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Perina D, Mikoč A, Ahel J, Ćetković H, Žaja R, Ahel I. Distribution of protein poly(ADP-ribosyl)ation systems across all domains of life. DNA Repair (Amst) 2014; 23:4-16. [PMID: 24865146 PMCID: PMC4245714 DOI: 10.1016/j.dnarep.2014.05.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/04/2014] [Accepted: 05/06/2014] [Indexed: 02/08/2023]
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification of proteins involved in regulation of many cellular pathways. Poly(ADP-ribose) (PAR) consists of chains of repeating ADP-ribose nucleotide units and is synthesized by the family of enzymes called poly(ADP-ribose) polymerases (PARPs). This modification can be removed by the hydrolytic action of poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3 (ARH3). Hydrolytic activity of macrodomain proteins (MacroD1, MacroD2 and TARG1) is responsible for the removal of terminal ADP-ribose unit and for complete reversion of protein ADP-ribosylation. Poly(ADP-ribosyl)ation is widely utilized in eukaryotes and PARPs are present in representatives from all six major eukaryotic supergroups, with only a small number of eukaryotic species that do not possess PARP genes. The last common ancestor of all eukaryotes possessed at least five types of PARP proteins that include both mono and poly(ADP-ribosyl) transferases. Distribution of PARGs strictly follows the distribution of PARP proteins in eukaryotic species. At least one of the macrodomain proteins that hydrolyse terminal ADP-ribose is also always present. Therefore, we can presume that the last common ancestor of all eukaryotes possessed a fully functional and reversible PAR metabolism and that PAR signalling provided the conditions essential for survival of the ancestral eukaryote in its ancient environment. PARP proteins are far less prevalent in bacteria and were probably gained through horizontal gene transfer. Only eleven bacterial species possess all proteins essential for a functional PAR metabolism, although it is not known whether PAR metabolism is truly functional in bacteria. Several dsDNA viruses also possess PARP homologues, while no PARP proteins have been identified in any archaeal genome. Our analysis of the distribution of enzymes involved in PAR metabolism provides insight into the evolution of these important signalling systems, as well as providing the basis for selection of the appropriate genetic model organisms to study the physiology of the specific human PARP proteins.
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Affiliation(s)
- Dragutin Perina
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Josip Ahel
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Roko Žaja
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb 10002, Croatia; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Abstract
DNA strand breaks arise continuously in cells and can lead to chromosome rearrangements and genome instability or cell death. The commonest DNA breaks are DNA single-strand breaks, which arise at a frequency of tens-of-thousands per cell each day and which can block the progression of RNA/DNA polymerases and disrupt gene transcription and genome duplication. If not rapidly repaired, SSBs can be converted into DNA double-strand breaks (DSBs) during genome duplication, eliciting a complex series of DNA damage responses that attempt to protect cells from irreversible replication fork collapse. DSBs are the most cytotoxic and clastogenic type of DNA breaks, and can also arise independently of DNA replication, albeit at a frequency several orders of magnitude lower than SSBs. Here, I discuss the evidence that DNA single- and double -strand break repair pathways, and cellular tolerance mechanisms for protecting replication forks during genome duplication, utilize signalling by protein ADP-ribosyltransferases to protect cells from the harmful impact of DNA strand breakage.
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Affiliation(s)
- K W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brigton BN1 9RQ, United Kingdom.
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Abstract
![]()
The
concept of synthetic lethality (the creation of a lethal phenotype
from the combined effects of mutations in two or more genes) has recently
been exploited in various efforts to develop new genotype-selective
anticancer therapeutics. These efforts include screening for novel
anticancer agents, identifying novel therapeutic targets, characterizing
mechanisms of resistance to targeted therapy, and improving efficacies
through the rational design of combination therapy. This review discusses
recent developments in synthetic lethality anticancer therapeutics,
including poly ADP-ribose polymerase inhibitors for BRCA1- and BRCA2-mutant cancers, checkpoint inhibitors
for p53 mutant cancers, and small molecule agents targeting RAS gene mutant cancers. Because cancers are caused by mutations
in multiple genes and abnormalities in multiple signaling pathways,
synthetic lethality for a specific tumor suppressor gene or oncogene
is likely cell context-dependent. Delineation of the mechanisms underlying
synthetic lethality and identification of treatment response biomarkers
will be critical for the success of synthetic lethality anticancer
therapy.
