1
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Khayat F, Alshmery M, Pal M, Oliver A, Bianchi A. Binding of the TRF2 iDDR motif to RAD50 highlights a convergent evolutionary strategy to inactivate MRN at telomeres. Nucleic Acids Res 2024; 52:7704-7719. [PMID: 38884214 PMCID: PMC11260466 DOI: 10.1093/nar/gkae509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/07/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024] Open
Abstract
Telomeres protect chromosome ends from unscheduled DNA repair, including from the MRN (MRE11, RAD50, NBS1) complex, which processes double-stranded DNA breaks (DSBs) via activation of the ATM kinase, promotes DNA end-tethering aiding the non-homologous end-joining (NHEJ) pathway, and initiates DSB resection through the MRE11 nuclease. A protein motif (MIN, for MRN inhibitor) inhibits MRN at budding yeast telomeres by binding to RAD50 and evolved at least twice, in unrelated telomeric proteins Rif2 and Taz1. We identify the iDDR motif of human shelterin protein TRF2 as a third example of convergent evolution for this telomeric mechanism for binding MRN, despite the iDDR lacking sequence homology to the MIN motif. CtIP is required for activation of MRE11 nuclease action, and we provide evidence for binding of a short C-terminal region of CtIP to a RAD50 interface that partly overlaps with the iDDR binding site, indicating that the interaction is mutually exclusive. In addition, we show that the iDDR impairs the DNA binding activity of RAD50. These results highlight direct inhibition of MRN action as a crucial role of telomeric proteins across organisms and point to multiple mechanisms enforced by the iDDR to disable the many activities of the MRN complex.
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Affiliation(s)
- Freddy Khayat
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Majedh Alshmery
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
- Department of Life Sciences, Hafr Al Batin University, Saudi Arabia
| | - Mohinder Pal
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
- School of Biosciences, University of Kent, Canterbury, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Alessandro Bianchi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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2
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Reginato G, Dello Stritto MR, Wang Y, Hao J, Pavani R, Schmitz M, Halder S, Morin V, Cannavo E, Ceppi I, Braunshier S, Acharya A, Ropars V, Charbonnier JB, Jinek M, Nussenzweig A, Ha T, Cejka P. HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nat Commun 2024; 15:5789. [PMID: 38987539 PMCID: PMC11237066 DOI: 10.1038/s41467-024-50080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The outcome of CRISPR-Cas-mediated genome modifications is dependent on DNA double-strand break (DSB) processing and repair pathway choice. Homology-directed repair (HDR) of protein-blocked DSBs requires DNA end resection that is initiated by the endonuclease activity of the MRE11 complex. Using reconstituted reactions, we show that Cas9 breaks are unexpectedly not directly resectable by the MRE11 complex. In contrast, breaks catalyzed by Cas12a are readily processed. Cas9, unlike Cas12a, bridges the broken ends, preventing DSB detection and processing by MRE11. We demonstrate that Cas9 must be dislocated after DNA cleavage to allow DNA end resection and repair. Using single molecule and bulk biochemical assays, we next find that the HLTF translocase directly removes Cas9 from broken ends, which allows DSB processing by DNA end resection or non-homologous end-joining machineries. Mechanistically, the activity of HLTF requires its HIRAN domain and the release of the 3'-end generated by the cleavage of the non-target DNA strand by the Cas9 RuvC domain. Consequently, HLTF removes the H840A but not the D10A Cas9 nickase. The removal of Cas9 H840A by HLTF explains the different cellular impact of the two Cas9 nickase variants in human cells, with potential implications for gene editing.
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Affiliation(s)
- Giordano Reginato
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Maria Rosaria Dello Stritto
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Yanbo Wang
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jingzhou Hao
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Swagata Halder
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
- Biological Systems Engineering, Plaksha University, Mohali, Punjab, 140306, India
| | - Vincent Morin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Elda Cannavo
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ilaria Ceppi
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Stefan Braunshier
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ananya Acharya
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Virginie Ropars
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Baptiste Charbonnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andrè Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
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3
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Lokanathan Balaji S, De Bragança S, Balaguer-Pérez F, Northall S, Wilkinson OJ, Aicart-Ramos C, Seetaloo N, Sobott F, Moreno-Herrero F, Dillingham MS. DNA binding and bridging by human CtIP in the healthy and diseased states. Nucleic Acids Res 2024:gkae538. [PMID: 38922686 DOI: 10.1093/nar/gkae538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The human DNA repair factor CtIP helps to initiate the resection of double-stranded DNA breaks for repair by homologous recombination, in part through its ability to bind and bridge DNA molecules. However, CtIP is a natively disordered protein that bears no apparent similarity to other DNA-binding proteins and so the structural basis for these activities remains unclear. In this work, we have used bulk DNA binding, single molecule tracking, and DNA bridging assays to study wild-type and variant CtIP proteins to better define the DNA binding domains and the effects of mutations associated with inherited human disease. Our work identifies a monomeric DNA-binding domain in the C-terminal region of CtIP. CtIP binds non-specifically to DNA and can diffuse over thousands of nucleotides. CtIP-mediated bridging of distant DNA segments is observed in single-molecule magnetic tweezers experiments. However, we show that binding alone is insufficient for DNA bridging, which also requires tetramerization via the N-terminal domain. Variant CtIP proteins associated with Seckel and Jawad syndromes display impaired DNA binding and bridging activities. The significance of these findings in the context of facilitating DNA break repair is discussed.
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Affiliation(s)
- Shreya Lokanathan Balaji
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Francisco Balaguer-Pérez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Sarah Northall
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Oliver John Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Neeleema Seetaloo
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Mark Simon Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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4
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He X, Brakebusch C. Regulation of Precise DNA Repair by Nuclear Actin Polymerization: A Chance for Improving Gene Therapy? Cells 2024; 13:1093. [PMID: 38994946 PMCID: PMC11240418 DOI: 10.3390/cells13131093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Although more difficult to detect than in the cytoplasm, it is now clear that actin polymerization occurs in the nucleus and that it plays a role in the specific processes of the nucleus such as transcription, replication, and DNA repair. A number of studies suggest that nuclear actin polymerization is promoting precise DNA repair by homologous recombination, which could potentially be of help for precise genome editing and gene therapy. This review summarizes the findings and describes the challenges and chances in the field.
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Affiliation(s)
| | - Cord Brakebusch
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark;
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5
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Nicolas Y, Bret H, Cannavo E, Acharya A, Cejka P, Borde V, Guerois R. Molecular insights into the activation of Mre11-Rad50 endonuclease activity by Sae2/CtIP. Mol Cell 2024; 84:2223-2237.e4. [PMID: 38870937 DOI: 10.1016/j.molcel.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 02/25/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
In Saccharomyces cerevisiae (S. cerevisiae), Mre11-Rad50-Xrs2 (MRX)-Sae2 nuclease activity is required for the resection of DNA breaks with secondary structures or protein blocks, while in humans, the MRE11-RAD50-NBS1 (MRN) homolog with CtIP is needed to initiate DNA end resection of all breaks. Phosphorylated Sae2/CtIP stimulates the endonuclease activity of MRX/N. Structural insights into the activation of the Mre11 nuclease are available only for organisms lacking Sae2/CtIP, so little is known about how Sae2/CtIP activates the nuclease ensemble. Here, we uncover the mechanism of Mre11 activation by Sae2 using a combination of AlphaFold2 structural modeling of biochemical and genetic assays. We show that Sae2 stabilizes the Mre11 nuclease in a conformation poised to cleave substrate DNA. Several designs of compensatory mutations establish how Sae2 activates MRX in vitro and in vivo, supporting the structural model. Finally, our study uncovers how human CtIP, despite considerable sequence divergence, employs a similar mechanism to activate MRN.
