1
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Rashid A, Qayum A, Bacha SAS, Liang Q, Liu Y, Kang L, Chi Z, Chi R, Han X, Ekumah JN, Virk MSU, Ren X, Ma H. Preparation and functional characterization of pullulan-sodium alginate composite film enhanced with ultrasound-assisted clove essential oil Nanoemulsions for effective preservation of cherries and mushrooms. Food Chem 2024; 457:140048. [PMID: 38917566 DOI: 10.1016/j.foodchem.2024.140048] [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: 01/13/2024] [Revised: 05/23/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
Abstract
Clove essential oil (CEO) exhibited potent antibacterial efficacy and are obtained from Eugenia caryophyllata tree flower buds. Herein, CEO nanoemulsions were prepared using various concentrations of casein protein treated with ultrasound for different time interval. The study demonstrated that CEO nanoemulsions with 5% casein protein subjected to ultrasound for 10 min displayed the most minimal particle size. The pullulan‑sodium alginate film incorporated with nanoemulsions treated with ultrasound exhibited enhanced physico-mechanical characteristics. Based on the structural analysis, the application of ultrasonic treatment improved intermolecular compatibility and organized molecular structure by strengthening hydrogen bonds. Furthermore, the composite film displayed remarkable efficacy against E. coli and S. aureus as well as longer retention of essential oils. The use of the developed films to protect cherry fruits and mushrooms produced promising results, emphasizing their potential in food packaging applications.
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Affiliation(s)
- Arif Rashid
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Abdul Qayum
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Syed Asim Shah Bacha
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Qiufang Liang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Yuxuan Liu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Lixin Kang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Zhuzhong Chi
- Jiangsu Nanxiang Agricultural Development Technology Co., Ltd, Danyang Huangtang City, Zhenjiang, Jiangsu 212327, China
| | - Runhao Chi
- Jiangsu Nanxiang Agricultural Development Technology Co., Ltd, Danyang Huangtang City, Zhenjiang, Jiangsu 212327, China
| | - Xu Han
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - John-Nelson Ekumah
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Muhammad Safi Ullah Virk
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
| | - Xiaofeng Ren
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China.
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China; Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, PR China
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2
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Hayashi R, Okumura H, Isono M, Yamauchi M, Unami D, Lusi RT, Yamamoto M, Kato Y, Uchihara Y, Shibata A. Inhibition of intracellular ATP synthesis impairs the recruitment of homologous recombination factors after ionizing radiation. JOURNAL OF RADIATION RESEARCH 2024; 65:263-271. [PMID: 38461549 PMCID: PMC11115441 DOI: 10.1093/jrr/rrae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/16/2024] [Indexed: 03/12/2024]
Abstract
Ionizing radiation (IR)-induced double-strand breaks (DSBs) are primarily repaired by non-homologous end joining or homologous recombination (HR) in human cells. DSB repair requires adenosine-5'-triphosphate (ATP) for protein kinase activities in the multiple steps of DSB repair, such as DNA ligation, chromatin remodeling, and DNA damage signaling via protein kinase and ATPase activities. To investigate whether low ATP culture conditions affect the recruitment of repair proteins at DSB sites, IR-induced foci were examined in the presence of ATP synthesis inhibitors. We found that p53 binding protein 1 foci formation was modestly reduced under low ATP conditions after IR, although phosphorylated histone H2AX and mediator of DNA damage checkpoint 1 foci formation were not impaired. Next, we examined the foci formation of breast cancer susceptibility gene I (BRCA1), replication protein A (RPA) and radiation 51 (RAD51), which are HR factors, in G2 phase cells following IR. Interestingly, BRCA1 and RPA foci in the G2 phase were significantly reduced under low ATP conditions compared to that under normal culture conditions. Notably, RAD51 foci were drastically impaired under low ATP conditions. These results suggest that HR does not effectively progress under low ATP conditions; in particular, ATP shortages impair downstream steps in HR, such as RAD51 loading. Taken together, these results suggest that the maintenance of cellular ATP levels is critical for DNA damage response and HR progression after IR.
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Affiliation(s)
- Ryota Hayashi
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Hikaru Okumura
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Mayu Isono
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Motohiro Yamauchi
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Unami
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Rahmartani Tania Lusi
- Department of Radiation Oncology, Faculty of Medicine Universitas Indonesia – Dr. Cipto Mangunkusumo National General Hospital, Jl. Diponegoro No.71, Jakarta Pusat, DKI Jakarta 10430, Indonesia
| | - Masamichi Yamamoto
- Department of Research Promotion and Management, National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita, Osaka 564-8565, Japan
| | - Yu Kato
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Yuki Uchihara
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Atsushi Shibata
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
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3
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Wu-Baer F, Wong M, Tschoe L, Lin CS, Jiang W, Zha S, Baer R. ATM/ATR Phosphorylation of CtIP on Its Conserved Sae2-like Domain Is Required for Genotoxin-Induced DNA Resection but Dispensable for Animal Development. Cells 2023; 12:2762. [PMID: 38067190 PMCID: PMC10706839 DOI: 10.3390/cells12232762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homology-directed repair (HDR) of double-strand DNA breaks (DSBs) is dependent on enzymatic resection of DNA ends by the Mre11/Rad50/Nbs1 complex. DNA resection is triggered by the CtIP/Sae2 protein, which allosterically promotes Mre11-mediated endonuclease DNA cleavage at a position internal to the DSB. Although the mechanics of resection, including the initial endonucleolytic step, are largely conserved in eucaryotes, CtIP and its functional counterpart in Saccharomyces cerevisiae (Sae2) share only a modest stretch of amino acid homology. Nonetheless, this stretch contains two highly conserved phosphorylation sites for cyclin-dependent kinases (T843 in mouse) and the damage-induced ATM/ATR kinases (T855 in mouse), both of which are required for DNA resection. To explore the function of ATM/ATR phosphorylation at Ctip-T855, we generated and analyzed mice expressing the Ctip-T855A mutant. Surprisingly, unlike Ctip-null mice and Ctip-T843A-expressing mice, both of which undergo embryonic lethality, homozygous CtipT855A/T855A mice develop normally. Nonetheless, they are hypersensitive to ionizing radiation, and CtipT855A/T855A mouse embryo fibroblasts from these mice display marked defects in DNA resection, chromosomal stability, and HDR-mediated repair of DSBs. Thus, although ATM/ATR phosphorylation of CtIP-T855 is not required for normal animal development, it enhances CtIP-mediated DNA resection in response to acute stress, such as genotoxin exposure.
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Affiliation(s)
- Foon Wu-Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Madeline Wong
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Lydia Tschoe
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Chyuan-Sheng Lin
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; (F.W.-B.); (M.W.); (L.T.); (W.J.); (S.Z.)