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Affiliation(s)
- Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, Unit 1489, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Boulevard, Houston, Texas 77030, United States
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Węsierska-Gądek J, Heinzl S. Interactions Between Ataxia Telangiectasia Mutated Kinase Inhibition, Poly(ADP-ribose) Polymerase-1 Inhibition and BRCA1 Status in Breast Cancer Cells. J Cancer Prev 2014; 19:125-36. [PMID: 25337581 PMCID: PMC4204161 DOI: 10.15430/jcp.2014.19.2.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/14/2014] [Accepted: 06/14/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cells harboring BRCA1/BRCA2 mutations are hypersensitive to inhibition of poly(ADP-ribose) polymerase-1 (PARP-1). We recently showed that interference with PARP-1 activity by NU1025 is strongly cytotoxic for BRCA1-positive BT-20 cells but not BRCA1-deficient SKBr-3 cells. These unexpected observations prompted speculation that other PARP-1 inhibitor(s) may be more cytotoxic towards SKBr-3 cells. In addition, interference with the DNA damage signaling pathway via (for instance) Ataxia telangiectasia mutated (ATM) kinase inhibition may induce synthetic lethality in DNA repair-deficient breast cancer cells and pharmacological interference with ATM activity may sensitize breast cancer cells to PARP-1 inactivation. METHODS We determined drug cytotoxicity in human MCF-7 and SKBr-3 breast cancer cells using the CellTiterGLO Luminescent cell viability assay and a Tecan multi-label, multitask plate counter to measure generated luminescence. Changes in cell cycle progression were monitored by flow cytometric measurement of DNA content in cells stained with propidium iodide. RESULTS Unlike NU1025, AZD2461, a new PARP-1 inhibitor, markedly reduced the numbers of living MCF-7 and SKBr-3 cells. ATM kinase inhibition (CP466722) was also cytotoxic for both MCF-7 and SKBr-3 cells. Furthermore, AZD2461 enhanced the cytotoxicity of CP466722 in both cell lines by inducing apoptosis, and concurrent inhibition of ATM and PARP-1 reduced cell proliferation more strongly than either single treatment. CONCLUSIONS Our data show that inhibition of PARP-1 by AZD2461 is synthetically lethal for NU1025-resistant MCF-7 and SKBr-3 breast cancer cells. They also indicate that DNA damage signaling is essential for survival of both SKBr-3 and MCF-7 cells, especially after inactivation of PARP-1.
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Affiliation(s)
- Józefa Węsierska-Gądek
- Cell Cycle Regulation Group, Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Austria
| | - Sarah Heinzl
- Cell Cycle Regulation Group, Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Austria
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Grundy GJ, Moulding HA, Caldecott KW, Rulten SL. One ring to bring them all--the role of Ku in mammalian non-homologous end joining. DNA Repair (Amst) 2014; 17:30-8. [PMID: 24680220 DOI: 10.1016/j.dnarep.2014.02.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/25/2014] [Indexed: 12/26/2022]
Abstract
The repair of DNA double strand breaks is essential for cell survival and several conserved pathways have evolved to ensure their rapid and efficient repair. The non-homologous end joining pathway is initiated when Ku binds to the DNA break site. Ku is an abundant nuclear heterodimer of Ku70 and Ku80 with a toroidal structure that allows the protein to slide over the broken DNA end and bind with high affinity. Once locked into placed, Ku acts as a tool-belt to recruit multiple interacting proteins, forming one or more non-homologous end joining complexes that act in a regulated manner to ensure efficient repair of DNA ends. Here we review the structure and functions of Ku and the proteins with which it interacts during non-homologous end joining.