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Affiliation(s)
- Yoann Nicolas
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Hélène Bret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elda Cannavo
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland.
| | - Valérie Borde
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France.
| | - Raphaël Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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6
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Liu Y, Lin Z, Yan J, Zhang X, Tong MH. A Rad50-null mutation in mouse germ cells causes reduced DSB formation, abnormal DSB end resection and complete loss of germ cells. Development 2024; 151:dev202312. [PMID: 38512324 DOI: 10.1242/dev.202312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The conserved MRE11-RAD50-NBS1/Xrs2 complex is crucial for DNA break metabolism and genome maintenance. Although hypomorphic Rad50 mutation mice showed normal meiosis, both null and hypomorphic rad50 mutation yeast displayed impaired meiosis recombination. However, the in vivo function of Rad50 in mammalian germ cells, particularly its in vivo role in the resection of meiotic double strand break (DSB) ends at the molecular level remains elusive. Here, we have established germ cell-specific Rad50 knockout mouse models to determine the role of Rad50 in mitosis and meiosis of mammalian germ cells. We find that Rad50-deficient spermatocytes exhibit defective meiotic recombination and abnormal synapsis. Mechanistically, using END-seq, we demonstrate reduced DSB formation and abnormal DSB end resection occurs in mutant spermatocytes. We further identify that deletion of Rad50 in gonocytes leads to complete loss of spermatogonial stem cells due to genotoxic stress. Taken together, our results reveal the essential role of Rad50 in mammalian germ cell meiosis and mitosis, and provide in vivo views of RAD50 function in meiotic DSB formation and end resection at the molecular level.
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Affiliation(s)
- Yuefang Liu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junyi Yan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xi Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Han Tong
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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7
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Galanti L, Peritore M, Gnügge R, Cannavo E, Heipke J, Palumbieri MD, Steigenberger B, Symington LS, Cejka P, Pfander B. Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination. Nat Commun 2024; 15:2890. [PMID: 38570537 PMCID: PMC10991553 DOI: 10.1038/s41467-024-46951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.
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Affiliation(s)
- Lorenzo Galanti
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Johannes Heipke
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Maria Dilia Palumbieri
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Boris Pfander
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany.
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8
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Alfano L, Iannuzzi CA, Barone D, Forte IM, Ragosta MC, Cuomo M, Mazzarotti G, Dell'Aquila M, Altieri A, Caporaso A, Roma C, Marra L, Boffo S, Indovina P, De Laurentiis M, Giordano A. CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice. Oncogene 2024; 43:1263-1273. [PMID: 38433256 DOI: 10.1038/s41388-024-02982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.
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Affiliation(s)
- Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy.
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Iris Maria Forte
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | | | - Maria Cuomo
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulio Mazzarotti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Milena Dell'Aquila
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Antonella Caporaso
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Laura Marra
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Paola Indovina
- Sbarro Research Health Organization, Candiolo, Torino, Italy
| | - Michelino De Laurentiis
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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9
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Merker L, Feller L, Dorn A, Puchta H. Deficiency of both classical and alternative end-joining pathways leads to a synergistic defect in double-strand break repair but not to an increase in homology-dependent gene targeting in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:242-254. [PMID: 38179887 DOI: 10.1111/tpj.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
In eukaryotes, double-strand breaks (DSBs) are either repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). In somatic plant cells, HR is very inefficient. Therefore, the vast majority of DSBs are repaired by two different pathways of NHEJ. The classical (cNHEJ) pathway depends on the heterodimer KU70/KU80, while polymerase theta (POLQ) is central to the alternative (aNHEJ) pathway. Surprisingly, Arabidopsis plants are viable, even when both pathways are impaired. However, they exhibit severe growth retardation and reduced fertility. Analysis of mitotic anaphases indicates that the double mutant is characterized by a dramatic increase in chromosome fragmentation due to defective DSB repair. In contrast to the single mutants, the double mutant was found to be highly sensitive to the DSB-inducing genotoxin bleomycin. Thus, both pathways can complement for each other efficiently in DSB repair. We speculated that in the absence of both NHEJ pathways, HR might be enhanced. This would be especially attractive for gene targeting (GT) in which predefined changes are introduced using a homologous template. Unexpectedly, the polq single mutant as well as the double mutant showed significantly lower GT frequencies in comparison to wildtype plants. Accordingly, we were able to show that elimination of both NHEJ pathways does not pose an attractive approach for Agrobacterium-mediated GT. However, our results clearly indicate that a loss of cNHEJ leads to an increase in GT frequency, which is especially drastic and attractive for practical applications, in which the in planta GT strategy is used.
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Affiliation(s)
- Laura Merker
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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10
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Locke AJ, Abou Farraj R, Tran C, Zeinali E, Mashayekhi F, Ali JYH, Glover JNM, Ismail IH. The role of RNF138 in DNA end resection is regulated by ubiquitylation and CDK phosphorylation. J Biol Chem 2024; 300:105709. [PMID: 38309501 PMCID: PMC10910129 DOI: 10.1016/j.jbc.2024.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Double-strand breaks (DSBs) are DNA lesions that pose a significant threat to genomic stability. The repair of DSBs by the homologous recombination (HR) pathway is preceded by DNA end resection, the 5' to 3' nucleolytic degradation of DNA away from the DSB. We and others previously identified a role for RNF138, a really interesting new gene finger E3 ubiquitin ligase, in stimulating DNA end resection and HR. Yet, little is known about how RNF138's function is regulated in the context of DSB repair. Here, we show that RNF138 is phosphorylated at residue T27 by cyclin-dependent kinase (CDK) activity during the S and G2 phases of the cell cycle. We also observe that RNF138 is ubiquitylated constitutively, with ubiquitylation occurring in part on residue K158 and rising during the S/G2 phases. Interestingly, RNF138 ubiquitylation decreases upon genotoxic stress. By mutating RNF138 at residues T27, K158, and the previously identified S124 ataxia telangiectasia mutated phosphorylation site (Han et al., 2016, ref. 22), we find that post-translational modifications at all three positions mediate DSB repair. Cells expressing the T27A, K158R, and S124A variants of RNF138 are impaired in DNA end resection, HR activity, and are more sensitive to ionizing radiation compared to those expressing wildtype RNF138. Our findings shed more light on how RNF138 activity is controlled by the cell during HR.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Caroline Tran
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jana Yasser Hafez Ali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
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11
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Matsuzaki S, Sakuma T, Yamamoto T. REMOVER-PITCh: microhomology-assisted long-range gene replacement with highly multiplexed CRISPR-Cas9. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00850-1. [PMID: 38334880 DOI: 10.1007/s11626-024-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
A variety of CRISPR-Cas9-based gene editing technologies have been developed, including gene insertion and gene replacement, and applied to the study and treatment of diseases. While numerous studies have been conducted to improve the efficiency of gene insertion and to expand the system in various ways, there have been relatively few reports on gene replacement technology; therefore, further improvements are still needed in this context. Here, we developed the REMOVER-PITCh system to establish an efficient long-range gene replacement method and demonstrated its utility at two genomic loci in human cultured cells. REMOVER-PITCh depends on microhomology-assisted gene insertion technology called PITCh with highly multiplexed CRISPR-Cas9. First, we achieved gene replacement of about 20-kb GUSB locus using this system. Second, by applying the previously established knock-in-enhancing platform, the LoAD system, along with REMOVER-PITCh, we achieved the replacement of a longer gene region of about 200 kb at the ARSB locus. Our REMOVER-PITCh system will make it possible to remove and incorporate a variety of sequences from and into the genome, respectively, which will facilitate the generation of various disease and humanized models.
