1
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Leu YL, Cheng SF, Wang TH, Feng CH, Chen YJ, Hsieh YC, Lan YH, Chen CC. Increasing DNA damage sensitivity through corylin-mediated inhibition of homologous recombination. Biomed Pharmacother 2024; 176:116864. [PMID: 38865847 DOI: 10.1016/j.biopha.2024.116864] [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: 03/24/2024] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND DNA repair allows the survival of cancer cells. Therefore, the development of DNA repair inhibitors is a critical need for sensitizing cancers to chemoradiation. Sae2CtIP has specific functions in initiating DNA end resection, as well as coordinating cell cycle checkpoints, and it also greatly interacts with the DDR at different levels. RESULTS In this study, we demonstrated that corylin, a potential sensitizer, causes deficiencies in DNA repair and DNA damage checkpoints in yeast cells. More specifically, corylin increases DNA damage sensitivity through the Sae2-dependent pathway and impairs the activation of Mec1-Ddc2, Rad53-p and γ-H2A. In breast cancer cells, corylin increases apoptosis and reduces proliferation following Dox treatment by inhibiting CtIP. Xenograft assays showed that treatment with corylin combined with Dox significantly reduced tumor growth in vivo. CONCLUSIONS Our findings herein delineate the mechanisms of action of corylin in regulating DNA repair and indicate that corylin has potential long-term clinical utility as a DDR inhibitor.
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Affiliation(s)
- Yann-Lii Leu
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Shu-Fang Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Tong-Hong Wang
- Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Chun-Hao Feng
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yu-Ju Chen
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yi-Cheng Hsieh
- Office of the Texas State Chemist, Texas A&M AgriLife Research, Texas A&M University System, College Station, TX 77843, USA
| | - Yu-Hsuan Lan
- Department of Pharmacy, College of Pharmacy, China Medical University, No.100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC.
| | - Chin-Chuan Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Healthy Aging Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC.
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2
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De Bragança S, Dillingham MS, Moreno-Herrero F. Recent insights into eukaryotic double-strand DNA break repair unveiled by single-molecule methods. Trends Genet 2023; 39:924-940. [PMID: 37806853 DOI: 10.1016/j.tig.2023.09.004] [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: 06/14/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Genome integrity and maintenance are essential for the viability of all organisms. A wide variety of DNA damage types have been described, but double-strand breaks (DSBs) stand out as one of the most toxic DNA lesions. Two major pathways account for the repair of DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Both pathways involve complex DNA transactions catalyzed by proteins that sequentially or cooperatively work to repair the damage. Single-molecule methods allow visualization of these complex transactions and characterization of the protein:DNA intermediates of DNA repair, ultimately allowing a comprehensive breakdown of the mechanisms underlying each pathway. We review current understanding of the HR and NHEJ responses to DSBs in eukaryotic cells, with a particular emphasis on recent advances through the use of single-molecule techniques.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Mark S Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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3
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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4
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Hamilton NA, Jehru AE, Samples WN, Wendel BM, Mokhtari PD, Courcelle CT, Courcelle J. chi sequences switch the RecBCD helicase-nuclease complex from degradative to replicative modes during the completion of DNA replication. J Biol Chem 2023; 299:103013. [PMID: 36781123 PMCID: PMC10025158 DOI: 10.1016/j.jbc.2023.103013] [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: 11/19/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase-nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with cross-over hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced-replication is processive, but uncoupled with respect to leading and lagging strand synthesis, and can be suppressed by ter sites which limit replisome progression. Our observations demonstrate that convergent replisomes create a substrate that is processed by RecBCD, and that chi, when encountered, switches RecBCD from a degradative to replicative function. We propose that chi serves to functionally differentiate DNA ends created during completion, which require degradation, from those created by chromosomal double-strand breaks, which require resynthesis.
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Affiliation(s)
| | - Avery E. Jehru
- Department of Biology, Portland State University, Portland, Oregon, USA
| | | | - Brian M. Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, Oregon, USA
- For correspondence: Justin Courcelle
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5
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Jagadeesan SK, Potter T, Al-Gafari M, Hooshyar M, Hewapathirana CM, Takallou S, Hajikarimlou M, Burnside D, Samanfar B, Moteshareie H, Smith M, Golshani A. Discovery and identification of genes involved in DNA damage repair in yeast. Gene 2022; 831:146549. [PMID: 35569766 DOI: 10.1016/j.gene.2022.146549] [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: 09/13/2021] [Revised: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 11/04/2022]
Abstract
DNA repair defects are common in tumour cells and can lead to misrepair of double-strand breaks (DSBs), posing a significant challenge to cellular integrity. The overall mechanisms of DSB have been known for decades. However, the list of the genes that affect the efficiency of DSB repair continues to grow. Additional factors that play a role in DSB repair pathways have yet to be identified. In this study, we present a computational approach to identify novel gene functions that are involved in DNA damage repair in Saccharomyces cerevisiae. Among the primary candidates, GAL7, YMR130W, and YHI9 were selected for further analysis since they had not previously been identified as being active in DNA repair pathways. Originally, GAL7 was linked to galactose metabolism. YHI9 and YMR130W encode proteins of unknown functions. Laboratory testing of deletion strains gal7Δ, ymr130wΔ, and yhi9Δ implicated all 3 genes in Homologous Recombination (HR) and/or Non-Homologous End Joining (NHEJ) repair pathways, and enhanced sensitivity to DNA damage-inducing drugs suggested involvement in the broader DNA damage repair machinery. A subsequent genetic interaction analysis revealed interconnections of these three genes, most strikingly through SIR2, SIR3 and SIR4 that are involved in chromatin regulation and DNA damage repair network.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Taylor Potter
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mohsen Hooshyar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | | | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Daniel Burnside
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Houman Moteshareie
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Myron Smith
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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6
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De Falco M, Porritiello A, Rota F, Scognamiglio V, Antonacci A, del Monaco G, De Felice M. The Finely Coordinated Action of SSB and NurA/HerA Complex Strictly Regulates the DNA End Resection Process in Saccharolobus solfataricus. Int J Mol Sci 2022; 23:ijms23052582. [PMID: 35269725 PMCID: PMC8910471 DOI: 10.3390/ijms23052582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
Generation of the 3' overhang is a critical step during homologous recombination (HR) and replication fork rescue processes. This event is usually performed by a series of DNA nucleases and/or helicases. The nuclease NurA and the ATPase HerA, together with the highly conserved MRE11/RAD50 proteins, play an important role in generating 3' single-stranded DNA during archaeal HR. Little is known, however, about HerA-NurA function and activation of this fundamental and complicated DNA repair process. Herein, we analyze the functional relationship among NurA, HerA and the single-strand binding protein SSB from Saccharolubus solfataricus. We demonstrate that SSB clearly inhibits NurA endonuclease activity and its exonuclease activities also when in combination with HerA. Moreover, we show that SSB binding to DNA is greatly stimulated by the presence of either NurA or NurA/HerA. In addition, if on the one hand NurA binding is not influenced, on the other hand, HerA binding is reduced when SSB is present in the reaction. In accordance with what has been observed, we have shown that HerA helicase activity is not stimulated by SSB. These data suggest that, in archaea, the DNA end resection process is governed by the strictly combined action of NurA, HerA and SSB.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
- Correspondence: (M.D.F.); (M.D.F.)
