101
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Delacôte F, Deriano L, Lambert S, Bertrand P, Saintigny Y, Lopez BS. Chronic exposure to sublethal doses of radiation mimetic Zeocin selects for clones deficient in homologous recombination. Mutat Res 2006; 615:125-33. [PMID: 17174359 DOI: 10.1016/j.mrfmmm.2006.11.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 10/30/2006] [Accepted: 11/17/2006] [Indexed: 01/27/2023]
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions leading to genome variability/instability. The balance between homologous recombination (HR) and non-homologous end-joining (NHEJ), two alternative DSB repair systems, is essential to ensure genome maintenance in mammalian cells. Here, we transfected CHO hamster cells with the pcDNA3.1/Zeo plasmid, and selected transfectants with Zeocin, a bleomycin analog which produces DSBs. Despite the presence of a Zeocin resistance gene in pcDNA3.1/Zeo, Zeocin induced 8-10 gamma-H2AX foci per cell. This shows that the Zeocin resistance gene failed to fully detoxify cells treated with Zeocin, and that during selection cells were submitted to a chronic sublethal DSB stress. Selected clones show decreases in both spontaneous and induced intrachromosomal HR. In contrast, in an in vitro assay, these clones show an increase in NHEJ products specific to the KU86 pathway. We selected cells, in the absence of pcDNA3.1/Zeo, with low and sublethal doses of Zeocin, producing a mean 8-10 gamma-H2AX foci per cell. Newly selected clones exhibited similar phenotypes: HR decrease accompanied by an increase in KU86-dependent NHEJ efficiency. Thus chronic exposure to sublethal numbers of DSBs selects cells whose HR versus NHEJ balance is altered. This may well have implications for radio- and chemotherapy, and for management of environmental hazards.
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Affiliation(s)
- Fabien Delacôte
- UMR CNRS/CEA 217, DSV, DRR, CEA, 18 route du panorama, 92265 Fontenay aux Roses, Cédex, France
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102
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Vodenicharov MD, Wellinger RJ. DNA degradation at unprotected telomeres in yeast is regulated by the CDK1 (Cdc28/Clb) cell-cycle kinase. Mol Cell 2006; 24:127-37. [PMID: 17018298 DOI: 10.1016/j.molcel.2006.07.035] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 06/09/2006] [Accepted: 07/17/2006] [Indexed: 11/20/2022]
Abstract
In the absence of functional telomeric cap protection, the ends of eukaryotic chromosomes are subject to DNA damage responses that lead to cell-cycle arrest and, eventually, genomic instability. However, the controlling activities responsible for the initiation of genome instability on unprotected telomeres remained unclear. Here we show that in budding yeast, unprotected telomeres undergo a tightly cell-cycle-regulated DNA degradation. Ablation of the function of essential capping proteins Cdc13p or Stn1p only caused telomere degradation in G2/M, but not in G1 of the cell cycle. Accordingly, G1-arrested cells with unprotected telomeres remained viable, while G2/M-arrested cells failed to recover. The data also show that completion of S phase and the activity of the S-Cdk1 kinase were required for telomere degradation. These results strongly suggest that after a loss of the telomere capping function, telomere-led genome instability is caused by tightly regulated cellular DNA repair attempts.
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Affiliation(s)
- Momchil D Vodenicharov
- Department of Microbiology, Faculty of Medicine, Université de Sherbrooke, 3001 12e Ave Nord, Sherbrooke, Québec J1H 5N4, Canada
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103
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Ahnesorg P, Jackson SP. The non-homologous end-joining protein Nej1p is a target of the DNA damage checkpoint. DNA Repair (Amst) 2006; 6:190-201. [PMID: 17101301 PMCID: PMC3338008 DOI: 10.1016/j.dnarep.2006.09.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 09/21/2006] [Accepted: 09/26/2006] [Indexed: 01/07/2023]
Abstract
DNA double-strand breaks (DSBs), which are generated by ionizing radiation (IR) and a range of other DNA damaging agents, are repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). Previous studies have shown that NHEJ in Saccharomyces cerevisiae requires the Yku70p-Yku80p heterodimer and a complex consisting of DNA Ligase IV, Lif1p and Nej1p. Here, we report that Nej1p is phosphorylated in response to DNA damage in a manner that relies on the DNA damage checkpoint kinases Mec1p, Rad53p and Dun1p. By using a mutational approach, we have identified a consensus Dun1p phosphorylation site in Nej1p, and mutation of conserved serine residues within it leads to decreased NHEJ efficiency. These data, together with previous findings that Rad55p--a protein involved in HR--is phosphorylated analogously, point to there being a broad signalling network connecting DNA damage checkpoint responses with the regulation of DNA DSB repair activities.
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Affiliation(s)
- Peter Ahnesorg
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, United Kingdom
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104
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Luke B, Versini G, Jaquenoud M, Zaidi IW, Kurz T, Pintard L, Pasero P, Peter M. The cullin Rtt101p promotes replication fork progression through damaged DNA and natural pause sites. Curr Biol 2006; 16:786-92. [PMID: 16631586 DOI: 10.1016/j.cub.2006.02.071] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 02/02/2006] [Accepted: 02/27/2006] [Indexed: 11/28/2022]
Abstract
Accurate and complete DNA replication is fundamental to maintain genome integrity. While the mechanisms and underlying machinery required to duplicate bulk genomic DNA are beginning to emerge, little is known about how cells replicate through damaged areas and special chromosomal regions such as telomeres, centromeres, and highly transcribed loci . Here, we have investigated the role of the yeast cullin Rtt101p in this process. We show that rtt101Delta cells accumulate spontaneous DNA damage and exhibit a G(2)/M delay, even though they are fully proficient to detect and repair chromosome breaks. Viability of rtt101Delta mutants depends on Rrm3p, a DNA helicase involved in displacing proteinaceous complexes at programmed pause sites . Moreover, rtt101Delta cells show hyperrecombination at forks arrested at replication fork barriers (RFBs) of ribosomal DNA. Finally, rtt101Delta mutants are sensitive to fork arrest induced by DNA alkylation, but not by nucleotide depletion. We therefore propose that the cullin Rtt101p promotes fork progression through obstacles such as DNA lesions or tightly bound protein-DNA complexes via a new mechanism involving ubiquitin-conjugation.
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Affiliation(s)
- Brian Luke
- Swiss Federal Institute of Technology Zurich (ETH), Institute of Biochemistry, ETH Hoenggerberg HPM G 10.0, Switzerland
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105
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Sonoda E, Hochegger H, Saberi A, Taniguchi Y, Takeda S. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst) 2006; 5:1021-9. [PMID: 16807135 DOI: 10.1016/j.dnarep.2006.05.022] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Repair of DNA double strand breaks (DSBs) plays a critical role in the maintenance of the genome. DSB arise frequently as a consequence of replication fork stalling and also due to the attack of exogenous agents. Repair of broken DNA is essential for survival. Two major pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ) have evolved to deal with these lesions, and are conserved from yeast to vertebrates. Despite the conservation of these pathways, their relative contribution to DSB repair varies greatly between these two species. HR plays a dominant role in any DSB repair in yeast, whereas NHEJ significantly contributes to DSB repair in vertebrates. This active NHEJ requires a regulatory mechanism to choose HR or NHEJ in vertebrate cells. In this review, we illustrate how HR and NHEJ are differentially regulated depending on the phase of cell cycle and on the nature of the DSB.
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Affiliation(s)
- Eiichiro Sonoda
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe Yoshida, Kyoto 606-8501, Japan
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106
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Abstract
DNA double-strand breaks (DSBs) are among the most deleterious types of damage that can occur in the genome of eukaryotic cells because failure to repair them can lead to loss of genetic information and chromosome rearrangements. DSBs can arise by failures in DNA replication and by exposure to environmental factors, such as ionizing radiations and radiomimetic chemicals. Moreover, they might arise when telomeres undergo extensive erosion, leading to the activation of the DNA damage response pathways and the onset of apoptosis and/or senescence. Importantly, DSBs can also form in a programmed manner during development. For example, meiotic recombination and rearrangement of the immunoglobulin genes in lymphocytes require the generation of site- or region-specific DSBs through the action of specific endonucleases. Efficient DSB repair is crucial in safeguarding genome integrity, whose maintenance in the face of DSBs involves branched signalling networks that switch on DNA damage checkpoints, activate DNA repair, induce chromatin reorganization and modulate numerous cellular processes. Not surprisingly, defects in these networks result in a variety of diseases ranging from severe genetic disorders to cancer predisposition and accelerated ageing.
