018-017-2697-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 12/15/2022]
Abstract
Mechanisms underlying anteroposterior body axis differences during adult tissue maintenance and regeneration are poorly understood. Here, we identify that post-translational modifications through the SUMO (Small Ubiquitin-like Modifier) machinery are evolutionarily conserved in the Lophotrocozoan Schmidtea mediterranea. Disruption of SUMOylation in adult animals by RNA-interference of the only SUMO E2 conjugating enzyme Ubc9 leads to a systemic increase in DNA damage and a remarkable regional defect characterized by increased cell death and loss of the posterior half of the body. We identified that Ubc9 is mainly expressed in planarian stem cells (neoblasts) but it is also transcribed in differentiated cells including neurons. Regeneration in Ubc9(RNAi) animals is impaired and associated with low neoblast proliferation. We present evidence indicating that Ubc9-induced regional cell death is preceded by alterations in transcription and spatial expression of repressors and activators of the Hedgehog signaling pathway. Our results demonstrate that SUMOylation acts as a regional-specific cue to regulate cell fate during tissue renewal and regeneration.
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Affiliation(s)
- Manish Thiruvalluvan
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Paul G Barghouth
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Assaf Tsur
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Néstor J Oviedo
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA.
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA.
- Health Sciences Research Institute, University of California, Merced, USA.
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23
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Andriuskevicius T, Kotenko O, Makovets S. Putting together and taking apart: assembly and disassembly of the Rad51 nucleoprotein filament in DNA repair and genome stability. Cell Stress 2018; 2:96-112. [PMID: 31225474 PMCID: PMC6551702 DOI: 10.15698/cst2018.05.134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Homologous recombination is a key mechanism providing both genome stability and genetic diversity in all living organisms. Recombinases play a central role in this pathway: multiple protein subunits of Rad51 or its orthologues bind single-stranded DNA to form a nucleoprotein filament which is essential for initiating recombination events. Multiple factors are involved in the regulation of this step, both positively and negatively. In this review, we discuss Rad51 nucleoprotein assembly and disassembly, how it is regulated and what functional significance it has in genome maintenance.
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Affiliation(s)
| | - Oleksii Kotenko
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
| | - Svetlana Makovets
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
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24
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Tsai CL, Liu WL, Hsu FM, Yang PS, Yen RF, Tzen KY, Cheng AL, Chen PJ, Cheng JCH. Targeting histone deacetylase 4/ubiquitin-conjugating enzyme 9 impairs DNA repair for radiosensitization of hepatocellular carcinoma cells in mice. Hepatology 2018. [PMID: 28646552 DOI: 10.1002/hep.29328] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Several strategies to improve the efficacy of radiation therapy against hepatocellular carcinoma (HCC) have been investigated. One approach is to develop radiosensitizing compounds. Because histone deacetylase 4 (HDAC4) is highly expressed in liver cancer and known to regulate oncogenesis through chromatin structure remodeling and controlling protein access to DNA, we postulated that HDAC4 inhibition might enhance radiation's effect on HCC cells. HCC cell lines (Huh7 and PLC5) and an ectopic xenograft were pretreated with HDAC inhibitor or short hairpin RNA to knock down expression of HDAC4 and then irradiated (2.5-10.0 Gy). We evaluated cell survival by a clonogenic assay; apoptosis by Annexin V immunofluorescence; γH2AX, Rad51, and HDAC4 by immunofluorescence staining; HDAC4, Rad51, and ubiquitin-conjugating enzyme 9 (Ubc9) in HCC cell nuclei by cell fractionation and confocal microscopy; physical interaction between HDAC4/Rad51/Ubc9 by immunoprecipitation; and the downstream targets of HDAC4 knockdown by immunoblotting. Both HDAC4 knockdown and HDAC inhibitor enhanced radiation-induced cell death and reduced homologous recombination repair of DNA double-strand breaks and protein kinase B activation, leading to increased apoptosis. HDAC4 knockdown with or without an HDAC inhibitor significantly delayed tumor growth in a radiation-treated xenograft model. Radiation stimulated nuclear translocation of Rad51 in an HDAC4-dependent manner and the binding of Ubc9 directly to HDAC4, which led to Ubc9 acetylation. Moreover, these effects were accompanied by HDAC4/Ubc9/Rad51 complex dissociation through inhibiting nuclear translocation. Conclusion: HDAC4 signaling blockade enhances radiation-induced lethality in HCC cells and xenografts. These findings raise the possibility that HDAC4/Ubc9/Rad51 complex in DNA repair may be a target for radiosensitization of HCC. (Hepatology 2018;67:586-599).