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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4
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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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Ceppi I, Cannavo E, Bret H, Camarillo R, Vivalda F, Thakur RS, Romero-Franco A, Sartori AA, Huertas P, Guérois R, Cejka P. PLK1 regulates CtIP and DNA2 interplay in long-range DNA end resection. Genes Dev 2023; 37:119-135. [PMID: 36746606 PMCID: PMC10069449 DOI: 10.1101/gad.349981.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
DNA double-strand break (DSB) repair is initiated by DNA end resection. CtIP acts in short-range resection to stimulate MRE11-RAD50-NBS1 (MRN) to endonucleolytically cleave 5'-terminated DNA to bypass protein blocks. CtIP also promotes the DNA2 helicase-nuclease to accelerate long-range resection downstream from MRN. Here, using AlphaFold2, we identified CtIP-F728E-Y736E as a separation-of-function mutant that is still proficient in conjunction with MRN but is not able to stimulate ssDNA degradation by DNA2. Accordingly, CtIP-F728E-Y736E impairs physical interaction with DNA2. Cellular assays revealed that CtIP-F728E-Y736E cells exhibit reduced DSB-dependent chromatin-bound RPA, impaired long-range resection, and increased sensitivity to DSB-inducing drugs. Previously, CtIP was shown to be targeted by PLK1 to inhibit long-range resection, yet the underlying mechanism was unclear. We show that the DNA2-interacting region in CtIP includes the PLK1 target site at S723. The integrity of S723 in CtIP is necessary for the stimulation of DNA2, and phosphorylation of CtIP by PLK1 in vitro is consequently inhibitory, explaining why PLK1 restricts long-range resection. Our data support a model in which CDK-dependent phosphorylation of CtIP activates resection by MRN in S phase, and PLK1-mediated phosphorylation of CtIP disrupts CtIP stimulation of DNA2 to attenuate long-range resection later at G2/M.
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Affiliation(s)
- Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
| | - Hélène Bret
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Rosa Camarillo
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Francesca Vivalda
- Institute of Molecular Cancer Research, University of Zürich, Zürich 8057, Switzerland
| | - Roshan Singh Thakur
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland
| | - Amador Romero-Franco
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zürich, Zürich 8057, Switzerland
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona 6500, Switzerland;
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland
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6
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Patterson-Fortin J, D'Andrea AD. Targeting Polymerase Theta (POLθ) for Cancer Therapy. Cancer Treat Res 2023; 186:285-298. [PMID: 37978141 DOI: 10.1007/978-3-031-30065-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Polymerase theta (POLθ) is the critical multi-domain enzyme in microhomology-mediated end-joining DNA double-stranded break repair. POLθ is expressed at low levels in normal tissue but is often overexpressed in cancers, especially in DNA repair deficient cancers, such as homologous-recombination cancers, rendering them exquisitely sensitive to POLθ inhibition secondary to synthetic lethality. Development of POLθ inhibitors is an active area of investigation with inhibitors of the N-terminal helicase domain or the C-terminal polymerase domain currently in clinical trial. Here, we review POLθ-mediated microhomology-mediated end-joining, the development of POLθ inhibitors, and the potential clinical uses of POLθ inhibitors.
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Affiliation(s)
- Jeffrey Patterson-Fortin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Harvard Medical School, Center for DNA Damage and Repair, Susan F. Smith Center for Women's Cancers (SFSCWC), The Fuller-American Cancer Society, Dana-Farber Cancer Institute, HIM 243, 450 Brookline Ave., Boston, MA, 02215, USA.
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7
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Qiu Z, Hao S, Song S, Zhang R, Yan T, Lu Z, Wang H, Jia Z, Zheng J. PLK1-mediated phosphorylation of PPIL2 regulates HR via CtIP. Front Cell Dev Biol 2022; 10:902403. [PMID: 36092721 PMCID: PMC9452783 DOI: 10.3389/fcell.2022.902403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR) is an error-free DNA double-strand break (DSB) repair pathway, which safeguards genome integrity and cell viability. Human C-terminal binding protein (CtBP)—interacting protein (CtIP) is a central regulator of the pathway which initiates the DNA end resection in HR. Ubiquitination modification of CtIP is known in some cases to control DNA resection and promote HR. However, it remains unclear how cells restrain CtIP activity in unstressed cells. We show that the ubiquitin E3 ligase PPIL2 is recruited to DNA damage sites through interactions with an HR-related protein ZNF830, implying PPIL2’s involvement in DNA repair. We found that PPIL2 interacts with and ubiquitinates CtIP at the K426 site, representing a hereunto unknown ubiquitination site. Ubiquitination of CtIP by PPIL2 suppresses HR and DNA resection. This inhibition of PPIL2 is also modulated by phosphorylation at multiple sites by PLK1, which reduces PPIL2 ubiquitination of CtIP. Our findings reveal new regulatory complexity in CtIP ubiquitination in DSB repair. We propose that the PPIL2-dependent CtIP ubiquitination prevents CtIP from interacting with DNA, thereby inhibiting HR.
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Affiliation(s)
- Zhiyu Qiu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shikai Song
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ruiling Zhang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Tingyu Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zhifang Lu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
- *Correspondence: Zongchao Jia, ; Jimin Zheng,
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, China
- *Correspondence: Zongchao Jia, ; Jimin Zheng,
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8
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Xue C, Salunkhe SJ, Tomimatsu N, Kawale AS, Kwon Y, Burma S, Sung P, Greene EC. Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing. Nat Commun 2022; 13:2248. [PMID: 35473934 PMCID: PMC9042962 DOI: 10.1038/s41467-022-29937-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Sameer J Salunkhe
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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10
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Mojumdar A, Adam N, Cobb JA. Nej1 interacts with Sae2 at DNA double-stranded breaks to inhibit DNA resection. J Biol Chem 2022; 298:101937. [PMID: 35429499 PMCID: PMC9117546 DOI: 10.1016/j.jbc.2022.101937] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The two major pathways of DNA double-strand break repair, nonhomologous end-joining and homologous recombination, are highly conserved from yeast to mammals. The regulation of 5′-DNA resection controls repair pathway choice and influences repair outcomes. Nej1 was first identified as a canonical NHEJ factor involved in stimulating the ligation of broken DNA ends, and more recently, it was shown to participate in DNA end-bridging and in the inhibition of 5′-resection mediated by the nuclease/helicase complex Dna2–Sgs1. Here, we show that Nej1 interacts with Sae2 to impact DSB repair in three ways. First, we show that Nej1 inhibits interaction of Sae2 with the Mre11–Rad50–Xrs2 complex and Sae2 localization to DSBs. Second, we found that Nej1 inhibits Sae2-dependent recruitment of Dna2 independently of Sgs1. Third, we determined that NEJ1 and SAE2 showed an epistatic relationship for end-bridging, an event that restrains broken DNA ends and reduces the frequency of genomic deletions from developing at the break site. Finally, we demonstrate that deletion of NEJ1 suppressed the synthetic lethality of sae2Δ sgs1Δ mutants, and that triple mutant viability was dependent on Dna2 nuclease activity. Taken together, these findings provide mechanistic insight to how Nej1 functionality inhibits the initiation of DNA resection, a role that is distinct from its involvement in end-joining repair at DSBs.