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Affiliation(s)
- Gabrielle J Grundy
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Hayley A Moulding
- School of Biochemistry, Medical Sciences, University Walk, Bristol BS8 1TD, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Stuart L Rulten
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
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Pears CJ, Lakin ND. Emerging models for DNA repair: Dictyostelium discoideum as a model for nonhomologous end-joining. DNA Repair (Amst) 2014; 17:121-31. [DOI: 10.1016/j.dnarep.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/09/2014] [Accepted: 01/24/2014] [Indexed: 02/03/2023]
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Beck C, Boehler C, Guirouilh Barbat J, Bonnet ME, Illuzzi G, Ronde P, Gauthier LR, Magroun N, Rajendran A, Lopez BS, Scully R, Boussin FD, Schreiber V, Dantzer F. PARP3 affects the relative contribution of homologous recombination and nonhomologous end-joining pathways. Nucleic Acids Res 2014; 42:5616-32. [PMID: 24598253 PMCID: PMC4027158 DOI: 10.1093/nar/gku174] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The repair of toxic double-strand breaks (DSB) is critical for the maintenance of genome integrity. The major mechanisms that cope with DSB are: homologous recombination (HR) and classical or alternative nonhomologous end joining (C-NHEJ versus A-EJ). Because these pathways compete for the repair of DSB, the choice of the appropriate repair pathway is pivotal. Among the mechanisms that influence this choice, deoxyribonucleic acid (DNA) end resection plays a critical role by driving cells to HR, while accurate C-NHEJ is suppressed. Furthermore, end resection promotes error-prone A-EJ. Increasing evidence define Poly(ADP-ribose) polymerase 3 (PARP3, also known as ARTD3) as an important player in cellular response to DSB. In this work, we reveal a specific feature of PARP3 that together with Ku80 limits DNA end resection and thereby helps in making the choice between HR and NHEJ pathways. PARP3 interacts with and PARylates Ku70/Ku80. The depletion of PARP3 impairs the recruitment of YFP-Ku80 to laser-induced DNA damage sites and induces an imbalance between BRCA1 and 53BP1. Both events result in compromised accurate C-NHEJ and a concomitant increase in DNA end resection. Nevertheless, HR is significantly reduced upon PARP3 silencing while the enhanced end resection causes mutagenic deletions during A-EJ. As a result, the absence of PARP3 confers hypersensitivity to anti-tumoral drugs generating DSB.
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Affiliation(s)
- Carole Beck
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Christian Boehler
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Josée Guirouilh Barbat
- Université Paris Sud, CNRS UMR8200, Institut de Cancérologie Gustave-Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Marie-Elise Bonnet
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Giuditta Illuzzi
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Philippe Ronde
- Laboratoire de biophotonique et pharmacologie, UMR 7213, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Laurent R Gauthier
- CEA DSV iRCM SCSR, Laboratoire de radiopathologie, INSERM, U967, 92265 Fontenay-aux-Roses, France
| | - Najat Magroun
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Anbazhagan Rajendran
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Bernard S Lopez
- Université Paris Sud, CNRS UMR8200, Institut de Cancérologie Gustave-Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Ralph Scully
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - François D Boussin
- CEA DSV iRCM SCSR, Laboratoire de radiopathologie, INSERM, U967, 92265 Fontenay-aux-Roses, France
| | - Valérie Schreiber
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
| | - Françoise Dantzer
- Poly(ADP-ribosyl)ation and Genome Integrity, Laboratoire d'Excellence Medalis, Equipe labellisée Ligue Nationale Contre Le Cancer, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 300 bld. S. Brant, BP10413, 67412 Illkirch, France
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Yao H, Sundar IK, Gorbunova V, Rahman I. P21-PARP-1 pathway is involved in cigarette smoke-induced lung DNA damage and cellular senescence. PLoS One 2013; 8:e80007. [PMID: 24244594 PMCID: PMC3823706 DOI: 10.1371/journal.pone.0080007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/07/2013] [Indexed: 12/20/2022] Open
Abstract
Persistent DNA damage triggers cellular senescence, which may play an important role in the pathogenesis of cigarette smoke (CS)-induced lung diseases. Both p21CDKN1A (p21) and poly(ADP-ribose) polymerase-1 (PARP-1) are involved in DNA damage and repair. However, the role of p21-PARP-1 axis in regulating CS-induced lung DNA damage and cellular senescence remains unknown. We hypothesized that CS causes DNA damage and cellular senescence through a p21-PARP-1 axis. To test this hypothesis, we determined the levels of γH2AX (a marker for DNA double-strand breaks) as well as non-homologous end joining proteins (Ku70 and Ku80) in lungs of mice exposed to CS. We found that the level of γH2AX was increased, whereas the level of Ku70 was reduced in lungs of CS-exposed mice. Furthermore, p21 deletion reduced the level of γH2AX, but augmented the levels of Ku70, Ku80, and PAR in lungs by CS. Administration of PARP-1 inhibitor 3-aminobenzamide increased CS-induced DNA damage, but lowered the levels of Ku70 and Ku80, in lungs of p21 knockout mice. Moreover, 3-aminobenzamide increased senescence-associated β-galactosidase activity, but decreased the expression of proliferating cell nuclear antigen in mouse lungs in response to CS. Interestingly, 3-aminobenzamide treatment had no effect on neutrophil influx into bronchoalveolar lavage fluid by CS. These results demonstrate that the p21-PARP-1 pathway is involved in CS-induced DNA damage and cellular senescence.