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Affiliation(s)
- Chiao-Ling Tsai
- Graduate Institutes of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Lin Liu
- Graduate Institutes of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Feng-Ming Hsu
- Graduate Institutes of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Sheng Yang
- Department of General Surgery, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ruoh-Fang Yen
- Department of Nuclear Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Molecular Imaging Center, National Taiwan University, Taipei, Taiwan
| | - Kai-Yuan Tzen
- Department of Nuclear Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of General Surgery, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ann-Lii Cheng
- Graduate Institutes of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan.,Cancer Research Center, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institutes of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jason Chia-Hsien Cheng
- Graduate Institutes of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan.,Graduate Institutes of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.,Cancer Research Center, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
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25
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Matunis MJ, Rodriguez MS. Concepts and Methodologies to Study Protein SUMOylation: An Overview. Methods Mol Biol 2018; 1475:3-22. [PMID: 27631794 DOI: 10.1007/978-1-4939-6358-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein modification by the small ubiquitin-related modifier (SUMO) was simultaneously discovered by several groups at the middle of the 1990s. Although distinct names were proposed including Sentrin, GMP1, PIC1, or SMT3, SUMO became the most popular. Early studies on the functions of SUMOylation focused on activities in the nucleus, including transcription activation, chromatin structure, and DNA repair. However, it is now recognized that SUMOylation affects a large diversity of cellular processes both in the nucleus and the cytoplasm and functions of SUMOylation appear to have undefined limits. SUMO-conjugating enzymes and specific proteases actively regulate the modification status of target proteins. The recent discoveries of ubiquitin-SUMO hybrid chains, multiple SUMO-interacting motifs, and macromolecular complexes regulated by SUMOylation underscore the high complexity of this dynamic reversible system. New conceptual frameworks suggested by these findings have motivated the development of new methodologies to study pre- and post-SUMOylation events in vitro and in vivo, using distinct model organisms. Here we summarize some of the new developments and methodologies in the field, particularly those that will be further elaborated on in the chapters integrating this book.
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Affiliation(s)
- Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe St., Room W8118, Baltimore, MD, 21205, USA.
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26
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Lee EJ, Hwang I, Lee JY, Park JN, Kim KC, Kim GH, Kang CM, Kim I, Lee SY, Kim HS. Hepatocyte Growth Factor Improves the Therapeutic Efficacy of Human Bone Marrow Mesenchymal Stem Cells via RAD51. Mol Ther 2017; 26:845-859. [PMID: 29398486 DOI: 10.1016/j.ymthe.2017.12.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
Human embryonic stem cell-derived mesenchymal stem cells (hE-MSCs) have greater proliferative capacity than other human mesenchymal stem cells (hMSCs), suggesting that they may have wider applications in regenerative cellular therapy. In this study, to uncover the anti-senescence mechanism in hE-MSCs, we compared hE-MSCs with adult bone marrow (hBM-MSCs) and found that hepatocyte growth factor (HGF) was more abundantly expressed in hE-MSCs than in hBM-MSCs and that it induced the transcription of RAD51 and facilitated its SUMOylation at K70. RAD51 induction/modification by HGF not only increased telomere length but also increased mtDNA replication, leading to increased ATP generation. Moreover, HGF-treated hBM-MSCs showed significantly better therapeutic efficacy than naive hBM-MSCs. Together, the data suggest that the RAD51-mediated effects of HGF prevent hMSC senescence by promoting telomere lengthening and inducing mtDNA replication and function, which opens the prospect of developing novel therapies for liver disease.
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Affiliation(s)
- Eun Ju Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Injoo Hwang
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong Nam Park
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Keun Cheon Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gi-Hwan Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chang-Mo Kang
- Korea Institute of Radiological & Medical Sciences, Seoul, Republic of Korea
| | - Irene Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seo-Yeon Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
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27
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Kochan JA, Desclos EC, Bosch R, Meister L, Vriend LE, van Attikum H, Krawczyk PM. Meta-analysis of DNA double-strand break response kinetics. Nucleic Acids Res 2017; 45:12625-12637. [PMID: 29182755 PMCID: PMC5728399 DOI: 10.1093/nar/gkx1128] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their functionality and underlying mechanisms of action. However, comparison and systemic interpretation of these data is challenging due to their scattered nature and differing experimental approaches. Here, we extracted, analyzed and compared the available results describing accumulation of 79 DSBR proteins at sites of DNA damage, which can be further explored using Cumulus (http://www.dna-repair.live/cumulus/)-the accompanying interactive online application. Despite large inter-study variability, our analysis revealed that the accumulation of most proteins starts immediately after damage induction, occurs in parallel and peaks within 15-20 min. Various DSBR pathways are characterized by distinct accumulation kinetics with major non-homologous end joining proteins being generally faster than those involved in homologous recombination, and signaling and chromatin remodeling factors accumulating with varying speeds. Our meta-analysis provides, for the first time, comprehensive overview of the temporal organization of the DSBR in mammalian cells and could serve as a reference for future mechanistic studies of this complex process.