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Affiliation(s)
- Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milan, Italy.
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107
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Kegel A, Martinez P, Carter SD, Åström SU. Genome wide distribution of illegitimate recombination events in Kluyveromyces lactis. Nucleic Acids Res 2006; 34:1633-45. [PMID: 16549875 PMCID: PMC1405753 DOI: 10.1093/nar/gkl064] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 01/21/2006] [Accepted: 02/28/2006] [Indexed: 11/13/2022] Open
Abstract
Illegitimate recombination (IR) is the process by which two DNA molecules not sharing homology to each other are joined. In Kluyveromyces lactis, integration of heterologous DNA occurred very frequently therefore constituting an excellent model organism to study IR. IR was completely dependent on the nonhomologous end-joining (NHEJ) pathway for DNA double strand break (DSB) repair and we detected no other pathways capable of mediating IR. NHEJ was very versatile, capable of repairing both blunt and non-complementary ends efficiently. Mapping the locations of genomic IR-events revealed target site preferences, in which intergenic regions (IGRs) and ribosomal DNA were overrepresented six-fold compared to open reading frames (ORFs). The IGR-events occurred predominantly within transcriptional regulatory regions. In a rad52 mutant strain IR still preferentially occurred at IGRs, indicating that DSBs in ORFs were not primarily repaired by homologous recombination (HR). Introduction of ectopic DSBs resulted in the efficient targeting of IR to these sites, strongly suggesting that IR occurred at spontaneous mitotic DSBs. The targeting efficiency was equal when ectopic breaks were introduced in an ORF or an IGR. We propose that spontaneous DSBs arise more frequently in transcriptional regulatory regions and in rDNA and such DSBs can be mapped by analyzing IR target sites.
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Affiliation(s)
- Andreas Kegel
- Department of Developmental Biology, Wennergren Institute, Stockholm UniversitySE-106 91 Stockholm, Sweden
| | - Paula Martinez
- Department of Developmental Biology, Wennergren Institute, Stockholm UniversitySE-106 91 Stockholm, Sweden
| | - Sidney D. Carter
- Department of Developmental Biology, Wennergren Institute, Stockholm UniversitySE-106 91 Stockholm, Sweden
| | - Stefan U. Åström
- Department of Developmental Biology, Wennergren Institute, Stockholm UniversitySE-106 91 Stockholm, Sweden
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108
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Hochegger H, Dejsuphong D, Fukushima T, Morrison C, Sonoda E, Schreiber V, Zhao GY, Saberi A, Masutani M, Adachi N, Koyama H, de Murcia G, Takeda S. Parp-1 protects homologous recombination from interference by Ku and Ligase IV in vertebrate cells. EMBO J 2006; 25:1305-14. [PMID: 16498404 PMCID: PMC1422167 DOI: 10.1038/sj.emboj.7601015] [Citation(s) in RCA: 208] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Accepted: 01/30/2006] [Indexed: 01/19/2023] Open
Abstract
Parp-1 and Parp-2 are activated by DNA breaks and have been implicated in the repair of DNA single-strand breaks (SSB). Their involvement in double-strand break (DSB) repair mediated by homologous recombination (HR) or nonhomologous end joining (NHEJ) remains unclear. We addressed this question using chicken DT40 cells, which have the advantage of carrying only a PARP-1 gene but not a PARP-2 gene. We found that PARP-1(-/-) DT40 mutants show reduced levels of HR and are sensitive to various DSB-inducing genotoxic agents. Surprisingly, this phenotype was strictly dependent on the presence of Ku, a DSB-binding factor that mediates NHEJ. PARP-1/KU70 double mutants were proficient in the execution of HR and displayed elevated resistance to DSB-inducing drugs. Moreover, we found deletion of Ligase IV, another NHEJ gene, suppressed the camptothecin of PARP-1(-/-) cells. Our results suggest a new critical function for Parp in minimizing the suppressive effects of Ku and the NHEJ pathway on HR.
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Affiliation(s)
- Helfrid Hochegger
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Donniphat Dejsuphong
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Toru Fukushima
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ciaran Morrison
- Department of Biochemistry and NCBES, National University of Ireland-Galway, Ireland
| | - Eiichiro Sonoda
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Valérie Schreiber
- Département Intégrité du génome de l'UMR7175 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Guang Yu Zhao
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Alihossein Saberi
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mitsuko Masutani
- ADP-ribosylation in Oncology Project, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Noritaka Adachi
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
| | - Hideki Koyama
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan
| | - Gilbert de Murcia
- Département Intégrité du génome de l'UMR7175 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Shunichi Takeda
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University; Sakyo-ku, 606-8501 Kyoto, Japan. Tel.: +81 75 753 4410; Fax: +81 75 753 4419; E-mail:
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109
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Pardo B, Ma E, Marcand S. Mismatch tolerance by DNA polymerase Pol4 in the course of nonhomologous end joining in Saccharomyces cerevisiae. Genetics 2006; 172:2689-94. [PMID: 16452137 PMCID: PMC1456414 DOI: 10.1534/genetics.105.053512] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In yeast, the nonhomologous end joining pathway (NHEJ) mobilizes the DNA polymerase Pol4 to repair DNA double-strand breaks when gap filling is required prior to ligation. Using telomere-telomere fusions caused by loss of the telomeric protein Rap1 and double-strand break repair on transformed DNA as assays for NHEJ between fully uncohesive ends, we show that Pol4 is able to extend a 3'-end whose last bases are mismatched, i.e., mispaired or unpaired, to the template strand.
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Affiliation(s)
- Benjamin Pardo
- Laboratoire de Radiobiologie de l'ADN, Service de Radiobiologie Moléculaire et Cellulaire, UMR217 du CNRS, CEA/Fontenay, Fontenay-aux-Roses, France
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110
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Pennaneach V, Putnam CD, Kolodner RD. Chromosome healing byde novotelomere addition inSaccharomyces cerevisiae. Mol Microbiol 2006; 59:1357-68. [PMID: 16468981 DOI: 10.1111/j.1365-2958.2006.05026.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The repair of spontaneous or induced DNA damage by homologous recombination (HR) in Saccharomyces cerevisiae will suppress chromosome rearrangements. Alternative chromosome healing pathways can result in chromosomal instability. One of these pathways is de novo telomere addition where the end of a broken chromosome is stabilized by telomerase-dependent addition of telomeres at non-telomeric sites. De novo telomere addition requires the recruitment of telomerase to chromosomal targets. Subsequently, annealing of the telomerase reverse transcriptase RNA-template (guide RNA) at short regions of homology is followed by extension of the nascent 3'-end of the broken chromosome to copy a short region of the telomerase guide RNA; multiple cycles of this process yield the new telomere. Proteins including Pif1 helicase, the single-stranded DNA-binding protein Cdc13 and the Ku heterocomplex are known to participate in native telomere functions and also regulate the de novo telomere addition reaction. Studies of the sequences added at de novo telomeres have lead to a detailed description of the annealing-extension-dissociation cycles that copy the telomerase guide RNA, which can explain the heterogeneity of telomeric repeats at de novo and native telomeres in S. cerevisiae.
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Affiliation(s)
- Vincent Pennaneach
- Ludwig Institute for Cancer Research, Department of Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, 92093-0669, USA
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111
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Pathways of DNA Double-Strand Break Repair in Mammalian Cells after Ionizing Radiation. Genome Integr 2006. [DOI: 10.1007/7050_011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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112
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Tsukuda T, Fleming AB, Nickoloff JA, Osley MA. Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 2005; 438:379-83. [PMID: 16292314 PMCID: PMC1388271 DOI: 10.1038/nature04148] [Citation(s) in RCA: 338] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 08/22/2005] [Indexed: 11/09/2022]
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for maintaining genome stability. Eukaryotic cells repair DSBs by both non-homologous end joining and homologous recombination. How chromatin structure is altered in response to DSBs and how such alterations influence DSB repair processes are important issues. In vertebrates, phosphorylation of the histone variant H2A.X occurs rapidly after DSB formation, spreads over megabase chromatin domains, and is required for stable accumulation of repair proteins at damage foci. In Saccharomyces cerevisiae, phosphorylation of the two principal H2A species is also signalled by DSB formation, which spreads approximately 40 kb in either direction from the DSB. Here we show that near a DSB phosphorylation of H2A is followed by loss of histones H2B and H3 and increased sensitivity of chromatin to digestion by micrococcal nuclease; however, phosphorylation of H2A and nucleosome loss occur independently. The DNA damage sensor MRX is required for histone loss, which also depends on INO80, a nucleosome remodelling complex. The repair protein Rad51 (ref. 6) shows delayed recruitment to DSBs in the absence of histone loss, suggesting that MRX-dependent nucleosome remodelling regulates the accessibility of factors directly involved in DNA repair by homologous recombination. Thus, MRX may regulate two pathways of chromatin changes: nucleosome displacement for efficient recruitment of homologous recombination proteins; and phosphorylation of H2A, which modulates checkpoint responses to DNA damage.
