151
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Alkema NG, Wisman GBA, van der Zee AGJ, van Vugt MATM, de Jong S. Studying platinum sensitivity and resistance in high-grade serous ovarian cancer: Different models for different questions. Drug Resist Updat 2015; 24:55-69. [PMID: 26830315 DOI: 10.1016/j.drup.2015.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/04/2015] [Accepted: 11/19/2015] [Indexed: 12/21/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) has the highest mortality rate among all gynecological cancers. Patients are generally diagnosed in an advanced stage with the majority of cases displaying platinum resistant relapses. Recent genomic interrogation of large numbers of HGSOC patient samples indicated high complexity in terms of genetic aberrations, intra- and intertumor heterogeneity and underscored their lack of targetable oncogenic mutations. Sub-classifications of HGSOC based on expression profiles, termed 'differentiated', 'immunoreactive', 'mesenchymal' and 'proliferative', were shown to have prognostic value. In addition, in almost half of all HGSOC patients, a deficiency in homologous recombination (HR) was found that potentially can be targeted using PARP inhibitors. Developing precision medicine requires advanced experimental models. In the current review, we discuss experimental HGSOC models in which resistance to platinum therapy and the use of novel therapeutics can be carefully studied. Panels of better-defined primary cell lines need to be established to capture the full spectrum of HGSOC subtypes. Further refinement of cell lines is obtained with a 3-dimensional culture model mimicking the tumor microenvironment. Alternatively, ex vivo ovarian tumor tissue slices are used. For in vivo studies, larger panels of ovarian cancer patient-derived xenografts (PDXs) are being established, encompassing all expression subtypes. Ovarian cancer PDXs grossly retain tumor heterogeneity and clinical response to platinum therapy is preserved. PDXs are currently used in drug screens and as avatars for patient response. The role of the immune system in tumor responses can be assessed using humanized PDXs and immunocompetent genetically engineered mouse models. Dynamic tracking of genetic alterations in PDXs as well as patients during treatment and after relapse is feasible by sequencing circulating cell-free tumor DNA and analyzing circulating tumor cells. We discuss how various models and methods can be combined to delineate the molecular mechanisms underlying platinum resistance and to select HGSOC patients other than BRCA1/2-mutation carriers that could potentially benefit from the synthetic lethality of PARP inhibitors. This integrated approach is a first step to improve therapy outcomes in specific subgroups of HGSOC patients.
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Affiliation(s)
- Nicolette G Alkema
- Department of Gynecologic Oncology, Cancer Research Centre Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - G Bea A Wisman
- Department of Gynecologic Oncology, Cancer Research Centre Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecologic Oncology, Cancer Research Centre Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, Cancer Research Centre Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Centre Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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152
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Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic Acids Res 2015; 44:669-82. [PMID: 26490958 PMCID: PMC4737138 DOI: 10.1093/nar/gkv1080] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
The DNA damage checkpoint pathway is activated in response to DNA lesions and replication stress to preserve genome integrity. However, hyper-activation of this surveillance system is detrimental to the cell, because it might prevent cell cycle re-start after repair, which may also lead to senescence. Here we show that the scaffold proteins Slx4 and Rtt107 limit checkpoint signalling at a persistent double-strand DNA break (DSB) and at uncapped telomeres. We found that Slx4 is recruited within a few kilobases of an irreparable DSB, through the interaction with Rtt107 and the multi-BRCT domain scaffold Dpb11. In the absence of Slx4 or Rtt107, Rad9 binding near the irreparable DSB is increased, leading to robust checkpoint signalling and slower nucleolytic degradation of the 5′ strand. Importantly, in slx4Δ sae2Δ double mutant cells these phenotypes are exacerbated, causing a severe Rad9-dependent defect in DSB repair. Our study sheds new light on the molecular mechanism that coordinates the processing and repair of DSBs with DNA damage checkpoint signalling, preserving genome integrity.
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Affiliation(s)
- Diego Dibitetto
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Matteo Ferrari
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Chetan C Rawal
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Attila Balint
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - TaeHyung Kim
- Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Federica Marini
- Department of Biosciences, University of Milan, 20133, Milano, Italy
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153
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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154
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015; 5:1137-54. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [Citation(s) in RCA: 605] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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155
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Rif1 binds to G quadruplexes and suppresses replication over long distances. Nat Struct Mol Biol 2015; 22:889-97. [PMID: 26436827 DOI: 10.1038/nsmb.3102] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022]
Abstract
Rif1 regulates replication timing and repair of double-strand DNA breaks. Using a chromatin immunoprecipitation-sequencing method, we identified 35 high-affinity Rif1-binding sites in fission yeast chromosomes. Binding sites tended to be located near dormant origins and to contain at least two copies of a conserved motif, CNWWGTGGGGG. Base substitution within these motifs resulted in complete loss of Rif1 binding and in activation of late-firing or dormant origins located up to 50 kb away. We show that Rif1-binding sites adopt G quadruplex-like structures in vitro, in a manner dependent on the conserved sequence and on other G tracts, and that purified Rif1 preferentially binds to this structure. These results suggest that Rif1 recognizes and binds G quadruplex-like structures at selected intergenic regions, thus generating local chromatin structures that may exert long-range suppressive effects on origin firing.
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156
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Castella M, Jacquemont C, Thompson EL, Yeo JE, Cheung RS, Huang JW, Sobeck A, Hendrickson EA, Taniguchi T. FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2. PLoS Genet 2015; 11:e1005563. [PMID: 26430909 PMCID: PMC4592014 DOI: 10.1371/journal.pgen.1005563] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
The Fanconi anemia (FA)-BRCA pathway mediates repair of DNA interstrand crosslinks. The FA core complex, a multi-subunit ubiquitin ligase, participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins, FANCD2 and FANCI (or the ID complex). However, the regulation of the FA core complex itself is poorly understood. Here we show that the FA core complex proteins are recruited to sites of DNA damage and form nuclear foci in S and G2 phases of the cell cycle. ATR kinase activity, an intact FA core complex and FANCM-FAAP24 were crucial for this recruitment. Surprisingly, FANCI, but not its partner FANCD2, was needed for efficient FA core complex foci formation. Monoubiquitination or ATR-dependent phosphorylation of FANCI were not required for the FA core complex recruitment, but FANCI deubiquitination by USP1 was. Additionally, BRCA1 was required for efficient FA core complex foci formation. These findings indicate that FANCI functions upstream of FA core complex recruitment independently of FANCD2, and alter the current view of the FA-BRCA pathway. Fanconi anemia is a genetic disease characterized by bone marrow failure, congenital malformations and cancer predisposition. Cells derived from Fanconi anemia patients have a dysfunctional FA-BRCA pathway and are deficient in the repair of a specific form of DNA damage, DNA interstrand-crosslinks, that are induced by certain chemotherapeutic drugs. Therefore, the study of FA-BRCA pathway regulation is essential for developing new treatments for Fanconi anemia patients and cancer patients in general. One of the first steps in the pathway is the detection of DNA lesions by the FA core complex. We have optimized a method to visualize the recruitment of the FA core complex to sites of DNA damage and, for the first time, explored how this process occurs. We have uncovered several factors that are required for this recruitment. Among them is a FA core complex substrate, FANCI. We report that non-phosphorylated FANCI, previously believed to be an inactive form, has an important role in the recruitment of the FA core complex and DNA interstrand-crosslink repair. Our findings change the current view of the FA-BRCA pathway and have implications for potential clinical strategies aimed at activating or inhibiting the FA-BRCA pathway.
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Affiliation(s)
- Maria Castella
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Celine Jacquemont
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elizabeth L. Thompson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Jung Eun Yeo
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Ronald S. Cheung
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jen-Wei Huang
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alexandra Sobeck
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Eric A. Hendrickson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Toshiyasu Taniguchi
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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157
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Saquilabon Cruz GM, Kong X, Silva BA, Khatibzadeh N, Thai R, Berns MW, Yokomori K. Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites. Nucleic Acids Res 2015; 44:e27. [PMID: 26424850 PMCID: PMC4756852 DOI: 10.1093/nar/gkv976] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023] Open
Abstract
Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affect the amounts and types of damage and the DDR. We compared different irradiation conditions using a femtosecond near-infrared laser and found distinct damage site recruitment thresholds for 53BP1 and TRF2 correlating with the dose-dependent increase of strand breaks and damage complexity. Low input-power microirradiation that induces relatively simple strand breaks led to robust recruitment of 53BP1 but not TRF2. In contrast, increased strand breaks with complex damage including crosslinking and base damage generated by high input-power microirradiation resulted in TRF2 recruitment to damage sites with no 53BP1 clustering. We found that poly(ADP-ribose) polymerase (PARP) activation distinguishes between the two damage states and that PARP activation is essential for rapid TRF2 recruitment while suppressing 53BP1 accumulation at damage sites. Thus, our results reveal that careful titration of laser irradiation conditions allows induction of varying amounts and complexities of DNA damage that are gauged by differential PARP activation regulating protein assembly at the damage site.