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Affiliation(s)
- Hongwei Yao
- Department of Environmental Medicine, Lung Biology and Disease Program, Rochester, New York, United States of America
- * E-mail: (HY); (IR)
| | - Isaac K. Sundar
- Department of Environmental Medicine, Lung Biology and Disease Program, Rochester, New York, United States of America
| | - Vera Gorbunova
- Department of Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Irfan Rahman
- Department of Environmental Medicine, Lung Biology and Disease Program, Rochester, New York, United States of America
- * E-mail: (HY); (IR)
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Predictive biomarkers for cancer therapy with PARP inhibitors. Oncogene 2013; 33:3894-907. [PMID: 24037533 DOI: 10.1038/onc.2013.352] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/09/2013] [Accepted: 07/12/2013] [Indexed: 12/17/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have raised high expectations for the treatment of multiple malignancies. PARP inhibitors, which can be used as monotherapies or in combination with DNA-damaging agents, are particularly efficient against tumors with defects in DNA repair mechanisms, in particular the homologous recombination pathway, for instance due to BRCA mutations. Thus, deficient DNA repair provides a framework for the success of PARP inhibitors in medical oncology. Here, we review encouraging results obtained in recent clinical trials investigating the safety and efficacy of PARP inhibitors as anticancer agents. We discuss emerging mechanisms of regulation of homologous recombination and how inhibition of DNA repair might be used in cancer therapy. We surmise that the identification of patients that are likely to benefit from PARP inhibition will improve the clinical use of PARP inhibitors in a defined target population. Thus, we will place special emphasis on biomarker discovery.
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61
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Barkauskaite E, Jankevicius G, Ladurner AG, Ahel I, Timinszky G. The recognition and removal of cellular poly(ADP-ribose) signals. FEBS J 2013; 280:3491-507. [PMID: 23711178 DOI: 10.1111/febs.12358] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/03/2013] [Accepted: 05/24/2013] [Indexed: 12/12/2022]
Abstract
Poly(ADP-ribosyl)ation is involved in the regulation of a variety of cellular pathways, including, but not limited to, transcription, chromatin, DNA damage and other stress signalling. Similar to other tightly regulated post-translational modifications, poly(ADP-ribosyl)ation employs 'writers', 'readers' and 'erasers' to confer regulatory functions. The generation of poly(ADP-ribose) is catalyzed by poly(ADP-ribose) polymerase enzymes, which use NAD(+) as a cofactor to sequentially transfer ADP-ribose units generating long polymers, which, in turn, can affect protein function or serve as a recruitment platform for additional factors. Historically, research has focused on poly(ADP-ribose) generation pathways, with knowledge about PAR recognition and degradation lagging behind. Over recent years, several discoveries have significantly furthered our understanding of poly(ADP-ribose) recognition and, even more so, of poly(ADP-ribose) degradation. In this review, we summarize current knowledge about the protein modules recognizing poly(ADP-ribose) and discuss the newest developments on the complete reversibility of poly(ADP-ribosyl)ation.
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Affiliation(s)
- Eva Barkauskaite
- Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
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Croset A, Cordelières FP, Berthault N, Buhler C, Sun JS, Quanz M, Dutreix M. Inhibition of DNA damage repair by artificial activation of PARP with siDNA. Nucleic Acids Res 2013; 41:7344-55. [PMID: 23761435 PMCID: PMC3753643 DOI: 10.1093/nar/gkt522] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the major early steps of repair is the recruitment of repair proteins at the damage site, and this is coordinated by a cascade of modifications controlled by phosphatidylinositol 3-kinase-related kinases and/or poly (ADP-ribose) polymerase (PARP). We used short interfering DNA molecules mimicking double-strand breaks (called Dbait) or single-strand breaks (called Pbait) to promote DNA-dependent protein kinase (DNA-PK) and PARP activation. Dbait bound and induced both PARP and DNA-PK activities, whereas Pbait acts only on PARP. Therefore, comparative study of the two molecules allows analysis of the respective roles of the two signaling pathways: both recruit proteins involved in single-strand break repair (PARP, XRCC1 and PCNA) and prevent their recruitment at chromosomal damage. Dbait, but not Pbait, also inhibits recruitment of proteins involved in double-strand break repair (53BP1, NBS1, RAD51 and DNA-PK). By these ways, Pbait and Dbait disorganize DNA repair, thereby sensitizing cells to various treatments. Single-strand breaks repair inhibition depends on direct trapping of the main proteins on both molecules. Double-strand breaks repair inhibition may be indirect, resulting from the phosphorylation of double-strand breaks repair proteins and chromatin targets by activated DNA-PK. The DNA repair inhibition by both molecules is confirmed by their synthetic lethality with BRCA mutations.