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Affiliation(s)
- Toyoko Tsukuda
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud Albuquerque, New Mexico 87131, USA
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113
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Ruan C, Workman JL, Simpson RT. The DNA repair protein yKu80 regulates the function of recombination enhancer during yeast mating type switching. Mol Cell Biol 2005; 25:8476-85. [PMID: 16166630 PMCID: PMC1265738 DOI: 10.1128/mcb.25.19.8476-8485.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recombination enhancer (RE) is essential for regulating donor preference during yeast mating type switching. In this study, by using minichromosome affinity purification (MAP) and mass spectrometry, we found that yeast Ku80p is associated with RE in MATa cells. Chromatin immunoprecipitation assays confirmed its occupancy in vivo. Deletion of YKU80 results in altered chromatin structure in the RE region and more importantly causes a dramatic decrease of HML usage in MATa cells. We also detect directional movement of yKu80p from the RE towards HML during switching. These results indicate a novel function of yeast Ku80p in regulating mating type switching.
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Affiliation(s)
- Chun Ruan
- Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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114
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Abstract
Nonhomologous end joining (NHEJ), the direct rejoining of DNA double-strand breaks, is closely associated with illegitimate recombination and chromosomal rearrangement. This has led to the concept that NHEJ is error prone. Studies with the yeast Saccharomyces cerevisiae have revealed that this model eukaryote has a classical NHEJ pathway dependent on Ku and DNA ligase IV, as well as alternative mechanisms for break rejoining. The evolutionary conservation of the Ku-dependent process includes several genes dedicated to this pathway, indicating that classical NHEJ at least is a strong contributor to fitness in the wild. Here we review how double-strand break structure, the yeast NHEJ proteins, and alternative rejoining mechanisms influence the accuracy of break repair. We also consider how the balance between NHEJ and homologous repair is regulated by cell state to promote genome preservation. The principles discussed are instructive to NHEJ in all organisms.
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Affiliation(s)
- James M Daley
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan 48109-0602, USA.
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115
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Michelson RJ, Rosenstein S, Weinert T. A telomeric repeat sequence adjacent to a DNA double-stranded break produces an anticheckpoint. Genes Dev 2005; 19:2546-59. [PMID: 16230525 PMCID: PMC1276729 DOI: 10.1101/gad.1293805] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Telomeres are complex structures that serve to protect chromosome ends. Here we provide evidence that in Saccharomyces cerevisiae telomeres may contain an anticheckpoint activity that prevents chromosome ends from signaling cell cycle arrest. We found that an internal tract of telomeric repeats inhibited DNA damage checkpoint signaling from adjacent double-strand breaks (DSBs); cell cycle arrest lasted 8-12 h from a normal DSB, whereas it lasted only 1-2 h from a DSB adjacent to a telomeric repeat. The shortened or abridged arrest was not the result of DNA repair, nor reduced amounts of single-stranded DNA, nor of adaptation. The molecular identity of this telomere repeat-associated anticheckpoint activity is unknown, though it is not dependent upon telomerase or telomere-proximal gene silencing. The anticheckpoint may inhibit the ATR yeast ortholog Mec1 because Rad9 and Rad53 became dephosphorylated and inactivated during the abridged arrest. The anticheckpoint acts regionally; it inhibited signaling from DNA breaks up to 0.6 kb away from the telomeric repeat but not from a DSB present on a separate chromosome. We propose that after formation of the DSB near the telomeric repeat, a mature telomere forms in 1-2 h, and the telomere then contains proteins that inhibit checkpoint signaling from nearby DNA breaks.
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Affiliation(s)
- Rhett J Michelson
- Molecular and Cellular Biology Department, University of Arizona, Tucson, Arizona 85721, USA
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116
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Chen S, Davies AA, Sagan D, Ulrich HD. The RING finger ATPase Rad5p of Saccharomyces cerevisiae contributes to DNA double-strand break repair in a ubiquitin-independent manner. Nucleic Acids Res 2005; 33:5878-86. [PMID: 16224103 PMCID: PMC1258175 DOI: 10.1093/nar/gki902] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Tolerance to replication-blocking DNA lesions is achieved by means of ubiquitylation of PCNA, the processivity clamp for replicative DNA polymerases, by components of the RAD6 pathway. In the yeast Saccharomyces cerevisiae the ubiquitin ligase (E3) responsible for polyubiquitylation of the clamp is the RING finger protein Rad5p. Interestingly, the RING finger, responsible for the protein's E3 activity, is embedded in a conserved DNA-dependent ATPase domain common to helicases and chromatin remodeling factors of the SWI/SNF family. Here, we demonstrate that the Rad5p ATPase domain provides the basis for a function of the protein in DNA double-strand break repair via a RAD52- and Ku-independent pathway mediated by the Mre11/Rad50/Xrs2 protein complex. This activity is distinct and separable from the contribution of the RING domain to ubiquitin conjugation to PCNA. Moreover, we show that the Rad5 protein physically associates with the single-stranded DNA regions at a processed double-strand break in vivo. Our observations suggest that Rad5p is a multifunctional protein that—by means of independent enzymatic activities inherent in its RING and ATPase domains—plays a modulating role in the coordination of repair events and replication fork progression in response to various different types of DNA lesions.
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Affiliation(s)
- Shuhua Chen
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Adelina A. Davies
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Daniel Sagan
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
| | - Helle D. Ulrich
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
- To whom correspondence should be addressed. Tel: +44 1707 62 5821; Fax: +44 1707 62 5550;
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117
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Skory CD. Inhibition of non-homologous end joining and integration of DNA upon transformation of Rhizopus oryzae. Mol Genet Genomics 2005; 274:373-83. [PMID: 16133163 DOI: 10.1007/s00438-005-0028-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 06/27/2005] [Indexed: 01/12/2023]
Abstract
Site-directed integration of DNA in the fungus Rhizopus has long been problematic because linearized plasmids used for transformation tend to replicate in high-molecular-weight concatenated structures, and rarely integrate into the chromosome. This work examines the methods that might interfere with the multimerization process, select against plasmids that had recircularized, and encourage strand invasion, hopefully leading to plasmid integration. In vitro methods were used to determine if the structure of the double-strand break had any effect on the ability to rejoin plasmid ends. In cell-free extracts, little difference in end-joining activity was found between linearized plasmids with 5' overhangs, 3' overhangs, or blunt ends. In addition, dephosphorylation of ends had no effect. Transformation of plasmids prepared in the same ways confirmed that they were easily religated in vivo, with almost all prototrophic isolates retaining autonomously replicated plasmids. It was possible to block religation by modifying the free ends of the linearized plasmids using oligonucleotide adapters which were blocked at the 3'-OH position and contained phosphorothioate nucleotides to make them nuclease-resistant. However, gene replacement, with repair of the auxotrophic mutation in the host chromosome, was the predominant event observed upon the transformation of these plasmids. The highest rates of integration were obtained with a plasmid containing a truncated, non-functional pyrG gene. Autonomous replication of this plasmid did not support prototrophic growth, but homologous recombination into the chromosome restored the function of the endogenous pyrG gene. All of the transformants obtained with this selective construct were found to have integrated the plasmid, with multicopy insertion being common.
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Affiliation(s)
- Christopher D Skory
- Bioproducts and Biocatalysis Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, IL 61604, USA
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118
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Abstract
Ataxia telangiectasia (AT) is a rare human disease characterized by extreme cellular sensitivity to radiation and a predisposition to cancer, with a hallmark of onset in early childhood. Several human diseases also share similar symptoms with AT albeit with different degrees of severity and different associated disorders. While all AT patients contain mutations in the AT-mutated gene (ATM), most other AT-like disorders are defective in genes encoding an MRN protein complex consisting of Mre11, Rad50 and Nbs1. Both ATM and MRN function as cellular sensors to DNA double-strand breaks, which lead to the recruitment and phosphorylation of an array of substrate proteins involved in DNA repair, apoptosis and cell-cycle checkpoints, as well as gene regulation, translation initiation and telomere maintenance. ATM is a member of the family of phosphatidylinositol 3-kinase-like protein kinases (PIKK), and the discovery of many ATM substrates provides the underlying mechanisms of heterologous symptoms among AT patients. This review article focuses on recent findings related to the initial recognition of double-strand breaks by ATM and MRN, as well as a DNA-dependent protein kinase complex consisting of the heterodimer Ku70/Ku80 and its catalytic subunit DNA-PKcs, another member of PIKK. This possible interaction suggests that a much greater complex is involved in sensing, transducing and co-ordinating cellular events in response to genome instability.