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Affiliation(s)
- Gladys Mae Saquilabon Cruz
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Bárbara Alcaraz Silva
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92617, USA
| | - Nima Khatibzadeh
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA
| | - Ryan Thai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Michael W Berns
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92617, USA Department of Biomedical Engineering and Surgery, University of California, Irvine, CA 92617, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
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158
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Hengeveld RCC, de Boer HR, Schoonen PM, de Vries EGE, Lens SMA, van Vugt MATM. Rif1 Is Required for Resolution of Ultrafine DNA Bridges in Anaphase to Ensure Genomic Stability. Dev Cell 2015; 34:466-74. [PMID: 26256213 DOI: 10.1016/j.devcel.2015.06.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 05/21/2015] [Accepted: 06/16/2015] [Indexed: 12/27/2022]
Abstract
Sister-chromatid disjunction in anaphase requires the resolution of DNA catenanes by topoisomerase II together with Plk1-interacting checkpoint helicase (PICH) and Bloom's helicase (BLM). We here identify Rif1 as a factor involved in the resolution of DNA catenanes that are visible as ultrafine DNA bridges (UFBs) in anaphase to which PICH and BLM localize. Rif1, which during interphase functions downstream of 53BP1 in DNA repair, is recruited to UFBs in a PICH-dependent fashion, but independently of 53BP1 or BLM. Similar to PICH and BLM, Rif1 promotes the resolution of UFBs: its depletion increases the frequency of nucleoplasmic bridges and RPA70-positive UFBs in late anaphase. Moreover, in the absence of Rif1, PICH, or BLM, more nuclear bodies with damaged DNA arise in ensuing G1 cells, when chromosome decatenation is impaired. Our data reveal a thus far unrecognized function for Rif1 in the resolution of UFBs during anaphase to protect genomic integrity.
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Affiliation(s)
- Rutger C C Hengeveld
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - H Rudolf de Boer
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9723 GZ Groningen, the Netherlands
| | - Pepijn M Schoonen
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9723 GZ Groningen, the Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9723 GZ Groningen, the Netherlands
| | - Susanne M A Lens
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9723 GZ Groningen, the Netherlands
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159
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Feng L, Li N, Li Y, Wang J, Gao M, Wang W, Chen J. Cell cycle-dependent inhibition of 53BP1 signaling by BRCA1. Cell Discov 2015; 1:15019. [PMID: 27462418 PMCID: PMC4860855 DOI: 10.1038/celldisc.2015.19] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/25/2015] [Indexed: 02/07/2023] Open
Abstract
DNA damage response mediator protein 53BP1 is a key regulator of non-homologous end-joining (NHEJ) repair. 53BP1 protects DNA broken ends from resection by recruiting two downstream factors, RIF1 (RAP1-interacting factor 1) and PTIP (Pax transactivation domain-interacting protein), to double-stranded breaks (DSBs) via ATM (ataxia telangiectasia mutated)-mediated 53BP1 phosphorylation, and competes with BRCA1-mediated homologous recombination (HR) repair in G1 phase. In contrast, BRCA1 antagonizes 53BP1-direct NHEJ repair in S/G2 phases. We and others have found that BRCA1 prevents the translocation of RIF1 to DSBs in S/G2 phases; however, the underlying mechanism remains unclear. Here we show that efficient ATM-dependent 53BP1 phosphorylation is restricted to the G1 phase of the cell cycle, as a consequence RIF1 and PTIP accumulation at DSB sites only occur in G1 phase. Mechanistically, both BRCT and RING domains of BRCA1 are required for the inhibition of 53BP1 phosphorylation in S and G2 phases. Thus, our findings reveal how BRCA1 antagonizes 53BP1 signaling to ensure that HR repair is the dominant repair pathway in S/G2 phases.
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Affiliation(s)
- Lin Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Nan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center , Houston, TX, USA
| | - Yujing Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; State Key Laboratory for Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiadong Wang
- Institute of Systems Biomedicine, Medical Isotopes Research Center, School of Basic Medical Sciences, Peking University , Beijing, China
| | - Min Gao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center , Houston, TX, USA
| | - Wenqi Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center , Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center , Houston, TX, USA
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160
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Ahn JW, Kim S, Na W, Baek SJ, Kim JH, Min K, Yeom J, Kwak H, Jeong S, Lee C, Kim SY, Choi CY. SERBP1 affects homologous recombination-mediated DNA repair by regulation of CtIP translation during S phase. Nucleic Acids Res 2015; 43:6321-33. [PMID: 26068472 PMCID: PMC4513868 DOI: 10.1093/nar/gkv592] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 05/13/2015] [Accepted: 05/24/2015] [Indexed: 11/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are the most severe type of DNA damage and are primarily repaired by non-homologous end joining (NHEJ) and homologous recombination (HR) in the G1 and S/G2 phase, respectively. Although CtBP-interacting protein (CtIP) is crucial in DNA end resection during HR following DSBs, little is known about how CtIP levels increase in an S phase-specific manner. Here, we show that Serpine mRNA binding protein 1 (SERBP1) regulates CtIP expression at the translational level in S phase. In response to camptothecin-mediated DNA DSBs, CHK1 and RPA2 phosphorylation, which are hallmarks of HR activation, was abrogated in SERBP1-depleted cells. We identified CtIP mRNA as a binding target of SERBP1 using RNA immunoprecipitation-coupled RNA sequencing, and confirmed SERBP1 binding to CtIP mRNA in S phase. SERBP1 depletion resulted in reduction of polysome-associated CtIP mRNA and concomitant loss of CtIP expression in S phase. These effects were reversed by reconstituting cells with wild-type SERBP1, but not by SERBP1 ΔRGG, an RNA binding defective mutant, suggesting regulation of CtIP translation by SERBP1 association with CtIP mRNA. These results indicate that SERBP1 affects HR-mediated DNA repair in response to DNA DSBs by regulation of CtIP translation in S phase.
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Affiliation(s)
- Jang-Won Ahn
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Sunjik Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Wooju Na
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Su-Jin Baek
- Human Genomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea Department of Functional Genomics, University of Science of Technology, Daejeon 305-350, Republic of Korea
| | - Jeong-Hwan Kim
- Human Genomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Keehong Min
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Jeonghun Yeom
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Hoyun Kwak
- Department of Molecular Biology, Dankook University, Yongin 448-701, Republic of Korea
| | - Sunjoo Jeong
- Department of Molecular Biology, Dankook University, Yongin 448-701, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Seon-Young Kim
- Human Genomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea Department of Functional Genomics, University of Science of Technology, Daejeon 305-350, Republic of Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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161
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Alagoz M, Katsuki Y, Ogiwara H, Ogi T, Shibata A, Kakarougkas A, Jeggo P. SETDB1, HP1 and SUV39 promote repositioning of 53BP1 to extend resection during homologous recombination in G2 cells. Nucleic Acids Res 2015. [PMID: 26206670 PMCID: PMC4652757 DOI: 10.1093/nar/gkv722] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent studies have shown that homologous recombination (HR) requires chromatin repression as well as relaxation at DNA double strand breaks (DSBs). HP1 and SUV39H1/2 are repressive factors essential for HR. Here, we identify SETDB1 as an additional compacting factor promoting HR. Depletion of HP1, SUV39, SETDB1 or BRCA1 confer identical phenotypes. The repressive factors, like BRCA1, are dispensable for the initiation of resection but promote the extension step causing diminished RPA or RAD51 foci and HR in irradiated G2 cells. Depletion of the compacting factors does not inhibit BRCA1 recruitment but at 8 h post IR, BRCA1 foci are smaller and aberrantly positioned compared to control cells. BRCA1 promotes 53BP1 repositioning to the periphery of enlarged foci and formation of a devoid core with BRCA1 becoming enlarged and localized internally to 53BP1. Depletion of the compacting factors precludes these changes at irradiation-induced foci. Thus, the repressive factors are required for BRCA1 function in promoting the repositioning of 53BP1 during HR. Additionally, depletion of these repressive factors in undamaged cells causes diminished sister chromatid association at centromeric sequences. We propose a model for how these findings may be functionally linked.
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Affiliation(s)
- Meryem Alagoz
- University of Sussex Genome Damage and Stability Centre, East Sussex, BN19RQ, UK
| | - Yoko Katsuki
- University of Sussex Genome Damage and Stability Centre, East Sussex, BN19RQ, UK
| | - Hideaki Ogiwara
- Division of Genome Biology, National Cancer Centre Japan Research Institute, Tokyo, 104-0045, Japan
| | - Tomoo Ogi
- Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Atsushi Shibata
- University of Sussex Genome Damage and Stability Centre, East Sussex, BN19RQ, UK
| | - Andreas Kakarougkas
- University of Sussex Genome Damage and Stability Centre, East Sussex, BN19RQ, UK Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, 11835, Egypt
| | - Penny Jeggo
- University of Sussex Genome Damage and Stability Centre, East Sussex, BN19RQ, UK
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162
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Sreesankar E, Bharathi V, Mishra RK, Mishra K. Drosophila Rif1 is an essential gene and controls late developmental events by direct interaction with PP1-87B. Sci Rep 2015; 5:10679. [PMID: 26022086 PMCID: PMC4448129 DOI: 10.1038/srep10679] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/16/2015] [Indexed: 11/24/2022] Open
Abstract
Rif1, identified as a regulator of telomerase in yeast, is an evolutionarily conserved protein and functions in diverse processes including telomere length regulation, epigenetic gene regulation, anti-checkpoint activity, DNA repair and establishing timing of firing at replication origins. Previously we had identified that all Rif1 homologues have PP1 interacting SILK-RVxF motif. In the present study, we show that Drosophila Rif1 is essential for normal fly development and loss of dRif1 impairs temporal regulation of initiation of DNA replication. In multiple tissues dRif1 colocalizes with HP1, a protein known to orchestrate timing of replication in fly. dRif1 associates with chromosomes in a mitotic stage-dependent manner coinciding with dephosphorylation of histones. Ectopic expression of dRif1 causes enlarged larval imaginal discs and early pupal lethality which is completely reversed by co-expression of PP1 87B, the major protein phosphatase in Drosophila, indicating genetic and functional interaction. These findings suggest that dRif1 is an adaptor for PP1 and functions by recruiting PP1 to multiple sites on the chromosome.
