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Stinson BM, Loparo JJ. Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. Annu Rev Biochem 2021; 90:137-164. [PMID: 33556282 DOI: 10.1146/annurev-biochem-080320-110356] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.
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Affiliation(s)
- Benjamin M Stinson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; ,
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2
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The Determinant of DNA Repair Pathway Choices in Ionising Radiation-Induced DNA Double-Strand Breaks. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4834965. [PMID: 32908893 PMCID: PMC7468606 DOI: 10.1155/2020/4834965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/13/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Ionising radiation- (IR-) induced DNA double-strand breaks (DSBs) are considered to be the deleterious DNA lesions that pose a serious threat to genomic stability. The major DNA repair pathways, including classical nonhomologous end joining, homologous recombination, single-strand annealing, and alternative end joining, play critical roles in countering and eliciting IR-induced DSBs to ensure genome integrity. If the IR-induced DNA DSBs are not repaired correctly, the residual or incorrectly repaired DSBs can result in genomic instability that is associated with certain human diseases. Although many efforts have been made in investigating the major mechanisms of IR-induced DNA DSB repair, it is still unclear what determines the choices of IR-induced DNA DSB repair pathways. In this review, we discuss how the mechanisms of IR-induced DSB repair pathway choices can operate in irradiated cells. We first briefly describe the main mechanisms of the major DNA DSB repair pathways and the related key repair proteins. Based on our understanding of the characteristics of IR-induced DNA DSBs and the regulatory mechanisms of DSB repair pathways in irradiated cells and recent advances in this field, We then highlight the main factors and associated challenges to determine the IR-induced DSB repair pathway choices. We conclude that the type and distribution of IR-induced DSBs, chromatin state, DNA-end structure, and DNA-end resection are the main determinants of the choice of the IR-induced DNA DSB repair pathway.
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Zhao L, Bao C, Shang Y, He X, Ma C, Lei X, Mi D, Sun Y. The Determinant of DNA Repair Pathway Choices in Ionising Radiation-Induced DNA Double-Strand Breaks. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: doi.org/10.1155/2020/4834965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionising radiation- (IR-) induced DNA double-strand breaks (DSBs) are considered to be the deleterious DNA lesions that pose a serious threat to genomic stability. The major DNA repair pathways, including classical nonhomologous end joining, homologous recombination, single-strand annealing, and alternative end joining, play critical roles in countering and eliciting IR-induced DSBs to ensure genome integrity. If the IR-induced DNA DSBs are not repaired correctly, the residual or incorrectly repaired DSBs can result in genomic instability that is associated with certain human diseases. Although many efforts have been made in investigating the major mechanisms of IR-induced DNA DSB repair, it is still unclear what determines the choices of IR-induced DNA DSB repair pathways. In this review, we discuss how the mechanisms of IR-induced DSB repair pathway choices can operate in irradiated cells. We first briefly describe the main mechanisms of the major DNA DSB repair pathways and the related key repair proteins. Based on our understanding of the characteristics of IR-induced DNA DSBs and the regulatory mechanisms of DSB repair pathways in irradiated cells and recent advances in this field, We then highlight the main factors and associated challenges to determine the IR-induced DSB repair pathway choices. We conclude that the type and distribution of IR-induced DSBs, chromatin state, DNA-end structure, and DNA-end resection are the main determinants of the choice of the IR-induced DNA DSB repair pathway.
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Affiliation(s)
- Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026 Liaoning, China
| | - Chengyu Bao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026 Liaoning, China
| | - Yuxuan Shang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026 Liaoning, China
| | - Xinye He
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026 Liaoning, China
| | - Chiyuan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dong Mi
- College of Science, Dalian Maritime University, Dalian, Liaoning, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026 Liaoning, China
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Serrano-Benítez A, Cortés-Ledesma F, Ruiz JF. "An End to a Means": How DNA-End Structure Shapes the Double-Strand Break Repair Process. Front Mol Biosci 2020; 6:153. [PMID: 31998749 PMCID: PMC6965357 DOI: 10.3389/fmolb.2019.00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022] Open
Abstract
Endogenously-arising DNA double-strand breaks (DSBs) rarely harbor canonical 5′-phosphate, 3′-hydroxyl moieties at the ends, which are, regardless of the pathway used, ultimately required for their repair. Cells are therefore endowed with a wide variety of enzymes that can deal with these chemical and structural variations and guarantee the formation of ligatable termini. An important distinction is whether the ends are directly “unblocked” by specific enzymatic activities without affecting the integrity of the DNA molecule and its sequence, or whether they are “processed” by unspecific nucleases that remove nucleotides from the termini. DNA end structure and configuration, therefore, shape the repair process, its requirements, and, importantly, its final outcome. Thus, the molecular mechanisms that coordinate and integrate the cellular response to blocked DSBs, although still largely unexplored, can be particularly relevant for maintaining genome integrity and avoiding malignant transformation and cancer.