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Affiliation(s)
- Lindsay G Ball
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK Canada, S7N 5E5
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119
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Kim JS, Krasieva TB, Kurumizaka H, Chen DJ, Taylor AMR, Yokomori K. Independent and sequential recruitment of NHEJ and HR factors to DNA damage sites in mammalian cells. J Cell Biol 2005; 170:341-7. [PMID: 16061690 PMCID: PMC2171485 DOI: 10.1083/jcb.200411083] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Accepted: 06/21/2005] [Indexed: 01/20/2023] Open
Abstract
Damage recognition by repair/checkpoint factors is the critical first step of the DNA damage response. DNA double strand breaks (DSBs) activate checkpoint signaling and are repaired by nonhomologous end-joining (NHEJ) and homologous recombination (HR) pathways. However, in vivo kinetics of the individual factor responses and the mechanism of pathway choice are not well understood. We report cell cycle and time course analyses of checkpoint activation by ataxia-telangiectasia mutated and damage site recruitment of the repair factors in response to laser-induced DSBs. We found that MRN acts as a DNA damage marker, continuously localizing at unrepaired damage sites. Damage recognition by NHEJ factors precedes that of HR factors. HR factor recruitment is not influenced by NHEJ factor assembly and occurs throughout interphase. Damage site retention of NHEJ factors is transient, whereas HR factors persist at unrepaired lesions, revealing unique roles of the two pathways in mammalian cells.
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Affiliation(s)
- Jong-Soo Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
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120
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Daley JM, Laan RLV, Suresh A, Wilson TE. DNA Joint Dependence of Pol X Family Polymerase Action in Nonhomologous End Joining. J Biol Chem 2005; 280:29030-7. [PMID: 15964833 DOI: 10.1074/jbc.m505277200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA double strand breaks (DSBs) can be rejoined directly by the nonhomologous end-joining (NHEJ) pathway of repair. Nucleases and polymerases are required to promote accurate NHEJ when the terminal bases of the DSB are damaged. The same enzymes also participate in imprecise rejoining and joining of incompatible ends, important mutagenic events. Previous work has shown that the Pol X family polymerase Pol4 is required for some but not all NHEJ events that require gap filling in Saccharomyces cerevisiae. Here, we systematically analyzed DSB end configurations and found that gaps on both strands and overhang polarity are the principal factors that determine whether a joint requires Pol4. DSBs with 3'-overhangs and a gap on each strand strongly depended on Pol4 for repair, DSBs with 5'-overhangs of the same sequence did not. Pol4 was not required when 3'-overhangs contained a gap on only one strand, however. Pol4 was equally required at 3'-overhangs of all lengths within the NHEJ-dependent range but was dispensable outside of this range, indicating that Pol4 is specific to NHEJ. Loss of Pol4 did not affect the rejoining of DSBs that utilized a recessed microhomology or DSBs bearing 5'-hydroxyls but no gap. Finally, mammalian Pol X polymerases were able to differentially complement a pol4 mutation depending on the joint structure, demonstrating that these polymerases can participate in yeast NHEJ but with distinct properties.
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Affiliation(s)
- James M Daley
- Graduate Program in Cellular and Molecular Biology and Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-0602, USA
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121
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Zhang X, Paull TT. The Mre11/Rad50/Xrs2 complex and non-homologous end-joining of incompatible ends in S. cerevisiae. DNA Repair (Amst) 2005; 4:1281-94. [PMID: 16043424 DOI: 10.1016/j.dnarep.2005.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2005] [Revised: 06/23/2005] [Accepted: 06/23/2005] [Indexed: 12/25/2022]
Abstract
In Saccharomyces cerevisiae, the Mre11/Rad50/Xrs2 (MRX) complex plays important roles in both homologous and non-homologous pathways of DNA repair. In this study, we investigated the role of the MRX complex and its enzymatic functions in non-homologous repair of DNA ends containing incompatible end structures. Using a plasmid transformation assay, we found that mre11 and rad50 null strains are extremely deficient in joining of incompatible DNA ends. Expression of the nuclease-deficient Mre11 mutant H125N fully complemented the mre11 strain for joining of mismatched ends in the absence of homology, while a mutant of Rad50 deficient in ATP-dependent activities exhibited levels of end-joining similar to a rad50 deletion strain. Although the majority of non-homologous end-joining (NHEJ) products isolated did not contain microhomologies, introduction of an 8bp microhomology at mismatched ends resulted in microhomology-mediated joining in all of the products recovered, demonstrating that a microhomology exerts a dominant effect on processing events that occur during NHEJ. Nuclease-deficient Mre11p was less efficient in promoting microhomology-mediated end-joining in comparison to its ability to stimulate non-microhomology-mediated events, suggesting that Mre11p influences, but is not essential for, microhomology-mediated repair. When the linearized DNA was transformed in the presence of an intact homologous plasmid to facilitate gap repair, there was no decrease in NHEJ products obtained, suggesting that NHEJ and homologous repair do not compete for DNA ends in vivo. These results suggest that the MRX complex is essential for joining of incompatible ends by NHEJ, and the ATP-dependent activities of Rad50 are critical for this process.
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Affiliation(s)
- Xiaoming Zhang
- Department of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station, A4800, Austin, TX 78712-0159, USA
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122
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Elliott B, Richardson C, Jasin M. Chromosomal translocation mechanisms at intronic alu elements in mammalian cells. Mol Cell 2005; 17:885-94. [PMID: 15780943 DOI: 10.1016/j.molcel.2005.02.028] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2004] [Revised: 02/04/2005] [Accepted: 02/24/2005] [Indexed: 01/05/2023]
Abstract
Repetitive elements comprise nearly half of the human genome. Chromosomal rearrangements involving these elements occur in somatic and germline cells and are causative for many diseases. To begin to understand the molecular mechanisms leading to these rearrangements in mammalian cells, we developed an intron-based system to specifically induce chromosomal translocations at Alu elements, the most numerous family of repetitive elements in humans. With this system, we found that when double-strand breaks (DSBs) were introduced adjacent to identical Alu elements, translocations occurred at high frequency and predominantly arose from repair by the single-strand annealing (SSA) pathway (85%). With diverged Alu elements, translocation frequency was unaltered, yet pathway usage shifted such that nonhomologous end joining (NHEJ) predominated as the translocation pathway (93%). These results emphasize the fluidity of mammalian DSB repair pathway usage. The intron-based system is highly adaptable to addressing a number of issues regarding molecular mechanisms of genomic rearrangements in mammalian cells.
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Affiliation(s)
- Beth Elliott
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
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123
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Abstract
Double-stranded DNA breaks (DSBs) are a particularly dangerous form of DNA damage because they can lead to chromosome loss, translocations or truncations. When DSBs occur, many proteins are recruited to the break site; these proteins serve to both initiate DNA repair and to activate a checkpoint response. Repair occurs via one of two pathways: non-homologous end-joining (NHEJ), in which broken DNA ends are directly ligated; or homologous recombination (HR), in which a homologous chromosome is used as a template in a replicative repair process. The checkpoint response is mediated by the phosphatidyl inositol 3-kinase-like kinases, Mec1 and Tel1 (ATR and ATM in humans, respectively). Two recent studies in yeast have significantly increased our understanding of when each of the proteins involved in these processes is localized to a break and, in addition, how their sequential localization is achieved. Specifically, these studies support and expand upon a model in which Tel1 and the NHEJ proteins are the first proteins to localize to the break to initiate signaling and attempt repair, but are subsequently replaced by Mec1 and the HR proteins. This transition is mediated by a cyclin-dependent kinase-dependent initiation of 5'-->3' processing (resection) of the DSB. Thus, the cell-cycle stage at which DSBs occur affects the way in which the DSBs are processed and recognized.