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Affiliation(s)
- Easwaran Sreesankar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad- 500 046, INDIA
| | | | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal road, Hyderabad-500 007, INDIA
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad- 500 046, INDIA
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163
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Replication stress in Mammalian cells and its consequences for mitosis. Genes (Basel) 2015; 6:267-98. [PMID: 26010955 PMCID: PMC4488665 DOI: 10.3390/genes6020267] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
The faithful transmission of genetic information to daughter cells is central to maintaining genomic stability and relies on the accurate and complete duplication of genetic material during each cell cycle. However, the genome is routinely exposed to endogenous and exogenous stresses that can impede the progression of replication. Such replication stress can be an early cause of cancer or initiate senescence. Replication stress, which primarily occurs during S phase, results in consequences during mitosis, jeopardizing chromosome segregation and, in turn, genomic stability. The traces of replication stress can be detected in the daughter cells during G1 phase. Alterations in mitosis occur in two types: 1) local alterations that correspond to breaks, rearrangements, intertwined DNA molecules or non-separated sister chromatids that are confined to the region of the replication dysfunction; 2) genome-wide chromosome segregation resulting from centrosome amplification (although centrosomes do not contain DNA), which amplifies the local replication stress to the entire genome. Here, we discuss the endogenous causes of replication perturbations, the mechanisms of replication fork restart and the consequences for mitosis, chromosome segregation and genomic stability.
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164
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Zhang D, Zhang X, Zeng M, Yuan J, Liu M, Yin Y, Wu X, Keefe DL, Liu L. Increased DNA damage and repair deficiency in granulosa cells are associated with ovarian aging in rhesus monkey. J Assist Reprod Genet 2015; 32:1069-78. [PMID: 25957622 DOI: 10.1007/s10815-015-0483-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/13/2015] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Ovarian aging is closely tied to the decline in ovarian follicular reserve and oocyte quality. During the prolonged reproductive lifespan of the female, granulosa cells connected with oocytes play critical roles in maintaining follicle reservoir, oocyte growth and follicular development. We tested whether double-strand breaks (DSBs) and repair in granulosa cells within the follicular reservoir are associated with ovarian aging. METHODS Ovaries were sectioned and processed for epi-fluorescence microscopy, confocal microscopy, and immunohistochemistry. DNA damage was revealed by immunstaining of γH2AX foci and telomere damage by γH2AX foci co-localized with telomere associated protein TRF2. DNA repair was indicated by BRCA1 immunofluorescence. RESULTS DSBs in granulosa cells increase and DSB repair ability, characterized by BRCA1 foci, decreases with advancing age. γH2AX foci increase in primordial, primary and secondary follicles with advancing age. Likewise, telomere damage increases with advancing age. In contrast, BRCA1 foci in granulosa cells of primordial, primary and secondary follicles decrease with monkey age. BRCA1 positive foci in the oocyte nuclei also decline with maternal age. CONCLUSIONS Increased DSBs and reduced DNA repair in granulosa cells may contribute to ovarian aging. Discovery of therapeutics that targets these pathways might help maintain follicle reserve and postpone ovarian dysfunction with age.
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Affiliation(s)
- Dongdong Zhang
- State Key Laboratory of Medicinal Chemical Biology; Collaborative Innovation Center for Biotherapy, College of Life Sciences, Nankai University, Tianjin, 300071, China
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165
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Abstract
DNA double-strand breaks (DSBs) in cells can undergo nucleolytic degradation to generate long 3' single-stranded DNA tails. This process is termed DNA end resection, and its occurrence effectively commits to break repair via homologous recombination, which entails the acquisition of genetic information from an intact, homologous donor DNA sequence. Recent advances, prompted by the identification of the nucleases that catalyze resection, have revealed intricate layers of functional redundancy, interconnectedness, and regulation. Here, we review the current state of the field with an emphasis on the major questions that remain to be answered. Topics addressed will include how resection initiates via the introduction of an endonucleolytic incision close to the break end, the molecular mechanism of the conserved MRE11 complex in conjunction with Sae2/CtIP within such a model, the role of BRCA1 and 53BP1 in regulating resection initiation in mammalian cells, the influence of chromatin in the resection process, and potential roles of novel factors.
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Affiliation(s)
- James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
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166
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Zong D, Callén E, Pegoraro G, Lukas C, Lukas J, Nussenzweig A. Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining. Nucleic Acids Res 2015; 43:4950-61. [PMID: 25916843 PMCID: PMC4446425 DOI: 10.1093/nar/gkv336] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/01/2015] [Indexed: 11/13/2022] Open
Abstract
DNA double strand breaks (DSBs) formed during S phase are preferentially repaired by homologous recombination (HR), whereas G1 DSBs, such as those occurring during immunoglobulin class switch recombination (CSR), are repaired by non-homologous end joining (NHEJ). The DNA damage response proteins 53BP1 and BRCA1 regulate the balance between NHEJ and HR. 53BP1 promotes CSR in part by mediating synapsis of distal DNA ends, and in addition, inhibits 5’ end resection. BRCA1 antagonizes 53BP1 dependent DNA end-blocking activity during S phase, which would otherwise promote mutagenic NHEJ and genome instability. Recently, it was shown that supra-physiological levels of the E3 ubiquitin ligase RNF168 results in the hyper-accumulation of 53BP1/BRCA1 which accelerates DSB repair. Here, we ask whether increased expression of RNF168 or 53BP1 impacts physiological versus mutagenic NHEJ. We find that the anti-resection activities of 53BP1 are rate-limiting for mutagenic NHEJ but not for physiological CSR. As heterogeneity in the expression of RNF168 and 53BP1 is found in human tumors, our results suggest that deregulation of the RNF168/53BP1 pathway could alter the chemosensitivity of BRCA1 deficient tumors.
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Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - Elsa Callén
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Center for Cancer Research, National Cancer Institute; National Institute of Health, Bethesda, MD 20892, USA
| | - Claudia Lukas
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Jiri Lukas
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - André Nussenzweig
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
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167
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Lin YH, Yuan J, Pei H, Liu T, Ann DK, Lou Z. KAP1 Deacetylation by SIRT1 Promotes Non-Homologous End-Joining Repair. PLoS One 2015; 10:e0123935. [PMID: 25905708 PMCID: PMC4408008 DOI: 10.1371/journal.pone.0123935] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/09/2015] [Indexed: 01/13/2023] Open
Abstract
Homologous recombination and non-homologous end joining are two major DNA double-strand-break repair pathways. While HR-mediated repair requires a homologous sequence as the guiding template to restore the damage site precisely, NHEJ-mediated repair ligates the DNA lesion directly and increases the risk of losing nucleotides. Therefore, how a cell regulates the balance between HR and NHEJ has become an important issue for maintaining genomic integrity over time. Here we report that SIRT1-dependent KAP1 deacetylation positively regulates NHEJ. We show that up-regulation of KAP1 attenuates HR efficiency while promoting NHEJ repair. Moreover, SIRT1-mediated KAP1 deacetylation further enhances the effect of NHEJ by stabilizing its interaction with 53BP1, which leads to increased 53BP1 focus formation in response to DNA damage. Taken together, our study suggests a SIRT1-KAP1 regulatory mechanism for HR-NHEJ repair pathway choice.