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Affiliation(s)
- Shu Matsuzaki
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624 Shimokotachi, Koda-Cho, Akitakata-Shi, Hiroshima, 739-1195, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
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12
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Möller C, Sharma R, Öz R, Reginato G, Cannavo E, Ceppi I, Sriram KK, Cejka P, Westerlund F. Xrs2/NBS1 promote end-bridging activity of the MRE11-RAD50 complex. Biochem Biophys Res Commun 2024; 695:149464. [PMID: 38217957 DOI: 10.1016/j.bbrc.2023.149464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/04/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
DNA double strand breaks (DSBs) can be detrimental to the cell and need to be efficiently repaired. A first step in DSB repair is to bring the free ends in close proximity to enable ligation by non-homologous end-joining (NHEJ), while the more precise, but less available, repair by homologous recombination (HR) requires close proximity of a sister chromatid. The human MRE11-RAD50-NBS1 (MRN) complex, Mre11-Rad50-Xrs2 (MRX) in yeast, is involved in both repair pathways. Here we use nanofluidic channels to study, on the single DNA molecule level, how MRN, MRX and their constituents interact with long DNA and promote DNA bridging. Nanofluidics is a suitable method to study reactions on DNA ends since no anchoring of the DNA end(s) is required. We demonstrate that NBS1 and Xrs2 play important, but differing, roles in the DNA tethering by MRN and MRX. NBS1 promotes DNA bridging by MRN consistent with tethering of a repair template. MRX shows a "synapsis-like" DNA end-bridging, stimulated by the Xrs2 subunit. Our results highlight the different ways MRN and MRX bridge DNA, and the results are in agreement with their key roles in HR and NHEJ, respectively, and contribute to the understanding of the roles of NBS1 and Xrs2 in DSB repair.
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Affiliation(s)
- Carl Möller
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Rajhans Sharma
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Robin Öz
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Giordano Reginato
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - Elda Cannavo
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - K K Sriram
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Petr Cejka
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden.
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13
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Waters KL, Spratt DE. New Discoveries on Protein Recruitment and Regulation during the Early Stages of the DNA Damage Response Pathways. Int J Mol Sci 2024; 25:1676. [PMID: 38338953 PMCID: PMC10855619 DOI: 10.3390/ijms25031676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Maintaining genomic stability and properly repairing damaged DNA is essential to staying healthy and preserving cellular homeostasis. The five major pathways involved in repairing eukaryotic DNA include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), and homologous recombination (HR). When these pathways do not properly repair damaged DNA, genomic stability is compromised and can contribute to diseases such as cancer. It is essential that the causes of DNA damage and the consequent repair pathways are fully understood, yet the initial recruitment and regulation of DNA damage response proteins remains unclear. In this review, the causes of DNA damage, the various mechanisms of DNA damage repair, and the current research regarding the early steps of each major pathway were investigated.
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Affiliation(s)
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
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14
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Chen Y, Wu J, Zhai L, Zhang T, Yin H, Gao H, Zhao F, Wang Z, Yang X, Jin M, Huang B, Ding X, Li R, Yang J, He Y, Wang Q, Wang W, Kloeber JA, Li Y, Hao B, Zhang Y, Wang J, Tan M, Li K, Wang P, Lou Z, Yuan J. Metabolic regulation of homologous recombination repair by MRE11 lactylation. Cell 2024; 187:294-311.e21. [PMID: 38128537 DOI: 10.1016/j.cell.2023.11.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 08/09/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
Lactylation is a lactate-induced post-translational modification best known for its roles in epigenetic regulation. Herein, we demonstrate that MRE11, a crucial homologous recombination (HR) protein, is lactylated at K673 by the CBP acetyltransferase in response to DNA damage and dependent on ATM phosphorylation of the latter. MRE11 lactylation promotes its binding to DNA, facilitating DNA end resection and HR. Inhibition of CBP or LDH downregulated MRE11 lactylation, impaired HR, and enhanced chemosensitivity of tumor cells in patient-derived xenograft and organoid models. A cell-penetrating peptide that specifically blocks MRE11 lactylation inhibited HR and sensitized cancer cells to cisplatin and PARPi. These findings unveil lactylation as a key regulator of HR, providing fresh insights into the ways in which cellular metabolism is linked to DSB repair. They also imply that the Warburg effect can confer chemoresistance through enhancing HR and suggest a potential therapeutic strategy of targeting MRE11 lactylation to mitigate the effects.
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Affiliation(s)
- Yuping Chen
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jinhuan Wu
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hui Yin
- Department of Thoracic Surgery, The First Affiliated Hospital of Shaoyang University, Shaoyang 422001, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhe Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaoning Yang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mingpeng Jin
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Bingsong Huang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Xin Ding
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Rui Li
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Jie Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yiming He
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Qianwen Wang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Yunxuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Zhang
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Shanghai 200072, China
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China.
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15
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Ahuja JS, Sandhu R, Huang L, Klein F, Börner GV. Temporal and Functional Relationship between Synaptonemal Complex Morphogenesis and Recombination during Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575218. [PMID: 38260343 PMCID: PMC10802607 DOI: 10.1101/2024.01.11.575218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
During prophase of meiosis I, programmed double strand breaks (DSBs) are processed into crossovers, a critical requirement for segregation of homologous chromosomes (homologs) and genome haploidization in sexually reproducing organisms. Crossovers form via homologous recombination in close temporospatial association with morphogenesis of the synaptonemal complex (SC), a proteinaceous structure that connects paired homologs along their length during the pachytene stage. Synapsis and recombination are a paradigm for the interplay between higher order chromosome structure and DNA metabolism, yet their temporal and functional relationship remains poorly understood. Probing linkage between these processes in budding yeast, we show that SC assembly is associated with a distinct threshold number of unstable D-loops. The transition from bona fide paranemic D-loops to plectonemic DSB single end invasions (SEIs) is completed during midpachynema, when the SC is fully assembled. Double Holliday junctions (dHJs) form at the time of desynapsis and are resolved into crossovers during diplonema. The SC central element component Zip1 shepherds recombination through three transitions, including DSB first end strand exchange and second end capture, as well as dHJ resolution. Zip1 mediates SEI formation independent of its polymerization whereas precocious Zip1 assembly interferes with double Holliday junction resolution. Together, our findings indicate that the synaptonemal complex controls recombination while assembled but also beyond its disassembly, possibly by establishing spatial constraints at recombination sites.
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16
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Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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17
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Kim S, Kim Y, Lee JY. Real-time single-molecule visualization using DNA curtains reveals the molecular mechanisms underlying DNA repair pathways. DNA Repair (Amst) 2024; 133:103612. [PMID: 38128155 DOI: 10.1016/j.dnarep.2023.103612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
The demand for direct observation of biomolecular interactions provides new insights into the molecular mechanisms underlying many biological processes. Single-molecule imaging techniques enable real-time visualization of individual biomolecules, providing direct observations of protein machines. Various single-molecule imaging techniques have been developed and have contributed to breakthroughs in biological research. One such technique is the DNA curtain, a novel, high-throughput, single-molecule platform that integrates lipid fluidity, nano-fabrication, microfluidics, and fluorescence imaging. Many DNA metabolic reactions, such as replication, transcription, and chromatin dynamics, have been studied using DNA curtains. In particular, the DNA curtain platform has been intensively applied in investigating the molecular details of DNA repair processes. This article reviews DNA curtain techniques and their applications for imaging DNA repair proteins.
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Affiliation(s)
- Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Youngseo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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18
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Wu-Baer F, Wong M, Tschoe L, Lin CS, Jiang W, Zha S, Baer R. ATM/ATR Phosphorylation of CtIP on Its Conserved Sae2-like Domain Is Required for Genotoxin-Induced DNA Resection but Dispensable for Animal Development. Cells 2023; 12:2762. [PMID: 38067190 PMCID: PMC10706839 DOI: 10.3390/cells12232762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homology-directed repair (HDR) of double-strand DNA breaks (DSBs) is dependent on enzymatic resection of DNA ends by the Mre11/Rad50/Nbs1 complex. DNA resection is triggered by the CtIP/Sae2 protein, which allosterically promotes Mre11-mediated endonuclease DNA cleavage at a position internal to the DSB. Although the mechanics of resection, including the initial endonucleolytic step, are largely conserved in eucaryotes, CtIP and its functional counterpart in Saccharomyces cerevisiae (Sae2) share only a modest stretch of amino acid homology. Nonetheless, this stretch contains two highly conserved phosphorylation sites for cyclin-dependent kinases (T843 in mouse) and the damage-induced ATM/ATR kinases (T855 in mouse), both of which are required for DNA resection. To explore the function of ATM/ATR phosphorylation at Ctip-T855, we generated and analyzed mice expressing the Ctip-T855A mutant. Surprisingly, unlike Ctip-null mice and Ctip-T843A-expressing mice, both of which undergo embryonic lethality, homozygous CtipT855A/T855A mice develop normally. Nonetheless, they are hypersensitive to ionizing radiation, and CtipT855A/T855A mouse embryo fibroblasts from these mice display marked defects in DNA resection, chromosomal stability, and HDR-mediated repair of DSBs. Thus, although ATM/ATR phosphorylation of CtIP-T855 is not required for normal animal development, it enhances CtIP-mediated DNA resection in response to acute stress, such as genotoxin exposure.