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Affiliation(s)
- Peter M Garber
- Cancer Research Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94115, USA
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124
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van Attikum H, Fritsch O, Hohn B, Gasser SM. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell 2005; 119:777-88. [PMID: 15607975 DOI: 10.1016/j.cell.2004.11.033] [Citation(s) in RCA: 458] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 11/01/2004] [Accepted: 11/11/2004] [Indexed: 11/22/2022]
Abstract
The budding yeast INO80 complex is a conserved ATP-dependent nucleosome remodeler containing actin-related proteins Arp5 and Arp8. Strains lacking INO80, ARP5, or ARP8 have defects in transcription. Here we show that these mutants are hypersensitive to DNA damaging agents and to double-strand breaks (DSBs) induced by the HO endonuclease. The checkpoint response and most transcriptional modulation associated with induction of DNA damage are unaffected by these mutations. Using chromatin immunoprecipitation we show that Ino80, Arp5, and Arp8 are recruited to an HO-induced DSB, where a phosphorylated form of H2A accumulates. Recruitment of Ino80 is compromised in cells lacking the H2A phosphoacceptor S129. Finally, we demonstrate that conversion of the DSB into ssDNA is compromised in arp8 and H2A mutants, which are both deficient for INO80 activity at the site of damage. These results implicate INO80-mediated chromatin remodeling directly at DSBs, where it appears to facilitate processing of the lesion.
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Affiliation(s)
- Haico van Attikum
- University of Geneva, Department of Molecular Biology and NCCR Frontiers in Genetics Program, Quai Ernest Ansermet 30, CH-1211 Geneva 4, Switzerland
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125
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Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE, Lichten M. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol 2005; 14:1703-11. [PMID: 15458641 PMCID: PMC4493763 DOI: 10.1016/j.cub.2004.09.047] [Citation(s) in RCA: 367] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 08/02/2004] [Accepted: 08/24/2004] [Indexed: 11/28/2022]
Abstract
BACKGROUND In response to DNA double-strand breaks (DSBs), eukaryotic cells rapidly phosphorylate histone H2A isoform H2AX at a C-terminal serine (to form gamma-H2AX) and accumulate repair proteins at or near DSBs. To date, these events have been defined primarily at the resolution of light microscopes, and the relationship between gamma-H2AX formation and repair protein recruitment remains to be defined. RESULTS We report here the first molecular-level characterization of regional chromatin changes that accompany a DSB formed by the HO endonuclease in Saccharomyces cerevisiae. Break induction provoked rapid gamma-H2AX formation and equally rapid recruitment of the Mre11 repair protein. gamma-H2AX formation was efficiently promoted by both Tel1p and Mec1p, the yeast ATM and ATR homologs; in G1-arrested cells, most gamma-H2AX formation was dependent on Tel1 and Mre11. gamma-H2AX formed in a large (ca. 50 kb) region surrounding the DSB. Remarkably, very little gamma-H2AX could be detected in chromatin within 1-2 kb of the break. In contrast, this region contains almost all the Mre11p and other repair proteins that bind as a result of the break. CONCLUSIONS Both Mec1p and Tel1p can respond to a DSB, with distinct roles for these checkpoint kinases at different phases of the cell cycle. Part of this response involves histone phosphorylation over large chromosomal domains; however, the distinct distributions of gamma-H2AX and repair proteins near DSBs indicate that localization of repair proteins to breaks is not likely to be the main function of this histone modification.
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Affiliation(s)
- Robert Shroff
- Laboratory of Biochemistry, Center for Cancer Research, National Cancer Institute, Building 37, Room 6124, Bethesda, Maryland 20892
| | - Ayelet Arbel-Eden
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454
| | - Duane Pilch
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Grzegorz Ira
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454
| | - William M. Bonner
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - John H. Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021
| | - James E. Haber
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454
| | - Michael Lichten
- Laboratory of Biochemistry, Center for Cancer Research, National Cancer Institute, Building 37, Room 6124, Bethesda, Maryland 20892
- Correspondence:
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126
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Dudásová Z, Dudás A, Chovanec M. Non-homologous end-joining factors of Saccharomyces cerevisiae. FEMS Microbiol Rev 2005; 28:581-601. [PMID: 15539075 DOI: 10.1016/j.femsre.2004.06.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 06/02/2004] [Accepted: 06/02/2004] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks (DSB) are considered to be a severe form of DNA damage, because if left unrepaired, they can cause a cell death and, if misrepaired, they can lead to genomic instability and, ultimately, the development of cancer in multicellular organisms. The budding yeast Saccharomyces cerevisiae repairs DSB primarily by homologous recombination (HR), despite the presence of the KU70, KU80, DNA ligase IV and XRCC4 homologues, essential factors of the mammalian non-homologous end-joining (NHEJ) machinery. S. cerevisiae, however, lacks clear DNA-PKcs and ARTEMIS homologues, two important additional components of mammalian NHEJ. On the other hand, S. cerevisiae is endowed with a regulatory NHEJ component, Nej1, which has not yet been found in other organisms. Furthermore, there is evidence in budding yeast for a requirement for the Mre11/Rad50/Xrs2 complex for NHEJ, which does not appear to be the case either in Schizosaccharomyces pombe or in mammals. Here, we comprehensively describe the functions of all the S. cerevisiae NHEJ components identified so far and present current knowledge about the NHEJ process in this organism. In addition, this review depicts S. cerevisiae as a powerful model system for investigating the utilization of either NHEJ or HR in DSB repair.
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Affiliation(s)
- Zuzana Dudásová
- Laboratory of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Vlárska 7, 833 91 Bratislava 37, Slovak Republic
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127
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Unal E, Arbel-Eden A, Sattler U, Shroff R, Lichten M, Haber JE, Koshland D. DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol Cell 2004; 16:991-1002. [PMID: 15610741 DOI: 10.1016/j.molcel.2004.11.027] [Citation(s) in RCA: 424] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 10/06/2004] [Accepted: 11/05/2004] [Indexed: 12/18/2022]
Abstract
The postreplicative repair of double-strand breaks (DSBs) is thought to require sister chromatid cohesion, provided by the cohesin complex along the chromosome arms. A further specialized role for cohesin in DSB repair is suggested by its de novo recruitment to regions of DNA damage in mammals. Here, we show in budding yeast that a single DSB induces the formation of a approximately 100 kb cohesin domain around the lesion. Our analyses suggest that the primary DNA damage checkpoint kinases Mec1p and Tel1p phosphorylate histone H2AX to generate a large domain, which is permissive for cohesin binding. Cohesin binding to the phospho-H2AX domain is enabled by Mre11p, a component of a critical repair complex, and Scc2p, a component of the cohesin loading machinery that is necessary for sister chromatid cohesion. We also provide evidence that the DSB-induced cohesin domain functions in postreplicative repair.
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Affiliation(s)
- Elçin Unal
- Howard Hughes Medical Institute, Department of Embryology, The Carnegie Institution of Washington, Baltimore, MD 21210, USA
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128
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Lisby M, Rothstein R. Localization of checkpoint and repair proteins in eukaryotes. Biochimie 2004; 87:579-89. [PMID: 15989975 DOI: 10.1016/j.biochi.2004.10.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 10/25/2004] [Indexed: 12/11/2022]
Abstract
In eukaryotes, the cellular response to DNA damage depends on the type of DNA structure being recognized by the checkpoint and repair machinery. DNA ends and single-stranded DNA are hallmarks of double-strand breaks and replication stress. These two structures are recognized by distinct sets of proteins, which are reorganized into a focal assembly at the lesion. Moreover, the composition of these foci is coordinated with cell cycle progression, reflecting the favoring of end-joining in the G1 phase and homologous recombination in S and G2. The assembly of proteins at sites of DNA damage is largely controlled by a network of protein-protein interactions, with the Mre11 complex initiating assembly at DNA ends and replication protein A directing recruitment to single-stranded DNA. This review summarizes current knowledge on the cellular organization of DSB repair and checkpoint proteins focusing on budding yeast and mammalian cells.