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Affiliation(s)
- Yi-Hui Lin
- Department of Biochemistry and Molecular Biology, Mayo Graduate School, Rochester, Minnesota, United States of America
| | - Jian Yuan
- Research Center for Translational Medicine, Tongji University School of Medicine, Shanghai, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huadong Pei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Tongzheng Liu
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - David K. Ann
- Department of Molecular Pharmacology and Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Zhenkun Lou
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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168
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Prakash R, Zhang Y, Feng W, Jasin M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol 2015; 7:a016600. [PMID: 25833843 DOI: 10.1101/cshperspect.a016600] [Citation(s) in RCA: 561] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks in mammalian cells, the defining step of which is homologous strand exchange directed by the RAD51 protein. The physiological importance of HR is underscored by the observation of genomic instability in HR-deficient cells and, importantly, the association of cancer predisposition and developmental defects with mutations in HR genes. The tumor suppressors BRCA1 and BRCA2, key players at different stages of HR, are frequently mutated in familial breast and ovarian cancers. Other HR proteins, including PALB2 and RAD51 paralogs, have also been identified as tumor suppressors. This review summarizes recent findings on BRCA1, BRCA2, and associated proteins involved in human disease with an emphasis on their molecular roles and interactions.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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169
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Batenburg NL, Thompson EL, Hendrickson EA, Zhu XD. Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation. EMBO J 2015; 34:1399-416. [PMID: 25820262 DOI: 10.15252/embj.201490041] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 03/11/2015] [Indexed: 11/09/2022] Open
Abstract
Mutations of CSB account for the majority of Cockayne syndrome (CS), a devastating hereditary disorder characterized by physical impairment, neurological degeneration and segmental premature aging. Here we report the generation of a human CSB-knockout cell line. We find that CSB facilitates HR and represses NHEJ. Loss of CSB or a CS-associated CSB mutation abrogating its ATPase activity impairs the recruitment of BRCA1, RPA and Rad51 proteins to damaged chromatin but promotes the formation of 53BP1-Rif1 damage foci in S and G2 cells. Depletion of 53BP1 rescues the formation of BRCA1 damage foci in CSB-knockout cells. In addition, knockout of CSB impairs the ATM- and Chk2-mediated DNA damage responses, promoting a premature entry into mitosis. Furthermore, we show that CSB accumulates at sites of DNA double-strand breaks (DSBs) in a transcription-dependent manner. The kinetics of DSB-induced chromatin association of CSB is distinct from that of its UV-induced chromatin association. These results reveal novel, important functions of CSB in regulating the DNA DSB repair pathway choice as well as G2/M checkpoint activation.
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Affiliation(s)
| | - Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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170
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Krajewska M, Fehrmann RSN, de Vries EGE, van Vugt MATM. Regulators of homologous recombination repair as novel targets for cancer treatment. Front Genet 2015; 6:96. [PMID: 25852742 PMCID: PMC4367534 DOI: 10.3389/fgene.2015.00096] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/23/2015] [Indexed: 12/20/2022] Open
Abstract
To cope with DNA damage, cells possess a complex signaling network called the ‘DNA damage response’, which coordinates cell cycle control with DNA repair. The importance of this network is underscored by the cancer predisposition that frequently goes along with hereditary mutations in DNA repair genes. One especially important DNA repair pathway in this respect is homologous recombination (HR) repair. Defects in HR repair are observed in various cancers, including hereditary breast, and ovarian cancer. Intriguingly, tumor cells with defective HR repair show increased sensitivity to chemotherapeutic reagents, including platinum-containing agents. These observations suggest that HR-proficient tumor cells might be sensitized to chemotherapeutics if HR repair could be therapeutically inactivated. HR repair is an extensively regulated process, which depends strongly on the activity of various other pathways, including cell cycle pathways, protein-control pathways, and growth factor-activated receptor signaling pathways. In this review, we discuss how the mechanistic wiring of HR is controlled by cell-intrinsic or extracellular pathways. Furthermore, we have performed a meta-analysis on available genome-wide RNA interference studies to identify additional pathways that control HR repair. Finally, we discuss how these HR-regulatory pathways may provide therapeutic targets in the context of radio/chemosensitization.
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Affiliation(s)
- Małgorzata Krajewska
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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171
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Wang J, Aroumougame A, Lobrich M, Li Y, Chen D, Chen J, Gong Z. PTIP associates with Artemis to dictate DNA repair pathway choice. Genes Dev 2015; 28:2693-8. [PMID: 25512557 PMCID: PMC4265673 DOI: 10.1101/gad.252478.114] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PARP inhibitors (PARPi) are being used in patients with BRCA1/2 mutations; however, doubly deficient BRCA1−/−53BP1−/− tumors become resistant to PARPis. 53BP1 and its known downstream effectors, PTIP and RIF1, lack enzymatic activities directly implicated in DNA repair. Wang et al. uncovered a nuclease, Artemis, as a PTIP-binding protein that trims DNA ends, promotes NHEJ, and directly competes with the HR repair pathway. Loss of Artemis restores PARPi resistance in BRCA1-deficient cells. PARP inhibitors (PARPis) are being used in patients with BRCA1/2 mutations. However, doubly deficient BRCA1−/−53BP1−/− cells or tumors become resistant to PARPis. Since 53BP1 or its known downstream effectors, PTIP and RIF1 (RAP1-interacting factor 1 homolog), lack enzymatic activities directly implicated in DNA repair, we decided to further explore the 53BP1-dependent pathway. In this study, we uncovered a nuclease, Artemis, as a PTIP-binding protein. Loss of Artemis restores PARPi resistance in BRCA1-deficient cells. Collectively, our data demonstrate that Artemis is the major downstream effector of the 53BP1 pathway, which prevents end resection and promotes nonhomologous end-joining and therefore directly competes with the homologous recombination repair pathway.
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Affiliation(s)
- Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Asaithamby Aroumougame
- Department of Radiation Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Markus Lobrich
- Radiation Biology and DNA Repair Laboratory, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Yujing Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Chen
- Department of Radiation Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA;
| | - Zihua Gong
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA;
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172
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Badie S, Carlos AR, Folio C, Okamoto K, Bouwman P, Jonkers J, Tarsounas M. BRCA1 and CtIP promote alternative non-homologous end-joining at uncapped telomeres. EMBO J 2015; 34:410-24. [PMID: 25582120 PMCID: PMC4339125 DOI: 10.15252/embj.201488947] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 10/29/2014] [Accepted: 11/25/2014] [Indexed: 12/15/2022] Open
Abstract
Loss of telomere protection occurs during physiological cell senescence and ageing, due to attrition of telomeric repeats and insufficient retention of the telomere-binding factor TRF2. Subsequently formed telomere fusions trigger rampant genomic instability leading to cell death or tumorigenesis. Mechanistically, telomere fusions require either the classical non-homologous end-joining (C-NHEJ) pathway dependent on Ku70/80 and LIG4, or the alternative non-homologous end-joining (A-NHEJ), which relies on PARP1 and LIG3. Here, we show that the tumour suppressor BRCA1, together with its interacting partner CtIP, both acting in end resection, also promotes end-joining of uncapped telomeres. BRCA1 and CtIP do not function in the ATM-dependent telomere damage signalling, nor in telomere overhang removal, which are critical for telomere fusions by C-NHEJ. Instead, BRCA1 and CtIP act in the same pathway as LIG3 to promote joining of de-protected telomeres by A-NHEJ. Our work therefore ascribes novel roles for BRCA1 and CtIP in end-processing and fusion reactions at uncapped telomeres, underlining the complexity of DNA repair pathways that act at chromosome ends lacking protective structures. Moreover, A-NHEJ provides a mechanism of previously unanticipated significance in telomere dysfunction-induced genome instability.
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Affiliation(s)
- Sophie Badie
- Telomere and Genome Stability Group, The CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Oxford, UK
| | - Ana Rita Carlos
- Telomere and Genome Stability Group, The CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Oxford, UK
| | - Cecilia Folio
- Telomere and Genome Stability Group, The CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Oxford, UK
| | - Keiji Okamoto
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter Bouwman
- Division of Molecular Pathology and Cancer Systems Biology Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Systems Biology Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Madalena Tarsounas
- Telomere and Genome Stability Group, The CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Oxford, UK
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173
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Wu W, Nishikawa H, Fukuda T, Vittal V, Asano M, Miyoshi Y, Klevit RE, Ohta T. Interaction of BARD1 and HP1 Is Required for BRCA1 Retention at Sites of DNA Damage. Cancer Res 2015; 75:1311-21. [PMID: 25634209 DOI: 10.1158/0008-5472.can-14-2796] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/31/2014] [Indexed: 12/12/2022]
Abstract
Stable retention of BRCA1/BARD1 complexes at sites of DNA damage is required for the proper response to DNA double-strand breaks (DSB). Here, we demonstrate that the BRCT domain of BARD1 is crucial for its retention through interaction with HP1. In response to DNA damage, BARD1 interacts with Lys9-dimethylated histone H3 (H3K9me2) in an ATM-dependent but RNF168-independent manner. This interaction is mediated primarily by HP1γ. A conserved HP1-binding motif in the BARD1 BRCT domain directly interacted with the chromoshadow domain of HP1 in vitro. Mutations in this motif (or simultaneous depletion of all three HP1 isoforms) disrupted retention of BARD1, BRCA1, and CtIP at DSB sites and allowed ectopic accumulation of RIF1, an effector of nonhomologous end-joining, at damaged loci in S-phase. UNC0638, a small-molecule inhibitor of histone lysine methyltransferase (HKMT), abolished retention and cooperated with the PARP inhibitor olaparib to block cancer cell growth. Taken together, our findings show how BARD1 promotes retention of the BRCA1/BARD1 complex at damaged DNA sites and suggest the use of HKMT inhibitors to leverage the application of PARP inhibitors to treat breast cancer.
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Affiliation(s)
- Wenwen Wu
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan. Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Hiroyuki Nishikawa
- Institute of Advanced Medical Science, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Takayo Fukuda
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Vinayak Vittal
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Masahide Asano
- Divisions of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Yasuo Miyoshi
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Hyogo, Japan
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan. Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, Japan.