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Affiliation(s)
- Amelie Croset
- Institut Curie, CNRS-UMR3347, INSERM-U1021, 91405 Orsay, France, DNA Therapeutics, Génopole, 91000 Evry, France, Institut Curie, CNRS-UMR3348, Plateforme PICT-IBiSA, 91405 Orsay, France and Museum National d'Histoire Naturelle, USM503, 75231 Paris, France
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63
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Detection and repair of ionizing radiation-induced DNA double strand breaks: new developments in nonhomologous end joining. Int J Radiat Oncol Biol Phys 2013; 86:440-9. [PMID: 23433795 DOI: 10.1016/j.ijrobp.2013.01.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/07/2013] [Indexed: 01/13/2023]
Abstract
DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.
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64
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Bremer S, Klein K, Sedlmaier A, Abouzied M, Gieselmann V, Franken S. Hepatoma-derived growth factor and nucleolin exist in the same ribonucleoprotein complex. BMC BIOCHEMISTRY 2013; 14:2. [PMID: 23305559 PMCID: PMC3551658 DOI: 10.1186/1471-2091-14-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/02/2013] [Indexed: 12/26/2022]
Abstract
BACKGROUND Hepatoma-derived growth factor (HDGF) is a protein which is highly expressed in a variety of tumours. HDGF has mitogenic, angiogenic, neurotrophic and antiapoptotic activity but the molecular mechanisms by which it exerts these activities are largely unknown nor has its biological function in tumours been elucidated. Mass spectrometry was performed to analyse the HDGFStrep-tag interactome. By Pull-down-experiments using different protein and nucleic acid constructs the interaction of HDGF and nucleolin was investigated further. RESULTS A number of HDGFStrep-tag copurifying proteins were identified which interact with RNA or are involved in the cellular DNA repair machinery. The most abundant protein, however, copurifying with HDGF in this approach was nucleolin. Therefore we focus on the characterization of the interaction of HDGF and nucleolin in this study. We show that expression of a cytosolic variant of HDGF causes a redistribution of nucleolin into the cytoplasm. Furthermore, formation of HDGF/nucleolin complexes depends on bcl-2 mRNA. Overexpression of full length bcl-2 mRNA increases the number of HDGF/nucleolin complexes whereas expression of only the bcl-2 coding sequence abolishes interaction completely. Further examination reveals that the coding sequence of bcl-2 mRNA together with either the 5' or 3' UTR is sufficient for formation of HDGF/nucleolin complexes. When bcl-2 coding sequence within the full length cDNA is replaced by a sequence coding for secretory alkaline phosphatase complex formation is not enhanced. CONCLUSION The results provide evidence for the existence of HDGF and nucleolin containing nucleoprotein complexes which formation depends on the presence of specific mRNAs. The nature of these RNAs and other components of the complexes should be investigated in future.
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Affiliation(s)
- Stephanie Bremer
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, Bonn, 53115, Germany
| | - Katharina Klein
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, Bonn, 53115, Germany
| | - Angela Sedlmaier
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, Bonn, 53115, Germany
| | - Mekky Abouzied
- Faculty of Pharmacy, University of El-Minia, El-Minia, Egypt
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, Bonn, 53115, Germany
| | - Sebastian Franken
- Institute of Biochemistry and Molecular Biology, University of Bonn, Nussallee 11, Bonn, 53115, Germany
- Present address: Life-Science-Inkubator, Ludwig-Erhard-Allee 2, Bonn, 53175, Germany
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Grundy GJ, Rulten SL, Zeng Z, Arribas-Bosacoma R, Iles N, Manley K, Oliver A, Caldecott KW. APLF promotes the assembly and activity of non-homologous end joining protein complexes. EMBO J 2013; 32:112-25. [PMID: 23178593 PMCID: PMC3545299 DOI: 10.1038/emboj.2012.304] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/29/2012] [Indexed: 11/08/2022] Open
Abstract
Non-homologous end joining (NHEJ) is critical for the maintenance of genetic integrity and DNA double-strand break (DSB) repair. NHEJ is regulated by a series of interactions between core components of the pathway, including Ku heterodimer, XLF/Cernunnos, and XRCC4/DNA Ligase 4 (Lig4). However, the mechanisms by which these proteins assemble into functional protein-DNA complexes are not fully understood. Here, we show that the von Willebrand (vWA) domain of Ku80 fulfills a critical role in this process by recruiting Aprataxin-and-PNK-Like Factor (APLF) into Ku-DNA complexes. APLF, in turn, functions as a scaffold protein and promotes the recruitment and/or retention of XRCC4-Lig4 and XLF, thereby assembling multi-protein Ku complexes capable of efficient DNA ligation in vitro and in cells. Disruption of the interactions between APLF and either Ku80 or XRCC4-Lig4 disrupts the assembly and activity of Ku complexes, and confers cellular hypersensitivity and reduced rates of chromosomal DSB repair in avian and human cells, respectively. Collectively, these data identify a role for the vWA domain of Ku80 and a molecular mechanism by which DNA ligase proficient complexes are assembled during NHEJ in mammalian cells, and reveal APLF to be a structural component of this critical DSB repair pathway.