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Affiliation(s)
- Almudena Serrano-Benítez
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain
| | - Felipe Cortés-Ledesma
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain.,Topology and DNA breaks Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Jose F Ruiz
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain.,Department of Plant Biochemistry and Molecular Biology, University of Seville, Seville, Spain
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Stinson BM, Moreno AT, Walter JC, Loparo JJ. A Mechanism to Minimize Errors during Non-homologous End Joining. Mol Cell 2019; 77:1080-1091.e8. [PMID: 31862156 DOI: 10.1016/j.molcel.2019.11.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/09/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
Abstract
Enzymatic processing of DNA underlies all DNA repair, yet inappropriate DNA processing must be avoided. In vertebrates, double-strand breaks are repaired predominantly by non-homologous end joining (NHEJ), which directly ligates DNA ends. NHEJ has the potential to be highly mutagenic because it uses DNA polymerases, nucleases, and other enzymes that modify incompatible DNA ends to allow their ligation. Using frog egg extracts that recapitulate NHEJ, we show that end processing requires the formation of a "short-range synaptic complex" in which DNA ends are closely aligned in a ligation-competent state. Furthermore, single-molecule imaging directly demonstrates that processing occurs within the short-range complex. This confinement of end processing to a ligation-competent complex ensures that DNA ends undergo ligation as soon as they become compatible, thereby minimizing mutagenesis. Our results illustrate how the coordination of enzymatic catalysis with higher-order structural organization of substrate maximizes the fidelity of DNA repair.
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Affiliation(s)
- Benjamin M Stinson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew T Moreno
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Krenning L, van den Berg J, Medema RH. Life or Death after a Break: What Determines the Choice? Mol Cell 2019; 76:346-358. [PMID: 31561953 DOI: 10.1016/j.molcel.2019.08.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 01/22/2023]
Abstract
DNA double-strand breaks (DSBs) pose a constant threat to genomic integrity. Such DSBs need to be repaired to preserve homeostasis at both the cellular and organismal levels. Hence, the DNA damage response (DDR) has evolved to repair these lesions and limit their toxicity. The initiation of DNA repair depends on the activation of the DDR, and we know that the strength of DDR signaling may differentially affect cellular viability. However, we do not fully understand what determines the cytotoxicity of a DSB. Recent work has identified genomic location, (in)correct DNA repair pathway usage, and cell-cycle position as contributors to DSB-induced cytotoxicity. In this review, we discuss how these determinants affect cytotoxicity, highlight recent discoveries, and identify open questions that could help to improve our understanding about cell fate decisions after a DNA DSB.
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Affiliation(s)
- Lenno Krenning
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jeroen van den Berg
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - René H Medema
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Efficient repair of DNA double strand breaks in individuals from high level natural radiation areas of Kerala coast, south-west India. Mutat Res 2017; 806:39-50. [PMID: 28963924 DOI: 10.1016/j.mrfmmm.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 08/14/2017] [Accepted: 09/11/2017] [Indexed: 11/21/2022]
Abstract
High level natural radiation areas (HLNRA) of Kerala coastal strip (55km long and 0.5km wide) in southwest India exhibit wide variations in the level of background dose (< 1.0-45.0mGy/year) due to thorium deposits in the beach sand. The areas with ≤1.5mGy/year are considered as normal level natural radiation area (NLNRA), whereas areas with >1.5mGy/year are HLNRA. Individuals belonging to HLNRA were stratified into two groups, Low dose group (LDG: 1.51-5.0mGy/year) and high dose group (HDG: >5.0mGy/year). The mean annual dose received by the individuals from NLNRA, LDG and HDG was 1.3±0.1, 2.7±0.9 and 9.4±2.3mGy/year, respectively. Induction and repair of DNA double strand breaks (DSBs) in terms of gamma-H2AX positive cells were analysed in peripheral blood mononuclear cells (PBMCs) using flow cytometry. Induction of DSBs was studied at low (0.25Gy) and high challenge doses (1.0 and 2.0Gy) of gamma radiation in 78 individuals {NLNRA, N=23; HLNRA (LDG, N=21 and HDG, N=34)}. Repair kinetics of DSBs were evaluated in PBMCs of 30 individuals belonging to NLNRA (N=8), LDG (N=7) and HDG (N=15) at low (0.25Gy) and high doses (2.0Gy) of gamma radiation. Transcription profile of DNA damage response (DDR) and DSB repair genes involved in non-homologous end joining (NHEJ) and homologous recombination repair (HRR) pathways was analysed after a challenge dose of 2.0Gy in PBMCs of NLNRA (N=10) and HDG, HLNRA (N=10) group. Our results revealed significantly lower induction and efficient repair of DSBs in HLNRA groups as compared to NLNRA. Transcription profile of DCLRE1C, XRCC4, NBS1 and CDK2 showed significant up-regulation (p≤0.05) in HDG at a challenge dose of 2.0Gy indicating active involvement of DDR and DSB repair pathways. In conclusion, lower induction and efficient repair of DNA DSBs in HLNRA groups is suggestive of an in vivo radio-adaptive response due to priming effect of chronic low dose radiation prevailing in this area.