| | - Alessandra Porritiello
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Federica Rota
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Viviana Scognamiglio
- Department of Chemical Sciences and Materials Technologies, Institute of Crystallography, National Research Council, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (V.S.); (A.A.)
| | - Amina Antonacci
- Department of Chemical Sciences and Materials Technologies, Institute of Crystallography, National Research Council, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (V.S.); (A.A.)
| | - Giovanni del Monaco
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Mariarita De Felice
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
- Correspondence: (M.D.F.); (M.D.F.)
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7
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De Falco M, De Felice M. Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea. Int J Mol Sci 2021; 22:ijms222413296. [PMID: 34948099 PMCID: PMC8708640 DOI: 10.3390/ijms222413296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.
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8
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Giaccherini C, Gaillard P. Control of structure-specific endonucleases during homologous recombination in eukaryotes. Curr Opin Genet Dev 2021; 71:195-205. [PMID: 34624742 DOI: 10.1016/j.gde.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023]
Abstract
Structure-Specific Endonucleases (SSE) are specialized DNA endonucleases that recognize and process DNA secondary structures without any strict dependency on the nucleotide sequence context. This enables them to act virtually anywhere in the genome and to make key contributions to the maintenance of genome stability by removing DNA structures that may stall essential cellular processes such as DNA replication, transcription, repair and chromosome segregation. During repair of double strand breaks by homologous recombination mechanisms, DNA secondary structures are formed and processed in a timely manner. Their homeostasis relies on the combined action of helicases, SSE and topoisomerases. In this review, we focus on how SSE contribute to DNA end resection, single-strand annealing and double-strand break repair, with an emphasis on how their action is fine-tuned in those processes.
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Affiliation(s)
- C Giaccherini
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - Phl Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France.
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9
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Wang XS, Menolfi D, Wu-Baer F, Fangazio M, Meyer SN, Shao Z, Wang Y, Zhu Y, Lee BJ, Estes VM, Cupo OM, Gautier J, Pasqualucci L, Dalla-Favera R, Baer R, Zha S. DNA damage-induced phosphorylation of CtIP at a conserved ATM/ATR site T855 promotes lymphomagenesis in mice. Proc Natl Acad Sci U S A 2021; 118:e2105440118. [PMID: 34521752 PMCID: PMC8463888 DOI: 10.1073/pnas.2105440118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 12/28/2022] Open
Abstract
CtIP is a DNA end resection factor widely implicated in alternative end-joining (A-EJ)-mediated translocations in cell-based reporter systems. To address the physiological role of CtIP, an essential gene, in translocation-mediated lymphomagenesis, we introduced the T855A mutation at murine CtIP to nonhomologous end-joining and Tp53 double-deficient mice that routinely succumbed to lymphomas carrying A-EJ-mediated IgH-Myc translocations. T855 of CtIP is phosphorylated by ATM or ATR kinases upon DNA damage to promote end resection. Here, we reported that the T855A mutation of CtIP compromised the neonatal development of Xrcc4-/-Tp53-/- mice and the IgH-Myc translocation-driven lymphomagenesis in DNA-PKcs-/-Tp53-/- mice. Mechanistically, the T855A mutation limits DNA end resection length without affecting hairpin opening, translocation frequency, or fork stability. Meanwhile, after radiation, CtIP-T855A mutant cells showed a consistent decreased Chk1 phosphorylation and defects in the G2/M cell cycle checkpoint. Consistent with the role of T855A mutation in lymphomagenesis beyond translocation, the CtIP-T855A mutation also delays splenomegaly in λ-Myc mice. Collectively, our study revealed a role of CtIP-T855 phosphorylation in lymphomagenesis beyond A-EJ-mediated chromosomal translocation.
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Affiliation(s)
- Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
- Graduate Program of Pathobiology and Molecular Medicine, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Demis Menolfi
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Foon Wu-Baer
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Marco Fangazio
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Stefanie N Meyer
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Zhengping Shao
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Yunyue Wang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Yimeng Zhu
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Olivia M Cupo
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
| | - Jean Gautier
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
- Department of Genetics and Development, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
- Department of Genetics and Development, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Richard Baer
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032;
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032
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10
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Lu R, Zhang H, Jiang YN, Wang ZQ, Sun L, Zhou ZW. Post-Translational Modification of MRE11: Its Implication in DDR and Diseases. Genes (Basel) 2021; 12:1158. [PMID: 34440334 PMCID: PMC8392716 DOI: 10.3390/genes12081158] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
Maintaining genomic stability is vital for cells as well as individual organisms. The meiotic recombination-related gene MRE11 (meiotic recombination 11) is essential for preserving genomic stability through its important roles in the resection of broken DNA ends, DNA damage response (DDR), DNA double-strand breaks (DSBs) repair, and telomere maintenance. The post-translational modifications (PTMs), such as phosphorylation, ubiquitination, and methylation, regulate directly the function of MRE11 and endow MRE11 with capabilities to respond to cellular processes in promptly, precisely, and with more diversified manners. Here in this paper, we focus primarily on the PTMs of MRE11 and their roles in DNA response and repair, maintenance of genomic stability, as well as their association with diseases such as cancer.
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Affiliation(s)
- Ruiqing Lu
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
| | - Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College; Kunming 650118, China;
| | - Yi-Nan Jiang
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
| | - Zhao-Qi Wang
- Leibniz Institute on Aging–Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07745 Jena, Germany
| | - Litao Sun
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhong-Wei Zhou
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
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11
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Al-Zain AM, Symington LS. The dark side of homology-directed repair. DNA Repair (Amst) 2021; 106:103181. [PMID: 34311272 DOI: 10.1016/j.dnarep.2021.103181] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
DNA double strand breaks (DSB) are cytotoxic lesions that can lead to genome rearrangements and genomic instability, which are hallmarks of cancer. The two main DSB repair pathways are non-homologous end joining and homologous recombination (HR). While HR is generally highly accurate, it has the potential for rearrangements that occur directly or through intermediates generated during the repair process. Whole genome sequencing of cancers has revealed numerous types of structural rearrangement signatures that are often indicative of repair mediated by sequence homology. However, it can be challenging to delineate repair mechanisms from sequence analysis of rearrangement end products from cancer genomes, or even model systems, because the same rearrangements can be generated by different pathways. Here, we review homology-directed repair pathways and their consequences. Exploring those pathways can lead to a greater understanding of rearrangements that occur in cancer cells.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, United States; Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, United States.