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Affiliation(s)
- Michael Lisby
- Institute of Molecular Biology, University of Copenhagen, Øster Farimagsgade 2 A, DK-1353 Copenhagen K, Denmark
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129
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Miller CA, Bill CA, Nickoloff JA. Characterization of palindromic loop mismatch repair tracts in mammalian cells. DNA Repair (Amst) 2004; 3:421-8. [PMID: 15010318 DOI: 10.1016/j.dnarep.2003.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2003] [Indexed: 01/03/2023]
Abstract
Single- and multi-base (loop) mismatches can arise in DNA by replication errors, during recombination, and by chemical modification of DNA. Single-base and loop mismatches of several nucleotides are efficiently repaired in mammalian cells by a nick-directed, MSH2-dependent mechanism. Larger loop mismatches (> or =12 bases) are repaired by an MSH2-independent mechanism. Prior studies have shown that 12- and 14-base palindromic loops are repaired with bias toward loop retention, and that repair bias is eliminated when five single-base mismatches flank the loop mismatch. Here we show that one single-base mismatch near a 12-base palindromic loop is sufficient to eliminate loop repair bias in wild-type, but not MSH2-defective mammalian cells. We also show that palindromic loop and single-base mismatches separated by 12 bases are repaired independently at least 10% of the time in wild-type cells, and at least 30% of the time in MSH2-defective cells. Palindromic loop and single-base mismatches separated by two bases were never repaired independently. These and other data indicate that loop repair tracts are variable in length. All tracts extend at least 2 bases, some extend <12 bases, and others >12 bases, on one side of the loop. These properties distinguish palindromic loop mismatch repair from the three known excision repair pathways: base excision repair which has one to six base tracts, nucleotide excision repair which has approximately 30 base tracts, and MSH2-dependent mismatch repair, which has tracts that extend for several hundred bases.
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Affiliation(s)
- Cheryl A Miller
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
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130
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Llorente B, Symington LS. The Mre11 nuclease is not required for 5' to 3' resection at multiple HO-induced double-strand breaks. Mol Cell Biol 2004; 24:9682-94. [PMID: 15485933 PMCID: PMC522228 DOI: 10.1128/mcb.24.21.9682-9694.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Current hypotheses suggest the Mre11 nuclease activity could be directly involved in double-strand break (DSB) resection in the presence of a large number of DSBs or limited to processing abnormal DNA ends. To distinguish between these possibilities, we used two methods to create large numbers of DSBs in Saccharomyces cerevisiae chromosomes, without introducing other substrates for the Mre11 nuclease. Multiple DSBs were created either by expressing the HO endonuclease in strains containing several HO cut sites embedded within randomly dispersed Ty1 elements or by phleomycin treatment. Analysis of resection by single-strand DNA formation in these systems showed no difference between strains containing MRE11 or the mre11-D56N nuclease defective allele, suggesting that the Mre11 nuclease is not involved in the extensive 5' to 3' resection of DSBs. We postulate that the ionizing radiation (IR) sensitivity of mre11 nuclease-defective mutants results from the accumulation of IR-induced DNA damage that is normally processed by the Mre11 nuclease. We also report that the processivity of 5' to 3' DSB resection and the yield of repaired products are affected by the number of DSBs in a dose-dependent manner. Finally, we show that the exonuclease Exo1 is involved in the processivity of 5' to 3' resection of an HO-induced DSB at the MAT locus.
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Affiliation(s)
- Bertrand Llorente
- Department of Microbiology, Columbia University Medical Center, 701 W. 168th St., New York, NY 10032, USA
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131
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Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W, Liberi G, Bressan D, Wan L, Hollingsworth NM, Haber JE, Foiani M. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 2004; 431:1011-7. [PMID: 15496928 PMCID: PMC4493751 DOI: 10.1038/nature02964] [Citation(s) in RCA: 554] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Accepted: 08/19/2004] [Indexed: 11/08/2022]
Abstract
A single double-strand break (DSB) induced by HO endonuclease triggers both repair by homologous recombination and activation of the Mec1-dependent DNA damage checkpoint in budding yeast. Here we report that DNA damage checkpoint activation by a DSB requires the cyclin-dependent kinase CDK1 (Cdc28) in budding yeast. CDK1 is also required for DSB-induced homologous recombination at any cell cycle stage. Inhibition of homologous recombination by using an analogue-sensitive CDK1 protein results in a compensatory increase in non-homologous end joining. CDK1 is required for efficient 5' to 3' resection of DSB ends and for the recruitment of both the single-stranded DNA-binding complex, RPA, and the Rad51 recombination protein. In contrast, Mre11 protein, part of the MRX complex, accumulates at unresected DSB ends. CDK1 is not required when the DNA damage checkpoint is initiated by lesions that are processed by nucleotide excision repair. Maintenance of the DSB-induced checkpoint requires continuing CDK1 activity that ensures continuing end resection. CDK1 is also important for a later step in homologous recombination, after strand invasion and before the initiation of new DNA synthesis.
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Affiliation(s)
- Grzegorz Ira
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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132
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Aylon Y, Liefshitz B, Kupiec M. The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J 2004; 23:4868-75. [PMID: 15549137 PMCID: PMC535085 DOI: 10.1038/sj.emboj.7600469] [Citation(s) in RCA: 305] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 10/12/2004] [Indexed: 11/09/2022] Open
Abstract
DNA double-strand breaks (DSBs) are dangerous lesions that can lead to genomic instability and cell death. Eukaryotic cells repair DSBs either by nonhomologous end-joining (NHEJ) or by homologous recombination. We investigated the ability of yeast cells (Saccharomyces cerevisiae) to repair a single, chromosomal DSB by recombination at different stages of the cell cycle. We show that cells arrested at the G1 phase of the cell cycle restrict homologous recombination, but are able to repair the DSB by NHEJ. Furthermore, we demonstrate that recombination ability does not require duplicated chromatids or passage through S phase, and is controlled at the resection step by Clb-CDK activity.
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Affiliation(s)
- Yael Aylon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Batia Liefshitz
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel. Tel.: +972 3 640 9031; Fax: +972 3 640 9407; E-mail:
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133
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Rapp A, Greulich KO. After double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available. J Cell Sci 2004; 117:4935-45. [PMID: 15367581 DOI: 10.1242/jcs.01355] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
After induction of DNA double-strand breaks (DSB) two repair systems, the error-prone 'nonhomologous end joining' (NHEJ) and the more accurate 'homologous recombination repair' (HRR) can compete for the same individual DSB site. In the human keratinocyte cell line, HaCaT, we have tested the spatial co-localisation and the temporal sequence of events. We used UV-A (365 nm) as a damaging agent, which can be applied in clearly defined doses and can lead to rare DSBs via propagation of clustered single-strand breaks (SSBs). DNA fragmentation and repair was measured by the Comet assay and persisting DSBs were quantified by the micronucleus assay. Direct DSB detection was performed by immunohistochemical labelling of gamma-H2AX, a phosphorylated histone that is assumed to form one foci per DSB. Intra- and inter-pathway interactions were quantified by co-localisation, FRET imaging and by co-immunoprecipitation (Co-IP) of XRCC4, DNA-PK and Ku70 as representatives of NHEJ, Rad51 and Rad52 for HRR and gamma-H2AX, Mre11 and Rad50 as representatives of both pathways. In G2 cells, where both systems are available, the temporal sequence after irradiation is: (1) gamma-H2AX (2) Mre11 (3) DNA-PK Rad51 (4) XRCC4. That is, the first two proteins involved in both pathways 'label' the damaged site and initiate repair, followed by the NHEJ, which is temporally overlapping with HRR activity. Taking all these observations together we suggest that a cell tries to repair DSBs with a combination of both HRR and NHEJ, if available.
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Affiliation(s)
- Alexander Rapp
- Institute of Molecular Biotechnology Jena, Beutenbergstr. 11, 07745, Germany.
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134
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Lisby M, Barlow JH, Burgess RC, Rothstein R. Choreography of the DNA Damage Response. Cell 2004; 118:699-713. [PMID: 15369670 DOI: 10.1016/j.cell.2004.08.015] [Citation(s) in RCA: 699] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 07/22/2004] [Accepted: 07/27/2004] [Indexed: 01/12/2023]
Abstract
DNA repair is an essential process for preserving genome integrity in all organisms. In eukaryotes, recombinational repair is choreographed by multiprotein complexes that are organized into centers (foci). Here, we analyze the cellular response to DNA double-strand breaks (DSBs) and replication stress in Saccharomyces cerevisiae. The Mre11 nuclease and the ATM-related Tel1 kinase are the first proteins detected at DSBs. Next, the Rfa1 single-strand DNA binding protein relocalizes to the break and recruits other key checkpoint proteins. Later and only in S and G2 phase, the homologous recombination machinery assembles at the site. Unlike the response to DSBs, Mre11 and recombination proteins are not recruited to hydroxyurea-stalled replication forks unless the forks collapse. The cellular response to DSBs and DNA replication stress is likely directed by the Mre11 complex detecting and processing DNA ends in conjunction with Sae2 and by RP-A recognizing single-stranded DNA and recruiting additional checkpoint and repair proteins.