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Affiliation(s)
- Jakub A. Kochan
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C.B. Desclos
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Luna Meister
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E.M. Vriend
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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28
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Fukuto A, Ikura M, Ikura T, Sun J, Horikoshi Y, Shima H, Igarashi K, Kusakabe M, Harata M, Horikoshi N, Kurumizaka H, Kiuchi Y, Tashiro S. SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites. Nucleus 2017; 9:87-94. [PMID: 29095668 PMCID: PMC5973225 DOI: 10.1080/19491034.2017.1395543] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone exchange and histone post-translational modifications play important roles in the regulation of DNA metabolism, by re-organizing the chromatin configuration. We previously demonstrated that the histone variant H2A.Z-2 is rapidly exchanged at damaged sites after DNA double strand break induction in human cells. In yeast, the small ubiquitin-like modifier (SUMO) modification of H2A.Z is involved in the DNA damage response. However, whether the SUMO modification regulates the exchange of human H2A.Z-2 at DNA damage sites remains unclear. Here, we show that H2A.Z-2 is SUMOylated in a damage-dependent manner, and the SUMOylation of H2A.Z-2 is suppressed by the depletion of the SUMO E3 ligase, PIAS4. Moreover, PIAS4 depletion represses the incorporation and eviction of H2A.Z-2 at damaged sites. These findings demonstrate that the PIAS4-mediated SUMOylation regulates the exchange of H2A.Z-2 at DNA damage sites.
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Affiliation(s)
- Atsuhiko Fukuto
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan.,b Department of Ophthalmology and Visual Science , Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Masae Ikura
- c Laboratory of Chromatin Regulatory Network, Department of Mutagenesis , Radiation Biology Center, Kyoto University , Kyoto , Japan
| | - Tsuyoshi Ikura
- c Laboratory of Chromatin Regulatory Network, Department of Mutagenesis , Radiation Biology Center, Kyoto University , Kyoto , Japan
| | - Jiying Sun
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
| | - Yasunori Horikoshi
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
| | - Hiroki Shima
- d Department of Biochemistry , Tohoku University Graduate School of Medicine , Sendai , Miyagi , Japan
| | - Kazuhiko Igarashi
- d Department of Biochemistry , Tohoku University Graduate School of Medicine , Sendai , Miyagi , Japan
| | - Masayuki Kusakabe
- e Laboratory of Molecular Biology, Graduate School of Agricultural Science , Tohoku University , Sendai , Miyagi , Japan
| | - Masahiko Harata
- e Laboratory of Molecular Biology, Graduate School of Agricultural Science , Tohoku University , Sendai , Miyagi , Japan
| | - Naoki Horikoshi
- f Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering , Waseda University, Shinjukuku , Tokyo , Japan.,g Present address; Department of Structural Biology, School of Medicine , Stanford University , Stanford , CA , USA
| | - Hitoshi Kurumizaka
- f Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering , Waseda University, Shinjukuku , Tokyo , Japan
| | - Yoshiaki Kiuchi
- b Department of Ophthalmology and Visual Science , Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Satoshi Tashiro
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
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29
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Bo T, Yamamori T, Suzuki M, Sakai Y, Yamamoto K, Inanami O. Calmodulin-dependent protein kinase II (CaMKII) mediates radiation-induced mitochondrial fission by regulating the phosphorylation of dynamin-related protein 1 (Drp1) at serine 616. Biochem Biophys Res Commun 2017; 495:1601-1607. [PMID: 29217195 DOI: 10.1016/j.bbrc.2017.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/02/2017] [Indexed: 12/11/2022]
Abstract
Mitochondrial dynamics are suggested to be indispensable for the maintenance of cellular quality and function in response to various stresses. While ionizing radiation (IR) stimulates mitochondrial fission, which is mediated by the mitochondrial fission protein, dynamin-related protein 1 (Drp1), it remains unclear how IR promotes Drp1 activation and subsequent mitochondrial fission. Therefore, we conducted this study to investigate these concerns. First, we found that X-irradiation triggered Drp1 phosphorylation at serine 616 (S616) but not at serine 637 (S637). Reconstitution analysis revealed that introduction of wild-type (WT) Drp1 recovered radiation-induced mitochondrial fission, which was absent in Drp1-deficient cells. Compared with cells transfected with WT or S637A Drp1, the change in mitochondrial shape following irradiation was mitigated in S616A Drp1-transfected cells. Furthermore, inhibition of CaMKII significantly suppressed Drp1 S616 phosphorylation and mitochondrial fission induced by IR. These results suggest that Drp1 phosphorylation at S616, but not at S637, is prerequisite for radiation-induced mitochondrial fission and that CaMKII regulates Drp1 phosphorylation at S616 following irradiation.
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Affiliation(s)
- Tomoki Bo
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tohru Yamamori
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
| | - Motofumi Suzuki
- Radiation and Cancer Biology Team, National Institutes for Quantum and Radiobiological Science and Technology, Chiba, Japan
| | - Yuri Sakai
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kumiko Yamamoto
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Osamu Inanami
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
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The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery. Nat Commun 2017; 8:1809. [PMID: 29180619 PMCID: PMC5703878 DOI: 10.1038/s41467-017-01900-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/23/2017] [Indexed: 12/14/2022] Open
Abstract
SUMO-targeted ubiquitin ligases (STUbLs) mediate the ubiquitylation of SUMOylated proteins to modulate their functions. In search of direct targets for the STUbL RNF4, we have developed TULIP (targets for ubiquitin ligases identified by proteomics) to covalently trap targets for ubiquitin E3 ligases. TULIP methodology could be widely employed to delineate E3 substrate wiring. Here we report that the single SUMO E2 Ubc9 and the SUMO E3 ligases PIAS1, PIAS2, PIAS3, ZNF451, and NSMCE2 are direct RNF4 targets. We confirm PIAS1 as a key RNF4 substrate. Furthermore, we establish the ubiquitin E3 ligase BARD1, a tumor suppressor and partner of BRCA1, as an indirect RNF4 target, regulated by PIAS1. Interestingly, accumulation of BARD1 at local sites of DNA damage increases upon knockdown of RNF4. Combined, we provide an insight into the role of the STUbL RNF4 to balance the role of SUMO signaling by directly targeting Ubc9 and SUMO E3 ligases. SUMO and ubiquitin are key signal transducers in several cellular processes including the DNA-damage response. Here the authors describe a method for selective enrichment of ubiquitin substrates for E3 ligases from complex cellular proteomes and identify the SUMO conjugation machinery as direct RNF4 substrates.