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174
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Xiong X, Du Z, Wang Y, Feng Z, Fan P, Yan C, Willers H, Zhang J. 53BP1 promotes microhomology-mediated end-joining in G1-phase cells. Nucleic Acids Res 2015; 43:1659-70. [PMID: 25586219 PMCID: PMC4330367 DOI: 10.1093/nar/gku1406] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alternative non-homologous end joining (alt-NHEJ) was originally identified as a backup repair mechanism in the absence of classical NHEJ (c-NHEJ) factors but recent studies have demonstrated that alt-NHEJ is active even when c-NHEJ as well as homologous recombination is available. The functions of 53BP1 in NHEJ processes are not well understood. Here, we report that 53BP1 promotes DNA double-strand break (DSB) repair and genomic stability not only in c-NHEJ-proficient but also -deficient human G1-phase cells. Using an array of repair substrates we show that these effects of 53BP1 are correlated with a promotion of microhomology-mediated end-joining (MMEJ), a subtype of alt-NHEJ, in G1-phase. Consistent with a specific role in MMEJ we confirm that 53BP1 status does not affect c-NHEJ. 53BP1 supports sequence deletion during MMEJ consistent with a putative role in facilitating end-resection. Interestingly, promotion of MMEJ by 53BP1 in G1-phase cells is only observed in the presence of functional BRCA1. Depletion of both 53BP1 and BRCA1 increases repair needing microhomology usage and augments loss of DNA sequence, suggesting that MMEJ is a highly regulated DSB repair process. Together, these findings significantly expand our understanding of the cell-cycle-dependent roles of 53BP1 in DSB repair.
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Affiliation(s)
- Xiahui Xiong
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, BRB 323, Cleveland, OH 44106, USA
| | - Zhanwen Du
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, BRB 323, Cleveland, OH 44106, USA
| | - Ying Wang
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, BRB 323, Cleveland, OH 44106, USA
| | - Zhihui Feng
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, BRB 323, Cleveland, OH 44106, USA
| | - Pan Fan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine,1650 Orleans Street, Baltimore, MD 21231, USA
| | - Chunhong Yan
- Department of Biochemistry and Molecular Biology, Georgia Regents University, 1410 Laney Walker Blvd., CN-2134, Augusta, GA 30912, USA
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Junran Zhang
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, BRB 323, Cleveland, OH 44106, USA
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175
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Ferrari M, Dibitetto D, De Gregorio G, Eapen VV, Rawal CC, Lazzaro F, Tsabar M, Marini F, Haber JE, Pellicioli A. Functional interplay between the 53BP1-ortholog Rad9 and the Mre11 complex regulates resection, end-tethering and repair of a double-strand break. PLoS Genet 2015; 11:e1004928. [PMID: 25569305 PMCID: PMC4287487 DOI: 10.1371/journal.pgen.1004928] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/30/2014] [Indexed: 12/29/2022] Open
Abstract
The Mre11-Rad50-Xrs2 nuclease complex, together with Sae2, initiates the 5'-to-3' resection of Double-Strand DNA Breaks (DSBs). Extended 3' single stranded DNA filaments can be exposed from a DSB through the redundant activities of the Exo1 nuclease and the Dna2 nuclease with the Sgs1 helicase. In the absence of Sae2, Mre11 binding to a DSB is prolonged, the two DNA ends cannot be kept tethered, and the DSB is not efficiently repaired. Here we show that deletion of the yeast 53BP1-ortholog RAD9 reduces Mre11 binding to a DSB, leading to Rad52 recruitment and efficient DSB end-tethering, through an Sgs1-dependent mechanism. As a consequence, deletion of RAD9 restores DSB repair either in absence of Sae2 or in presence of a nuclease defective MRX complex. We propose that, in cells lacking Sae2, Rad9/53BP1 contributes to keep Mre11 bound to a persistent DSB, protecting it from extensive DNA end resection, which may lead to potentially deleterious DNA deletions and genome rearrangements.
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Affiliation(s)
- Matteo Ferrari
- Department of Biosciences, University of Milan, Milano, Italy
| | - Diego Dibitetto
- Department of Biosciences, University of Milan, Milano, Italy
| | | | - Vinay V Eapen
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Chetan C Rawal
- Department of Biosciences, University of Milan, Milano, Italy
| | | | - Michael Tsabar
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Federica Marini
- Department of Biosciences, University of Milan, Milano, Italy
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
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176
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Li P, Ma X, Adams IR, Yuan P. A tight control of Rif1 by Oct4 and Smad3 is critical for mouse embryonic stem cell stability. Cell Death Dis 2015; 6:e1588. [PMID: 25569105 PMCID: PMC4669749 DOI: 10.1038/cddis.2014.551] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/03/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Prolonged culture of embryonic stem cells (ESCs) leads them to adopt embryonal carcinoma cell features, creating enormous dangers for their further application. The mechanism involved in ESC stability has not, however, been extensively studied. We previously reported that SMAD family member 3 (Smad3) has an important role in maintaining mouse ESC stability, as depletion of Smad3 results in cancer cell-like properties in ESCs and Smad3-/- ESCs are prone to grow large, malignant teratomas. To understand how Smad3 contributes to ESC stability, we performed microarray analysis to compare the transcriptome of wild-type and Smad3-/- ESCs. We found that Rif1 (RAP1-associated protein 1), a factor important for genomic stability, is significantly upregulated in Smad3-/- ESCs. The expression level of Rif1 needs to be tightly controlled in ESCs, as a low level of Rif1 is associated with ESC differentiation, but a high level of Rif1 is linked to ESC transformation. In ESCs, Oct4 activates Rif1, whereas Smad3 represses its expression. Oct4 recruits Smad3 to bind to Rif1 promoter, but Smad3 joining facilitates the loading of a polycomb complex that generates a repressive epigenetic modification on Rif1 promoter, and thus maintains the expression of Rif1 at a proper level in ESCs. Interestingly, Rif1 short hairpin RNA (shRNA)-transduced Smad3-/- ESCs showed less malignant properties than the control shRNA-transduced Smad3-/- ESCs, suggesting a critical role of Rif1 in maintaining the stability of ESCs during proliferation.
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Affiliation(s)
- P Li
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - X Ma
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - I R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - P Yuan
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China [4] School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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177
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Barton O, Naumann SC, Diemer-Biehs R, Künzel J, Steinlage M, Conrad S, Makharashvili N, Wang J, Feng L, Lopez BS, Paull TT, Chen J, Jeggo PA, Löbrich M. Polo-like kinase 3 regulates CtIP during DNA double-strand break repair in G1. ACTA ACUST UNITED AC 2014; 206:877-94. [PMID: 25267294 PMCID: PMC4178966 DOI: 10.1083/jcb.201401146] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plk3 phosphorylates CtIP in G1 in a damage-inducible manner and is required with CtIP for the repair of complex double-strand breaks and regulation of resection-mediated end-joining pathways. DNA double-strand breaks (DSBs) are repaired by nonhomologous end joining (NHEJ) or homologous recombination (HR). The C terminal binding protein–interacting protein (CtIP) is phosphorylated in G2 by cyclin-dependent kinases to initiate resection and promote HR. CtIP also exerts functions during NHEJ, although the mechanism phosphorylating CtIP in G1 is unknown. In this paper, we identify Plk3 (Polo-like kinase 3) as a novel DSB response factor that phosphorylates CtIP in G1 in a damage-inducible manner and impacts on various cellular processes in G1. First, Plk3 and CtIP enhance the formation of ionizing radiation-induced translocations; second, they promote large-scale genomic deletions from restriction enzyme-induced DSBs; third, they are required for resection and repair of complex DSBs; and finally, they regulate alternative NHEJ processes in Ku−/− mutants. We show that mutating CtIP at S327 or T847 to nonphosphorylatable alanine phenocopies Plk3 or CtIP loss. Plk3 binds to CtIP phosphorylated at S327 via its Polo box domains, which is necessary for robust damage-induced CtIP phosphorylation at S327 and subsequent CtIP phosphorylation at T847.
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Affiliation(s)
- Olivia Barton
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Steffen C Naumann
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Ronja Diemer-Biehs
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Julia Künzel
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Monika Steinlage
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Sandro Conrad
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Nodar Makharashvili
- The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Jiadong Wang
- Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Lin Feng
- Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Bernard S Lopez
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Sud, F-94805 Villejuif, France
| | - Tanya T Paull
- The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Junjie Chen
- Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Penny A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, England, UK
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
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178
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Abstract
DNA double-strand break (DSB) repair is not only key to genome stability but is also an important anticancer target. Through an shRNA library-based screening, we identified ubiquitin-conjugating enzyme H7 (UbcH7, also known as Ube2L3), a ubiquitin E2 enzyme, as a critical player in DSB repair. UbcH7 regulates both the steady-state and replicative stress-induced ubiquitination and proteasome-dependent degradation of the tumor suppressor p53-binding protein 1 (53BP1). Phosphorylation of 53BP1 at the N terminus is involved in the replicative stress-induced 53BP1 degradation. Depletion of UbcH7 stabilizes 53BP1, leading to inhibition of DSB end resection. Therefore, UbcH7-depleted cells display increased nonhomologous end-joining and reduced homologous recombination for DSB repair. Accordingly, UbcH7-depleted cells are sensitive to DNA damage likely because they mainly used the error-prone nonhomologous end-joining pathway to repair DSBs. Our studies reveal a novel layer of regulation of the DSB repair choice and propose an innovative approach to enhance the effect of radiotherapy or chemotherapy through stabilizing 53BP1.