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Affiliation(s)
- Aditya Mojumdar
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada
| | - Nancy Adam
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine; University of Calgary; 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada.
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11
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Park D, Gharghabi M, Reczek CR, Plow R, Yungvirt C, Aldaz CM, Huebner K. Wwox Binding to the Murine Brca1-BRCT Domain Regulates Timing of Brip1 and CtIP Phospho-Protein Interactions with This Domain at DNA Double-Strand Breaks, and Repair Pathway Choice. Int J Mol Sci 2022; 23:ijms23073729. [PMID: 35409089 PMCID: PMC8999063 DOI: 10.3390/ijms23073729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Wwox-deficient human cells show elevated homologous recombination, leading to resistance to killing by double-strand break-inducing agents. Human Wwox binds to the Brca1 981-PPLF-984 Wwox-binding motif, likely blocking the pChk2 phosphorylation site at Brca1-S988. This phosphorylation site is conserved across mammalian species; the PPLF motif is conserved in primates but not in rodents. We now show that murine Wwox does not bind Brca1 near the conserved mouse Brca1 phospho-S971 site, leaving it open for Chk2 phosphorylation and Brca1 activation. Instead, murine Wwox binds to Brca1 through its BRCT domain, where pAbraxas, pBrip1, and pCtIP, of the A, B, and C binding complexes, interact to regulate double-strand break repair pathway response. In Wwox-deficient mouse cells, the Brca1-BRCT domain is thus accessible for immediate binding of these phospho-proteins. We confirm elevated homologous recombination in Wwox-silenced murine cells, as in human cells. Wwox-deficient murine cells showed increased ionizing radiation-induced Abraxas, Brca1, and CtIP foci and long resected single-strand DNA, early after ionizing radiation. Wwox deletion increased the basal level of Brca1-CtIP interaction and the expression level of the MRN-CtIP protein complex, key players in end-resection, and facilitated Brca1 release from foci. Inhibition of phospho-Chk2 phosphorylation of Brca1-S971 delays the end-resection; the delay of premature end-resection by combining Chk2 inhibition with ionizing radiation or carboplatin treatment restored ionizing radiation and platinum sensitivity in Wwox-deficient murine cells, as in human cells, supporting the use of murine in vitro and in vivo models in preclinical cancer treatment research.
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Affiliation(s)
- Dongju Park
- Department of Cancer Biology and Genetics, The Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (M.G.); (R.P.); (C.Y.)
- Correspondence: (D.P.); (K.H.); Tel.: +1-614-685-9124 (D.P.); +1-614-292-4850 (K.H.)
| | - Mehdi Gharghabi
- Department of Cancer Biology and Genetics, The Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (M.G.); (R.P.); (C.Y.)
- Department of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Colleen R. Reczek
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA;
| | - Rebecca Plow
- Department of Cancer Biology and Genetics, The Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (M.G.); (R.P.); (C.Y.)
| | - Charles Yungvirt
- Department of Cancer Biology and Genetics, The Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (M.G.); (R.P.); (C.Y.)
| | - C. Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX 77054, USA;
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; (M.G.); (R.P.); (C.Y.)
- Correspondence: (D.P.); (K.H.); Tel.: +1-614-685-9124 (D.P.); +1-614-292-4850 (K.H.)
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12
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Shen J, Zhao Y, Pham NT, Li Y, Zhang Y, Trinidad J, Ira G, Qi Z, Niu H. Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble. Nat Commun 2022; 13:359. [PMID: 35042867 PMCID: PMC8766458 DOI: 10.1038/s41467-021-27940-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single-stranded DNA (ssDNA) commonly occurs as intermediates in DNA metabolic pathways. The ssDNA binding protein, RPA, not only protects the integrity of ssDNA, but also directs the downstream factor that signals or repairs the ssDNA intermediate. However, it remains unclear how these enzymes/factors outcompete RPA to access ssDNA. Using the budding yeast Saccharomyces cerevisiae as a model system, we find that Dna2 — a key nuclease in DNA replication and repair — employs a bimodal interface to act with RPA both in cis and in trans. The cis-activity makes RPA a processive unit for Dna2-catalyzed ssDNA digestion, where RPA delivers its bound ssDNA to Dna2. On the other hand, activity in trans is mediated by an acidic patch on Dna2, which enables it to function with a sub-optimal amount of RPA, or to overcome DNA secondary structures. The trans-activity mode is not required for cell viability, but is necessary for effective double strand break (DSB) repair. RPA protects the integrity of single stranded DNA during DNA repair processes. Here the authors show how RPA actively participates in DNA transactions through its interactions with the endonuclease Dna2.
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Affiliation(s)
- Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Yiling Zhao
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Nhung Tuyet Pham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuxi Li
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Yixiang Zhang
- Department of Chemistry, Biological Mass Spectrometry Facility, Indiana University, Bloomington, IN, 47405, USA
| | - Jonathan Trinidad
- Department of Chemistry, Biological Mass Spectrometry Facility, Indiana University, Bloomington, IN, 47405, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
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13
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van de Kamp G, Heemskerk T, Kanaar R, Essers J. DNA Double Strand Break Repair Pathways in Response to Different Types of Ionizing Radiation. Front Genet 2021; 12:738230. [PMID: 34659358 PMCID: PMC8514742 DOI: 10.3389/fgene.2021.738230] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/30/2021] [Indexed: 01/12/2023] Open
Abstract
The superior dose distribution of particle radiation compared to photon radiation makes it a promising therapy for the treatment of tumors. However, the cellular responses to particle therapy and especially the DNA damage response (DDR) is not well characterized. Compared to photons, particles are thought to induce more closely spaced DNA lesions instead of isolated lesions. How this different spatial configuration of the DNA damage directs DNA repair pathway usage, is subject of current investigations. In this review, we describe recent insights into induction of DNA damage by particle radiation and how this shapes DNA end processing and subsequent DNA repair mechanisms. Additionally, we give an overview of promising DDR targets to improve particle therapy.