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12
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Ren J, Wu Y, Wang Y, Zhao Y, Li Y, Hao S, Lin L, Zhang S, Xu X, Wang H. CtIP suppresses primary microRNA maturation and promotes metastasis of colon cancer cells in a xenograft mouse model. J Biol Chem 2021; 296:100707. [PMID: 33901493 PMCID: PMC8164041 DOI: 10.1016/j.jbc.2021.100707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022] Open
Abstract
miRNAs are important regulators of eukaryotic gene expression. The post-transcriptional maturation of miRNAs is controlled by the Drosha-DiGeorge syndrome critical region gene 8 (DGCR8) microprocessor. Dysregulation of miRNA biogenesis has been implicated in the pathogenesis of human diseases, including cancers. C-terminal-binding protein-interacting protein (CtIP) is a well-known DNA repair factor that promotes the processing of DNA double-strand break (DSB) to initiate homologous recombination-mediated DSB repair. However, it was unclear whether CtIP has other unknown cellular functions. Here, we aimed to uncover the roles of CtIP in miRNA maturation and cancer cell metastasis. We found that CtIP is a potential regulatory factor that suppresses the processing of miRNA primary transcripts (pri-miRNA). CtIP directly bound to both DGCR8 and pri-miRNAs through a conserved Sae2-like domain, reduced the binding of Drosha to DGCR8 and pri-miRNA substrate, and inhibited processing activity of Drosha complex. CtIP depletion significantly increased the expression levels of a subset of mature miRNAs, including miR-302 family members that are associated with tumor progression and metastasis in several cancer types. We also found that CtIP-inhibited miRNAs, such as miR-302 family members, are not crucial for DSB repair. However, increase of miR-302b levels or loss of CtIP function severely suppressed human colon cancer cell line tumor cell metastasis in a mouse xenograft model. These studies reveal a previously unrecognized mechanism of CtIP in miRNA processing and tumor metastasis that represents a new function of CtIP in cancer.
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Affiliation(s)
- Jianping Ren
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yan Wu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Ya Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Lixiu Lin
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuyuan Zhang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China.
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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14
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021. [DOI: 10.3389/fcell.2021.640755 order by 1-- znbp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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15
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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16
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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17
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021. [DOI: 10.3389/fcell.2021.640755 order by 1-- azli] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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18
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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20
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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21
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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22
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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23
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021; 9:640755. [PMID: 33718381 PMCID: PMC7947261 DOI: 10.3389/fcell.2021.640755] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund-Thomson syndrome (RTS), Baller-Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Affiliation(s)
- Huiming Lu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Anthony J. Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, United States
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24
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Cheblal A, Challa K, Seeber A, Shimada K, Yoshida H, Ferreira HC, Amitai A, Gasser SM. DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement. Mol Cell 2020; 80:311-326.e4. [PMID: 32970994 DOI: 10.1016/j.molcel.2020.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/02/2023]
Abstract
To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR. The loss of nucleosome remodeler INO80-C did the opposite. To see whether enhanced HDR depends on DSB mobility or the global chromatin response, we tested the ubiquitin ligase mutant uls1Δ, which selectively impairs local but not global movement in response to a DSB. Strand invasion occurs in uls1Δ cells with wild-type kinetics, arguing that global histone depletion rather than DSB movement is rate limiting for HDR. Impaired break movement in uls1Δ correlates with elevated MRX and cohesin loading, despite normal resection and checkpoint activation.
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Affiliation(s)
- Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Present address: Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA 02138, USA
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Haruka Yoshida
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland.
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Mosbach V, Viterbo D, Descorps-Declère S, Poggi L, Vaysse-Zinkhöfer W, Richard GF. Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal deletions. PLoS Genet 2020; 16:e1008924. [PMID: 32673314 PMCID: PMC7413560 DOI: 10.1371/journal.pgen.1008924] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/07/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Microsatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ~2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used the Streptococcus pyogenes Cas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal deletions around the repeat tract. These deletions depended on RAD50, RAD52, DNL4 and SAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in a rad50Δ strain, whereas they were impaired in a sae2Δ mutant, only on the DSB end containing most of the repeat tract. This observation demonstrates that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end. In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfere with gene conversion too. Altogether, these data show that SpCas9 may not be the best choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome. With the discovery of highly specific DNA endonucleases such as TALEN and CRISPR-Cas systems, gene editing has become an attractive approach to address genetic disorders. Myotonic dystrophy type 1 (Steinert disease) is due to a large expansion of a CTG trinucleotide repeat in the DMPK gene. At the present time, despite numerous therapeutic attempts, this dramatic neurodegenerative disorder still has no cure. In the present work, we tried to use the Cas9 endonuclease to induce a double-strand break within the expanded CTG repeat of the DMPK gene integrated in the yeast genome. Surprisingly, this break induced chromosomal deletions around the repeat tract. These deletions were local and involved non-homologous joining of the two DNA ends, or more extensive involving homologous recombination between repeated elements upstream and downstream the break. Using yeast genetics, we investigated the genetic requirements for these deletions and found that the triplet repeat tract altered the capacity of the repair machinery to faithfully repair the double-strand break. These results have implications for future gene therapy approaches in human patients.
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Affiliation(s)
| | | | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Paris, France
| | - Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
| | - Wilhelm Vaysse-Zinkhöfer
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
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Limiting the DNA Double-Strand Break Resectosome for Genome Protection. Trends Biochem Sci 2020; 45:779-793. [PMID: 32513599 DOI: 10.1016/j.tibs.2020.05.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022]
Abstract
DNA double-strand break (DSB) resection, once thought to be a simple enzymatic process, is emerging as a highly complex series of coordinated activities required to maintain genome integrity. Progress in cell biology, biochemistry, and genetics has deciphered the precise resecting activities, the regulatory components, and their ability to properly channel the resected DNA to the appropriate DNA repair pathway. Herein, we review the mechanisms of regulation of DNA resection, with an emphasis on negative regulators that prevent single-strand (ss)DNA accumulation to maintain genome stability. Interest in targeting DNA resection inhibitors is emerging because their inactivation leads to poly(ADP-ribose) polymerase inhibitor (PARPi) resistance. We also present detailed regulation of DNA resection machineries, their analysis by functional assays, and their impact on disease and PARPi resistance.