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Morris JR, Garvin AJ. SUMO in the DNA Double-Stranded Break Response: Similarities, Differences, and Cooperation with Ubiquitin. J Mol Biol 2017; 429:3376-3387. [PMID: 28527786 DOI: 10.1016/j.jmb.2017.05.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022]
Abstract
In recent years, our knowledge of the varied role that ubiquitination plays in promoting signal amplification, novel protein interactions, and protein turnover has progressed rapidly. This is particularly remarkable in the examination of how DNA double-stranded breaks (DSBs) are repaired, with many components of the ubiquitin (Ub) conjugation, de-conjugation, and recognition machinery now identified as key factors in DSB repair. In addition, a member of the Ub-like family, small Ub-like modifier (SUMO), has also been recognised as integral for efficient repair. Here, we summarise our emerging understanding of SUMOylation both as a distinct modification and as a cooperative modification with Ub, using the cellular response to DNA DSBs as the primary setting to compare these modifications.
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Affiliation(s)
- Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK
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Garvin AJ, Morris JR. SUMO, a small, but powerful, regulator of double-strand break repair. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160281. [PMID: 28847818 PMCID: PMC5577459 DOI: 10.1098/rstb.2016.0281] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
The response to a DNA double-stranded break in mammalian cells is a process of sensing and signalling the lesion. It results in halting the cell cycle and local transcription and in the mediation of the DNA repair process itself. The response is launched through a series of post-translational modification signalling events coordinated by phosphorylation and ubiquitination. More recently modifications of proteins by Small Ubiquitin-like MOdifier (SUMO) isoforms have also been found to be key to coordination of the response (Morris et al. 2009 Nature462, 886-890 (doi:10.1038/nature08593); Galanty et al. 2009 Nature462, 935-939 (doi:10.1038/nature08657)). However our understanding of the role of SUMOylation is slight compared with our growing knowledge of how ubiquitin drives signal amplification and key chromatin interactions. In this review we consider our current knowledge of how SUMO isoforms, SUMO conjugation machinery, SUMO proteases and SUMO-interacting proteins contribute to directing altered chromatin states and to repair-protein kinetics at a double-stranded DNA lesion in mammalian cells. We also consider the gaps in our understanding.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Browning CL, Wise JP. Prolonged exposure to particulate chromate inhibits RAD51 nuclear import mediator proteins. Toxicol Appl Pharmacol 2017; 331:101-107. [PMID: 28554658 PMCID: PMC5568470 DOI: 10.1016/j.taap.2017.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022]
Abstract
Particulate hexavalent chromium (Cr(VI)) is a human lung carcinogen and a human health concern. The induction of structural chromosome instability is considered to be a driving mechanism of Cr(VI)-induced carcinogenesis. Homologous recombination repair protects against Cr(VI)-induced chromosome damage, due to its highly accurate repair of Cr(VI)-induced DNA double strand breaks. However, recent studies demonstrate Cr(VI) inhibits homologous recombination repair through the misregulation of RAD51. RAD51 is an essential protein in HR repair that facilitates the search for a homologous sequence. Recent studies show prolonged Cr(VI) exposure prevents proper RAD51 subcellular localization, causing it to accumulate in the cytoplasm. Since nuclear import of RAD51 is crucial to its function, this study investigated the effect of Cr(VI) on the RAD51 nuclear import mediators, RAD51C and BRCA2. We show acute (24h) Cr(VI) exposure induces the proper localization of RAD51C and BRCA2. In contrast, prolonged (120h) exposure increased the cytoplasmic localization of both proteins, although RAD51C localization was more severely impaired. These results correlate temporally with the previously reported Cr(VI)-induced RAD51 cytoplasmic accumulation. In addition, we found Cr(VI) does not inhibit interaction between RAD51 and its nuclear import mediators. Altogether, our results suggest prolonged Cr(VI) exposure inhibits the nuclear import of RAD51C, and to a lesser extent, BRCA2, which results in the cytoplasmic accumulation of RAD51. Cr(VI)-induced inhibition of nuclear import may play a key role in its carcinogenic mechanism since the nuclear import of many tumor suppressor proteins and DNA repair proteins is crucial to their function.
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Affiliation(s)
- Cynthia L Browning
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, United States; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, United States.
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, United States; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, United States.
