1
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Lama-Diaz T, Blanco MG. Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase. Nucleic Acids Res 2024; 52:6928-6944. [PMID: 38783074 PMCID: PMC11229318 DOI: 10.1093/nar/gkae400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
In budding yeast, the integrity of both the nuclear and mitochondrial genomes relies on dual-targeted isoforms of the conserved Pif1 helicase, generated by alternative translation initiation (ATI) of PIF1 mRNA from two consecutive AUG codons flanking a mitochondrial targeting signal. Here, we demonstrate that ribosomal leaky scanning is the specific ATI mechanism that produces not only these, but also novel, previously uncharacterized Pif1 isoforms. Both in-frame, downstream AUGs as well as near-cognate start codons contribute to the generation of these alternative isoforms. This has crucial implications for the rational design of genuine separation-of-function alleles and provides an explanation for the suboptimal behaviour of the widely employed mitochondrial- (pif1-m1) and nuclear-deficient (pif1-m2) alleles, with mutations in the first or second AUG codon, respectively. We have taken advantage of this refined model to develop improved versions of these alleles, which will serve as valuable tools to elucidate novel functions of this helicase and to disambiguate previously described genetic interactions of PIF1 in the context of nuclear and mitochondrial genome stability.
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Affiliation(s)
- Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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2
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Yamamoto H, Hirasawa A. Homologous Recombination Deficiencies and Hereditary Tumors. Int J Mol Sci 2021; 23:348. [PMID: 35008774 PMCID: PMC8745585 DOI: 10.3390/ijms23010348] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination (HR) is a vital process for repairing DNA double-strand breaks. Germline variants in the HR pathway, comprising at least 10 genes, such as BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK2, NBS1(NBN), PALB2, RAD51C, and RAD51D, lead to inherited susceptibility to specific types of cancers, including those of the breast, ovaries, prostate, and pancreas. The penetrance of germline pathogenic variants of each gene varies, whereas all their associated protein products are indispensable for maintaining a high-fidelity DNA repair system by HR. The present review summarizes the basic molecular mechanisms and components that collectively play a role in maintaining genomic integrity against DNA double-strand damage and their clinical implications on each type of hereditary tumor.
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Affiliation(s)
- Hideki Yamamoto
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
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3
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Roy U, Kwon Y, Marie L, Symington L, Sung P, Lisby M, Greene EC. The Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination. Mol Cell 2021; 81:1043-1057.e8. [PMID: 33421364 PMCID: PMC8262405 DOI: 10.1016/j.molcel.2020.12.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/02/2020] [Accepted: 12/10/2020] [Indexed: 12/29/2022]
Abstract
Homologous recombination (HR) is essential for maintenance of genome integrity. Rad51 paralogs fulfill a conserved but undefined role in HR, and their mutations are associated with increased cancer risk in humans. Here, we use single-molecule imaging to reveal that the Saccharomyces cerevisiae Rad51 paralog complex Rad55-Rad57 promotes assembly of Rad51 recombinase filament through transient interactions, providing evidence that it acts like a classical molecular chaperone. Srs2 is an ATP-dependent anti-recombinase that downregulates HR by actively dismantling Rad51 filaments. Contrary to the current model, we find that Rad55-Rad57 does not physically block the movement of Srs2. Instead, Rad55-Rad57 promotes rapid re-assembly of Rad51 filaments after their disruption by Srs2. Our findings support a model in which Rad51 is in flux between free and single-stranded DNA (ssDNA)-bound states, the rate of which is controlled dynamically though the opposing actions of Rad55-Rad57 and Srs2.