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Affiliation(s)
- Foon Wu-Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Madeline Wong
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Lydia Tschoe
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Chyuan-Sheng Lin
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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19
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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20
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Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT. Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Nat Commun 2023; 14:5759. [PMID: 37717054 PMCID: PMC10505227 DOI: 10.1038/s41467-023-41544-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5' strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site-a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
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Affiliation(s)
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Hannah K Barnes
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Phillip R Woolley
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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21
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van de Kooij B, van der Wal FJ, Rother MB, Creixell P, Stout M, Wiegant W, Joughin BA, Vornberger J, van Vugt MA, Altmeyer M, Yaffe MB, van Attikum H. The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556391. [PMID: 37732274 PMCID: PMC10508776 DOI: 10.1101/2023.09.05.556391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological DNA damaging processes. DSBs are also generated as intermediates during the repair of interstrand crosslinks (ICLs). In this context, the Fanconi anemia (FA) core complex, which is effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether the FA core complex also promotes HR at ICL-independent DSBs remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen with cells carrying the DSB-repair reporter DSB-Spectrum. Using isogenic cell-line models, we validated the HR-function of FANCL and Ube2T, and demonstrated a similar function for their ubiquitination-substrate FANCD2. We further show that FANCL and Ube2T are directly recruited to DSBs and are required for the accumulation of FANCD2 at these break sites. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of the nuclease CtIP at DSBs, and consequently for optimal end-resection and Rad51 loading. CtIP overexpression rescues HR in FANCL-deficient cells, validating that FANCL primarily regulates HR by promoting CtIP recruitment. Together, these data demonstrate that the FA core complex and FANCD2 have a dual genome maintenance function by promoting repair of DSBs as well as the repair of ICLs.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Current address: Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Fenna J. van der Wal
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Magdalena B. Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Pau Creixell
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Merula Stout
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Brian A. Joughin
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Vornberger
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Marcel A.T.M. van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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22
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Myler LR, Toia B, Vaughan CK, Takai K, Matei AM, Wu P, Paull TT, de Lange T, Lottersberger F. DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres. Nat Struct Mol Biol 2023; 30:1346-1356. [PMID: 37653239 PMCID: PMC10497418 DOI: 10.1038/s41594-023-01072-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Telomeres replicated by leading-strand synthesis lack the 3' overhang required for telomere protection. Surprisingly, resection of these blunt telomeres is initiated by the telomere-specific 5' exonuclease Apollo rather than the Mre11-Rad50-Nbs1 (MRN) complex, the nuclease that acts at DNA breaks. Without Apollo, leading-end telomeres undergo fusion, which, as demonstrated here, is mediated by alternative end joining. Here, we show that DNA-PK and TRF2 coordinate the repression of MRN at blunt mouse telomeres. DNA-PK represses an MRN-dependent long-range resection, while the endonuclease activity of MRN-CtIP, which could cleave DNA-PK off of blunt telomere ends, is inhibited in vitro and in vivo by the iDDR of TRF2. AlphaFold-Multimer predicts a conserved association of the iDDR with Rad50, potentially interfering with CtIP binding and MRN endonuclease activation. We propose that repression of MRN-mediated resection is a conserved aspect of telomere maintenance and represents an ancient feature of DNA-PK and the iDDR.
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Affiliation(s)
- Logan R Myler
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Beatrice Toia
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Cara K Vaughan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Kaori Takai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Andreea M Matei
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Peng Wu
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA.
| | - Francisca Lottersberger
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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23
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Bian X, Sun C, Cheng J, Hong B. Targeting DNA Damage Repair and Immune Checkpoint Proteins for Optimizing the Treatment of Endometrial Cancer. Pharmaceutics 2023; 15:2241. [PMID: 37765210 PMCID: PMC10536053 DOI: 10.3390/pharmaceutics15092241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 09/29/2023] Open
Abstract
The dependence of cancer cells on the DNA damage response (DDR) pathway for the repair of endogenous- or exogenous-factor-induced DNA damage has been extensively studied in various cancer types, including endometrial cancer (EC). Targeting one or more DNA damage repair protein with small molecules has shown encouraging treatment efficacy in preclinical and clinical models. However, the genes coding for DDR factors are rarely mutated in EC, limiting the utility of DDR inhibitors in this disease. In the current review, we recapitulate the functional role of the DNA repair system in the development and progression of cancer. Importantly, we discuss strategies that target DDR proteins, including PARP, CHK1 and WEE1, as monotherapies or in combination with cytotoxic agents in the treatment of EC and highlight the compounds currently being evaluated for their efficacy in EC in clinic. Recent studies indicate that the application of DNA damage agents in cancer cells leads to the activation of innate and adaptive immune responses; targeting immune checkpoint proteins could overcome the immune suppressive environment in tumors. We further summarize recently revolutionized immunotherapies that have been completed or are now being evaluated for their efficacy in advanced EC and propose future directions for the development of DDR-based cancer therapeutics in the treatment of EC.
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Affiliation(s)
- Xing Bian
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Chuanbo Sun
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Jin Cheng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Bo Hong
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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24
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Sun JKL, Wong GCN, Chow KHM. Cross-talk between DNA damage response and the central carbon metabolic network underlies selective vulnerability of Purkinje neurons in ataxia-telangiectasia. J Neurochem 2023; 166:654-677. [PMID: 37319113 DOI: 10.1111/jnc.15881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023]
Abstract
Cerebellar ataxia is often the first and irreversible outcome in the disease of ataxia-telangiectasia (A-T), as a consequence of selective cerebellar Purkinje neuronal degeneration. A-T is an autosomal recessive disorder resulting from the loss-of-function mutations of the ataxia-telangiectasia-mutated ATM gene. Over years of research, it now becomes clear that functional ATM-a serine/threonine kinase protein product of the ATM gene-plays critical roles in regulating both cellular DNA damage response and central carbon metabolic network in multiple subcellular locations. The key question arises is how cerebellar Purkinje neurons become selectively vulnerable when all other cell types in the brain are suffering from the very same defects in ATM function. This review intended to comprehensively elaborate the unexpected linkages between these two seemingly independent cellular functions and the regulatory roles of ATM involved, their integrated impacts on both physical and functional properties, hence the introduction of selective vulnerability to Purkinje neurons in the disease will be addressed.
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Affiliation(s)
- Jacquelyne Ka-Li Sun
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
| | - Genper Chi-Ngai Wong
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
| | - Kim Hei-Man Chow
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong
- Nexus of Rare Neurodegenerative Diseases, The Chinese University of Hong Kong, Hong Kong
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25
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Leung W, Simoneau A, Saxena S, Jackson J, Patel PS, Limbu M, Vindigni A, Zou L. ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms. Cell Rep 2023; 42:112792. [PMID: 37454295 PMCID: PMC10529362 DOI: 10.1016/j.celrep.2023.112792] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/06/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
The ATR kinase safeguards genomic integrity during S phase, but how ATR protects DNA replication forks remains incompletely understood. Here, we combine four distinct assays to analyze ATR functions at ongoing and newly assembled replication forks upon replication inhibition by hydroxyurea. At ongoing forks, ATR inhibitor (ATRi) increases MRE11- and EXO1-mediated nascent DNA degradation from PrimPol-generated, single-stranded DNA (ssDNA) gaps. ATRi also exposes template ssDNA through fork uncoupling and nascent DNA degradation. Electron microscopy reveals that ATRi reduces reversed forks by increasing gap-dependent nascent DNA degradation. At new forks, ATRi triggers MRE11- and CtIP-initiated template DNA degradation by EXO1, exposing nascent ssDNA. Upon PARP inhibition, ATRi preferentially exacerbates gap-dependent nascent DNA degradation at ongoing forks in BRCA1/2-deficient cells and disrupts the restored gap protection in BRCA1-deficient, PARP-inhibitor-resistant cells. Thus, ATR protects ongoing and new forks through distinct mechanisms, providing an extended view of ATR's functions in stabilizing replication forks.