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27
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Ceppi I, Howard SM, Kasaciunaite K, Pinto C, Anand R, Seidel R, Cejka P. CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection. Proc Natl Acad Sci U S A 2020; 117:8859-8869. [PMID: 32241893 PMCID: PMC7183222 DOI: 10.1073/pnas.2001165117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To repair a DNA double-strand break by homologous recombination, 5'-terminated DNA strands must first be resected to reveal 3'-overhangs. This process is initiated by a short-range resection catalyzed by MRE11-RAD50-NBS1 (MRN) stimulated by CtIP, which is followed by a long-range step involving EXO1 or DNA2 nuclease. DNA2 is a bifunctional enzyme that contains both single-stranded DNA (ssDNA)-specific nuclease and motor activities. Upon DNA unwinding by Bloom (BLM) or Werner (WRN) helicase, RPA directs the DNA2 nuclease to degrade the 5'-strand. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single-molecule biochemistry, we show that CtIP also dramatically stimulates the adenosine 5'-triphosphate (ATP) hydrolysis-driven motor activity of DNA2 involved in the long-range resection step. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. Accordingly, the stimulatory effect of CtIP is only observed with wild-type DNA2, but not the helicase-deficient variant. Similarly to the function of CtIP to promote MRN, also the DNA2 stimulatory effect is facilitated by CtIP phosphorylation. The domain of CtIP required to promote DNA2 is located in the central region lacking in lower eukaryotes and is fully separable from domains involved in the stimulation of MRN. These results establish how CtIP couples both MRE11-dependent short-range and DNA2-dependent long-range resection and define the involvement of the motor activity of DNA2 in this process. Our data might help explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.
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Affiliation(s)
- Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
- Institute of Biochemistry, Department of Biology, ETH, Zürich, 8093, Switzerland
| | - Sean M Howard
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
| | - Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zürich, Zürich, 8057, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, 04103, Germany
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, 6500, Switzerland;
- Institute of Biochemistry, Department of Biology, ETH, Zürich, 8093, Switzerland
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28
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Langston RE, Palazzola D, Bonnell E, Wellinger RJ, Weinert T. Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping. PLoS Genet 2020; 16:e1008733. [PMID: 32287268 PMCID: PMC7205313 DOI: 10.1371/journal.pgen.1008733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 05/07/2020] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
In budding yeast, Cdc13, Stn1, and Ten1 form the telomere-binding heterotrimer CST complex. Here we investigate the role of Cdc13/CST in maintaining genome stability by using a Chr VII disome system that can generate recombinants, chromosome loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitive CDC13 allele, cdc13F684S, unstable chromosomes frequently arise from problems in or near a telomere. We found that, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes that are then the source for additional chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or chromosome loss). We observed that genome instability arises from a defect in Cdc13’s function during DNA replication, not Cdc13’s putative post-replication telomere capping function. The molecular nature of the initial unstable chromosomes formed by a Cdc13-defect involves ssDNA and does not involve homologous recombination nor non-homologous end joining; we speculate the original unstable chromosome may be a one-ended double strand break. This system defines a link between Cdc13’s function during DNA replication and genome stability in the form of unstable chromosomes, that then progress to form other chromosome changes. Eukaryotic chromosomes are linear molecules with specialized end structures called telomeres. Telomeres contain both unique repetitive DNA sequences and specialized proteins that solve several biological problems by differentiating chromosomal ends from internal breaks, thus preventing chromosome instability. When telomeres are defective, the entire chromosome can become unstable and change, causing mutations and pathology (cancer, aging, etc.). Here we study how a defect in specific telomere proteins causes chromosomal rearrangements, using the model organism Saccharomyces cerevisiae (budding or brewer’s yeast). We find that when specific telomere proteins are defective, errors in DNA replication generate a type of damage that likely involves extensive single-stranded DNA that forms inherently unstable chromosomes, subject to many subsequent instances of instability (e.g. allelic recombinants, chromosome loss, truncations, dicentrics). The telomere protein Cdc13 is part of a protein complex called CST that is conserved in most organisms including mammalian cells. The technical capacity of studies in budding yeast allow a detailed, real-time examination of how telomere defects compromise chromosome stability in a single cell cycle, generating lessons likely relevant to how human telomeres keep human chromosomes stable.
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Affiliation(s)
- Rachel E. Langston
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Dominic Palazzola
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Erin Bonnell
- Department of Microbiology and Infectiology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Raymund J. Wellinger
- Department of Microbiology and Infectiology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ted Weinert
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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Rai R, Gu P, Broton C, Kumar-Sinha C, Chen Y, Chang S. The Replisome Mediates A-NHEJ Repair of Telomeres Lacking POT1-TPP1 Independently of MRN Function. Cell Rep 2019; 29:3708-3725.e5. [PMID: 31825846 PMCID: PMC7001145 DOI: 10.1016/j.celrep.2019.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 09/22/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Telomeres use shelterin to protect chromosome ends from activating the DNA damage sensor MRE11-RAD50-NBS1 (MRN), repressing ataxia-telangiectasia, mutated (ATM) and ATM and Rad3-related (ATR) dependent DNA damage checkpoint responses. The MRE11 nuclease is thought to be essential for the resection of the 5' C-strand to generate the microhomologies necessary for alternative non-homologous end joining (A-NHEJ) repair. In the present study, we uncover DNA damage signaling and repair pathways engaged by components of the replisome complex to repair dysfunctional telomeres. In cells lacking MRN, single-stranded telomeric overhangs devoid of POT1-TPP1 do not recruit replication protein A (RPA), ATR-interacting protein (ATRIP), and RAD 51. Rather, components of the replisome complex, including Claspin, Proliferating cell nuclear antigen (PCNA), and Downstream neighbor of SON (DONSON), initiate DNA-PKcs-mediated p-CHK1 activation and A-NHEJ repair. In addition, Claspin directly interacts with TRF2 and recruits EXO1 to newly replicated telomeres to promote 5' end resection. Our data indicate that MRN is dispensable for the repair of dysfunctional telomeres lacking POT1-TPP1 and highlight the contributions of the replisome in telomere repair.
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Affiliation(s)
- Rekha Rai
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
| | - Peili Gu
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Cayla Broton
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Tri-Institutional MD/PhD Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Yong Chen
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Sandy Chang
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
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30
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Keener R, Connelly CJ, Greider CW. Tel1 Activation by the MRX Complex Is Sufficient for Telomere Length Regulation but Not for the DNA Damage Response in Saccharomyces cerevisiae. Genetics 2019; 213:1271-1288. [PMID: 31645360 PMCID: PMC6893380 DOI: 10.1534/genetics.119.302713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Previous models suggested that regulation of telomere length in Saccharomyces cerevisiae by Tel1(ATM) and Mec1(ATR) would parallel the established pathways regulating the DNA damage response. Here, we provide evidence that telomere length regulation differs from the DNA damage response in both the Tel1 and Mec1 pathways. We found that Rad53 mediates a Mec1 telomere length regulation pathway but is dispensable for Tel1 telomere length regulation, whereas in the DNA damage response, Rad53 is regulated by both Mec1 and Tel1 Using epistasis analysis with a Tel1 hypermorphic allele, Tel1-hy909, we found that the MRX complex is not required downstream of Tel1 for telomere elongation but is required downstream of Tel1 for the DNA damage response. Our data suggest that nucleolytic telomere end processing is not a required step for telomerase to elongate telomeres.