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179
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Dulev S, Tkach J, Lin S, Batada NN. SET8 methyltransferase activity during the DNA double-strand break response is required for recruitment of 53BP1. EMBO Rep 2014; 15:1163-74. [PMID: 25252681 PMCID: PMC4253490 DOI: 10.15252/embr.201439434] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 12/29/2022] Open
Abstract
DNA double-strand breaks (DSBs) activate a signaling pathway known as the DNA damage response (DDR) which via protein-protein interactions and post-translational modifications recruit signaling proteins, such as 53BP1, to chromatin flanking the lesion. Depletion of the SET8 methyltransferase prevents accumulation of 53BP1 at DSBs; however, this phenotype has been attributed to the role of SET8 in generating H4K20 methylation across the genome, which is required for 53BP1 binding to chromatin, prior to DNA damage. Here, we report that SET8 acts directly at DSBs during the DNA damage response (DDR). SET8 accumulates at DSBs and is enzymatically active at DSBs. Depletion of SET8 just prior to the induction of DNA damage abrogates 53BP1's accumulation at DSBs, suggesting that SET8 acts during DDR. SET8's occupancy at DSBs is regulated by histone deacetylases (HDACs). Finally, SET8 is functionally required for efficient repair of DSBs specifically via the non-homologous end-joining pathway (NHEJ). Our findings reveal that SET8's active role during DDR at DSBs is required for 53BP1's accumulation.
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Affiliation(s)
- Stanimir Dulev
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Johnny Tkach
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sichun Lin
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Nizar N Batada
- Ontario Institute for Cancer Research, Toronto, ON, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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180
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Liu T, Huang J. Quality control of homologous recombination. Cell Mol Life Sci 2014; 71:3779-97. [PMID: 24858417 PMCID: PMC11114062 DOI: 10.1007/s00018-014-1649-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022]
Abstract
Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR.
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Affiliation(s)
- Ting Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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181
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Doksani Y, de Lange T. The role of double-strand break repair pathways at functional and dysfunctional telomeres. Cold Spring Harb Perspect Biol 2014; 6:a016576. [PMID: 25228584 DOI: 10.1101/cshperspect.a016576] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Telomeres have evolved to protect the ends of linear chromosomes from the myriad of threats posed by the cellular DNA damage signaling and repair pathways. Mammalian telomeres have to block nonhomologous end joining (NHEJ), thus preventing chromosome fusions; they need to control homologous recombination (HR), which could change telomere lengths; they have to avoid activating the ATM (ataxia telangiectasia mutated) and ATR (ATM- and RAD3-related) kinase pathways, which could induce cell cycle arrest; and they have to protect chromosome ends from hyperresection. Recent studies of telomeres have provided insights into the mechanisms of NHEJ and HR, how these double-strand break (DSB) repair pathways can be thwarted, and how telomeres have co-opted DNA repair factors to help in the protection of chromosome ends. These aspects of telomere biology are reviewed here with particular emphasis on recombination, the main focus of this collection.
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Affiliation(s)
- Ylli Doksani
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, New York 10065
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, New York 10065
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182
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Klement K, Goodarzi AA. DNA double strand break responses and chromatin alterations within the aging cell. Exp Cell Res 2014; 329:42-52. [PMID: 25218945 DOI: 10.1016/j.yexcr.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022]
Abstract
Cellular senescence is a state of permanent replicative arrest that allows cells to stay viable and metabolically active but resistant to apoptotic and mitogenic stimuli. Specific, validated markers can identify senescent cells, including senescence-associated β galactosidase activity, chromatin alterations, cell morphology changes, activated p16- and p53-dependent signaling and permanent cell cycle arrest. Senescence is a natural consequence of DNA replication-associated telomere erosion, but can also be induced prematurely by telomere-independent events such as failure to repair DNA double strand breaks. Here, we review the molecular pathways of senescence onset, focussing on the changes in chromatin organization that are associated with cellular senescence, particularly senescence-associated heterochromatin foci formation. We also discuss the altered dynamics of the DNA double strand break response within the context of aging cells. Appreciating how, mechanistically, cellular senescence is induced, and how changes to chromatin organization and DNA repair contributes to this, is fundamental to our understanding of the normal and premature human aging processes associated with loss of organ and tissue function in humans.
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Affiliation(s)
- Karolin Klement
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Aaron A Goodarzi
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1.
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183
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Böhm S, Bernstein KA. The role of post-translational modifications in fine-tuning BLM helicase function during DNA repair. DNA Repair (Amst) 2014; 22:123-32. [PMID: 25150915 DOI: 10.1016/j.dnarep.2014.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Abstract
RecQ-like helicases are a highly conserved family of proteins which are critical for preserving genome integrity. Genome instability is considered a hallmark of cancer and mutations within three of the five human RECQ genes cause hereditary syndromes that are associated with cancer predisposition. The human RecQ-like helicase BLM has a central role in DNA damage signaling, repair, replication, and telomere maintenance. BLM and its budding yeast orthologue Sgs1 unwind double-stranded DNA intermediates. Intriguingly, BLM functions in both a pro- and anti-recombinogenic manner upon replicative damage, acting on similar substrates. Thus, BLM activity must be intricately controlled to prevent illegitimate recombination events that could have detrimental effects on genome integrity. In recent years it has become evident that post-translational modifications (PTMs) of BLM allow a fine-tuning of its function. To date, BLM phosphorylation, ubiquitination, and SUMOylation have been identified, in turn regulating its subcellular localization, protein-protein interactions, and protein stability. In this review, we will discuss the cellular context of when and how these different modifications of BLM occur. We will reflect on the current model of how PTMs control BLM function during DNA damage repair and compare this to what is known about post-translational regulation of the budding yeast orthologue Sgs1. Finally, we will provide an outlook toward future research, in particular to dissect the cross-talk between the individual PTMs on BLM.
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Affiliation(s)
- Stefanie Böhm
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| | - Kara Anne Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States.
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184
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Abstract
RecA/Rad51 catalyzed pairing of homologous DNA strands, initiated by polymerization of the recombinase on single-stranded DNA (ssDNA), is a universal feature of homologous recombination (HR). Generation of ssDNA from a double-strand break (DSB) requires nucleolytic degradation of the 5'-terminated strands to generate 3'-ssDNA tails, a process referred to as 5'-3' end resection. The RecBCD helicase-nuclease complex is the main end-processing machine in Gram-negative bacteria. Mre11-Rad50 and Mre11-Rad50-Xrs2/Nbs1 can play a direct role in end resection in archaea and eukaryota, respectively, by removing end-blocking lesions and act indirectly by recruiting the helicases and nucleases responsible for extensive resection. In eukaryotic cells, the initiation of end resection has emerged as a critical regulatory step to differentiate between homology-dependent and end-joining repair of DSBs.
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185
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Abstract
SIGNIFICANCE Ionizing radiation (IR) is an effective and commonly employed treatment in the management of more than half of human malignancies. Because IR's ability to control tumors mainly relies on DNA damage, the cell's DNA damage response and repair (DRR) processes may hold the key to determining tumor responses. IR-induced DNA damage activates a number of DRR signaling cascades that control cell cycle arrest, DNA repair, and the cell's fate. DNA double-strand breaks (DSBs) generated by IR are the most lethal form of damage, and are mainly repaired via either homologous recombination (HR) or nonhomologous end-joining (NHEJ) pathways. RECENT ADVANCES In recent years, immense effort to understand and exploit the differences in the use of these repair pathways between tumors and normal cells will allow for an increase in tumor cell killing and a decrease in normal tissue injury. CRITICAL ISSUES Regulation of the two major DSB repair mechanisms (HR and NHEJ) and new strategies, which may improve the therapeutic ratio of radiation by differentially targeting HR and NHEJ function in tumor and normal tissues, is of intense interest currently, and is the focus of this article. FUTURE DIRECTIONS By utilizing the strategies outlined above, it may be possible to exploit differences between tumor and somatic cell DRR pathways, specifically their DSB repair mechanisms, to improve the therapeutic ratio of IR.
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Affiliation(s)
- Wil L Santivasi
- Department of Radiation Oncology, The Ohio State University College of Medicine , Columbus, Ohio
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186
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Gupta A, Hunt CR, Hegde ML, Chakraborty S, Chakraborty S, Udayakumar D, Horikoshi N, Singh M, Ramnarain DB, Hittelman WN, Namjoshi S, Asaithamby A, Hazra TK, Ludwig T, Pandita RK, Tyler JK, Pandita TK. MOF phosphorylation by ATM regulates 53BP1-mediated double-strand break repair pathway choice. Cell Rep 2014; 8:177-89. [PMID: 24953651 DOI: 10.1016/j.celrep.2014.05.044] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 04/24/2014] [Accepted: 05/21/2014] [Indexed: 01/09/2023] Open
Abstract
Cell-cycle phase is a critical determinant of the choice between DNA damage repair by nonhomologous end-joining (NHEJ) or homologous recombination (HR). Here, we report that double-strand breaks (DSBs) induce ATM-dependent MOF (a histone H4 acetyl-transferase) phosphorylation (p-T392-MOF) and that phosphorylated MOF colocalizes with γ-H2AX, ATM, and 53BP1 foci. Mutation of the phosphorylation site (MOF-T392A) impedes DNA repair in S and G2 phase but not G1 phase cells. Expression of MOF-T392A also blocks the reduction in DSB-associated 53BP1 seen in wild-type S/G2 phase cells, resulting in enhanced 53BP1 and reduced BRCA1 association. Decreased BRCA1 levels at DSB sites correlates with defective repairosome formation, reduced HR repair, and decreased cell survival following irradiation. These data support a model whereby ATM-mediated MOF-T392 phosphorylation modulates 53BP1 function to facilitate the subsequent recruitment of HR repair proteins, uncovering a regulatory role for MOF in DSB repair pathway choice during S/G2 phase.