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Branzei D, Szakal B. Building up and breaking down: mechanisms controlling recombination during replication. Crit Rev Biochem Mol Biol 2017; 52:381-394. [PMID: 28325102 DOI: 10.1080/10409238.2017.1304355] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis. There is a profound connection between replication and recombination: recombination proteins protect replication forks from nuclease-mediated degradation of the nascent DNA strands and facilitate replication completion in cells challenged by DNA damage. Moreover, in case of fork collapse and formation of double strand breaks (DSBs), the recombination factors present or recruited to the fork facilitate HR-mediated DSB repair, which is primarily error-free. Disruption of HR is inexorably linked to genome instability, but the premature activation of HR during replication often leads to genome rearrangements. Faithful replication necessitates the downregulation of HR and disruption of active RAD51 filaments at replication forks, but upon persistent fork stalling, building up of HR is critical for the reorganization of the replication fork and for filling-in of the gaps associated with discontinuous replication induced by DNA lesions. Here we summarize and reflect on our understanding of the mechanisms that either suppress recombination or locally enhance it during replication, and the principles that underlie this regulation.
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Affiliation(s)
- Dana Branzei
- a IFOM, the FIRC Institute of Molecular Oncology , Milan , Italy
| | - Barnabas Szakal
- a IFOM, the FIRC Institute of Molecular Oncology , Milan , Italy
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Abstract
Post-translational protein modification by small ubiquitin-like modifier (SUMO), termed sumoylation, is an important mechanism in cellular responses to stress and one that appears to be upregulated in many cancers. Here, we examine the role of sumoylation in tumorigenesis as a possibly necessary safeguard that protects the stability and functionality of otherwise easily misregulated gene expression programmes and signalling pathways of cancer cells.
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Affiliation(s)
- Jacob-Sebastian Seeler
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Institut Pasteur, 28 rue de Dr Roux, 75724 Paris Cedex 15, France
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Institut Pasteur, 28 rue de Dr Roux, 75724 Paris Cedex 15, France
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36
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The mechanism of Jurkat cells apoptosis induced by Aggregatibacter actinomycetemcomitans cytolethal distending toxin. Apoptosis 2017; 22:841-851. [DOI: 10.1007/s10495-017-1357-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Zeng Q, Wang Z, Liu C, Gong Z, Yang L, Jiang L, Ma Z, Qian Y, Yang Y, Kang H, Hong S, Bu Y, Hu G. Knockdown of NFBD1/MDC1 enhances chemosensitivity to cisplatin or 5-fluorouracil in nasopharyngeal carcinoma CNE1 cells. Mol Cell Biochem 2016; 418:137-46. [DOI: 10.1007/s11010-016-2739-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/15/2016] [Indexed: 01/13/2023]
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38
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García-Rodríguez N, Wong RP, Ulrich HD. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress. Front Genet 2016; 7:87. [PMID: 27242895 PMCID: PMC4865505 DOI: 10.3389/fgene.2016.00087] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022] Open
Abstract
Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse.
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Puhr M, Hoefer J, Eigentler A, Dietrich D, van Leenders G, Uhl B, Hoogland M, Handle F, Schlick B, Neuwirt H, Sailer V, Kristiansen G, Klocker H, Culig Z. PIAS1 is a determinant of poor survival and acts as a positive feedback regulator of AR signaling through enhanced AR stabilization in prostate cancer. Oncogene 2016; 35:2322-32. [PMID: 26257066 PMCID: PMC4865476 DOI: 10.1038/onc.2015.292] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/10/2015] [Accepted: 07/06/2015] [Indexed: 01/19/2023]
Abstract
Novel drugs like Abiraterone or Enzalutamide, which target androgen receptor (AR) signaling to improve androgen deprivation therapy (ADT), have been developed during the past years. However, the application of these drugs is limited because of occurrence of inherent or acquired therapy resistances during the treatment. Thus, identification of new molecular targets is urgently required to improve current therapeutic prostate cancer (PCa) treatment strategies. PIAS1 (protein inhibitor of activated STAT1 (signal transducer and activator of transcription-1)) is known to be an important cell cycle regulator and PIAS1-mediated SUMOylation is essential for DNA repair. In this context, elevated PIAS1 expression has already been associated with cancer initiation. Thus, in the present study, we addressed the question of whether PIAS1 targeting can be used as a basis for an improved PCa therapy in combination with anti-androgens. We show that PIAS1 significantly correlates with AR expression in PCa tissue and in cell lines and demonstrate that high PIAS1 levels predict shorter relapse-free survival. Our patient data are complemented by mechanistic and functional in vitro experiments that identify PIAS1 as an androgen-responsive gene and a crucial factor for AR signaling via prevention of AR degradation. Furthermore, PIAS1 knockdown is sufficient to decrease cell proliferation as well as cell viability. Strikingly, Abiraterone or Enzalutamide treatment in combination with PIAS1 depletion is even more effective than single-drug treatment in multiple PCa cell models, rendering PIAS1 as a promising target protein for a combined treatment approach to improve future PCa therapies.