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Affiliation(s)
- Gerarda van de Kamp
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands.,Oncode Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tim Heemskerk
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands.,Oncode Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands.,Oncode Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Radiation Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
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14
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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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15
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ZGRF1 promotes end resection of DNA homologous recombination via forming complex with BRCA1/EXO1. Cell Death Discov 2021; 7:260. [PMID: 34552057 PMCID: PMC8458317 DOI: 10.1038/s41420-021-00633-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/08/2022] Open
Abstract
To maintain genomic stability, the mammalian cells has evolved a coordinated response to DNA damage, including activation of DNA repair and cell cycle checkpoint processes. Exonuclease 1 (EXO1)-dependent excision of DNA ends is important for the initiation of homologous recombination (HR) repair of DNA breaks, which is thought to play a key role in activating the ATR-CHK1 pathway to induce G2/M cell cycle arrest. But the mechanism is still not fully understood. Here, we report that ZGRF1 forms complexes with EXO1 as well as other repair proteins and promotes DNA repair through HR. ZGRF1 is recruited to DNA damage sites in a MDC1-RNF8-BRCA1 dependent manner. Furthermore, ZGRF1 is important for the recruitment of RPA2 to DNA damage sites and the following ATR-CHK1 mediated G2/M checkpoint in response to irradiation. ZGRF1 null cells show increased sensitivity to many DNA-damaging agents, especially PARPi and irradiation. Collectively,our findings identify ZGRF1 as a novel regulator of DNA end resection and G2/M checkpoint. ZGRF1 is a potential target of radiation and PARPi cancer therapy.
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16
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Yannuzzi I, Butler MA, Fernandez J, LaRocque JR. The Role of Drosophila CtIP in Homology-Directed Repair of DNA Double-Strand Breaks. Genes (Basel) 2021; 12:genes12091430. [PMID: 34573412 PMCID: PMC8468788 DOI: 10.3390/genes12091430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a particularly genotoxic type of DNA damage that can result in chromosomal aberrations. Thus, proper repair of DSBs is essential to maintaining genome integrity. DSBs can be repaired by non-homologous end joining (NHEJ), where ends are processed before joining through ligation. Alternatively, DSBs can be repaired through homology-directed repair, either by homologous recombination (HR) or single-strand annealing (SSA). Both types of homology-directed repair are initiated by DNA end resection. In cultured human cells, the protein CtIP has been shown to play a role in DNA end resection through its interactions with CDK, BRCA1, DNA2, and the MRN complex. To elucidate the role of CtIP in a multicellular context, CRISPR/Cas9 genome editing was used to create a DmCtIPΔ allele in Drosophila melanogaster. Using the DSB repair reporter assay direct repeat of white (DR-white), a two-fold decrease in HR in DmCtIPΔ/Δ mutants was observed when compared to heterozygous controls. However, analysis of HR gene conversion tracts (GCTs) suggests DmCtIP plays a minimal role in determining GCT length. To assess the function of DmCtIP on both short (~550 bp) and long (~3.6 kb) end resection, modified homology-directed SSA repair assays were implemented, resulting in a two-fold decrease in SSA repair in both short and extensive end resection requirements in the DmCtIPΔ/Δ mutants compared to heterozygote controls. Through these analyses, we affirmed the importance of end resection on DSB repair pathway choice in multicellular systems, described the function of DmCtIP in short and extensive DNA end resection, and determined the impact of end resection on GCT length during HR.
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Affiliation(s)
- Ian Yannuzzi
- Biology Department, Georgetown College, Georgetown University, Washington, DC 20057, USA;
| | - Margaret A. Butler
- Georgetown University Medical Center, Department of Human Science, Georgetown University, Washington, DC 20057, USA; (M.A.B.); (J.F.)
| | - Joel Fernandez
- Georgetown University Medical Center, Department of Human Science, Georgetown University, Washington, DC 20057, USA; (M.A.B.); (J.F.)
| | - Jeannine R. LaRocque
- Georgetown University Medical Center, Department of Human Science, Georgetown University, Washington, DC 20057, USA; (M.A.B.); (J.F.)
- Correspondence:
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17
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DNA end resection during homologous recombination. Curr Opin Genet Dev 2021; 71:99-105. [PMID: 34329854 DOI: 10.1016/j.gde.2021.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Exposure to environmental mutagens but also cell-endogenous processes can create DNA double-strand breaks (DSBs) in a cell's genome. DSBs need to be repaired accurately and timely to ensure genomic integrity and cell survival. One major DSB repair mechanism, called homologous recombination, relies on the nucleolytic degradation of the 5'-terminated strands in a process termed end resection. Here, we review new insights into end resection with a focus on the mechanistic interplay of the nucleases, helicases, and accessory factors involved.
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18
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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19
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Begum NA, Haque F, Stanlie A, Husain A, Mondal S, Nakata M, Taniguchi T, Taniguchi H, Honjo T. Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition. EMBO J 2021; 40:e106393. [PMID: 33938017 PMCID: PMC8204862 DOI: 10.15252/embj.2020106393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement mediated by switch (S) region transcription, activation-induced cytidine deaminase (AID)-induced DNA breaks, and their resolution by non-homologous end joining (NHEJ)-mediated DNA repair. Due to the complex nature of the recombination process, numerous cofactors are intimately involved, making it important to identify rate-limiting factors that impact on DNA breaking and/or repair. Using an siRNA-based loss-of-function screen of genes predicted to encode PHD zinc-finger-motif proteins, we identify the splicing factor Phf5a/Sf3b14b as a novel modulator of the DNA repair step of CSR. Loss of Phf5a severely impairs AID-induced recombination, but does not perturb DNA breaks and somatic hypermutation. Phf5a regulates NHEJ-dependent DNA repair by preserving chromatin integrity to elicit optimal DNA damage response and subsequent recruitment of NHEJ factors at the S region. Phf5a stabilizes the p400 histone chaperone complex at the locus, which in turn promotes deposition of H2A variant such as H2AX and H2A.Z that are critical for the early DNA damage response and NHEJ, respectively. Depletion of Phf5a or p400 blocks the repair of both AID- and I-SceI-induced DNA double-strand breaks, supporting an important contribution of this axis to programmed as well as aberrant recombination.
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Affiliation(s)
- Nasim A Begum
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Farazul Haque
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Andre Stanlie
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- BioMedicine DesignPfizer Inc.CambridgeMAUSA
| | - Afzal Husain
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of BiochemistryFaculty of Life SciencesAligarh Muslim UniversityAligarhIndia
| | - Samiran Mondal
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of ChemistryRammohan CollegeKolkataIndia
| | - Mikiyo Nakata
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Takako Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Hisaaki Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Tasuku Honjo
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
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20
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Lyu X, Sang PB, Chai W. CST in maintaining genome stability: Beyond telomeres. DNA Repair (Amst) 2021; 102:103104. [PMID: 33780718 PMCID: PMC8081025 DOI: 10.1016/j.dnarep.2021.103104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
The human CST (CTC1-STN1-TEN1) complex is an RPA-like single-stranded DNA binding protein complex. While its telomeric functions have been well investigated, numerous studies have revealed that hCST also plays important roles in maintaining genome stability beyond telomeres. Here, we review and discuss recent discoveries on CST in various global genome maintenance pathways, including findings on the CST supercomplex structure, its functions in unperturbed DNA replication, stalled replication, double-strand break repair, and the ATR-CHK1 activation pathway. By summarizing these recent discoveries, we hope to offer new insights into genome maintenance mechanisms and the pathogenesis of CST mutation-associated diseases.
