101
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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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102
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Catalytic and noncatalytic roles of the CtIP endonuclease in double-strand break end resection. Mol Cell 2014; 54:1022-1033. [PMID: 24837676 DOI: 10.1016/j.molcel.2014.04.011] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/11/2013] [Accepted: 04/04/2014] [Indexed: 12/22/2022]
Abstract
The carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) is known to function in 5' strand resection during homologous recombination, similar to the budding yeast Sae2 protein, but its role in this process is unclear. Here, we characterize recombinant human CtIP and find that it exhibits 5' flap endonuclease activity on branched DNA structures, independent of the MRN complex. Phosphorylation of CtIP at known damage-dependent sites and other sites is essential for its catalytic activity, although the S327 and T847 phosphorylation sites are dispensable. A catalytic mutant of CtIP that is deficient in endonuclease activity exhibits wild-type levels of homologous recombination at restriction enzyme-generated breaks but is deficient in processing topoisomerase adducts and radiation-induced breaks in human cells, suggesting that the nuclease activity of CtIP is specifically required for the removal of DNA adducts at sites of DNA breaks.
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103
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Murina O, von Aesch C, Karakus U, Ferretti LP, Bolck HA, Hänggi K, Sartori AA. FANCD2 and CtIP cooperate to repair DNA interstrand crosslinks. Cell Rep 2014; 7:1030-8. [PMID: 24794434 DOI: 10.1016/j.celrep.2014.03.069] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 03/04/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022] Open
Abstract
The resolution of DNA interstrand crosslinks (ICLs) requires a complex interplay between several processes of DNA metabolism, including the Fanconi anemia (FA) pathway and homologous recombination (HR). FANCD2 monoubiquitination and CtIP-dependent DNA-end resection represent key events in FA and HR activation, respectively, but very little is known about their functional relationship. Here, we show that CtIP physically interacts with both FANCD2 and ubiquitin and that monoubiquitinated FANCD2 tethers CtIP to damaged chromatin, which helps channel DNA double-strand breaks generated during ICL processing into the HR pathway. Consequently, CtIP mutants defective in FANCD2 binding fail to associate with damaged chromatin, which leads to increased levels of nonhomologous end-joining activity and ICL hypersensitivity. Interestingly, we also observe that CtIP depletion aggravates the genomic instability in FANCD2-deficient cells. Thus, our data indicate that FANCD2 primes CtIP-dependent resection during HR after ICL induction but that CtIP helps prevent illegitimate recombination in FA cells.
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Affiliation(s)
- Olga Murina
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christine von Aesch
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ufuk Karakus
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lorenza P Ferretti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Hella A Bolck
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Kay Hänggi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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104
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Phosphorylation of EXO1 by CDKs 1 and 2 regulates DNA end resection and repair pathway choice. Nat Commun 2014; 5:3561. [PMID: 24705021 PMCID: PMC4041212 DOI: 10.1038/ncomms4561] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/05/2014] [Indexed: 12/23/2022] Open
Abstract
Resection of DNA double-strand breaks (DSBs) is a pivotal step during which the choice between NHEJ and HR DNA repair pathways is made. Although CDKs are known to control initiation of resection, their role in regulating long-range resection remains elusive. Here we show that CDKs 1/2 phosphorylate the long-range resection nuclease EXO1 at four C-terminal S/TP sites during S/G2 phases of the cell cycle. Impairment of EXO1 phosphorylation attenuates resection, chromosomal integrity, cell survival and HR, but augments NHEJ upon DNA damage. In contrast, cells expressing phospho-mimic EXO1 are proficient in resection even after CDK inhibition and favour HR over NHEJ. Mutation of cyclin-binding sites on EXO1 attenuates CDK binding and EXO1 phosphorylation, causing a resection defect that can be rescued by phospho-mimic mutations. Mechanistically, phosphorylation of EXO1 augments its recruitment to DNA breaks possibly via interactions with BRCA1. In summary, phosphorylation of EXO1 by CDKs is a novel mechanism regulating repair pathway choice.
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105
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Averbeck NB, Ringel O, Herrlitz M, Jakob B, Durante M, Taucher-Scholz G. DNA end resection is needed for the repair of complex lesions in G1-phase human cells. Cell Cycle 2014; 13:2509-16. [PMID: 25486192 PMCID: PMC4615131 DOI: 10.4161/15384101.2015.941743] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/01/2014] [Indexed: 11/19/2022] Open
Abstract
Repair of DNA double strand breaks (DSBs) is influenced by the chemical complexity of the lesion. Clustered lesions (complex DSBs) are generally considered more difficult to repair and responsible for early and late cellular effects after exposure to genotoxic agents. Resection is commonly used by the cells as part of the homologous recombination (HR) pathway in S- and G2-phase. In contrast, DNA resection in G1-phase may lead to an error-prone microhomology-mediated end joining. We induced DNA lesions with a wide range of complexity by irradiation of mammalian cells with X-rays or accelerated ions of different velocity and mass. We found replication protein A (RPA) foci indicating DSB resection both in S/G2- and G1-cells, and the fraction of resection-positive cells correlates with the severity of lesion complexity throughout the cell cycle. Besides RPA, Ataxia telangiectasia and Rad3-related (ATR) was recruited to complex DSBs both in S/G2- and G1-cells. Resection of complex DSBs is driven by meiotic recombination 11 homolog A (MRE11), CTBP-interacting protein (CtIP), and exonuclease 1 (EXO1) but seems not controlled by the Ku heterodimer or by phosphorylation of H2AX. Reduced resection capacity by CtIP depletion increased cell killing and the fraction of unrepaired DSBs after exposure to densely ionizing heavy ions, but not to X-rays. We conclude that in mammalian cells resection is essential for repair of complex DSBs in all phases of the cell-cycle and targeting this process sensitizes mammalian cells to cytotoxic agents inducing clustered breaks, such as in heavy-ion cancer therapy.