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Affiliation(s)
- M Puhr
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - J Hoefer
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - A Eigentler
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - D Dietrich
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - G van Leenders
- Institute of Pathology Erasmus Medical Center, Rotterdam, The Netherlands
| | - B Uhl
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - M Hoogland
- Institute of Pathology Erasmus Medical Center, Rotterdam, The Netherlands
| | - F Handle
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - B Schlick
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - H Neuwirt
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck, Austria
| | - V Sailer
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - G Kristiansen
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - H Klocker
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Z Culig
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
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40
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PIAS1 binds p300 and behaves as a coactivator or corepressor of the transcription factor c-Myb dependent on SUMO-status. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:705-18. [PMID: 27032383 DOI: 10.1016/j.bbagrm.2016.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/08/2016] [Accepted: 03/23/2016] [Indexed: 12/21/2022]
Abstract
The PIAS proteins (Protein Inhibitor of Activated STATs) constitute a family of multifunctional nuclear proteins operating as SUMO E3 ligases and being involved in a multitude of interactions. They participate in a range of biological processes, also beyond their well-established role in the immune system and cytokine signalling. They act both as transcriptional corepressors and coactivators depending on the context. In the present work, we investigated mechanisms by which PIAS1 causes activation or repression of c-Myb dependent target genes. Analysis of global expression data shows that c-Myb and PIAS1 knockdowns affect a subset of common targets, but with a dual outcome consistent with a role of PIAS1 as either a corepressor or coactivator. Our mechanistic studies show that PIAS1 engages in a novel interaction with the acetyltransferase and coactivator p300. Interaction and ChIP analysis suggest a bridging function where PIAS1 enhances p300 recruitment to c-Myb-bound sites through interaction with both proteins. In addition, the E3 activity of PIAS1 enhances further its coactivation. Remarkably, the SUMO status of c-Myb had a decisive role, indicating a SUMO-dependent switch in the way PIAS1 affects c-Myb, either as a coactivator or corepressor. Removal of the two major SUMO-conjugation sites in c-Myb (2KR mutant), which enhances its activity significantly, turned PIAS1 into a corepressor. Also, p300 was less efficiently recruited to chromatin by c-Myb-2KR. We propose that PIAS1 acts as a "protein inhibitor of activated c-Myb" in the absence of SUMOylation while, in its presence, PIAS behaves as a "protein activator of repressed c-Myb".
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Puhr M, Hoefer J, Neuwirt H, Eder IE, Kern J, Schäfer G, Geley S, Heidegger I, Klocker H, Culig Z. PIAS1 is a crucial factor for prostate cancer cell survival and a valid target in docetaxel resistant cells. Oncotarget 2015; 5:12043-56. [PMID: 25474038 PMCID: PMC4322998 DOI: 10.18632/oncotarget.2658] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/27/2014] [Indexed: 11/25/2022] Open
Abstract
Occurrence of an inherent or acquired resistance to the chemotherapeutic drug docetaxel is a major burden for patients suffering from different kinds of malignancies, including castration resistant prostate cancer (PCa). In the present study we address the question whether PIAS1 targeting can be used to establish a basis for improved PCa treatment. The expression status and functional relevance of PIAS1 was evaluated in primary tumors, in metastatic lesions, in tissue of patients after docetaxel chemotherapy, and in docetaxel resistant cells. Patient data were complemented by functional studies on PIAS1 knockdown in vitro as well as in chicken chorioallantoic membrane and mouse xenograft in vivo models. PIAS1 was found to be overexpressed in local and metastatic PCa and its expression was further elevated in tumors after docetaxel treatment as well as in docetaxel resistant cells. Furthermore, PIAS1 knockdown experiments revealed an increased expression of tumor suppressor p21 and declined expression of anti-apoptotic protein Mcl1, which caused diminished cell proliferation and tumor growth in vitro and in vivo. In summary, the presented data indicate that PIAS1 is crucial for parental and docetaxel resistant PCa cell survival and is therefore a promising new target for treatment of primary, metastatic, and chemotherapy resistant PCa.
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Affiliation(s)
- Martin Puhr
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Julia Hoefer
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hannes Neuwirt
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck, Austria
| | - Iris E Eder
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johann Kern
- Oncotyrol Laboratory for Tumor Biology and Angiogenesis, Innsbruck, Austria
| | - Georg Schäfer
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Geley
- Division of Molecular Pathophysiology, Innsbruck Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Isabel Heidegger
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helmut Klocker
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zoran Culig
- Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
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42
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Wang Z, Zeng Q, Chen T, Liao K, Bu Y, Hong S, Hu G. Silencing NFBD1/MDC1 enhances the radiosensitivity of human nasopharyngeal cancer CNE1 cells and results in tumor growth inhibition. Cell Death Dis 2015; 6:e1849. [PMID: 26247734 PMCID: PMC4558506 DOI: 10.1038/cddis.2015.214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/16/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022]
Abstract
NFBD1 functions in cell cycle checkpoint activation and DNA repair following ionizing radiation (IR). In this study, we defined the NFBD1 as a tractable molecular target to radiosensitize nasopharyngeal carcinoma (NPC) cells. Silencing NFBD1 using lentivirus-mediated shRNA-sensitized NPC cells to radiation in a dose-dependent manner, increasing apoptotic cell death, decreasing clonogenic survival and delaying DNA damage repair. Furthermore, downregulation of NFBD1 inhibited the amplification of the IR-induced DNA damage signal, and failed to accumulate and retain DNA damage-response proteins at the DNA damage sites, which leaded to defective checkpoint activation following DNA damage. We also implicated the involvement of NFBD1 in IR-induced Rad51 and DNA-dependent protein kinase catalytic subunit foci formation. Xenografts models in nude mice showed that silencing NFBD1 significantly enhanced the antitumor activity of IR, leading to tumor growth inhibition of the combination therapy. Our studies suggested that a combination of gene therapy and radiation therapy may be an effective strategy for human NPC treatment.