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Affiliation(s)
- Wendy Leung
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Parasvi S Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mangsi Limbu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA.
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26
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Calheiros J, Corbo V, Saraiva L. Overcoming therapeutic resistance in pancreatic cancer: Emerging opportunities by targeting BRCAs and p53. Biochim Biophys Acta Rev Cancer 2023; 1878:188914. [PMID: 37201730 DOI: 10.1016/j.bbcan.2023.188914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Pancreatic cancer (PC) is characterized by (epi)genetic and microenvironmental alterations that negatively impact the treatment outcomes. New targeted therapies have been pursued to counteract the therapeutic resistance in PC. Aiming to seek for new therapeutic options for PC, several attempts have been undertaken to exploit BRCA1/2 and TP53 deficiencies as promising actionable targets. The elucidation of the pathogenesis of PC highlighted the high prevalence of p53 mutations and their connection with the aggressiveness and therapeutic resistance of PC. Additionally, PC is associated with dysfunctions in several DNA repair-related genes, including BRCA1/2, which sensitize tumours to DNA-damaging agents. In this context, poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) were approved for mutant BRCA1/2 PC patients. However, acquired drug resistance has become a major drawback of PARPi. This review emphasizes the importance of targeting defective BRCAs and p53 pathways for advancing personalized PC therapy, with particular focus on how this approach may provide an opportunity to tackle PC resistance.
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Affiliation(s)
- Juliana Calheiros
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Vincenzo Corbo
- Department of Engineering for Innovation Medicine (DIMI), University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Lucília Saraiva
- LAQV/REQUIMTE, Laboratόrio de Microbiologia, Departamento de Ciências Biolόgicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
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27
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Campos A, Ramos F, Iglesias L, Delgado C, Merino E, Esperilla-Muñoz A, Correa-Bordes J, Clemente-Blanco A. Cdc14 phosphatase counteracts Cdk-dependent Dna2 phosphorylation to inhibit resection during recombinational DNA repair. Nat Commun 2023; 14:2738. [PMID: 37173316 PMCID: PMC10182099 DOI: 10.1038/s41467-023-38417-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cyclin-dependent kinase (Cdk) stimulates resection of DNA double-strand breaks ends to generate single-stranded DNA (ssDNA) needed for recombinational DNA repair. Here we show in Saccharomyces cerevisiae that lack of the Cdk-counteracting phosphatase Cdc14 produces abnormally extended resected tracts at the DNA break ends, involving the phosphatase in the inhibition of resection. Over-resection in the absence of Cdc14 activity is bypassed when the exonuclease Dna2 is inactivated or when its Cdk consensus sites are mutated, indicating that the phosphatase restrains resection by acting through this nuclease. Accordingly, mitotically activated Cdc14 promotes Dna2 dephosphorylation to exclude it from the DNA lesion. Cdc14-dependent resection inhibition is essential to sustain DNA re-synthesis, thus ensuring the appropriate length, frequency, and distribution of the gene conversion tracts. These results establish a role for Cdc14 in controlling the extent of resection through Dna2 regulation and demonstrate that the accumulation of excessively long ssDNA affects the accurate repair of the broken DNA by homologous recombination.
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Affiliation(s)
- Adrián Campos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Facundo Ramos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Lydia Iglesias
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Celia Delgado
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Eva Merino
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | | | - Jaime Correa-Bordes
- Departamento de Ciencias Biomédicas, Universidad de Extremadura, Badajoz, Spain
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain.
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28
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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29
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Otahalova B, Volkova Z, Soukupova J, Kleiblova P, Janatova M, Vocka M, Macurek L, Kleibl Z. Importance of Germline and Somatic Alterations in Human MRE11, RAD50, and NBN Genes Coding for MRN Complex. Int J Mol Sci 2023; 24:ijms24065612. [PMID: 36982687 PMCID: PMC10051278 DOI: 10.3390/ijms24065612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The MRE11, RAD50, and NBN genes encode for the nuclear MRN protein complex, which senses the DNA double strand breaks and initiates the DNA repair. The MRN complex also participates in the activation of ATM kinase, which coordinates DNA repair with the p53-dependent cell cycle checkpoint arrest. Carriers of homozygous germline pathogenic variants in the MRN complex genes or compound heterozygotes develop phenotypically distinct rare autosomal recessive syndromes characterized by chromosomal instability and neurological symptoms. Heterozygous germline alterations in the MRN complex genes have been associated with a poorly-specified predisposition to various cancer types. Somatic alterations in the MRN complex genes may represent valuable predictive and prognostic biomarkers in cancer patients. MRN complex genes have been targeted in several next-generation sequencing panels for cancer and neurological disorders, but interpretation of the identified alterations is challenging due to the complexity of MRN complex function in the DNA damage response. In this review, we outline the structural characteristics of the MRE11, RAD50 and NBN proteins, the assembly and functions of the MRN complex from the perspective of clinical interpretation of germline and somatic alterations in the MRE11, RAD50 and NBN genes.
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Affiliation(s)
- Barbora Otahalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University in Prague, 12800 Prague, Czech Republic
| | - Zuzana Volkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine and General University Hospital in Prague, 12853 Prague, Czech Republic
- Correspondence: ; Tel.: +420-22496-4287
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30
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Mre11-Rad50: the DNA end game. Biochem Soc Trans 2023; 51:527-538. [PMID: 36892213 DOI: 10.1042/bst20220754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The Mre11-Rad50-(Nbs1/Xrs2) complex is an evolutionarily conserved factor for the repair of DNA double-strand breaks and other DNA termini in all kingdoms of life. It is an intricate DNA associated molecular machine that cuts, among other functions, a large variety of free and obstructed DNA termini for DNA repair by end joining or homologous recombination, yet leaves undamaged DNA intact. Recent years have brought progress in both the structural and functional analyses of Mre11-Rad50 orthologs, revealing mechanisms of DNA end recognition, endo/exonuclease activities, nuclease regulation and DNA scaffolding. Here, I review our current understanding and recent progress on the functional architecture Mre11-Rad50 and how this chromosome associated coiled-coil ABC ATPase acts as DNA topology specific endo-/exonuclease.
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31
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Rinaldi C, Pizzul P, Casari E, Mangiagalli M, Tisi R, Longhese MP. The Ku complex promotes DNA end-bridging and this function is antagonized by Tel1/ATM kinase. Nucleic Acids Res 2023; 51:1783-1802. [PMID: 36762474 PMCID: PMC9976877 DOI: 10.1093/nar/gkad062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by either homologous recombination (HR) or non-homologous end-joining (NHEJ). NHEJ is induced by the binding to DSBs of the Ku70-Ku80 heterodimer, which acts as a hub for the recruitment of downstream NHEJ components. An important issue in DSB repair is the maintenance of the DSB ends in close proximity, a function that in yeast involves the MRX complex and Sae2. Here, we provide evidence that Ku contributes to keep the DNA ends tethered to each other. The ku70-C85Y mutation, which increases Ku affinity for DNA and its persistence very close to the DSB ends, enhances DSB end-tethering and suppresses the end-tethering defect of sae2Δ cells. Impairing histone removal around DSBs either by eliminating Tel1 kinase activity or nucleosome remodelers enhances Ku persistence at DSBs and DSB bridging, suggesting that Tel1 antagonizes the Ku function in supporting end-tethering by promoting nucleosome removal and possibly Ku sliding inwards. As Ku provides a block to DSB resection, this Tel1 function can be important to regulate the mode by which DSBs are repaired.