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Affiliation(s)
- Xinxing Lyu
- Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China; Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States.
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21
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Mendez-Dorantes C, Tsai LJ, Jahanshir E, Lopezcolorado FW, Stark JM. BLM has Contrary Effects on Repeat-Mediated Deletions, based on the Distance of DNA DSBs to a Repeat and Repeat Divergence. Cell Rep 2021; 30:1342-1357.e4. [PMID: 32023454 PMCID: PMC7085117 DOI: 10.1016/j.celrep.2020.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/08/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Repeat-mediated deletions (RMDs) often involve repetitive elements (e.g., short interspersed elements) with sequence divergence that is separated by several kilobase pairs (kbps). We have examined RMDs induced by DNA double-strand breaks (DSBs) under varying conditions of repeat sequence divergence (identical versus 1% and 3% divergent) and DSB/repeat distance (16 bp–28.4 kbp). We find that the BLM helicase promotes RMDs with long DSB/repeat distances (e.g., 28.4 kbp), which is consistent with a role in extensive DSB end resection, because the resection nucleases EXO1 and DNA2 affect RMDs similarly to BLM. In contrast, BLM suppresses RMDs with sequence divergence and intermediate (e.g., 3.3 kbp) DSB/repeat distances, which supports a role in heteroduplex rejection. The role of BLM in heteroduplex rejection is not epistatic with MSH2 and is independent of the annealing factor RAD52. Accordingly, the role of BLM on RMDs is substantially affected by DSB/repeat distance and repeat sequence divergence. Mendez-Dorantes et al. identify the BLM helicase as a key regulator of repeat-mediated deletions (RMDs). BLM, EXO1, and DNA2 mediate RMDs with remarkably long DNA break/repeat distances. BLM suppresses RMDs with sequence divergence that is optimal with a long non-homologous tail and is independent of MSH2 and RAD52.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - L Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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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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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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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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25
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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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26
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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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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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29
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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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30
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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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31
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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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32
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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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Shen W, Ma Y, Qi H, Wang W, He J, Xiao F, Zhu H, He S. Kinetics model of DNA double-strand break repair in eukaryotes. DNA Repair (Amst) 2021; 100:103035. [PMID: 33618125 DOI: 10.1016/j.dnarep.2020.103035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022]
Abstract
This manuscript outlines the kinetics of two main repair pathways of DNA double-strand break (DSB) in eukaryotes: non-homologous end joining (NHEJ) and homologous recombination repair (HRR). In this review, we discuss the precise study of recruitment kinetics of repair proteins based on the latest technologies in the past two decades. Then we simulate the theoretical description of the DNA repair process by mathematical models. In our study, the consecutive reactions chain (CRC) model and continuous-time random walk (CTRW) model have been unified by us, so that we can obtain the function of the number of intermediates with time in the same framework of equations, overcome the incompatibility between the two models. On this basis, we propose a data fitting workflow using these both models. Finally, we give an overview of different real-time quantitative methods and the new mechanism complexity that can be found from the corresponding dynamic models.
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Affiliation(s)
- Wangtao Shen
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China
| | - Yun Ma
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China.
| | - Huizhou Qi
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Function Laboratory Center, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Wuzhou Wang
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Junyan He
- Department of Radiation Oncology, The First Affiliated Hospital of University of South China, Hengyang, 421001, China
| | - Fangzhu Xiao
- Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Hui Zhu
- Institute of Engineering Mathematics, Mathematics and Physics College, University of South China, Hengyang, 421001, China
| | - Shuya He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China.
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Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
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Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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35
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Lodovichi S, Cervelli T, Pellicioli A, Galli A. Inhibition of DNA Repair in Cancer Therapy: Toward a Multi-Target Approach. Int J Mol Sci 2020; 21:E6684. [PMID: 32932697 PMCID: PMC7554826 DOI: 10.3390/ijms21186684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Alterations in DNA repair pathways are one of the main drivers of cancer insurgence. Nevertheless, cancer cells are more susceptible to DNA damage than normal cells and they rely on specific functional repair pathways to survive. Thanks to advances in genome sequencing, we now have a better idea of which genes are mutated in specific cancers and this prompted the development of inhibitors targeting DNA repair players involved in pathways essential for cancer cells survival. Currently, the pivotal concept is that combining the inhibition of mechanisms on which cancer cells viability depends is the most promising way to treat tumorigenesis. Numerous inhibitors have been developed and for many of them, efficacy has been demonstrated either alone or in combination with chemo or radiotherapy. In this review, we will analyze the principal pathways involved in cell cycle checkpoint and DNA repair focusing on how their alterations could predispose to cancer, then we will explore the inhibitors developed or in development specifically targeting different proteins involved in each pathway, underscoring the rationale behind their usage and how their combination and/or exploitation as adjuvants to classic therapies could help in patients clinical outcome.
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Affiliation(s)
- Samuele Lodovichi
- Bioscience Department, University of Milan, Via Celoria 26, 20131 Milan, Italy;
| | - Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy;
| | - Achille Pellicioli
- Bioscience Department, University of Milan, Via Celoria 26, 20131 Milan, Italy;
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy;
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36
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Yang H, Ren S, Yu S, Pan H, Li T, Ge S, Zhang J, Xia N. Methods Favoring Homology-Directed Repair Choice in Response to CRISPR/Cas9 Induced-Double Strand Breaks. Int J Mol Sci 2020; 21:E6461. [PMID: 32899704 PMCID: PMC7555059 DOI: 10.3390/ijms21186461] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/15/2022] Open
Abstract
Precise gene editing is-or will soon be-in clinical use for several diseases, and more applications are under development. The programmable nuclease Cas9, directed by a single-guide RNA (sgRNA), can introduce double-strand breaks (DSBs) in target sites of genomic DNA, which constitutes the initial step of gene editing using this novel technology. In mammals, two pathways dominate the repair of the DSBs-nonhomologous end joining (NHEJ) and homology-directed repair (HDR)-and the outcome of gene editing mainly depends on the choice between these two repair pathways. Although HDR is attractive for its high fidelity, the choice of repair pathway is biased in a biological context. Mammalian cells preferentially employ NHEJ over HDR through several mechanisms: NHEJ is active throughout the cell cycle, whereas HDR is restricted to S/G2 phases; NHEJ is faster than HDR; and NHEJ suppresses the HDR process. This suggests that definitive control of outcome of the programmed DNA lesioning could be achieved through manipulating the choice of cellular repair pathway. In this review, we summarize the DSB repair pathways, the mechanisms involved in choice selection based on DNA resection, and make progress in the research investigating strategies that favor Cas9-mediated HDR based on the manipulation of repair pathway choice to increase the frequency of HDR in mammalian cells. The remaining problems in improving HDR efficiency are also discussed. This review should facilitate the development of CRISPR/Cas9 technology to achieve more precise gene editing.