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Affiliation(s)
- Z Wang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Q Zeng
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - T Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - K Liao
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Y Bu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research, China Center, Chongqing Medical University, Chongqing, China
| | - S Hong
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - G Hu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Okimoto S, Sun J, Fukuto A, Horikoshi Y, Matsuda S, Matsuda T, Ikura M, Ikura T, Machida S, Kurumizaka H, Miyamoto Y, Oka M, Yoneda Y, Kiuchi Y, Tashiro S. hCAS/CSE1L regulates RAD51 distribution and focus formation for homologous recombinational repair. Genes Cells 2015; 20:681-94. [PMID: 26123175 DOI: 10.1111/gtc.12262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/14/2015] [Indexed: 01/05/2023]
Abstract
Homologous recombinational repair (HR) is one of the major repair systems for DNA double-strand breaks. RAD51 is a key molecule in HR, and the RAD51 concentration in the cell nucleus increases after DNA damage induction. However, the mechanism that regulates the intracellular distribution of RAD51 is still unclear. Here, we show that hCAS/CSE1L associates with RAD51 in human cells. We found that hCAS/CSE1L negatively regulates the nuclear protein level of RAD51 under normal conditions. hCAS/CSE1L is also required to repress the DNA damage-induced focus formation of RAD51. Moreover, we show that hCAS/CSE1L plays roles in the regulation of the HR activity and in chromosome stability. These findings suggest that hCAS/CSE1L is responsible for controlling the HR activity by directly interacting with RAD51.
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Affiliation(s)
- Satoshi Okimoto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan.,Department of Ophthalmology and Visual Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan.,Department of Ophthalmology and Visual Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Shun Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan
| | - Masae Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoichi Miyamoto
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Masahiro Oka
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Yoshihiro Yoneda
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Yoshiaki Kiuchi
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, 734-8551, Japan
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44
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Liu NA, Sun J, Kono K, Horikoshi Y, Ikura T, Tong X, Haraguchi T, Tashiro S. Regulation of homologous recombinational repair by lamin B1 in radiation-induced DNA damage. FASEB J 2015; 29:2514-25. [PMID: 25733566 DOI: 10.1096/fj.14-265546] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/13/2015] [Indexed: 01/05/2023]
Abstract
DNA double-strand breaks (DSBs) are the major lethal lesion induced by ionizing radiation (IR). RAD51-dependent homologous recombination (HR) is one of the most important pathways in DSB repair and genome integrity maintenance. However, the mechanism of HR regulation by RAD51 remains unclear. To understand the mechanism of RAD51-dependent HR, we searched for interacting partners of RAD51 by a proteomics analysis and identified lamin B1 in human cells. Lamins are nuclear lamina proteins that play important roles in the structural organization of the nucleus and the regulation of chromosome functions. Immunoblotting analyses revealed that siRNA-mediated lamin B1 depletion repressed the DNA damage-dependent increase of RAD51 after IR. The repression was abolished by the proteasome inhibitor MG132, suggesting that lamin B1 stabilizes RAD51 by preventing proteasome-mediated degradation in cells with IR-induced DNA damage. We also showed that lamin B1 depletion repressed RAD51 focus formation and decreased the survival rates after IR. On the basis of these results, we propose that lamin B1 promotes DSB repair and cell survival by maintaining the RAD51 protein levels for HR upon DSB induction after IR.