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Affiliation(s)
- Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Marco Mangiagalli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
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Mengoli V, Ceppi I, Sanchez A, Cannavo E, Halder S, Scaglione S, Gaillard P, McHugh PJ, Riesen N, Pettazzoni P, Cejka P. WRN helicase and mismatch repair complexes independently and synergistically disrupt cruciform DNA structures. EMBO J 2023; 42:e111998. [PMID: 36541070 PMCID: PMC9890227 DOI: 10.15252/embj.2022111998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The Werner Syndrome helicase, WRN, is a promising therapeutic target in cancers with microsatellite instability (MSI). Long-term MSI leads to the expansion of TA nucleotide repeats proposed to form cruciform DNA structures, which in turn cause DNA breaks and cell lethality upon WRN downregulation. Here we employed biochemical assays to show that WRN helicase can efficiently and directly unfold cruciform structures, thereby preventing their cleavage by the SLX1-SLX4 structure-specific endonuclease. TA repeats are particularly prone to form cruciform structures, explaining why these DNA sequences are preferentially broken in MSI cells upon WRN downregulation. We further demonstrate that the activity of the DNA mismatch repair (MMR) complexes MutSα (MSH2-MSH6), MutSβ (MSH2-MSH3), and MutLα (MLH1-PMS2) similarly decreases the level of DNA cruciforms, although the mechanism is different from that employed by WRN. When combined, WRN and MutLα exhibited higher than additive effects in in vitro cruciform processing, suggesting that WRN and the MMR proteins may cooperate. Our data explain how WRN and MMR defects cause genome instability in MSI cells with expanded TA repeats, and provide a mechanistic basis for their recently discovered synthetic-lethal interaction with promising applications in precision cancer therapy.
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Affiliation(s)
- Valentina Mengoli
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Ilaria Ceppi
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Aurore Sanchez
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Elda Cannavo
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Swagata Halder
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Sarah Scaglione
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Pierre‐Henri Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Nathalie Riesen
- Roche Pharma Research & Early Development pREDRoche Innovation CenterBaselSwitzerland
| | | | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)BellinzonaSwitzerland
- Department of Biology, Institute of BiochemistryEidgenössische Technische Hochschule (ETH)ZürichSwitzerland
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Ceppi I, Cannavo E, Bret H, Camarillo R, Vivalda F, Thakur RS, Romero-Franco A, Sartori AA, Huertas P, Guérois R, Cejka P. PLK1 regulates CtIP and DNA2 interplay in long-range DNA end resection. Genes Dev 2023; 37:119-135. [PMID: 36746606 PMCID: PMC10069449 DOI: 10.1101/gad.349981.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
DNA double-strand break (DSB) repair is initiated by DNA end resection. CtIP acts in short-range resection to stimulate MRE11-RAD50-NBS1 (MRN) to endonucleolytically cleave 5'-terminated DNA to bypass protein blocks. CtIP also promotes the DNA2 helicase-nuclease to accelerate long-range resection downstream from MRN. Here, using AlphaFold2, we identified CtIP-F728E-Y736E as a separation-of-function mutant that is still proficient in conjunction with MRN but is not able to stimulate ssDNA degradation by DNA2. Accordingly, CtIP-F728E-Y736E impairs physical interaction with DNA2. Cellular assays revealed that CtIP-F728E-Y736E cells exhibit reduced DSB-dependent chromatin-bound RPA, impaired long-range resection, and increased sensitivity to DSB-inducing drugs. Previously, CtIP was shown to be targeted by PLK1 to inhibit long-range resection, yet the underlying mechanism was unclear. We show that the DNA2-interacting region in CtIP includes the PLK1 target site at S723. The integrity of S723 in CtIP is necessary for the stimulation of DNA2, and phosphorylation of CtIP by PLK1 in vitro is consequently inhibitory, explaining why PLK1 restricts long-range resection. Our data support a model in which CDK-dependent phosphorylation of CtIP activates resection by MRN in S phase, and PLK1-mediated phosphorylation of CtIP disrupts CtIP stimulation of DNA2 to attenuate long-range resection later at G2/M.
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Affiliation(s)
- Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
| | - Hélène Bret
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Rosa Camarillo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Francesca Vivalda
- Institute of Molecular Cancer Research, University of Zürich, Zürich 8057, Switzerland
| | - Roshan Singh Thakur
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
| | - Amador Romero-Franco
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zürich, Zürich 8057, Switzerland
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland;
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
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ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
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Patterson-Fortin J, D'Andrea AD. Targeting Polymerase Theta (POLθ) for Cancer Therapy. Cancer Treat Res 2023; 186:285-298. [PMID: 37978141 DOI: 10.1007/978-3-031-30065-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Polymerase theta (POLθ) is the critical multi-domain enzyme in microhomology-mediated end-joining DNA double-stranded break repair. POLθ is expressed at low levels in normal tissue but is often overexpressed in cancers, especially in DNA repair deficient cancers, such as homologous-recombination cancers, rendering them exquisitely sensitive to POLθ inhibition secondary to synthetic lethality. Development of POLθ inhibitors is an active area of investigation with inhibitors of the N-terminal helicase domain or the C-terminal polymerase domain currently in clinical trial. Here, we review POLθ-mediated microhomology-mediated end-joining, the development of POLθ inhibitors, and the potential clinical uses of POLθ inhibitors.
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Affiliation(s)
- Jeffrey Patterson-Fortin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Harvard Medical School, Center for DNA Damage and Repair, Susan F. Smith Center for Women's Cancers (SFSCWC), The Fuller-American Cancer Society, Dana-Farber Cancer Institute, HIM 243, 450 Brookline Ave., Boston, MA, 02215, USA.
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36
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Kim H, Kim D, Choi H, Shin G, Lee JK. Deubiquitinase USP2 stabilizes the MRE11-RAD50-NBS1 complex at DNA double-strand break sites by counteracting the ubiquitination of NBS1. J Biol Chem 2022; 299:102752. [PMID: 36436562 PMCID: PMC9758435 DOI: 10.1016/j.jbc.2022.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex plays essential roles in the cellular response to DNA double-strand breaks (DSBs), which are the most cytotoxic DNA lesions, and is a target of various modifications and controls. Recently, lysine 48-linked ubiquitination of NBS1, resulting in premature disassembly of the MRN complex from DSB sites, was observed in cells lacking RECQL4 helicase activity. However, the role and control of this ubiquitination during the DSB response in cells with intact RECQL4 remain unknown. Here, we showed that USP2 counteracts this ubiquitination and stabilizes the MRN complex during the DSB response. By screening deubiquitinases that increase the stability of the MRN complex in RECQL4-deficient cells, USP2 was identified as a new deubiquitinase that acts at DSB sites to counteract NBS1 ubiquitination. We determined that USP2 is recruited to DSB sites in a manner dependent on ATM, a major checkpoint kinase against DSBs, and stably interacts with NBS1 and RECQL4 in immunoprecipitation experiments. Phosphorylation of two critical residues in the N terminus of USP2 by ATM is required for its recruitment to DSBs and its interaction with RECQL4. While inactivation of USP2 alone does not substantially influence the DSB response, we found that inactivation of USP2 and USP28, another deubiquitinase influencing NBS1 ubiquitination, results in premature disassembly of the MRN complex from DSB sites as well as defects in ATM activation and homologous recombination repair abilities. These results suggest that deubiquitinases counteracting NBS1 ubiquitination are essential for the stable maintenance of the MRN complex and proper cellular response to DSBs.
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Affiliation(s)
- Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Dongmin Kim
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Hyemin Choi
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea; Department of Biology Education, Seoul National University, Seoul, Korea.