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Affiliation(s)
- Arun Gupta
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Clayton R Hunt
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | | | - Sharmistha Chakraborty
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sharmistha Chakraborty
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Durga Udayakumar
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Nobuo Horikoshi
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Mayank Singh
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deepti B Ramnarain
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Walter N Hittelman
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarita Namjoshi
- Department of Biochemistry, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aroumougame Asaithamby
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tapas K Hazra
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thomas Ludwig
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Raj K Pandita
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jessica K Tyler
- Department of Biochemistry, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tej K Pandita
- Deparment of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA.
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187
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Abstract
Rif1 protein is present in eukaryotic cells from yeast to human. In yeast, Rif1 is important for telomere homeostasis. Despite conservation in its domain organization, human Rif1 is not part of the telomere complex but was recently reported to work at DNA double‐strand breaks (DSBs) with 53BP1 to inhibit 5′ strand degradation (resection) and stimulate a subset of nonhomologous end‐joining (NHEJ) reactions. Martina et al report in this issue of EMBO reports that yeast Rif1 is also recruited to DSBs, but in contrast to its human counterpart, it promotes resection. The authors propose that Rif1 stimulates resection by limiting the access of Rad9, an ortholog of 53BP1, to DSBs.
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Affiliation(s)
- Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of MedicineHouston, TX, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
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188
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Liu C, Srihari S, Cao KAL, Chenevix-Trench G, Simpson PT, Ragan MA, Khanna KK. A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Res 2014; 42:6106-27. [PMID: 24792170 PMCID: PMC4041457 DOI: 10.1093/nar/gku284] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 02/06/2023] Open
Abstract
DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pathways, triggering cancerous potential in cells. Selective killing of cancer cells by sensitizing them to further DNA damage, especially by induction of DSBs, therefore requires careful modulation of DSB-repair pathways. Here, we review the latest knowledge on the two DSB-repair pathways, homologous recombination and non-homologous end joining in human, describing in detail the functions of their components and the key mechanisms contributing to the repair. Such an in-depth characterization of these pathways enables a more mechanistic understanding of how cells respond to therapies, and suggests molecules and processes that can be explored as potential therapeutic targets. One such avenue that has shown immense promise is via the exploitation of synthetic lethal relationships, for which the BRCA1-PARP1 relationship is particularly notable. Here, we describe how this relationship functions and the manner in which cancer cells acquire therapy resistance by restoring their DSB repair potential.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kim-Anh Lê Cao
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
| | | | - Peter T Simpson
- The University of Queensland Centre for Clinical Research, Herston, Brisbane, QLD 4029, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kum Kum Khanna
- Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
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189
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Polato F, Callen E, Wong N, Faryabi R, Bunting S, Chen HT, Kozak M, Kruhlak MJ, Reczek CR, Lee WH, Ludwig T, Baer R, Feigenbaum L, Jackson S, Nussenzweig A. CtIP-mediated resection is essential for viability and can operate independently of BRCA1. ACTA ACUST UNITED AC 2014; 211:1027-36. [PMID: 24842372 PMCID: PMC4042650 DOI: 10.1084/jem.20131939] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In contrast to BRCA1, CtIP has indispensable roles in promoting resection and embryonic development. Homologous recombination (HR) is initiated by DNA end resection, a process in which stretches of single-strand DNA (ssDNA) are generated and used for homology search. Factors implicated in resection include nucleases MRE11, EXO1, and DNA2, which process DNA ends into 3′ ssDNA overhangs; helicases such as BLM, which unwind DNA; and other proteins such as BRCA1 and CtIP whose functions remain unclear. CDK-mediated phosphorylation of CtIP on T847 is required to promote resection, whereas CDK-dependent phosphorylation of CtIP-S327 is required for interaction with BRCA1. Here, we provide evidence that CtIP functions independently of BRCA1 in promoting DSB end resection. First, using mouse models expressing S327A or T847A mutant CtIP as a sole species, and B cells deficient in CtIP, we show that loss of the CtIP-BRCA1 interaction does not detectably affect resection, maintenance of genomic stability or viability, whereas T847 is essential for these functions. Second, although loss of 53BP1 rescues the embryonic lethality and HR defects in BRCA1-deficient mice, it does not restore viability or genome integrity in CtIP−/− mice. Third, the increased resection afforded by loss of 53BP1 and the rescue of BRCA1-deficiency depend on CtIP but not EXO1. Finally, the sensitivity of BRCA1-deficient cells to poly ADP ribose polymerase (PARP) inhibition is partially rescued by the phospho-mimicking mutant CtIP (CtIP-T847E). Thus, in contrast to BRCA1, CtIP has indispensable roles in promoting resection and embryonic development.
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Affiliation(s)
- Federica Polato
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elsa Callen
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nancy Wong
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Robert Faryabi
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Samuel Bunting
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Hua-Tang Chen
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Marina Kozak
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael J Kruhlak
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Colleen R Reczek
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032
| | - Wen-Hwa Lee
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697
| | - Thomas Ludwig
- Ohio State University Wexner Medical Center, Columbus, OH 43210
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032
| | - Lionel Feigenbaum
- Science Applications International Corporation-Frederick National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21704
| | - Stephen Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England, UK The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England, UK The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, England, UK
| | - André Nussenzweig
- Laboratory of Genome Integrity, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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190
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Radhakrishnan SK, Jette N, Lees-Miller SP. Non-homologous end joining: emerging themes and unanswered questions. DNA Repair (Amst) 2014; 17:2-8. [PMID: 24582502 PMCID: PMC4084493 DOI: 10.1016/j.dnarep.2014.01.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 11/25/2022]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation induced DNA double strand breaks in human cells. Here, we discuss current insights into the mechanism of NHEJ and the interplay between NHEJ and other pathways for repair of IR-induced DNA damage.
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Affiliation(s)
- Sarvan Kumar Radhakrishnan
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Nicholas Jette
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1.
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191
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Abstract
Since DNA double-strand breaks (DSBs) contribute to the genomic instability that drives cancer development, DSB repair pathways serve as important mechanisms for tumor suppression. Thus, genetic lesions, such as BRCA1 and BRCA2 mutations, that disrupt DSB repair are often associated with cancer susceptibility. In addition, recent evidence suggests that DSB "mis-repair", in which DSBs are resolved by an inappropriate repair pathway, can also promote genomic instability and presumably tumorigenesis. This notion has gained currency from recent cancer genome sequencing studies which have uncovered numerous chromosomal rearrangements harboring pathological DNA repair signatures. In this perspective, we discuss the factors that regulate DSB repair pathway choice and their consequences for genome stability and cancer.
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Affiliation(s)
- Tomas Aparicio
- Institute for Cancer Genetics & Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Richard Baer
- Institute for Cancer Genetics & Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics & Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
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192
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Orthwein A, Fradet-Turcotte A, Noordermeer SM, Canny MD, Brun CM, Strecker J, Escribano-Diaz C, Durocher D. Mitosis inhibits DNA double-strand break repair to guard against telomere fusions. Science 2014; 344:189-93. [PMID: 24652939 DOI: 10.1126/science.1248024] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitotic cells inactivate DNA double-strand break (DSB) repair, but the rationale behind this suppression remains unknown. Here, we unravel how mitosis blocks DSB repair and determine the consequences of repair reactivation. Mitotic kinases phosphorylate the E3 ubiquitin ligase RNF8 and the nonhomologous end joining factor 53BP1 to inhibit their recruitment to DSB-flanking chromatin. Restoration of RNF8 and 53BP1 accumulation at mitotic DSB sites activates DNA repair but is, paradoxically, deleterious. Aberrantly controlled mitotic DSB repair leads to Aurora B kinase-dependent sister telomere fusions that produce dicentric chromosomes and aneuploidy, especially in the presence of exogenous genotoxic stress. We conclude that the capacity of mitotic DSB repair to destabilize the genome explains the necessity for its suppression during mitosis, principally due to the fusogenic potential of mitotic telomeres.