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Affiliation(s)
| | - Stuart L Rulten
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Zhihong Zeng
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | | | - Natasha Iles
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Katie Manley
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Antony Oliver
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
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66
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Couto CAM, Hsu DW, Teo R, Rakhimova A, Lempidaki S, Pears CJ, Lakin ND. Nonhomologous end-joining promotes resistance to DNA damage in the absence of an ADP-ribosyltransferase that signals DNA single strand breaks. J Cell Sci 2013; 126:3452-61. [DOI: 10.1242/jcs.128769] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ADP-ribosylation of proteins at DNA lesions by ADP-ribosyltransferases (ARTs) is an early response to DNA damage. The best defined role of ADP-ribosylation in the DNA damage response is in repair of single strand breaks (SSBs). Recently, we initiated a study of how ADP-ribosylation regulates DNA repair in Dictyostelium and found that whilst two ARTs (Adprt1b and Adprt2) are required for tolerance of cells to SSBs, a third ART (Adprt1a) promotes nonhomologous end-joining (NHEJ). Here we report that disruption of adprt2 results in accumulation of DNA damage throughout the cell cycle following exposure to agents that induce base damage and DNA SSBs. Although ADP-ribosylation is evident in adprt2− cells exposed to MMS, disruption of adprt1a and adprt2 in combination abrogates this response and further sensitises cells to this agent, indicating that in the absence of Adprt2, Adprt1a signals MMS-induced DNA lesions to promote resistance of cells to DNA damage. As a consequence of defective signalling of SSBs by Adprt2, Adprt1a is required to assemble NHEJ factors in chromatin and disruption of the NHEJ pathway in combination with adprt2 increases sensitivity of cells to MMS. Taken together, these data indicate overlapping functions between different ARTs in signalling DNA damage and illustrate a critical requirement for NHEJ in maintaining cell viability in the absence of an effective SSB response.
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67
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Abstract
DNA is constantly being damaged from endogenous and exogenous sources and efficient repair of different types of DNA lesions is essential for the survival of the organism. Dictyostelium is highly resistant to DNA damage and its genome sequence has revealed the presence of multiple repair pathways conserved with vertebrates but lost in other genetically tractable invertebrate models. As such, Dictyostelium is a powerful model organism to study selected human DNA repair pathways and may provide insights into the molecular basis of how cells become resistant to DNA damage. Here we describe a range of assays used to study DNA repair in Dictyostelium. Genes required for repair of DNA damage can be identified and analyzed by comparing the ability of control or mutant cells to survive exposure to genotoxic agents that induce different types of DNA lesion. We also describe assays that assess the presence of markers for DNA repair within chromatin either in the form of posttranslational modification of proteins at sites of damage or the recruitment of repair factors to DNA lesions. Finally, we also describe more direct assays to assess repair of DNA double-strand breaks by either homologous recombination or non-homologous end joining.
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68
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Gassman NR, Stefanick DF, Kedar PS, Horton JK, Wilson SH. Hyperactivation of PARP triggers nonhomologous end-joining in repair-deficient mouse fibroblasts. PLoS One 2012; 7:e49301. [PMID: 23145148 PMCID: PMC3492265 DOI: 10.1371/journal.pone.0049301] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/08/2012] [Indexed: 01/20/2023] Open
Abstract
Regulation of poly(ADP-ribose) (PAR) synthesis and turnover is critical to determining cell fate after genotoxic stress. Hyperactivation of PAR synthesis by poly(ADP-ribose) polymerase-1 (PARP-1) occurs when cells deficient in DNA repair are exposed to genotoxic agents; however, the function of this hyperactivation has not been adequately explained. Here, we examine PAR synthesis in mouse fibroblasts deficient in the base excision repair enzyme DNA polymerase β (pol β). The extent and duration of PARP-1 activation was measured after exposure to either the DNA alkylating agent, methyl methanesulfonate (MMS), or to low energy laser-induced DNA damage. There was strong DNA damage-induced hyperactivation of PARP-1 in pol β nullcells, but not in wild-type cells. In the case of MMS treatment, PAR synthesis did not lead to cell death in the pol β null cells, but instead resulted in increased PARylation of the nonhomologous end-joining (NHEJ) protein Ku70 and increased association of Ku70 with PARP-1. Inhibition of the NHEJ factor DNA-PK, under conditions of MMS-induced PARP-1 hyperactivation, enhanced necrotic cell death. These data suggest that PARP-1 hyperactivation is a protective mechanism triggering the classical-NHEJ DNA repair pathway when the primary alkylated base damage repair pathway is compromised.