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Affiliation(s)
- Ning-Ang Liu
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Jiying Sun
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Kazuteru Kono
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasunori Horikoshi
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tsuyoshi Ikura
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Xing Tong
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tokuko Haraguchi
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Satoshi Tashiro
- *Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, and Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Hiroshima, Japan; Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan; Laboratory Center, Medical College of Soochow University, Suzhou, China; and Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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46
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 347] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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47
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Nishibuchi I, Suzuki H, Kinomura A, Sun J, Liu NA, Horikoshi Y, Shima H, Kusakabe M, Harata M, Fukagawa T, Ikura T, Ishida T, Nagata Y, Tashiro S. Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2. Int J Radiat Oncol Biol Phys 2014; 89:736-44. [PMID: 24969791 DOI: 10.1016/j.ijrobp.2014.03.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/13/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023]
Abstract
PURPOSE The reorganization of damaged chromatin plays an important role in the regulation of the DNA damage response. A recent study revealed the presence of 2 vertebrate H2A.Z isoforms, H2A.Z-1 and H2A.Z-2. However, the roles of the vertebrate H2A.Z isoforms are still unclear. Thus, in this study we examined the roles of the vertebrate H2A.Z isoforms in chromatin reorganization after the induction of DNA double-strand breaks (DSBs). METHODS AND MATERIALS To examine the dynamics of H2A.Z isoforms at damaged sites, we constructed GM0637 cells stably expressing each of the green fluorescent protein (GFP)-labeled H2A.Z isoforms, and performed fluorescence recovery after photobleaching (FRAP) analysis and inverted FRAP analysis in combination with microirradiation. Immunofluorescence staining using an anti-RAD51 antibody was performed to study the kinetics of RAD51 foci formation after 2-Gy irradiation of wild-type (WT), H2A.Z-1- and H2A.Z-2-deficient DT40 cells. Colony-forming assays were also performed to compare the survival rates of WT, H2A.Z-1-, and H2A.Z-2-deficient DT40 cells with control, and H2A.Z-1- and H2A.Z-2-depleted U2OS cells after irradiation. RESULTS FRAP analysis revealed that H2A.Z-2 was incorporated into damaged chromatin just after the induction of DSBs, whereas H2A.Z-1 remained essentially unchanged. Inverted FRAP analysis showed that H2A.Z-2 was released from damaged chromatin. These findings indicated that H2A.Z-2 was exchanged at DSB sites immediately after the induction of DSBs. RAD51 focus formation after ionizing irradiation was disturbed in H2A.Z-2-deficient DT40 cells but not in H2A.Z-1-deficient cells. The survival rate of H2A.Z-2-deficient cells after irradiation was lower than those of WT and H2A.Z-1- DT40 cells. Similar to DT40 cells, H2A.Z-2-depleted U2OS cells were also radiation-sensitive compared to control and H2A.Z-1-depleted cells. CONCLUSIONS We found that vertebrate H2A.Z-2 is involved in the regulation of the DNA damage response at a very early stage, via the damaged chromatin reorganization required for RAD51 focus formation.
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Affiliation(s)
- Ikuno Nishibuchi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Department of Radiation Oncology, Hiroshima Prefectural Hospital, Hiroshima, Japan
| | - Hidekazu Suzuki
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Ning-Ang Liu
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
| | - Hiroki Shima
- Department of Biochemistry, Graduate School of Medical Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tatsuo Fukagawa
- Department of Molecular Genetics, National Institute of Genetics and The Graduate University for Advanced Studies, Mishima, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Takafumi Ishida
- Department of Cardiovascular Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasushi Nagata
- Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan.
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48
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Hu Y, Parvin JD. Small ubiquitin-like modifier (SUMO) isoforms and conjugation-independent function in DNA double-strand break repair pathways. J Biol Chem 2014; 289:21289-95. [PMID: 24966330 DOI: 10.1074/jbc.c114.582122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small ubiquitin-like modifier (SUMO) proteins act in DNA double-strand break (DSB) repair, but the pathway specificity of the three major isoforms has not been defined. In experiments in which we depleted the endogenous SUMO protein by RNAi, we found that SUMO1 functioned in all subpathways of either homologous recombination (HR) or non-homologous end joining (NHEJ), whereas SUMO2/3 was required for the major NHEJ pathway, called conservative NHEJ, but dispensable in other DSB repair pathways. To our surprise, we found that depletion of UBC9, the unique SUMO E2 enzyme, had no effect in HR or alternative NHEJ (Alt-NHEJ) but was required for conservative NHEJ. Consistent with this result, both non-conjugatable mutant and wild-type SUMO1 proteins functioned similarly in HR and Alt-NHEJ. These results detail the functional roles of specific SUMO isoforms in DSB repair in mammalian cells and reveal that SUMO1 functions in HR or Alt-NHEJ as a free protein and not as a protein conjugate.
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Affiliation(s)
- Yiheng Hu
- From the Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210
| | - Jeffrey D Parvin
- From the Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210
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49
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Richard P, Manley JL. SETX sumoylation: A link between DNA damage and RNA surveillance disrupted in AOA2. Rare Dis 2014; 2:e27744. [PMID: 25054092 PMCID: PMC4091563 DOI: 10.4161/rdis.27744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/18/2013] [Accepted: 01/06/2014] [Indexed: 01/09/2023] Open
Abstract
Senataxin (SETX) is a putative RNA:DNA helicase that is mutated in two distinct juvenile neurological disorders, AOA2 and ALS4. SETX is involved in the response to oxidative stress and is suggested to resolve R loops formed at transcription termination sites or at sites of collisions between the transcription and replication machineries. R loops are hybrids between RNA and DNA that are believed to lead to DNA damage and genomic instability. We discovered that Rrp45, a core component of the exosome, is a SETX-interacting protein and that the interaction depends on modification of SETX by sumoylation. Importantly, we showed that AOA2 but not ALS4 mutations prevented both SETX sumoylation and the Rrp45 interaction. We also found that upon replication stress induction, SETX and Rrp45 co-localize in nuclear foci that constitute sites of R-loop formation generated by transcription and replication machinery collisions. We suggest that SETX links transcription, DNA damage and RNA surveillance, and discuss here how this link can be relevant to AOA2 disease.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences; Columbia University; New York, NY USA
| | - James L Manley
- Department of Biological Sciences; Columbia University; New York, NY USA
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