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Affiliation(s)
| | | | | | | | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Disease, Collaborative Innovation Centers of Biological Products, School of Public Health, Xiamen University, Xiamen 361102, China; (H.Y.); (S.R.); (S.Y.); (H.P.); (J.Z.); (N.X.)
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Abstract
The DNA of our cells is constantly exposed to various types of damaging agents. One of the most critical types of damage is when both strands of the DNA break, and thus such breaks need to be efficiently repaired. It is known that CtIP promotes nucleases in DNA break repair. Here we show that CtIP can also hold the two DNA strands together in solution when DNA is free to move, using novel methodology that allows the monitoring of thousands of single DNA molecules in nanofabricated devices. DNA bridging likely facilitates the enzymatic repair steps and identifies novel CtIP functions that are crucial for repairing broken DNA. The early steps of DNA double-strand break (DSB) repair in human cells involve the MRE11-RAD50-NBS1 (MRN) complex and its cofactor, phosphorylated CtIP. The roles of these proteins in nucleolytic DSB resection are well characterized, but their role in bridging the DNA ends for efficient and correct repair is much less explored. Here we study the binding of phosphorylated CtIP, which promotes the endonuclease activity of MRN, to single long (∼50 kb) DNA molecules using nanofluidic channels and compare it to the yeast homolog Sae2. CtIP bridges DNA in a manner that depends on the oligomeric state of the protein, and truncated mutants demonstrate that the bridging depends on CtIP regions distinct from those that stimulate the nuclease activity of MRN. Sae2 is a much smaller protein than CtIP, and its bridging is significantly less efficient. Our results demonstrate that the nuclease cofactor and structural functions of CtIP may depend on the same protein population, which may be crucial for CtIP functions in both homologous recombination and microhomology-mediated end-joining.
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38
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Howard SM, Ceppi I, Anand R, Geiger R, Cejka P. The internal region of CtIP negatively regulates DNA end resection. Nucleic Acids Res 2020; 48:5485-5498. [PMID: 32347940 PMCID: PMC7261161 DOI: 10.1093/nar/gkaa273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/05/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both short and long-range resection. The structure of CtIP differs from its orthologues in yeast, as it contains a large internal unstructured region. Here, we conducted a domain analysis of CtIP to define the function of the internal region in DNA end resection. We found that residues 350-600 were entirely dispensable for resection in vitro. A mutant lacking these residues was unexpectedly more efficient than full-length CtIP in DNA end resection and homologous recombination in vivo, and consequently conferred resistance to lesions induced by the topoisomerase poison camptothecin, which require high MRN-CtIP-dependent resection activity for repair. This suggested that the internal CtIP region, further mapped to residues 550-600, may mediate a negative regulatory function to prevent over resection in vivo. The CtIP internal deletion mutant exhibited sensitivity to other DNA-damaging drugs, showing that upregulated resection may be instead toxic under different conditions. These experiments together identify a region within the central CtIP domain that negatively regulates DNA end resection.
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Affiliation(s)
- Sean Michael Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
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39
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Mechanism and significance of chromosome damage repair by homologous recombination. Essays Biochem 2020; 64:779-790. [DOI: 10.1042/ebc20190093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/29/2022]
Abstract
Abstract
Homologous recombination (HR) is a major, conserved pathway of chromosome damage repair. It not only fulfills key functions in the removal of deleterious lesions such as DNA double-strand breaks (DSBs) and interstrand cross-links (ICLs), but also in replication fork repair and protection. Several familial and acquired cancer predisposition syndromes stem from defects in HR. In particular, individuals with mutations in HR genes exhibit predisposition to breast, ovarian, pancreatic, and prostate cancers, and they also show signs of accelerated aging. However, aberrant and untimely HR events can lead to the loss of heterozygosity, genomic rearrangements, and cytotoxic nucleoprotein intermediates. Thus, it is critically important that HR be tightly regulated. In addition to DNA repair, HR is also involved in meiotic chromosome segregation and telomere maintenance in cells that lack telomerase. In this review, we focus on the role of HR in DSB repair (DSBR) and summarize the current state of the field.
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40
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DNA Damage: From Threat to Treatment. Cells 2020; 9:cells9071665. [PMID: 32664329 PMCID: PMC7408370 DOI: 10.3390/cells9071665] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022] Open
Abstract
DNA is the source of genetic information, and preserving its integrity is essential in order to sustain life. The genome is continuously threatened by different types of DNA lesions, such as abasic sites, mismatches, interstrand crosslinks, or single-stranded and double-stranded breaks. As a consequence, cells have evolved specialized DNA damage response (DDR) mechanisms to sustain genome integrity. By orchestrating multilayer signaling cascades specific for the type of lesion that occurred, the DDR ensures that genetic information is preserved overtime. In the last decades, DNA repair mechanisms have been thoroughly investigated to untangle these complex networks of pathways and processes. As a result, key factors have been identified that control and coordinate DDR circuits in time and space. In the first part of this review, we describe the critical processes encompassing DNA damage sensing and resolution. In the second part, we illustrate the consequences of partial or complete failure of the DNA repair machinery. Lastly, we will report examples in which this knowledge has been instrumental to develop novel therapies based on genome editing technologies, such as CRISPR-Cas.
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41
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DNA double-strand break end resection: a critical relay point for determining the pathway of repair and signaling. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s42764-020-00017-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractA DNA double-strand break (DSB) is considered the most critical DNA lesion because it causes cell death and severe mutations if it is not repaired or repaired incorrectly. Accumulating evidence has shown that the majority of DSBs are repaired by DNA non-homologous end joining (NHEJ), the first utilized repair pathway in human cells. In contrast, the repair pathway is sometimes diverted into using homologous recombination (HR), which has increased precision under specific circumstances: e.g., when DSBs are generated at transcriptionally active loci or are not readily repaired due to the complexity of damage at the DSB ends or due to highly compacted chromatin. DSB end resection (resection) is considered the most critical turning point for directing repair towards HR. After resection, the HR process is finalized by RAD51 loading and recombination. Thus, understanding the process of resection is critically important to understand the regulation of the choice of DSB repair pathway. In addition, resection is also an important factor influencing DNA damage signaling because unresected ends preferentially activate ATM, whereas longer resected ends activate ATR. Thus, DSB end resection is a key relay point that determines the repair pathway and the signal balance. In this review, we summarize the mechanism underlying DSB end resection and further discuss how it is involved in cancer therapy.