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Affiliation(s)
- Michael Lisby
- Department of Genetics and Development, Columbia University, College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032, USA
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135
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Abstract
Genome stability is of primary importance for the survival and proper functioning of all organisms. Double-strand breaks (DSBs) arise spontaneously during growth, or can be created by external insults. In response to even a single DSB, organisms must trigger a series of events to promote repair of the DNA damage in order to survive and restore chromosomal integrity. In doing so, cells must regulate a fine balance between potentially competing DSB repair pathways. These are generally classified as either homologous recombination (HR) or non-homologous end joining (NHEJ). The yeast Saccharomyces cerevisiae is an ideal model organism for studying these repair processes. Indeed, much of what we know today on the mechanisms of repair in eukaryotes come from studies carried out in budding yeast. Many of the proteins involved in the various repair pathways have been isolated and the details of their mode of action are currently being unraveled at the molecular level. In this review, we focus on exciting new work eminating from yeast research that provides fresh insights into the DSB repair process. This recent work supplements and complements the wealth of classical genetic research that has been performed in yeast systems over the years. Given the conservation of the repair mechanisms and genes throughout evolution, these studies have profound implications for other eukaryotic organisms.
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Affiliation(s)
- Yael Aylon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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136
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Aylon Y, Kupiec M. New insights into the mechanism of homologous recombination in yeast. Mutat Res 2004; 566:231-48. [PMID: 15082239 DOI: 10.1016/j.mrrev.2003.10.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2003] [Accepted: 10/02/2003] [Indexed: 01/09/2023]
Abstract
Genome stability is of primary importance for the survival and proper functioning of all organisms. Double-strand breaks (DSBs) arise spontaneously during growth, or can be created by external insults. Repair of DSBs by homologous recombination provides an efficient and fruitful pathway to restore chromosomal integrity. Exciting new work in yeast has lately provided insights into this complex process. Many of the proteins involved in recombination have been isolated and the details of the repair mechanism are now being unraveled at the molecular level. In this review, we focus on recent studies which dissect the recombinational repair of a single broken chromosome. After DSB formation, a decision is made regarding the mechanism of repair (recombination or non-homologous end-joining). This decision is under genetic control. Once committed to the recombination pathway, the broken chromosomal ends are resected by a still unclear mechanism in which the DNA damage checkpoint protein Rad24 participates. At this stage several proteins are recruited to the broken ends, including Rad51p, Rad52p, Rad55p, Rad57p, and possibly Rad54p. A genomic search for homology ensues, followed by strand invasion, promoted by the Rad51 filament with the participation of Rad55p, Rad57p and Rad54p. DNA synthesis then takes place, restoring the resected ends. Crossing-over formation depends on the length of the homologous recombining sequences, and is usually counteracted by the activity of the mismatch repair system. Given the conservation of the repair mechanisms and genes throughout evolution, these studies have profound implications for other eukaryotic organisms.
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Affiliation(s)
- Yael Aylon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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137
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Abstract
In eukaryotes, recombinational repair is choreographed by multiprotein complexes that are organized into focal assemblies. These foci are highly dynamic giga-dalton structures capable of simultaneously repairing multiple DNA lesions. Moreover, the composition of these repair centers depends on the nature of the DNA lesion and is tightly coordinated with progression of the cell cycle. Components of DNA repair centers are regulated by post-translational modifications such as phosphorylation, ubiquitination and sumoylation. Repair foci progress through four distinct stages: first, DNA damage recognition and binding of DNA ends by the Mre11 complex and Ku70/80; second, end-processing and binding of single-stranded DNA by replication protein A, which recruits checkpoint proteins; third, recombinational repair during S and G(2) phase; and fourth, disassembly of foci and resumption of the cell cycle.
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Affiliation(s)
- Michael Lisby
- Department of Genetics & Development, Columbia University, College of Physicians & Surgeons, 701 West 168th Street, New York, NY 10032-2704, USA
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138
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Lee GS, Neiditch MB, Salus SS, Roth DB. RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell 2004; 117:171-84. [PMID: 15084256 DOI: 10.1016/s0092-8674(04)00301-0] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 01/30/2004] [Accepted: 02/12/2004] [Indexed: 11/28/2022]
Abstract
The two major pathways for repairing double-strand breaks (DSBs), homologous recombination and nonhomologous end joining (NHEJ), have traditionally been thought to operate in different stages of the cell cycle. This division of labor is not absolute, however, and precisely what governs the choice of pathway to repair a given DSB has remained enigmatic. We pursued this question by studying the site-specific DSBs created during V(D)J recombination, which relies on classical NHEJ to repair the broken ends. We show that mutations that form unstable RAG postcleavage complexes allow DNA ends to participate in both homologous recombination and the error-prone alternative NHEJ pathway. By abrogating a key function of the complex, these mutations reveal it to be a molecular shepherd that guides DSBs to the proper pathway. We also find that RAG-mediated nicks efficiently stimulate homologous recombination and discuss the implications of these findings for oncogenic chromosomal rearrangements, evolution, and gene targeting.
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Affiliation(s)
- Gregory S Lee
- The Skirball Institute of Biomolecular Medicine, Lab 2-10 and Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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139
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Abstract
Werner syndrome (WS) is one of three heritable human genetic instability/cancer predisposition syndromes that result from mutations in a member of the gene family encoding human RecQ helicases. Cellular defects are a prominent part of the WS phenotype. Here we review recent work to identify in vivo functions of the WS protein and discuss how loss of function leads to cellular defects. These new results provide clues to the origin of cell lineage-specific defects in WS patients and suggest a broader role for Werner protein function in determining disease risk in the general population.
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Affiliation(s)
- Raymond J Monnat
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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140
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Skory CD. Repair of plasmid DNA used for transformation of Rhizopus oryzae by gene conversion. Curr Genet 2004; 45:302-10. [PMID: 15007626 DOI: 10.1007/s00294-004-0494-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 02/06/2004] [Accepted: 02/13/2004] [Indexed: 10/26/2022]
Abstract
Techniques for genetic manipulation of the filamentous fungus Rhizopus have been hampered due to a lack of understanding regarding the recombination and replication mechanisms that affect the fate of introduced DNA. The ability to target chromosomal integration of a plasmid has been difficult because DNA transformed into Rhizopus rarely integrates and is autonomously replicated in a high molecular weight concatenated arrangement (i.e., series or chain). Linearization of the plasmid prior to transformation at a site having homology with the genomic DNA yields the highest frequency of integration, but repair of the double-strand break by end-joining is still the predominant event. We recently attempted to circumvent replication of the plasmid by introducing frameshift mutations in pyrG, the R. oryzae orotidine-5'-monophosphate decarboxylase gene used for selection of the vector. It was hypothesized that autonomous replication of the mutated plasmids would be incapable of restoring prototrophic growth, since the genomic pyrG also contained a mutation. However, homologous integration of the plasmid results in duplication of the pyrG gene, which can create a functional copy of pyrG if both the genomic and plasmid mutations are paired on the same duplicate copy. While this event was detected in one of the isolates, it represented less than 8% of the total transformants. The majority of transformants contained plasmid replicating autonomously in a concatenated arrangement. Sequence analysis showed that prototrophic growth was restored by repairing the non-functional pyrG sequence in the plasmid, while the genomic pyrG gene was unaltered. Frequent transfer of the genomic pyrG mutation to the plasmid suggests that gene conversion is likely occurring by recombination pathways involving break-induced replication or synthesis-dependent strand annealing.
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Affiliation(s)
- Christopher D Skory
- Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604, USA.
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141
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Yu J, Marshall K, Yamaguchi M, Haber JE, Weil CF. Microhomology-dependent end joining and repair of transposon-induced DNA hairpins by host factors in Saccharomyces cerevisiae. Mol Cell Biol 2004; 24:1351-64. [PMID: 14729978 PMCID: PMC321453 DOI: 10.1128/mcb.24.3.1351-1364.2004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Revised: 10/15/2003] [Accepted: 10/31/2003] [Indexed: 12/20/2022] Open
Abstract
The maize, cut-and-paste transposon Ac/Ds is mobile in Saccharomyces cerevisiae, and DNA sequences of repair products provide strong genetic evidence that hairpin intermediates form in host DNA during this transposition, similar to those formed for V(D)J coding joints in vertebrates. Both DNA strands must be broken for Ac/Ds to excise, suggesting that double-strand break (DSB) repair pathways should be involved in repair of excision sites. In the absence of homologous template, as expected, Ac excisions are repaired by nonhomologous end joining (NHEJ) that can involve microhomologies close to the broken ends. However, unlike repair of endonuclease-induced DSBs, repair of Ac excisions in the presence of homologous template occurs by gene conversion only about half the time, the remainder being NHEJ events. Analysis of transposition in mutant yeast suggests roles for the Mre11/Rad50 complex, SAE2, NEJ1, and the Ku complex in repair of excision sites. Separation-of-function alleles of MRE11 suggest that its endonuclease function is more important in this repair than either its exonuclease or Rad50-binding properties. In addition, the interstrand cross-link repair gene PSO2 plays a role in end joining hairpin ends that is not seen in repair of linearized plasmids and may be involved in positioning transposase cleavage at the transposon ends.