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Affiliation(s)
- Rebecca Keener
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Carla J Connelly
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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31
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Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
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Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
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32
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Saatchi F, Kirchmaier AL. Tolerance of DNA Replication Stress Is Promoted by Fumarate Through Modulation of Histone Demethylation and Enhancement of Replicative Intermediate Processing in Saccharomyces cerevisiae. Genetics 2019; 212:631-654. [PMID: 31123043 PMCID: PMC6614904 DOI: 10.1534/genetics.119.302238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Fumarase is a well-characterized TCA cycle enzyme that catalyzes the reversible conversion of fumarate to malate. In mammals, fumarase acts as a tumor suppressor, and loss-of-function mutations in the FH gene in hereditary leiomyomatosis and renal cell cancer result in the accumulation of intracellular fumarate-an inhibitor of α-ketoglutarate-dependent dioxygenases. Fumarase promotes DNA repair by nonhomologous end joining in mammalian cells through interaction with the histone variant H2A.Z, and inhibition of KDM2B, a H3 K36-specific histone demethylase. Here, we report that Saccharomyces cerevisiae fumarase, Fum1p, acts as a response factor during DNA replication stress, and fumarate enhances survival of yeast lacking Htz1p (H2A.Z in mammals). We observed that exposure to DNA replication stress led to upregulation as well as nuclear enrichment of Fum1p, and raising levels of fumarate in cells via deletion of FUM1 or addition of exogenous fumarate suppressed the sensitivity to DNA replication stress of htz1Δ mutants. This suppression was independent of modulating nucleotide pool levels. Rather, our results are consistent with fumarate conferring resistance to DNA replication stress in htz1Δ mutants by inhibiting the H3 K4-specific histone demethylase Jhd2p, and increasing H3 K4 methylation. Although the timing of checkpoint activation and deactivation remained largely unaffected by fumarate, sensors and mediators of the DNA replication checkpoint were required for fumarate-dependent resistance to replication stress in the htz1Δ mutants. Together, our findings imply metabolic enzymes and metabolites aid in processing replicative intermediates by affecting chromatin modification states, thereby promoting genome integrity.
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Affiliation(s)
- Faeze Saatchi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
| | - Ann L Kirchmaier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
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Scully R, Panday A, Elango R, Willis NA. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol 2019; 20:698-714. [PMID: 31263220 DOI: 10.1038/s41580-019-0152-0] [Citation(s) in RCA: 766] [Impact Index Per Article: 153.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 11/09/2022]
Abstract
The major pathways of DNA double-strand break (DSB) repair are crucial for maintaining genomic stability. However, if deployed in an inappropriate cellular context, these same repair functions can mediate chromosome rearrangements that underlie various human diseases, ranging from developmental disorders to cancer. The two major mechanisms of DSB repair in mammalian cells are non-homologous end joining (NHEJ) and homologous recombination. In this Review, we consider DSB repair-pathway choice in somatic mammalian cells as a series of 'decision trees', and explore how defective pathway choice can lead to genomic instability. Stalled, collapsed or broken DNA replication forks present a distinctive challenge to the DSB repair system. Emerging evidence suggests that the 'rules' governing repair-pathway choice at stalled replication forks differ from those at replication-independent DSBs.
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Affiliation(s)
- Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
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34
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Liu X, Wang XS, Lee BJ, Wu-Baer FK, Lin X, Shao Z, Estes VM, Gautier J, Baer R, Zha S. CtIP is essential for early B cell proliferation and development in mice. J Exp Med 2019; 216:1648-1663. [PMID: 31097467 PMCID: PMC6605744 DOI: 10.1084/jem.20181139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/10/2018] [Accepted: 04/24/2019] [Indexed: 11/08/2022] Open
Abstract
B cell development requires efficient proliferation and successful assembly and modifications of the immunoglobulin gene products. CtIP is an essential gene implicated in end resection and DNA repair. Here, we show that CtIP is essential for early B cell development but dispensable in naive B cells. CtIP loss is well tolerated in G1-arrested B cells and during V(D)J recombination, but in proliferating B cells, CtIP loss leads to a progressive cell death characterized by ATM hyperactivation, G2/M arrest, genomic instability, and 53BP1 nuclear body formation, indicating that the essential role of CtIP during proliferation underscores its stage-specific requirement in B cells. B cell proliferation requires phosphorylation of CtIP at T847 presumably by CDK, but not its interaction with CtBP or Rb or its nuclease activity. CtIP phosphorylation by ATM/ATR at T859 (T855 in mice) promotes end resection in G1-arrested cells but is dispensable for B cell development and class switch recombination, suggesting distinct roles for T859 and T847 phosphorylation in B cell development.
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Affiliation(s)
- Xiangyu Liu
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Pathobiology and Human Disease Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Foon K Wu-Baer
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Zhengping Shao
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jean Gautier
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Richard Baer
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
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35
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Hamilton NA, Wendel BM, Weber EA, Courcelle CT, Courcelle J. RecBCD, SbcCD and ExoI process a substrate created by convergent replisomes to complete DNA replication. Mol Microbiol 2019; 111:1638-1651. [PMID: 30883946 PMCID: PMC6561825 DOI: 10.1111/mmi.14242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/11/2022]
Abstract
The accurate completion of DNA replication on the chromosome requires RecBCD and structure specific SbcCD and ExoI nucleases. However, the substrates and mechanism by which this reaction occurs remains unknown. Here we show that these completion enzymes operate on plasmid substrates containing two replisomes, but are not required for plasmids containing one replisome. Completion on the two-replisome plasmids requires RecBCD, but does not require RecA and no broken intermediates accumulate in its absence, indicating that the completion reaction occurs normally in the absence of any double-strand breaks. Further, similar to the chromosome, we show that when the normal completion reaction is prevented, an aberrant RecA-mediated recombination process leads to amplifications that drive most of the instabilities associated with the two-replisome substrates. The observations imply that the substrate SbcCD, ExoI and RecBCD act upon in vivo is created specifically by two convergent replisomes, and demonstrate that the function of RecBCD in completing replication is independent of double-strand break repair, and likely promotes joining of the strands of the convergent replication forks.