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Affiliation(s)
- Natalie R. Gassman
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Donna F. Stefanick
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Padmini S. Kedar
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Julie K. Horton
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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69
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van Vuurden DG, Hulleman E, Meijer OLM, Wedekind LE, Kool M, Witt H, Vandertop PW, Würdinger T, Noske DP, Kaspers GJL, Cloos J. PARP inhibition sensitizes childhood high grade glioma, medulloblastoma and ependymoma to radiation. Oncotarget 2012; 2:984-96. [PMID: 22184287 PMCID: PMC3282104 DOI: 10.18632/oncotarget.362] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Poly ADP-ribose polymerase (PARP) is a protein involved in single strand break repair. Recently, PARP inhibitors have shown considerable promise in the treatment of several cancers, both in monotherapy and in combination with cytotoxic agents. Synthetic lethal action of PARP inhibitors has been observed in tumors with mutations in double strand break repair pathways. In addition, PARP inhibition potentially enhances sensitivity of tumor cells to DNA damaging agents, including radiotherapy. Aim of this study is to determine the radiosensitizing properties of the PARP inhibitor Olaparib in childhood medulloblastoma, ependymoma and high grade glioma (HGG). Increased PARP1 expression was observed in medulloblastoma, ependymoma and HGG, as compared to non-neoplastic brain tissue. Pediatric high grade glioma, medulloblastoma and ependymoma gene expression profiling revealed that high PARP1 expression is associated with poor prognosis. Cell growth inhibition assays with Olaparib resulted in differential sensitivity, with IC50 values ranging from 1.4 to 8.4 μM, irrespective of tumor type and PARP1 protein expression. Sensitization to radiation was observed in medulloblastoma, ependymoma and HGG cell lines with subcytotoxic concentrations of Olaparib, which coincided with persistence of double strand breaks. Combining PARP inhibitors with radiotherapy in clinical studies in childhood high grade brain tumors may improve therapeutic outcome.
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Affiliation(s)
- Dannis G van Vuurden
- Department of Pediatric Oncology / Hematology, Neuro-oncology Research Group, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.
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70
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Finn K, Lowndes NF, Grenon M. Eukaryotic DNA damage checkpoint activation in response to double-strand breaks. Cell Mol Life Sci 2012; 69:1447-73. [PMID: 22083606 PMCID: PMC11115150 DOI: 10.1007/s00018-011-0875-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 10/19/2011] [Accepted: 10/20/2011] [Indexed: 02/07/2023]
Abstract
Double-strand breaks (DSBs) are the most detrimental form of DNA damage. Failure to repair these cytotoxic lesions can result in genome rearrangements conducive to the development of many diseases, including cancer. The DNA damage response (DDR) ensures the rapid detection and repair of DSBs in order to maintain genome integrity. Central to the DDR are the DNA damage checkpoints. When activated by DNA damage, these sophisticated surveillance mechanisms induce transient cell cycle arrests, allowing sufficient time for DNA repair. Since the term "checkpoint" was coined over 20 years ago, our understanding of the molecular mechanisms governing the DNA damage checkpoint has advanced significantly. These pathways are highly conserved from yeast to humans. Thus, significant findings in yeast may be extrapolated to vertebrates, greatly facilitating the molecular dissection of these complex regulatory networks. This review focuses on the cellular response to DSBs in Saccharomyces cerevisiae, providing a comprehensive overview of how these signalling pathways function to orchestrate the cellular response to DNA damage and preserve genome stability in eukaryotic cells.