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37
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Mann A, Ramirez-Otero MA, De Antoni A, Hanthi YW, Sannino V, Baldi G, Falbo L, Schrempf A, Bernardo S, Loizou J, Costanzo V. POLθ prevents MRE11-NBS1-CtIP-dependent fork breakage in the absence of BRCA2/RAD51 by filling lagging-strand gaps. Mol Cell 2022; 82:4218-4231.e8. [PMID: 36400008 DOI: 10.1016/j.molcel.2022.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/16/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
POLθ promotes repair of DNA double-strand breaks (DSBs) resulting from collapsed forks in homologous recombination (HR) defective tumors. Inactivation of POLθ results in synthetic lethality with the loss of HR genes BRCA1/2, which induces under-replicated DNA accumulation. However, it is unclear whether POLθ-dependent DNA replication prevents HR-deficiency-associated lethality. Here, we isolated Xenopus laevis POLθ and showed that it processes stalled Okazaki fragments, directly visualized by electron microscopy, thereby suppressing ssDNA gaps accumulating on lagging strands in the absence of RAD51 and preventing fork reversal. Inhibition of POLθ DNA polymerase activity leaves fork gaps unprotected, enabling their cleavage by the MRE11-NBS1-CtIP endonuclease, which produces broken forks with asymmetric single-ended DSBs, hampering BRCA2-defective cell survival. These results reveal a POLθ-dependent genome protection function preventing stalled forks rupture and highlight possible resistance mechanisms to POLθ inhibitors.
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Affiliation(s)
- Anjali Mann
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Miguel Angel Ramirez-Otero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna De Antoni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Yodhara Wijesekara Hanthi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Vincenzo Sannino
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Giorgio Baldi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Lucia Falbo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna Schrempf
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Sara Bernardo
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Joanna Loizou
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Vincenzo Costanzo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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38
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Kapoor-Vazirani P, Rath SK, Liu X, Shu Z, Bowen NE, Chen Y, Haji-Seyed-Javadi R, Daddacha W, Minten EV, Danelia D, Farchi D, Duong DM, Seyfried NT, Deng X, Ortlund EA, Kim B, Yu DS. SAMHD1 deacetylation by SIRT1 promotes DNA end resection by facilitating DNA binding at double-strand breaks. Nat Commun 2022; 13:6707. [PMID: 36344525 PMCID: PMC9640623 DOI: 10.1038/s41467-022-34578-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) has a dNTPase-independent function in promoting DNA end resection to facilitate DNA double-strand break (DSB) repair by homologous recombination (HR); however, it is not known if upstream signaling events govern this activity. Here, we show that SAMHD1 is deacetylated by the SIRT1 sirtuin deacetylase, facilitating its binding with ssDNA at DSBs, to promote DNA end resection and HR. SIRT1 complexes with and deacetylates SAMHD1 at conserved lysine 354 (K354) specifically in response to DSBs. K354 deacetylation by SIRT1 promotes DNA end resection and HR but not SAMHD1 tetramerization or dNTPase activity. Mechanistically, K354 deacetylation by SIRT1 promotes SAMHD1 recruitment to DSBs and binding to ssDNA at DSBs, which in turn facilitates CtIP ssDNA binding, leading to promotion of genome integrity. These findings define a mechanism governing the dNTPase-independent resection function of SAMHD1 by SIRT1 deacetylation in promoting HR and genome stability.
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Affiliation(s)
- Priya Kapoor-Vazirani
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sandip K Rath
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhen Shu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yitong Chen
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ramona Haji-Seyed-Javadi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Waaqo Daddacha
- Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA
| | - Elizabeth V Minten
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Diana Danelia
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniela Farchi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xingming Deng
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David S Yu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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39
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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40
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Jiang Y. Contribution of Microhomology to Genome Instability: Connection between DNA Repair and Replication Stress. Int J Mol Sci 2022; 23:12937. [PMID: 36361724 PMCID: PMC9657218 DOI: 10.3390/ijms232112937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) is a highly mutagenic pathway to repair double-strand breaks (DSBs). MMEJ was thought to be a backup pathway of homologous recombination (HR) and canonical nonhomologous end joining (C-NHEJ). However, it attracts more attention in cancer research due to its special function of microhomology in many different aspects of cancer. In particular, it is initiated with DNA end resection and upregulated in homologous recombination-deficient cancers. In this review, I summarize the following: (1) the recent findings and contributions of MMEJ to genome instability, including phenotypes relevant to MMEJ; (2) the interaction between MMEJ and other DNA repair pathways; (3) the proposed mechanistic model of MMEJ in DNA DSB repair and a new connection with microhomology-mediated break-induced replication (MMBIR); and (4) the potential clinical application by targeting MMEJ based on synthetic lethality for cancer therapy.
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Affiliation(s)
- Yuning Jiang
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22903, USA
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41
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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42
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Jeong SY, Hariharasudhan G, Kim MJ, Lim JY, Jung SM, Choi EJ, Chang IY, Kee Y, You HJ, Lee JH. SIAH2 regulates DNA end resection and replication fork recovery by promoting CtIP ubiquitination. Nucleic Acids Res 2022; 50:10469-10486. [PMID: 36155803 PMCID: PMC9561274 DOI: 10.1093/nar/gkac808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/19/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Human CtIP maintains genomic integrity primarily by promoting 5′ DNA end resection, an initial step of the homologous recombination (HR). A few mechanisms have been suggested as to how CtIP recruitment to damage sites is controlled, but it is likely that we do not yet have full understanding of the process. Here, we provide evidence that CtIP recruitment and functioning are controlled by the SIAH2 E3 ubiquitin ligase. We found that SIAH2 interacts and ubiquitinates CtIP at its N-terminal lysine residues. Mutating the key CtIP lysine residues impaired CtIP recruitment to DSBs and stalled replication forks, DSB end resection, overall HR repair capacity of cells, and recovery of stalled replication forks, suggesting that the SIAH2-induced ubiquitination is important for relocating CtIP to sites of damage. Depleting SIAH2 consistently phenocopied these results. Overall, our work suggests that SIAH2 is a new regulator of CtIP and HR repair, and emphasizes that SIAH2-mediated recruitment of the CtIP is an important step for CtIP’s function during HR repair.
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Affiliation(s)
- Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Gurusamy Hariharasudhan
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Min-Ji Kim
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Ji-Yeon Lim
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sung Mi Jung
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Eun-Ji Choi
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Younghoon Kee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Ho Jin You
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Jung-Hee Lee
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
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43
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Gómez-Cabello D, Pappas G, Aguilar-Morante D, Dinant C, Bartek J. CtIP-dependent nascent RNA expression flanking DNA breaks guides the choice of DNA repair pathway. Nat Commun 2022; 13:5303. [PMID: 36085345 PMCID: PMC9463442 DOI: 10.1038/s41467-022-33027-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
The RNA world is changing our views about sensing and resolution of DNA damage. Here, we develop single-molecule DNA/RNA analysis approaches to visualize how nascent RNA facilitates the repair of DNA double-strand breaks (DSBs). RNA polymerase II (RNAPII) is crucial for DSB resolution in human cells. DSB-flanking, RNAPII-generated nascent RNA forms RNA:DNA hybrids, guiding the upstream DNA repair steps towards favouring the error-free Homologous Recombination (HR) pathway over Non-Homologous End Joining. Specific RNAPII inhibitor, THZ1, impairs recruitment of essential HR proteins to DSBs, implicating nascent RNA in DNA end resection, initiation and execution of HR repair. We further propose that resection factor CtIP interacts with and helps re-activate RNAPII when paused by the RNA:DNA hybrids, collectively promoting faithful repair of chromosome breaks to maintain genomic integrity. RNA has been implicated in DNA repair. This work shows that the interplay of RNAPII-generated nascent RNA, RNA:DNA hybrids and the resection factor CtIP guide DNA double strand break repair pathway choice towards error-free homologous recombination.
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Affiliation(s)
- Daniel Gómez-Cabello
- Genome Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen, DK-2100, Denmark. .,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain. .,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
| | - George Pappas
- Genome Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen, DK-2100, Denmark
| | - Diana Aguilar-Morante
- Genome Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen, DK-2100, Denmark.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Christoffel Dinant
- Genome Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen, DK-2100, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, Copenhagen, DK-2100, Denmark. .,Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Scheele's vag 2, Stockholm, 17177, Sweden.