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Reginato G, Cejka P. The MRE11 complex: A versatile toolkit for the repair of broken DNA. DNA Repair (Amst) 2020; 91-92:102869. [PMID: 32480356 DOI: 10.1016/j.dnarep.2020.102869] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
Abstract
When DNA breaks, the ends need to be stabilized and processed to facilitate subsequent repair, which can occur by either direct but error-prone end-joining with another broken DNA molecule or a more accurate homology-directed repair by the recombination machinery. At the same time, the presence of broken DNA triggers a signaling cascade that regulates the repair events and cellular progression through the cell cycle. The MRE11 nuclease, together with RAD50 and NBS1 forms a complex termed MRN that participates in all these processes. Although MRE11 was first identified more than 20 years ago, deep insights into its mechanism of action and regulation are much more recent. Here we review how MRE11 functions within MRN, and how the complex is further regulated by CtIP and its phosphorylation in a cell cycle dependent manner. We describe how RAD50, NBS1 and CtIP convert MRE11, exhibiting per se a 3'→5' exonuclease activity, into an ensemble that instead degrades primarily the 5'-terminated strand by endonucleolytic cleavage at DNA break sites to generate 3' overhangs, as required for the initiation of homologous recombination. The unique mechanism of DNA end resection by MRN-CtIP makes it a very flexible toolkit to process DNA breaks with a variety of secondary structures and protein blocks. Such a block can also be the Ku heterodimer, and emerging evidence suggests that MRN-CtIP may often need to remove Ku from DNA ends before initiating homologous recombination. Misregulation of DNA break repair results in mutations and chromosome rearrangements that can drive cancer development. Therefore, a detailed understanding of the underlying processes is highly relevant for human health.
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Affiliation(s)
- Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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43
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Daley JM, Tomimatsu N, Hooks G, Wang W, Miller AS, Xue X, Nguyen KA, Kaur H, Williamson E, Mukherjee B, Hromas R, Burma S, Sung P. Specificity of end resection pathways for double-strand break regions containing ribonucleotides and base lesions. Nat Commun 2020; 11:3088. [PMID: 32555206 PMCID: PMC7303207 DOI: 10.1038/s41467-020-16903-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 05/29/2020] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand break repair by homologous recombination begins with nucleolytic resection of the 5’ DNA strand at the break ends. Long-range resection is catalyzed by EXO1 and BLM-DNA2, which likely have to navigate through ribonucleotides and damaged bases. Here, we show that a short stretch of ribonucleotides at the 5’ terminus stimulates resection by EXO1. Ribonucleotides within a 5’ flap are resistant to cleavage by DNA2, and extended RNA:DNA hybrids inhibit both strand separation by BLM and resection by EXO1. Moreover, 8-oxo-guanine impedes EXO1 but enhances resection by BLM-DNA2, and an apurinic/apyrimidinic site stimulates resection by BLM-DNA2 and DNA strand unwinding by BLM. Accordingly, depletion of OGG1 or APE1 leads to greater dependence of DNA resection on DNA2. Importantly, RNase H2A deficiency impairs resection overall, which we attribute to the accumulation of long RNA:DNA hybrids at DNA ends. Our results help explain why eukaryotic cells possess multiple resection nucleases. DNA double-strand break repair by homologous recombination initiates with nucleolytic resection of the 5’ DNA strand at the break ends. Here, the authors reveal that the lesion context influences the action and efficiency of the long range resection factors EXO1 and BLM-DNA2.
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Affiliation(s)
- James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA. .,Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
| | - Nozomi Tomimatsu
- Department of Neurosurgery, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Grace Hooks
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA.,Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA.,Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA.,Regeneron, Rensselaer, NY, 12144, USA
| | - Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA.,Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Kevin A Nguyen
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA.,David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Hardeep Kaur
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Elizabeth Williamson
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Bipasha Mukherjee
- Department of Neurosurgery, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA. .,Department of Neurosurgery, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06510, USA. .,Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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44
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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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45
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Nath S, Nagaraju G. FANCJ helicase promotes DNA end resection by facilitating CtIP recruitment to DNA double-strand breaks. PLoS Genet 2020; 16:e1008701. [PMID: 32251466 PMCID: PMC7162537 DOI: 10.1371/journal.pgen.1008701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/16/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
FANCJ helicase mutations are known to cause hereditary breast and ovarian cancers as well as bone marrow failure syndrome Fanconi anemia. FANCJ plays an important role in the repair of DNA inter-strand crosslinks and DNA double-strand breaks (DSBs) by homologous recombination (HR). Nonetheless, the molecular mechanism by which FANCJ controls HR mediated DSB repair is obscure. Here, we show that FANCJ promotes DNA end resection by recruiting CtIP to the sites of DSBs. This recruitment of CtIP is dependent on FANCJ K1249 acetylation. Notably, FANCJ acetylation is dependent on FANCJ S990 phosphorylation by CDK. The CDK mediated phosphorylation of FANCJ independently facilitates its interaction with BRCA1 at damaged DNA sites and promotes DNA end resection by CtIP recruitment. Strikingly, mutational studies reveal that ATP binding competent but hydrolysis deficient FANCJ partially supports end resection, indicating that in addition to the scaffolding role of FANCJ in CtIP recruitment, its helicase activity is important for promoting end resection. Together, these data unravel a novel function of FANCJ helicase in DNA end resection and provide mechanistic insights into its role in repairing DSBs by HR and in genome maintenance. Homologous recombination has been considered as an error-free pathway in repairing DSBs and maintaining genome stability. Cyclin-dependent kinases (CDKs) and various factors including MRE11, CtIP, EXO1, and BLM helicase participate in DNA end resection to promote HR mediated DSB repair. Despite the identification of FANCJ helicase role in HR and tumor suppression, the molecular mechanism by which FANCJ helicase participates in HR is obscure. Here, we show that FANCJ helicase controls DNA end resection by recruiting CtIP to the sites of DSBs. The loading of CtIP is dependent on FANCJ acetylation which is mediated by CDK dependent phosphorylation of FANCJ. Moreover, in addition to FANCJ mediated CtIP recruitment, its helicase activity is also essential for DNA end resection. Our data identify FANCJ as a novel player in the DNA end resection and provide insights into its role in HR mediated DSB repair.