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Affiliation(s)
- Nicklas A. Hamilton
- To whom correspondence should be addressed: Department of Biology, Portland State University, PO Box 751 Portland, Oregon, 97207-0751;
| | | | - Emma A. Weber
- Department of Biology, Portland State University, Portland, OR 97201
| | | | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR 97201
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36
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Chen BR, Quinet A, Byrum AK, Jackson J, Berti M, Thangavel S, Bredemeyer AL, Hindi I, Mosammaparast N, Tyler JK, Vindigni A, Sleckman BP. XLF and H2AX function in series to promote replication fork stability. J Cell Biol 2019; 218:2113-2123. [PMID: 31123184 PMCID: PMC6605786 DOI: 10.1083/jcb.201808134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/03/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Chen et al. show that XLF functions to limit fork reversal during DNA replication. H2AX prevents MRE11-dependent replication stress in XLF-deficient cells, suggesting that H2AX prevents the resection of regressed arms at reversed forks. XRCC4-like factor (XLF) is a non-homologous end joining (NHEJ) DNA double strand break repair protein. However, XLF deficiency leads to phenotypes in mice and humans that are not necessarily consistent with an isolated defect in NHEJ. Here we show that XLF functions during DNA replication. XLF undergoes cell division cycle 7–dependent phosphorylation; associates with the replication factor C complex, a critical component of the replisome; and is found at replication forks. XLF deficiency leads to defects in replication fork progression and an increase in fork reversal. The additional loss of H2AX, which protects DNA ends from resection, leads to a requirement for ATR to prevent an MRE11-dependent loss of newly synthesized DNA and activation of DNA damage response. Moreover, H2ax−/−:Xlf−/− cells exhibit a marked dependence on the ATR kinase for survival. We propose that XLF and H2AX function in series to prevent replication stress induced by the MRE11-dependent resection of regressed arms at reversed replication forks.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea K Byrum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Matteo Berti
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Saravanabhavan Thangavel
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea L Bredemeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Issa Hindi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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37
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Andres SN, Li ZM, Erie DA, Williams RS. Ctp1 protein-DNA filaments promote DNA bridging and DNA double-strand break repair. J Biol Chem 2019; 294:3312-3320. [PMID: 30626735 DOI: 10.1074/jbc.ra118.006759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/26/2018] [Indexed: 12/13/2022] Open
Abstract
The Ctp1 protein in Schizosaccharomyces pombe is essential for DNA double-strand break (DSB) repair by homologous recombination. Fission yeast Ctp1 and its budding yeast (Sae2) and human (CtIP) homologs control Mre11-Rad50-Nbs1 nuclease complex activity and harbor DNA-binding and -bridging activities. However, the molecular basis for Ctp1-DNA transactions remains undefined. Here, we report atomic force microscopy (AFM) imaging of S. pombe Ctp1-DNA complexes revealing that Ctp1 polymerizes on dsDNA molecules and forms synaptic filaments that bridge two dsDNA strands. We observed that Ctp1 DNA filaments are typified by an average filament length of ∼180 bp of dsDNA and a Ctp1 tetramer footprint of ∼15 bp. Biochemical results characterizing Ctp1 variants with impaired DNA-binding or -bridging properties were consistent with Ctp1-mediated DNA bridging requiring the intact and correctly folded Ctp1 tetramer. Furthermore, mutations altering Ctp1 oligomerization and DNA bridging in vitro conferred cell sensitivity to DSB-producing agents. Together, these results support an important role for Ctp1-regulated DNA strand coordination required for DNA DSB repair in S. pombe.
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Affiliation(s)
- Sara N Andres
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Zimeng M Li
- the Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27695, and
| | - Dorothy A Erie
- the Department of Chemistry, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - R Scott Williams
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709,
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38
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Wilkinson OJ, Martín-González A, Kang H, Northall SJ, Wigley DB, Moreno-Herrero F, Dillingham MS. CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair. eLife 2019; 8:42129. [PMID: 30601117 PMCID: PMC6344080 DOI: 10.7554/elife.42129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/01/2019] [Indexed: 12/16/2022] Open
Abstract
CtIP is involved in the resection of broken DNA during the S and G2 phases of the cell cycle for repair by recombination. Acting with the MRN complex, it plays a particularly important role in handling complex DNA end structures by localised nucleolytic processing of DNA termini in preparation for longer range resection. Here we show that human CtIP is a tetrameric protein adopting a dumbbell architecture in which DNA binding domains are connected by long coiled-coils. The protein complex binds two short DNA duplexes with high affinity and bridges DNA molecules in trans. DNA binding is potentiated by dephosphorylation and is not specific for DNA end structures per se. However, the affinity for linear DNA molecules is increased if the DNA terminates with complex structures including forked ssDNA overhangs and nucleoprotein conjugates. This work provides a biochemical and structural basis for the function of CtIP at complex DNA breaks.
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Affiliation(s)
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Haejoo Kang
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Sarah J Northall
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
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39
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Lamarche BJ, Orazio NI, Goben B, Meisenhelder J, You Z, Weitzman MD, Hunter T. Repair of protein-linked DNA double strand breaks: Using the adenovirus genome as a model substrate in cell-based assays. DNA Repair (Amst) 2018; 74:80-90. [PMID: 30583959 DOI: 10.1016/j.dnarep.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
The DNA double strand breaks (DSBs) created during meiotic recombination and during some types of chemotherapy contain protein covalently attached to their 5' termini. Removal of the end-blocking protein is a prerequisite to DSB processing by non-homologous end-joining or homologous recombination. One mechanism for removing the protein involves CtIP-stimulated Mre11-catalyzed nicking of the protein-linked strand distal to the DSB terminus, releasing the end-blocking protein while it remains covalently attached to an oligonucleotide. Much of what is known about this repair process has recently been deciphered through in vitro reconstitution studies. We present here a novel model system based on adenovirus (Ad), which contains the Ad terminal protein covalently linked to the 5' terminus of its dsDNA genome, for studying the repair of 5' protein-linked DSBs in vivo. It was previously shown that the genome of Ad mutants that lack early region 4 (E4) can be joined into concatemers in vivo, suggesting that the Ad terminal protein had been removed from the genome termini prior to ligation. Here we show that during infection with the E4-deleted Ad mutant dl1004, the Ad terminal protein is removed in a manner that recapitulates removal of end-blocking proteins from cellular DSBs. In addition to displaying a dependence on CtIP, and Mre11 acting as the endonuclease, the protein-linked oligonucleotides that are released from the viral genome are similar in size to the oligos that remain attached to Spo11 and Top2 after they are removed from the 5' termini of DSBs during meiotic recombination and etoposide chemotherapy, respectively. The single nucleotide resolution that is possible with this assay, combined with the single sequence context in which the lesion is presented, make it a useful tool for further refining our mechanistic understanding of how blocking proteins are removed from the 5' termini of DSBs.