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44
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Zhang T, Yang H, Zhou Z, Bai Y, Wang J, Wang W. Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin. Nat Commun 2022; 13:5133. [PMID: 36050397 PMCID: PMC9436968 DOI: 10.1038/s41467-022-32920-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
DNA end resection is delicately regulated through various types of post-translational modifications to initiate homologous recombination, but the involvement of SUMOylation in this process remains incompletely understood. Here, we show that MRE11 requires SUMOylation to shield it from ubiquitin-mediated degradation when resecting damaged chromatin. Upon DSB induction, PIAS1 promotes MRE11 SUMOylation on chromatin to initiate DNA end resection. Then, MRE11 is deSUMOylated by SENP3 mainly after it has moved away from DSB sites. SENP3 deficiency results in MRE11 degradation failure and accumulation on chromatin, causing genome instability. We further show that cancer-related MRE11 mutants with impaired SUMOylation exhibit compromised DNA repair ability. Thus, we demonstrate that MRE11 SUMOylation in coordination with ubiquitylation is dynamically controlled by PIAS1 and SENP3 to facilitate DNA end resection and maintain genome stability. DNA end resection initiating DNA repair by homologous recombination needs to be delicately regulated. This study shows the interplay between SUMOylation and ubiquitylation maintains MRE11 homeostasis on chromatin, thus facilitating genome stability.
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Affiliation(s)
- Tao Zhang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Han Yang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zenan Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yongtai Bai
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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45
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Halder S, Sanchez A, Ranjha L, Reginato G, Ceppi I, Acharya A, Anand R, Cejka P. Double-stranded DNA binding function of RAD51 in DNA protection and its regulation by BRCA2. Mol Cell 2022; 82:3553-3565.e5. [PMID: 36070766 DOI: 10.1016/j.molcel.2022.08.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
RAD51 and the breast cancer suppressor BRCA2 have critical functions in DNA double-strand (dsDNA) break repair by homologous recombination and the protection of newly replicated DNA from nucleolytic degradation. The recombination function of RAD51 requires its binding to single-stranded DNA (ssDNA), whereas binding to dsDNA is inhibitory. Using reconstituted MRE11-, EXO1-, and DNA2-dependent nuclease reactions, we show that the protective function of RAD51 unexpectedly depends on its binding to dsDNA. The BRC4 repeat of BRCA2 abrogates RAD51 binding to dsDNA and accordingly impairs the function of RAD51 in protection. The BRCA2 C-terminal RAD51-binding segment (TR2) acts in a dominant manner to overcome the effect of BRC4. Mechanistically, TR2 stabilizes RAD51 binding to dsDNA, even in the presence of BRC4, promoting DNA protection. Our data suggest that RAD51's dsDNA-binding capacity may have evolved together with its function in replication fork protection and provide a mechanistic basis for the DNA-protection function of BRCA2.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland.
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46
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Qiu Z, Hao S, Song S, Zhang R, Yan T, Lu Z, Wang H, Jia Z, Zheng J. PLK1-mediated phosphorylation of PPIL2 regulates HR via CtIP. Front Cell Dev Biol 2022; 10:902403. [PMID: 36092721 PMCID: PMC9452783 DOI: 10.3389/fcell.2022.902403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR) is an error-free DNA double-strand break (DSB) repair pathway, which safeguards genome integrity and cell viability. Human C-terminal binding protein (CtBP)—interacting protein (CtIP) is a central regulator of the pathway which initiates the DNA end resection in HR. Ubiquitination modification of CtIP is known in some cases to control DNA resection and promote HR. However, it remains unclear how cells restrain CtIP activity in unstressed cells. We show that the ubiquitin E3 ligase PPIL2 is recruited to DNA damage sites through interactions with an HR-related protein ZNF830, implying PPIL2’s involvement in DNA repair. We found that PPIL2 interacts with and ubiquitinates CtIP at the K426 site, representing a hereunto unknown ubiquitination site. Ubiquitination of CtIP by PPIL2 suppresses HR and DNA resection. This inhibition of PPIL2 is also modulated by phosphorylation at multiple sites by PLK1, which reduces PPIL2 ubiquitination of CtIP. Our findings reveal new regulatory complexity in CtIP ubiquitination in DSB repair. We propose that the PPIL2-dependent CtIP ubiquitination prevents CtIP from interacting with DNA, thereby inhibiting HR.
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Affiliation(s)
- Zhiyu Qiu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shikai Song
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ruiling Zhang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Tingyu Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zhifang Lu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
- *Correspondence: Zongchao Jia, ; Jimin Zheng,
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, China
- *Correspondence: Zongchao Jia, ; Jimin Zheng,
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47
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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48
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Kolobynina KG, Rapp A, Cardoso MC. Chromatin Ubiquitination Guides DNA Double Strand Break Signaling and Repair. Front Cell Dev Biol 2022; 10:928113. [PMID: 35865631 PMCID: PMC9294282 DOI: 10.3389/fcell.2022.928113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is the context for all DNA-based molecular processes taking place in the cell nucleus. The initial chromatin structure at the site of the DNA damage determines both, lesion generation and subsequent activation of the DNA damage response (DDR) pathway. In turn, proceeding DDR changes the chromatin at the damaged site and across large fractions of the genome. Ubiquitination, besides phosphorylation and methylation, was characterized as an important chromatin post-translational modification (PTM) occurring at the DNA damage site and persisting during the duration of the DDR. Ubiquitination appears to function as a highly versatile “signal-response” network involving several types of players performing various functions. Here we discuss how ubiquitin modifiers fine-tune the DNA damage recognition and response and how the interaction with other chromatin modifications ensures cell survival.
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49
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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50
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Kissling VM, Reginato G, Bianco E, Kasaciunaite K, Tilma J, Cereghetti G, Schindler N, Lee SS, Guérois R, Luke B, Seidel R, Cejka P, Peter M. Mre11-Rad50 oligomerization promotes DNA double-strand break repair. Nat Commun 2022; 13:2374. [PMID: 35501303 PMCID: PMC9061753 DOI: 10.1038/s41467-022-29841-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/01/2022] [Indexed: 11/08/2022] Open
Abstract
The conserved Mre11-Rad50 complex is crucial for the detection, signaling, end tethering and processing of DNA double-strand breaks. While it is known that Mre11-Rad50 foci formation at DNA lesions accompanies repair, the underlying molecular assembly mechanisms and functional implications remained unclear. Combining pathway reconstitution in electron microscopy, biochemical assays and genetic studies, we show that S. cerevisiae Mre11-Rad50 with or without Xrs2 forms higher-order assemblies in solution and on DNA. Rad50 mediates such oligomerization, and mutations in a conserved Rad50 beta-sheet enhance or disrupt oligomerization. We demonstrate that Mre11-Rad50-Xrs2 oligomerization facilitates foci formation, DNA damage signaling, repair, and telomere maintenance in vivo. Mre11-Rad50 oligomerization does not affect its exonuclease activity but drives endonucleolytic cleavage at multiple sites on the 5'-DNA strand near double-strand breaks. Interestingly, mutations in the human RAD50 beta-sheet are linked to hereditary cancer predisposition and our findings might provide insights into their potential role in chemoresistance.
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Affiliation(s)
- Vera M Kissling
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Giordano Reginato
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500, Bellinzona, Switzerland
| | - Eliana Bianco
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Janny Tilma
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Gea Cereghetti
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Natalie Schindler
- Institute for Developmental and Neurobiology (IDN), Johannes Gutenberg University, 55128, Mainz, Germany
| | - Sung Sik Lee
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
- Scientific Center for Optical and Electron Microscopy, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Brian Luke
- Institute for Developmental and Neurobiology (IDN), Johannes Gutenberg University, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Petr Cejka
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland.
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500, Bellinzona, Switzerland.
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland.
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