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Affiliation(s)
- Karen Finn
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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71
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De Vos M, Schreiber V, Dantzer F. The diverse roles and clinical relevance of PARPs in DNA damage repair: current state of the art. Biochem Pharmacol 2012; 84:137-46. [PMID: 22469522 DOI: 10.1016/j.bcp.2012.03.018] [Citation(s) in RCA: 368] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/19/2012] [Accepted: 03/22/2012] [Indexed: 12/17/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) catalyzed poly(ADP-ribosyl)ation is one of the earliest post-translational modification of proteins detectable at sites of DNA strand interruptions. The considerable recent progress in the science of PARP in the last decade and the discovery of a PARP superfamily (17 members) has introduced this modification as a key mechanism regulating a wide variety of cellular processes including among others transcription, regulation of chromatin dynamics, telomere homeostasis, differentiation and cell death. However, the most extensive studied and probably the best characterized role is in DNA repair where it plays pivotal roles in the processing and resolution of the damaged DNA. Although much of the focus has been on PARP1 in DNA repair, recent advances highlight the emergence of other DNA-dependent PARPs (i.e. PARP2, PARP3 and possibly Tankyrase) in this process. Here we will summarize the recent insights into the molecular functions of these PARPs in different DNA repair pathways in which they emerge as specific actors. Furthermore, the DNA repair functions of PARP1 have stimulated another area of intense research in the field with the development of potent and selective PARP1 inhibitors to promote genome instability and cell death in tumor cells. Their current use in clinical trials have demonstrated potentiation of antitumoral drugs and cytotoxicity in repair deficient tumor cells.
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Affiliation(s)
- Mike De Vos
- UMR7242-CNRS-Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg, bld. S. Brant, BP10413, 67412 Illkirch, France
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72
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Shao Z, Davis AJ, Fattah KR, So S, Sun J, Lee KJ, Harrison L, Yang J, Chen DJ. Persistently bound Ku at DNA ends attenuates DNA end resection and homologous recombination. DNA Repair (Amst) 2012; 11:310-6. [PMID: 22265216 DOI: 10.1016/j.dnarep.2011.12.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 10/24/2022]
Abstract
DNA double strand breaks (DSBs) are repaired by non-homologous end joining (NHEJ) or homologous recombination (HR). The DNA cell cycle stage and resection of the DSB ends are two key mechanisms which are believed to push DSB repair to the HR pathway. Here, we show that the NHEJ factor Ku80 associates with DSBs in S phase, when HR is thought to be the preferred repair pathway, and its dynamics/kinetics at DSBs is similar to those observed for Ku80 in non-S phase in mammalian cells. A Ku homolog from Mycobacterium tuberculosis binds to and is retained at DSBs in S phase and was used as a tool to determine if blocking DNA ends affects end resection and HR in mammalian cells. A decrease in DNA end resection, as marked by IR-induced RPA, BrdU, and Rad51 focus formation, and HR are observed when Ku deficient rodent cells are complemented with Mt-Ku. Together, this data suggests that Ku70/80 binds to DSBs in all cell cycle stages and is likely actively displaced from DSB ends to free the DNA ends for DNA end resection and thus HR to occur.
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Affiliation(s)
- Zhengping Shao
- Division of Molecular Radiation Biology, Department of Radiation Oncology, The University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, TX 75390, USA
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73
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Pears CJ, Couto CAM, Wang HY, Borer C, Kiely R, Lakin ND. The role of ADP-ribosylation in regulating DNA double-strand break repair. Cell Cycle 2012; 11:48-56. [PMID: 22186780 DOI: 10.4161/cc.11.1.18793] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
ADP-ribosylation is the post translational modification of proteins catalysed by ADP-ribosyltransferases (ARTs). ADP-ribosylation has been implicated in a wide variety of cellular processes including cell growth and differentiation, apoptosis and transcriptional regulation. Perhaps the best characterised role, however, is in DNA repair and genome stability where ADP-ribosylation promotes resolution of DNA single strand breaks. Although ADP-ribosylation also occurs at DNA double strand breaks (DSBs), which ARTs catalyse this reaction and the molecular basis of how this modification regulates their repair remains a matter of debate. Here we review recent advances in our understanding of how ADP-ribosylation regulates DSB repair. Specifically, we highlight studies using the genetic model organism Dictyostelium, in addition to vertebrate cells that identify a third ART that accelerates DSB repair by non-homologous end-joining through promoting the interaction of repair factors with DNA lesions. The implications of these data with regards to how ADP-ribosylation regulates DNA repair and genome stability are discussed.
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74
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Short B. PARP retains Ku at double-strand breaks. J Biophys Biochem Cytol 2011. [PMCID: PMC3153645 DOI: 10.1083/jcb.1943iti1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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