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Affiliation(s)
- Jianhua Yu
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907-1150, USA
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142
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Wang X, Haber JE. Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. PLoS Biol 2004; 2:E21. [PMID: 14737196 PMCID: PMC314472 DOI: 10.1371/journal.pbio.0020021] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2003] [Accepted: 11/21/2003] [Indexed: 01/03/2023] Open
Abstract
The single-stranded DNA (ssDNA)-binding protein replication protein A (RPA) is essential for both DNA replication and recombination. Chromatin immunoprecipitation techniques were used to visualize the kinetics and extent of RPA binding following induction of a double-strand break (DSB) and during its repair by homologous recombination in yeast. RPA assembles at the HO endonuclease-cut MAT locus simultaneously with the appearance of the DSB, and binding spreads away from the DSB as 5′ to 3′ exonuclease activity creates more ssDNA. RPA binding precedes binding of the Rad51 recombination protein. The extent of RPA binding is greater when Rad51 is absent, supporting the idea that Rad51 displaces RPA from ssDNA. RPA plays an important role during RAD51-mediated strand invasion of the MAT ssDNA into the donor sequence HML. The replication-proficient but recombination-defective rfa1-t11 (K45E) mutation in the large subunit of RPA is normal in facilitating Rad51 filament formation on ssDNA, but is unable to achieve synapsis between MAT and HML. Thus, RPA appears to play a role in strand invasion as well as in facilitating Rad51 binding to ssDNA, possibly by stabilizing the displaced ssDNA. By studying the repair of double-strand DNA breaks in vivo, evidence of a new role for the DNA-binding protein RPA has been discovered
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Affiliation(s)
- Xuan Wang
- 1Rosenstiel Center and Department of Biology, Brandeis UniversityWaltham, MassachusettsUnited States of America
| | - James E Haber
- 1Rosenstiel Center and Department of Biology, Brandeis UniversityWaltham, MassachusettsUnited States of America
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143
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Abstract
The protective "cap" that assembles at chromosome ends recruits and controls an intricate network of biochemical activities, each one critical for telomere structure and the maintenance of genomic stability. Recent studies have uncovered the components of telomere caps and have started to define the pathways that lead from telomere dysfunction to chromosomal catastrophe.
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Affiliation(s)
- Miguel Godinho Ferreira
- Telomere Biology Laboratory, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
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144
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Lieber MR, Ma Y, Pannicke U, Schwarz K. Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol 2003; 4:712-20. [PMID: 14506474 DOI: 10.1038/nrm1202] [Citation(s) in RCA: 696] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Non-homologous DNA end-joining (NHEJ)--the main pathway for repairing double-stranded DNA breaks--functions throughout the cell cycle to repair such lesions. Defects in NHEJ result in marked sensitivity to ionizing radiation and ablation of lymphocytes, which rely on NHEJ to complete the rearrangement of antigen-receptor genes. NHEJ is typically imprecise, a characteristic that is useful for immune diversification in lymphocytes, but which might also contribute to some of the genetic changes that underlie cancer and ageing.
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Affiliation(s)
- Michael R Lieber
- Norris Comprehensive Cancer Center, Department of Pathology, University of Southern California School of Medicine, 1441 Eastlake Avenue, MS 9176, Los Angeles, California 90089, USA.
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145
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Anti-aging medicine literaturewatch. JOURNAL OF ANTI-AGING MEDICINE 2003; 6:45-64. [PMID: 12971397 DOI: 10.1089/109454503765361588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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146
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Kibe T, Tomita K, Matsuura A, Izawa D, Kodaira T, Ushimaru T, Uritani M, Ueno M. Fission yeast Rhp51 is required for the maintenance of telomere structure in the absence of the Ku heterodimer. Nucleic Acids Res 2003; 31:5054-63. [PMID: 12930956 PMCID: PMC212814 DOI: 10.1093/nar/gkg718] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Schizosaccharomyces pombe Ku70-Ku80 heterodimer is required for telomere length regulation. Lack of pku70+ results in telomere shortening and striking rearrangements of telomere-associated sequences. We found that the rearrangements of telomere-associated sequences in pku80+ mutants are Rhp51 dependent, but not Rad50 dependent. Rhp51 bound to telomere ends when the Ku heterodimer was not present at telomere ends. We also found that the single-stranded G-rich tails increased in S phase in wild-type strains, while deletion of pku70+ increased the single-stranded overhang in both G2 and S phase. Based on these observations, we propose that Rhp51 binds to the G-rich overhang and promotes homologous pairing between two different telomere ends in the absence of Ku heterodimer. Moreover, pku80 rhp51 double mutants showed a significantly reduced telomere hybridization signal. Our results suggest that, although Ku heterodimer sequesters Rhp51 from telomere ends to inhibit homologous recombination activity, Rhp51 plays important roles for the maintenance of telomere ends in the absence of the Ku heterodimer.
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Affiliation(s)
- Tatsuya Kibe
- Department of Chemistry, Shizuoka University, 836 Oya, Shizuoka 422-8529, Japan
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147
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Sugawara N, Wang X, Haber JE. In vivo roles of Rad52, Rad54, and Rad55 proteins in Rad51-mediated recombination. Mol Cell 2003; 12:209-19. [PMID: 12887906 DOI: 10.1016/s1097-2765(03)00269-7] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Repairing a double-strand break by homologous recombination requires binding of the strand exchange protein Rad51p to ssDNA, followed by synapsis with a homologous donor. Here we used chromatin immunoprecipitation to monitor the in vivo association of Saccharomyces cerevisiae Rad51p with both the cleaved MATa locus and the HML alpha donor. Localization of Rad51p to MAT precedes its association with HML, providing evidence of the time needed for the Rad51 filament to search the genome for a homologous sequence. Rad51p binding to ssDNA requires Rad52p. The absence of Rad55p delays Rad51p binding to ssDNA and prevents strand invasion and localization of Rad51p to HML alpha. Lack of Rad54p does not significantly impair Rad51p recruitment to MAT or its initial association with HML alpha; however, Rad54p is required at or before the initiation of DNA synthesis after synapsis has occurred at the 3' end of the invading strand.
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Affiliation(s)
- Neal Sugawara
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA
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148
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Palmer S, Schildkraut E, Lazarin R, Nguyen J, Nickoloff JA. Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional. Nucleic Acids Res 2003; 31:1164-73. [PMID: 12582235 PMCID: PMC150237 DOI: 10.1093/nar/gkg219] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Revised: 12/17/2002] [Accepted: 12/17/2002] [Indexed: 11/12/2022] Open
Abstract
Gene conversion is a common outcome of double-strand break (DSB) repair in yeast. Prior studies revealed that DSB-induced gene conversion tracts are often short (<53 bp), unidirectional, and biased toward promoter-proximal (5') markers. In those studies, broken ends had short, non-homologous termini. For the present study we created plasmid x chromosome, chromosomal direct repeat and allelic recombination substrates in which donor alleles carried mutant HO sites (HOinc--not cleaved) at the same position as cleavable HO sites in recipient alleles. In these substrates, broken ends are almost completely homologous to donor alleles, differing only at the three HOinc mutations. These mutations serve as markers very close to, or within, the four-base overhang produced by HO nuclease. We identified extremely short tracts (<12 bp) and many tracts were highly directional, extending <2 bp on one side of the DSB. We thought that terminal homology would promote bidirectional tracts, but found instead that unidirectional tracts were more frequent. Interestingly, substrates with terminal homology displayed enhanced 3' conversion, and in several cases conversion bias was reversed toward 3' markers. These results are discussed in relation to factors that may influence tract length and directionality, including heteroduplex DNA formation, transcription, replication and mismatch repair.
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Affiliation(s)
- Sean Palmer
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
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