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Affiliation(s)
- Brandon J Lamarche
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA; Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Nicole I Orazio
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Brittany Goben
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Jill Meisenhelder
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Matthew D Weitzman
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA.
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA.
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40
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Oh J, Symington LS. Role of the Mre11 Complex in Preserving Genome Integrity. Genes (Basel) 2018; 9:E589. [PMID: 30501098 PMCID: PMC6315862 DOI: 10.3390/genes9120589] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous lesions that threaten genome integrity and cell survival. The DNA damage response (DDR) safeguards the genome by sensing DSBs, halting cell cycle progression and promoting repair through either non-homologous end joining (NHEJ) or homologous recombination (HR). The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex is central to the DDR through its structural, enzymatic, and signaling roles. The complex tethers DNA ends, activates the Tel1/ATM kinase, resolves protein-bound or hairpin-capped DNA ends, and maintains telomere homeostasis. In addition to its role at DSBs, MRX/N associates with unperturbed replication forks, as well as stalled replication forks, to ensure complete DNA synthesis and to prevent chromosome rearrangements. Here, we summarize the significant progress made in characterizing the MRX/N complex and its various activities in chromosome metabolism.
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Affiliation(s)
- Julyun Oh
- Biological Sciences Program, Columbia University, New York, NY 10027, USA.
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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41
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Regulatory control of DNA end resection by Sae2 phosphorylation. Nat Commun 2018; 9:4016. [PMID: 30275497 PMCID: PMC6167383 DOI: 10.1038/s41467-018-06417-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/29/2018] [Indexed: 12/31/2022] Open
Abstract
DNA end resection plays a critical function in DNA double-strand break repair pathway choice. Resected DNA ends are refractory to end-joining mechanisms and are instead channeled to homology-directed repair. Using biochemical, genetic, and imaging methods, we show that phosphorylation of Saccharomyces cerevisiae Sae2 controls its capacity to promote the Mre11-Rad50-Xrs2 (MRX) nuclease to initiate resection of blocked DNA ends by at least two distinct mechanisms. First, DNA damage and cell cycle-dependent phosphorylation leads to Sae2 tetramerization. Second, and independently, phosphorylation of the conserved C-terminal domain of Sae2 is a prerequisite for its physical interaction with Rad50, which is also crucial to promote the MRX endonuclease. The lack of this interaction explains the phenotype of rad50S mutants defective in the processing of Spo11-bound DNA ends during meiotic recombination. Our results define how phosphorylation controls the initiation of DNA end resection and therefore the choice between the key DNA double-strand break repair mechanisms. It has previously been established that DNA end resection in yeast and in humans is under CDK control. Here the authors explain how phosphorylation regulates the capacity of Sae2 — the yeast orthologue of human CtIP — to promote DNA end resection.
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42
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Ramakrishnan S, Kockler Z, Evans R, Downing BD, Malkova A. Single-strand annealing between inverted DNA repeats: Pathway choice, participating proteins, and genome destabilizing consequences. PLoS Genet 2018; 14:e1007543. [PMID: 30091972 PMCID: PMC6103520 DOI: 10.1371/journal.pgen.1007543] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/21/2018] [Accepted: 07/06/2018] [Indexed: 11/19/2022] Open
Abstract
Double strand DNA breaks (DSBs) are dangerous events that can result from various causes including environmental assaults or the collapse of DNA replication. While the efficient and precise repair of DSBs is essential for cell survival, faulty repair can lead to genetic instability, making the choice of DSB repair an important step. Here we report that inverted DNA repeats (IRs) placed near a DSB can channel its repair from an accurate pathway that leads to gene conversion to instead a break-induced replication (BIR) pathway that leads to genetic instabilities. The effect of IRs is explained by their ability to form unusual DNA structures when present in ssDNA that is formed by DSB resection. We demonstrate that IRs can form two types of unusual DNA structures, and the choice between these structures depends on the length of the spacer separating IRs. In particular, IRs separated by a long (1-kb) spacer are predominantly involved in inter-molecular single-strand annealing (SSA) leading to the formation of inverted dimers; IRs separated by a short (12-bp) spacer participate in intra-molecular SSA, leading to the formation of fold-back (FB) structures. Both of these structures interfere with an accurate DSB repair by gene conversion and channel DSB repair into BIR, which promotes genomic destabilization. We also report that different protein complexes participate in the processing of FBs containing short (12-bp) versus long (1-kb) ssDNA loops. Specifically, FBs with short loops are processed by the MRX-Sae2 complex, whereas the Rad1-Rad10 complex is responsible for the processing of long loops. Overall, our studies uncover the mechanisms of genomic destabilization resulting from re-routing DSB repair into unusual pathways by IRs. Given the high abundance of IRs in the human genome, our findings may contribute to the understanding of IR-mediated genomic destabilization associated with human disease. Efficient and accurate repair of double-strand DNA breaks (DSBs), resulting from the exposure of cells to ionizing radiation or various chemicals, is crucial for cell survival. Conversely, faulty DSB repair can generate genomic instability that can lead to birth defects or cancer in humans. Here we demonstrate that inverted DNA repeats (IRs) placed in the vicinity of a DSB, interfere with the accurate repair of DSBs and promote genomic rearrangements and chromosome loss. This results from annealing between inverted repeats, located either in different DNA molecules or in the same molecule. In addition, we describe a new role for the Rad1-Rad10 protein complex in processing fold-back (FB) structures formed by intra-molecular annealing involving IRs separated by long spacers. In contrast, FBs with short spacers are processed by the Mre11-Rad50-Xrs2/-Sae2 complex. Overall, we describe several pathways of DSB promoted interaction between IRs that can lead to genomic instability. Given the large number of IRs in the human genome, our findings are relevant to the mechanisms driving genomic destabilization in humans contributing to the development of cancer and other diseases.
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Affiliation(s)
- Sreejith Ramakrishnan
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
- Indiana University Purdue University Indianapolis, Indianapolis, IN, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Zachary Kockler
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
| | - Robert Evans
- Indiana University Purdue University Indianapolis, Indianapolis, IN, United States of America
| | - Brandon D. Downing
- Indiana University Purdue University Indianapolis, Indianapolis, IN, United States of America
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
- Indiana University Purdue University Indianapolis, Indianapolis, IN, United States of America
- * E-mail:
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43
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Paull TT. 20 Years of Mre11 Biology: No End in Sight. Mol Cell 2018; 71:419-427. [PMID: 30057197 DOI: 10.1016/j.molcel.2018.06.033] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/18/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023]
Abstract
The Mre11 nuclease has been the subject of intensive investigation for the past 20 years because of the central role that Mre11/Rad50 complexes play in genome maintenance. The last two decades of work on this complex has led to a much deeper understanding of the structure, biochemical activities, and regulation of Mre11/Rad50 complexes from archaea, bacteria, and eukaryotic cells. This review will discuss some of the important findings over recent years that have illuminated roles for the Mre11 nuclease in these different contexts as well as the insights from structural biology that have helped us to understand its mechanisms of action.