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Key Words
- ATM, Ataxia telangiectasia mutated
- ATR, Ataxia telangiectasia and Rad3-related
- BLM, Bloom syndrome protein
- BRCA1, breast cancer 1, early onset
- CENP-F, centromere protein F
- CtIP
- CtIP, CTBP-interacting protein
- DAPI, 4',6-diamidino-2-phenylindole
- DSB, double strand break
- EXO1
- EXO1, exonuclease 1
- FCS, fetal calf serum
- HR, homologous recombination
- IR, ionizing radiation
- LET, linear energy transfer
- MEF, mouse embryonic fibroblasts
- MMEJ, microhomology-mediated end joining
- MRE11
- MRE11, meiotic recombination 11 homolog A
- NHEJ, none homologous end joining
- PARP, poly (ADP-ribose) polymerase
- RAD51, DNA repair protein RAD51 homolog 1
- RPA, replication protein A
- WRN, Werner syndrome
- complex DNA damage
- double-strand break repair
- kd, knockdown
- resection in G1-phase
- siRNA, small interfering RNA
- ssDNA, single stranded DNA
- wt, wild-type
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Affiliation(s)
- Nicole B Averbeck
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
| | - Oliver Ringel
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
| | - Maren Herrlitz
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
| | - Burkhard Jakob
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
| | - Marco Durante
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
- Department of Condensed Matter Physics; Technische Universität Darmstadt; Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH; Planckstraße 1; Darmstadt, Germany
- Department of Biology; Technische Universität Darmstadt; Darmstadt, Germany
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106
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De Lorenzo SB, Patel AG, Hurley RM, Kaufmann SH. The Elephant and the Blind Men: Making Sense of PARP Inhibitors in Homologous Recombination Deficient Tumor Cells. Front Oncol 2013; 3:228. [PMID: 24062981 PMCID: PMC3769628 DOI: 10.3389/fonc.2013.00228] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/21/2013] [Indexed: 12/31/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an important component of the base excision repair (BER) pathway as well as a regulator of homologous recombination (HR) and non-homologous end-joining (NHEJ). Previous studies have demonstrated that treatment of HR-deficient cells with PARP inhibitors results in stalled and collapsed replication forks. Consequently, HR-deficient cells are extremely sensitive to PARP inhibitors. Several explanations have been advanced to explain this so-called synthetic lethality between HR deficiency and PARP inhibition: (i) reduction of BER activity leading to enhanced DNA double-strand breaks, which accumulate in the absence of HR; (ii) trapping of inhibited PARP1 at sites of DNA damage, which prevents access of other repair proteins; (iii) failure to initiate HR by poly(ADP-ribose) polymer-dependent BRCA1 recruitment; and (iv) activation of the NHEJ pathway, which selectively induces error-prone repair in HR-deficient cells. Here we review evidence regarding these various explanations for the ability of PARP inhibitors to selectively kill HR-deficient cancer cells and discuss their potential implications.
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107
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Shiotani B, Nguyen HD, Håkansson P, Maréchal A, Tse A, Tahara H, Zou L. Two distinct modes of ATR activation orchestrated by Rad17 and Nbs1. Cell Rep 2013; 3:1651-62. [PMID: 23684611 DOI: 10.1016/j.celrep.2013.04.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 04/05/2013] [Accepted: 04/19/2013] [Indexed: 11/15/2022] Open
Abstract
The ATM- and Rad3-related (ATR) kinase is a master regulator of the DNA damage response, yet how ATR is activated toward different substrates is still poorly understood. Here, we show that ATR phosphorylates Chk1 and RPA32 through distinct mechanisms at replication-associated DNA double-stranded breaks (DSBs). In contrast to the rapid phosphorylation of Chk1, RPA32 is progressively phosphorylated by ATR at Ser33 during DSB resection prior to the phosphorylation of Ser4/Ser8 by DNA-PKcs. Surprisingly, despite its reliance on ATR and TopBP1, substantial RPA32 Ser33 phosphorylation occurs in a Rad17-independent but Nbs1-dependent manner in vivo and in vitro. Importantly, the role of Nbs1 in RPA32 phosphorylation can be separated from ATM activation and DSB resection, and it is dependent upon the interaction of Nbs1 with RPA. An Nbs1 mutant that is unable to bind RPA fails to support proper recovery of collapsed replication forks, suggesting that the Nbs1-mediated mode of ATR activation is important for the repair of replication-associated DSBs.
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Affiliation(s)
- Bunsyo Shiotani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.
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