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Yang K, Guo R, Xu D. Non-homologous end joining: advances and frontiers. Acta Biochim Biophys Sin (Shanghai) 2016; 48:632-40. [PMID: 27217473 DOI: 10.1093/abbs/gmw046] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
DNA double-strand breaks (DSBs) are the most serious form of DNA damage. In human cells, non-homologous end joining (NHEJ) is the major pathway for the repair of DSBs. Different types of DSBs result in different subsets of NHEJ repair strategies. These variations in NHEJ repair strategies depend on numerous elements, such as the flexible recruitment of NHEJ-related proteins, the complexity of the DSB ends, and the spatial- and temporal-ordered formation of the multi-protein complex. On the one hand, current studies of DNA DSBs repair focus on the repair pathway choices between homologous recombination and classic or alternative NHEJ. On the other hand, increasing researches have also deepened the significance and dug into the cross-links between the NHEJ pathway and the area of genome organization and aging. Although remarkable progress has been made in elucidating the underlying principles during the past decades, the detailed mechanism of action in response to different types of DSBs remains largely unknown and needs further evaluation in the future study.
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Affiliation(s)
- Kai Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Rong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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Klymiuk N, Fezert P, Wünsch A, Kurome M, Kessler B, Wolf E. Homologous recombination contributes to the repair of zinc-finger-nuclease induced double strand breaks in pig primary cells and facilitates recombination with exogenous DNA. J Biotechnol 2014; 177:74-81. [DOI: 10.1016/j.jbiotec.2014.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/13/2014] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
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DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (Amst) 2014; 17:21-9. [PMID: 24680878 DOI: 10.1016/j.dnarep.2014.02.020] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 11/23/2022]
Abstract
DNA double stranded breaks (DSBs) are the most cytoxic DNA lesion as the inability to properly repair them can lead to genomic instability and tumorigenesis. The prominent DSB repair pathway in humans is non-homologous end-joining (NHEJ). In the simplest sense, NHEJ mediates the direct re-ligation of the broken DNA molecule. However, NHEJ is a complex and versatile process that can repair DSBs with a variety of damages and ends via the utilization of a significant number of proteins. In this review we will describe the important factors and mechanisms modulating NHEJ with emphasis given to the versatility of this repair process and the DNA-PK complex.
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Barnard S, Bouffler S, Rothkamm K. The shape of the radiation dose response for DNA double-strand break induction and repair. Genome Integr 2013; 4:1. [PMID: 23522792 PMCID: PMC3616853 DOI: 10.1186/2041-9414-4-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/18/2013] [Indexed: 12/22/2022] Open
Abstract
DNA double-strand breaks are among the most deleterious lesions induced by ionising radiation. A range of inter-connected cellular response mechanisms has evolved to enable their efficient repair and thus protect the cell from the harmful consequences of un- or mis-repaired breaks which may include early effects such as cell killing and associated acute toxicities and late effects such as cancer. A number of studies suggest that the induction and repair of double-strand breaks may not always occur linearly with ionising radiation dose. Here we have aimed to identify and discuss some of the biological and methodological factors that can potentially modify the shape of the dose response curve obtained for these endpoints using the most common assays for double-strand breaks, pulsed-field gel electrophoresis and microscopic scoring of radiation-induced foci.
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Affiliation(s)
- Stephen Barnard
- Health Protection Agency Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot, Oxon OX11 0RQ, UK.
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