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Affiliation(s)
- Tanya T Paull
- Howard Hughes Medical Institute; Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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44
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Trinucleotide repeat instability during double-strand break repair: from mechanisms to gene therapy. Curr Genet 2018; 65:17-28. [DOI: 10.1007/s00294-018-0865-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 07/01/2018] [Indexed: 12/26/2022]
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45
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Daley JM, Jimenez-Sainz J, Wang W, Miller AS, Xue X, Nguyen KA, Jensen RB, Sung P. Enhancement of BLM-DNA2-Mediated Long-Range DNA End Resection by CtIP. Cell Rep 2018; 21:324-332. [PMID: 29020620 DOI: 10.1016/j.celrep.2017.09.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/24/2023] Open
Abstract
DNA double-strand break repair by homologous recombination entails the resection of DNA ends to reveal ssDNA tails, which are used to invade a homologous DNA template. CtIP and its yeast ortholog Sae2 regulate the nuclease activity of MRE11 in the initial stage of resection. Deletion of CtIP in the mouse or SAE2 in yeast engenders a more severe phenotype than MRE11 nuclease inactivation, indicative of a broader role of CtIP/Sae2. Here, we provide biochemical evidence that CtIP promotes long-range resection via the BLM-DNA2 pathway. Specifically, CtIP interacts with BLM and enhances its helicase activity, and it enhances DNA cleavage by DNA2. Thus, CtIP influences multiple aspects of end resection beyond MRE11 regulation.
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Affiliation(s)
- James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Judit Jimenez-Sainz
- Department of Therapeutic Radiobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kevin A Nguyen
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
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46
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De Falco M, Massa F, Rossi M, De Felice M. The Sulfolobus solfataricus RecQ-like DNA helicase Hel112 inhibits the NurA/HerA complex exonuclease activity. Extremophiles 2018; 22:581-589. [PMID: 29488113 DOI: 10.1007/s00792-018-1018-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/21/2018] [Indexed: 02/03/2023]
Abstract
ATPase/Helicases and nucleases play important roles in DNA end-resection, a critical step during homologous recombination repair in all organisms. In hyperthermophilic archaea the exo-endonuclease NurA and the ATPase HerA cooperate with the highly conserved Mre11-Rad50 complex in 3' single-stranded DNA (ssDNA) end processing to coordinate repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA complex. In this study we demonstrate that the NurA exonuclease activity is inhibited by the Sulfolobus solfataricus RecQ-like Hel112 helicase. Inhibition occurs both in the presence and in the absence of HerA, but is much stronger when NurA is in complex with HerA. In contrast, the endonuclease activity of NurA is not affected by the presence of Hel112. Taken together these results suggest that the functional interaction between NurA/HerA and Hel112 is important for DNA end-resection in archaeal homologous recombination.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
| | - Federica Massa
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
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47
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TALEN-Induced Double-Strand Break Repair of CTG Trinucleotide Repeats. Cell Rep 2018; 22:2146-2159. [DOI: 10.1016/j.celrep.2018.01.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 12/19/2017] [Accepted: 01/25/2018] [Indexed: 11/19/2022] Open
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48
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Abstract
Accurate repair of DNA double-strand breaks (DSBs) is carried out by homologous recombination. In order to repair DNA breaks by the recombination pathway, the 5'-terminated DNA strand at DSB sites must be first nucleolytically processed to produce 3'-overhang. The process is termed DNA end resection and involves the interplay of several nuclease complexes. DNA end resection commits DSB repair to the recombination pathway including a process termed single-strand annealing, as resected DNA ends are generally nonligatable by the competing nonhomologous end-joining machinery. Biochemical reconstitution experiments provided invaluable mechanistic insights into the DNA end resection pathways. In this chapter, we describe preparation procedures of key proteins involved in DNA end resection in human cells, including the MRE11-RAD50-NBS1 complex, phosphorylated variant of CtIP, the DNA2 nuclease-helicase with its helicase partners Bloom (BLM) or Werner (WRN), as well as the single-stranded DNA-binding protein replication protein A. The availability of recombinant DNA end resection factors will help to further elucidate resection mechanisms and regulatory processes that may involve novel protein partners and posttranslational modifications.
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Affiliation(s)
- Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland; Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
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49
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Ranjha L, Howard SM, Cejka P. Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes. Chromosoma 2018; 127:187-214. [PMID: 29327130 DOI: 10.1007/s00412-017-0658-1] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/16/2022]
Abstract
DNA double-strand breaks arise accidentally upon exposure of DNA to radiation and chemicals or result from faulty DNA metabolic processes. DNA breaks can also be introduced in a programmed manner, such as during the maturation of the immune system, meiosis, or cancer chemo- or radiotherapy. Cells have developed a variety of repair pathways, which are fine-tuned to the specific needs of a cell. Accordingly, vegetative cells employ mechanisms that restore the integrity of broken DNA with the highest efficiency at the lowest cost of mutagenesis. In contrast, meiotic cells or developing lymphocytes exploit DNA breakage to generate diversity. Here, we review the main pathways of eukaryotic DNA double-strand break repair with the focus on homologous recombination and its various subpathways. We highlight the differences between homologous recombination and end-joining mechanisms including non-homologous end-joining and microhomology-mediated end-joining and offer insights into how these pathways are regulated. Finally, we introduce noncanonical functions of the recombination proteins, in particular during DNA replication stress.
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Affiliation(s)
- Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sean M Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland. .,Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
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50
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Abstract
DNA end resection initiates the largely accurate repair of DNA double-strand breaks (DSBs) by homologous recombination. Specifically, recombination requires the formation of 3' overhangs at DSB sites, which is carried out by nucleases that specifically degrade 5'-terminated DNA. In most cases, DNA end resection is a two-step process, comprising of initial short-range followed by more processive long-range resection. In this chapter, we describe selected assays that reconstitute both the short- and long-range pathways. First, we define methods to study the exonuclease and endonuclease activities of the MRE11-RAD50-NBS1 (MRN) complex in conjunction with phosphorylated cofactor CtIP. This reaction is particularly important to initiate processing of DNA breaks and to recruit components belonging to the subsequent long-range pathway. Next, we describe assays that reconstitute the concerted reactions of Bloom (BLM) or Werner (WRN) helicases that function together with the DNA2 nuclease-helicase, and which are as a complex capable to resect DNA of kilobases in length. The reconstituted reactions allow us to understand how the resection pathways function at the molecular level. The assays will be invaluable to define regulatory mechanisms and to identify inhibitory compounds, which may be valuable in cancer therapy.
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Affiliation(s)
- Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland; Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
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