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Affiliation(s)
- Alexandre Orthwein
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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193
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Sukackaite R, Jensen MR, Mas PJ, Blackledge M, Buonomo SB, Hart DJ. Structural and biophysical characterization of murine rif1 C terminus reveals high specificity for DNA cruciform structures. J Biol Chem 2014; 289:13903-11. [PMID: 24634216 DOI: 10.1074/jbc.m114.557843] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian Rif1 is a key regulator of DNA replication timing, double-stranded DNA break repair, and replication fork restart. Dissecting the molecular functions of Rif1 is essential to understand how it regulates such diverse processes. However, Rif1 is a large protein that lacks well defined functional domains and is predicted to be largely intrinsically disordered; these features have hampered recombinant expression of Rif1 and subsequent functional characterization. Here we applied ESPRIT (expression of soluble proteins by random incremental truncation), an in vitro evolution-like approach, to identify high yielding soluble fragments encompassing conserved regions I and II (CRI and CRII) at the C-terminal region of murine Rif1. NMR analysis showed CRI to be intrinsically disordered, whereas CRII is partially folded. CRII binds cruciform DNA with high selectivity and micromolar affinity and thus represents a functional DNA binding domain. Mutational analysis revealed an α-helical region of CRII to be important for cruciform DNA binding and identified critical residues. Thus, we present the first structural study of the mammalian Rif1, identifying a domain that directly links its function to DNA binding. The high specificity of Rif1 for cruciform structures is significant given the role of this key protein in regulating origin firing and DNA repair.
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Affiliation(s)
- Rasa Sukackaite
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France, the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Malene Ringkjøbing Jensen
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Philippe J Mas
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France
| | - Martin Blackledge
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Sara B Buonomo
- the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Darren J Hart
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France,
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194
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Leung JW, Agarwal P, Canny MD, Gong F, Robison AD, Finkelstein IJ, Durocher D, Miller KM. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling. PLoS Genet 2014; 10:e1004178. [PMID: 24603765 PMCID: PMC3945288 DOI: 10.1371/journal.pgen.1004178] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/31/2013] [Indexed: 12/23/2022] Open
Abstract
Histone ubiquitinations are critical for the activation of the DNA damage response (DDR). In particular, RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119, respectively. However, it remains to be defined how the ubiquitin pathway engages chromatin to provide regulation of ubiquitin targeting of specific histone residues. Here we identify the nucleosome acid patch as a critical chromatin mediator of H2A/H2AX ubiquitination (ub). The acidic patch is required for RNF168- and RING1B/BMI1-dependent H2A/H2AXub in vivo. The acidic patch functions within the nucleosome as nucleosomes containing a mutated acidic patch exhibit defective H2A/H2AXub by RNF168 and RING1B/BMI1 in vitro. Furthermore, direct perturbation of the nucleosome acidic patch in vivo by the expression of an engineered acidic patch interacting viral peptide, LANA, results in defective H2AXub and RNF168-dependent DNA damage responses including 53BP1 and BRCA1 recruitment to DNA damage. The acidic patch therefore is a critical nucleosome feature that may serve as a scaffold to integrate multiple ubiquitin signals on chromatin to compose selective ubiquitinations on histones for DNA damage signaling.
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Affiliation(s)
- Justin W Leung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Poonam Agarwal
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Marella D Canny
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Fade Gong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Aaron D Robison
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel Durocher
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kyle M Miller
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
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195
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Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
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Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
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196
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53BP1, BRCA1, and the choice between recombination and end joining at DNA double-strand breaks. Mol Cell Biol 2014; 34:1380-8. [PMID: 24469398 DOI: 10.1128/mcb.01639-13] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
When DNA double-strand breaks occur, the cell cycle stage has a major influence on the choice of the repair pathway employed. Specifically, nonhomologous end joining is the predominant mechanism used in the G1 phase of the cell cycle, while homologous recombination becomes fully activated in S phase. Studies over the past 2 decades have revealed that the aberrant joining of replication-associated breaks leads to catastrophic genome rearrangements, revealing an important role of DNA break repair pathway choice in the preservation of genome integrity. 53BP1, first identified as a DNA damage checkpoint protein, and BRCA1, a well-known breast cancer tumor suppressor, are at the center of this choice. Research on how these proteins function at the DNA break site has advanced rapidly in the recent past. Here, we review what is known regarding how the repair pathway choice is made, including the mechanisms that govern the recruitment of each critical factor, and how the cell transitions from end joining in G1 to homologous recombination in S/G2.
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197
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Kumar R, Cheok CF. RIF1: a novel regulatory factor for DNA replication and DNA damage response signaling. DNA Repair (Amst) 2014; 15:54-9. [PMID: 24462468 DOI: 10.1016/j.dnarep.2013.12.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 12/30/2022]
Abstract
DNA double strand breaks (DSBs) are highly toxic to the cells and accumulation of DSBs results in several detrimental effects in various cellular processes which can lead to neurological, immunological and developmental disorders. Failure of the repair of DSBs spurs mutagenesis and is a driver of tumorigenesis, thus underscoring the importance of the accurate repair of DSBs. Two major canonical DSB repair pathways are the non-homologous end joining (NHEJ) and homologous recombination (HR) pathways. 53BP1 and BRCA1 are the key mediator proteins which coordinate with other components of the DNA repair machinery in the NHEJ and HR pathways respectively, and their exclusive recruitment to DNA breaks/ends potentially decides the choice of repair by either NHEJ or HR. Recently, Rap1 interacting factor 1 has been identified as an important component of the DNA repair pathway which acts downstream of the ATM/53BP1 to inhibit the 5'-3' end resection of broken DNA ends, in-turn facilitating NHEJ repair and inhibiting homology directed repair. Rif1 is conserved from yeast to humans but its function has evolved from telomere length regulation in yeast to the maintenance of genome integrity in mammalian cells. Recently its role in the maintenance of genomic integrity has been expanded to include the regulation of chromatin structure, replication timing and intra-S phase checkpoint. We present a summary of these important findings highlighting the various aspects of Rif1 functions and discuss the key implications for genomic integrity.
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Affiliation(s)
- Ramesh Kumar
- IFOM-p53Lab Joint Research Laboratory, 8A Biomedical Grove, #06-38, Immunos, A*STAR, S138648 Singapore, Singapore; IFOM, The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
| | - Chit Fang Cheok
- IFOM-p53Lab Joint Research Laboratory, 8A Biomedical Grove, #06-38, Immunos, A*STAR, S138648 Singapore, Singapore; IFOM, The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, S117597 Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, S639798 Singapore, Singapore.
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198
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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199
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Abstract
DNA double-strand break (DSB) signalling and repair is crucial to preserve genomic integrity and maintain cellular homeostasis. p53-binding protein 1 (53BP1) is an important regulator of the cellular response to DSBs that promotes the end-joining of distal DNA ends, which is induced during V(D)J and class switch recombination as well as during the fusion of deprotected telomeres. New insights have been gained into the mechanisms underlying the recruitment of 53BP1 to damaged chromatin and how 53BP1 promotes non-homologous end-joining-mediated DSB repair while preventing homologous recombination. From these studies, a model is emerging in which 53BP1 recruitment requires the direct recognition of a DSB-specific histone code and its influence on pathway choice is mediated by mutual antagonism with breast cancer 1 (BRCA1).
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Affiliation(s)
- Stephanie Panier
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms, London EN6 3LD, UK
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms, London EN6 3LD, UK
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Helchowski CM, Skow LF, Roberts KH, Chute CL, Canman CE. A small ubiquitin binding domain inhibits ubiquitin-dependent protein recruitment to DNA repair foci. Cell Cycle 2013; 12:3749-58. [PMID: 24107634 PMCID: PMC3905067 DOI: 10.4161/cc.26640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
The rapid ubiquitination of chromatin surrounding DNA double-stranded breaks (DSB) drives the formation of large structures called ionizing radiation-induced foci (IRIF), comprising many DNA damage response (DDR) proteins. This process is regulated by RNF8 and RNF168 ubiquitin ligases and is thought to be necessary for DNA repair and activation of signaling pathways involved in regulating cell cycle checkpoints. Here we demonstrate that it is possible to interfere with ubiquitin-dependent recruitment of DDR factors by expressing proteins containing ubiquitin binding domains (UBDs) that bind to lysine 63-linked polyubiquitin chains. Expression of the E3 ubiquitin ligase RAD18 prevented chromatin spreading of 53BP1 at DSBs, and this phenomenon was dependent upon the integrity of the RAD18 UBD. An isolated RAD18 UBD interfered with 53BP1 chromatin spreading, as well as other important DDR mediators, including RAP80 and the BRCA1 tumor suppressor protein, consistent with the model that the RAD18 UBD is blocking access of proteins to ubiquitinated chromatin. Using the RAD18 UBD as a tool to impede localization of 53BP1 and BRCA1 to repair foci, we found that DDR signaling, DNA DSB repair, and radiosensitivity were unaffected. We did find that activated ATM (S1981P) and phosphorylated SMC1 (a specific target of ATM) were not detectable in DNA repair foci, in addition to upregulated homologous recombination repair, revealing 2 DDR responses that are dependent upon chromatin spreading of certain DDR factors at DSBs. These data demonstrate that select UBDs containing targeting motifs may be useful probes in determining the biological significance of protein-ubiquitin interactions.
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Affiliation(s)
- Corey M Helchowski
- Department of Pharmacology; University of Michigan Medical School; Ann Arbor, MI USA
| | - Laura F Skow
- Department of Pharmacology; University of Michigan Medical School; Ann Arbor, MI USA
| | - Katelyn H Roberts
- Department of Pharmacology; University of Michigan Medical School; Ann Arbor, MI USA
| | - Colleen L Chute
- Department of Pharmacology; University of Michigan Medical School; Ann Arbor, MI USA
| | - Christine E Canman
- Department of Pharmacology; University of Michigan Medical School; Ann Arbor, MI USA
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