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Affiliation(s)
- Sarmi Nath
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail:
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46
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Stroik S, Kurtz K, Hendrickson EA. CtIP is essential for telomere replication. Nucleic Acids Res 2019; 47:8927-8940. [PMID: 31378812 PMCID: PMC6755089 DOI: 10.1093/nar/gkz652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
The maintenance of telomere length is critical to longevity and survival. Specifically, the failure to properly replicate, resect, and/or form appropriate telomeric structures drives telomere shortening and, in turn, genomic instability. The endonuclease CtIP is a DNA repair protein that is well-known to promote genome stability through the resection of endogenous DNA double-stranded breaks. Here, we describe a novel role for CtIP. We show that in the absence of CtIP, human telomeres shorten rapidly to non-viable lengths. This telomere dysfunction results in an accumulation of fusions, breaks, and frank telomere loss. Additionally, CtIP suppresses the generation of circular, extrachromosomal telomeric DNA. These latter structures appear to arise from arrested DNA replication forks that accumulate in the absence of CtIP. Hence, CtIP is required for faithful replication through telomeres via its roles at stalled replication tracts. Our findings demonstrate a new role for CtIP as a protector of human telomere integrity.
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Affiliation(s)
- Susanna Stroik
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kevin Kurtz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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47
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Xue C, Daley JM, Xue X, Steinfeld J, Kwon Y, Sung P, Greene EC. Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates. Nucleic Acids Res 2019; 47:11225-11237. [PMID: 31544923 PMCID: PMC6868385 DOI: 10.1093/nar/gkz810] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/06/2019] [Accepted: 09/17/2019] [Indexed: 11/12/2022] Open
Abstract
Bloom helicase (BLM) and its orthologs are essential for the maintenance of genome integrity. BLM defects represent the underlying cause of Bloom Syndrome, a rare genetic disorder that is marked by strong cancer predisposition. BLM deficient cells accumulate extensive chromosomal aberrations stemming from dysfunctions in homologous recombination (HR). BLM participates in several HR stages and helps dismantle potentially harmful HR intermediates. However, much remains to be learned about the molecular mechanisms of these BLM-mediated regulatory effects. Here, we use DNA curtains to directly visualize the activity of BLM helicase on single molecules of DNA. Our data show that BLM is a robust helicase capable of rapidly (∼70-80 base pairs per second) unwinding extensive tracts (∼8-10 kilobases) of double-stranded DNA (dsDNA). Importantly, we find no evidence for BLM activity on single-stranded DNA (ssDNA) that is bound by replication protein A (RPA). Likewise, our results show that BLM can neither associate with nor translocate on ssDNA that is bound by the recombinase protein RAD51. Moreover, our data reveal that the presence of RAD51 also blocks BLM translocation on dsDNA substrates. We discuss our findings within the context of potential regulator roles for BLM helicase during DNA replication and repair.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - James M Daley
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Justin Steinfeld
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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48
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Alfano L, Caporaso A, Altieri A, Dell'Aquila M, Landi C, Bini L, Pentimalli F, Giordano A. Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation. Nucleic Acids Res 2019; 47:4068-4085. [PMID: 30799487 PMCID: PMC6486545 DOI: 10.1093/nar/gkz076] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/24/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
DNA double strand break (DSB) repair through homologous recombination (HR) is crucial to maintain genome stability. DSB resection generates a single strand DNA intermediate, which is crucial for the HR process. We used a synthetic DNA structure, mimicking a resection intermediate, as a bait to identify proteins involved in this process. Among these, LC/MS analysis identified the RNA binding protein, HNRNPD. We found that HNRNPD binds chromatin, although this binding occurred independently of DNA damage. However, upon damage, HNRNPD re-localized to γH2Ax foci and its silencing impaired CHK1 S345 phosphorylation and the DNA end resection process. Indeed, HNRNPD silencing reduced: the ssDNA fraction upon camptothecin treatment; AsiSI-induced DSB resection; and RPA32 S4/8 phosphorylation. CRISPR/Cas9-mediated HNRNPD knockout impaired in vitro DNA resection and sensitized cells to camptothecin and olaparib treatment. We found that HNRNPD interacts with the heterogeneous nuclear ribonucleoprotein SAF-A previously associated with DNA damage repair. HNRNPD depletion resulted in an increased amount of RNA:DNA hybrids upon DNA damage. Both the expression of RNase H1 and RNA pol II inhibition recovered the ability to phosphorylate RPA32 S4/8 in HNRNPD knockout cells upon DNA damage, suggesting that RNA:DNA hybrid resolution likely rescues the defective DNA damage response of HNRNPD-depleted cells.
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Affiliation(s)
- Luigi Alfano
- Oncology Research Center of Mercogliano (CROM); Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli, Italia
| | - Antonella Caporaso
- Department of Medical Biotechnologies, University of Siena, Siena, Italia.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italia
| | - Milena Dell'Aquila
- Department of Medical Biotechnologies, University of Siena, Siena, Italia
| | - Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italia
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italia
| | - Francesca Pentimalli
- Oncology Research Center of Mercogliano (CROM); Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli, Italia
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italia.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
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49
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Densham RM, Morris JR. Moving Mountains-The BRCA1 Promotion of DNA Resection. Front Mol Biosci 2019; 6:79. [PMID: 31552267 PMCID: PMC6733915 DOI: 10.3389/fmolb.2019.00079] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) occur in our cells in the context of chromatin. This type of lesion is toxic, entirely preventing genome continuity and causing cell death or terminal arrest. Several repair mechanisms can act on DNA surrounding a DSB, only some of which carry a low risk of mutation, so that which repair process is utilized is critical to the stability of genetic material of cells. A key component of repair outcome is the degree of DNA resection directed to either side of the break site. This in turn determines the subsequent forms of repair in which DNA homology plays a part. Here we will focus on chromatin and chromatin-bound complexes which constitute the "mountains" that block resection, with a particular focus on how the breast and ovarian cancer predisposition protein-1 (BRCA1) contributes to repair outcomes through overcoming these blocks.
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Affiliation(s)
| | - Joanna R. Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, United Kingdom
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50
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Tarnauskaitė Ž, Bicknell LS, Marsh JA, Murray JE, Parry DA, Logan CV, Bober MB, de Silva DC, Duker AL, Sillence D, Wise C, Jackson AP, Murina O, Reijns MAM. Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Hum Mutat 2019; 40:1063-1070. [PMID: 31045292 PMCID: PMC6773220 DOI: 10.1002/humu.23776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/15/2019] [Accepted: 04/28/2019] [Indexed: 11/11/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterized by the extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report the identification of four MPD individuals with biallelic variants in DNA2, which encodes an adenosine triphosphate (ATP)-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.
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Affiliation(s)
- Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Louise S. Bicknell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jennie E. Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Clare V. Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael B. Bober
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - Deepthi C. de Silva
- Department of Physiology, Faculty of MedicineUniversity of KelaniyaColomboSri Lanka
| | - Angela L. Duker
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - David Sillence
- Discipline of Genomic Medicine, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
- Western Sydney Genetics ProgramSydney Children's Hospitals NetworkWestmeadAustralia
| | - Carol Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal ResearchTexas Scottish, Rite Hospital for ChildrenDallasTexas
- McDermott Center for Human Growth and DevelopmentUniversity of Texas, Southwestern Medical CenterDallasTexas
- Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTexas
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
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