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Affiliation(s)
- Upasana Roy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lea Marie
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Lorraine Symington
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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4
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ATP hydrolysis by yeast Hsp104 determines protein aggregate dissolution and size in vivo. Nat Commun 2020; 11:5226. [PMID: 33067463 PMCID: PMC7568574 DOI: 10.1038/s41467-020-19104-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/28/2020] [Indexed: 12/23/2022] Open
Abstract
Signs of proteostasis failure often entwine with those of metabolic stress at the cellular level. Here, we study protein sequestration during glucose deprivation-induced ATP decline in Saccharomyces cerevisiae. Using live-cell imaging, we find that sequestration of misfolded proteins and nascent polypeptides into two distinct compartments, stress granules, and Q-bodies, is triggered by the exhaustion of ATP. Both compartments readily dissolve in a PKA-dependent manner within minutes of glucose reintroduction and ATP level restoration. We identify the ATP hydrolase activity of Hsp104 disaggregase as the critical ATP-consuming process determining compartments abundance and size, even in optimal conditions. Sequestration of proteins into distinct compartments during acute metabolic stress and their retrieval during the recovery phase provide a competitive fitness advantage, likely promoting cell survival during stress. The sequestration of misfolded protein into insoluble aggregates occurs under conditions of proteotoxic stress. Here the authors observe that a reduction in cellular ATP promotes protein sequestration into two separate compartments: Q-bodies and stress granules; and identify Hsp104 as a critical ATP-consuming process that determines those compartments abundance and size.
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5
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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Ip K, Yadin R, George KW. High-Throughput DNA Assembly Using Yeast Homologous Recombination. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2205:79-89. [PMID: 32809194 DOI: 10.1007/978-1-0716-0908-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Yeast homologous recombination is a reliable, low-cost, and efficient method for DNA assembly. Using homology regions as short as 24 base pairs, constructs of up to 12 unique parts can be assembled into a diverse range of vectors. The simplicity and robustness of this protocol make it amenable to laboratory automation and high-throughput operations. Here we describe a high-throughput protocol to generate DNA parts through PCR, assemble them into a vector via yeast transformation, and "shuttle" the resulting plasmid constructs into E. coli for storage and propagation. Though this protocol is intended for high-throughput workflows, it can be easily adapted for bench-scale DNA assembly.
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7
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Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. Mitochondrial DNA and temperature tolerance in lager yeasts. SCIENCE ADVANCES 2019; 5:eaav1869. [PMID: 30729163 PMCID: PMC6353617 DOI: 10.1126/sciadv.aav1869] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/03/2019] [Indexed: 06/01/2023]
Abstract
A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Paterna, Valencia, Spain
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xueying C. Li
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C. Fay
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
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8
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Szymanski EA. Who are the users of synthetic DNA? Using metaphors to activate microorganisms at the center of synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:15. [PMID: 30006902 PMCID: PMC6045561 DOI: 10.1186/s40504-018-0080-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology, a multidisciplinary field involving designing and building with DNA, often designs and builds in microorganisms. The role of these microorganisms tends to be understood through metaphors making the microbial cell like a machine and emphasizing its passivity: cells are described as platforms, chassis, and computers. Here, I point to the efficacy of such metaphors in enacting the microorganism as a particular kind of (non-)participant in the research process, and I suggest the utility of employing metaphors that make microorganisms a different kind of thing-active participants, contributors, and even collaborators in scientific research. This suggestion is worth making, I argue, because enabling the activity of the microorganism generates opportunities for learning from microorganisms in ways that may help explain currently unexplained phenomena in synthetic biology and suggest new experimental directions. Moreover, "activating the microorganism" reorients relationships between human scientists and nonhuman experimental participants away from control over nonhuman creatures and toward respect for and listening to them, generating conditions of possibility for exploring what responsible research means when humans try to be responsible toward and even with creatures across species boundaries.
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Affiliation(s)
- Erika Amethyst Szymanski
- Science, Technology, and Innovation Studies, University of Edinburgh, Edinburgh, UK.
- Chisholm House, High School Yards, Edinburgh, EH1 1LZ, UK.
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9
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Crickard JB, Kaniecki K, Kwon Y, Sung P, Lisby M, Greene EC. Regulation of Hed1 and Rad54 binding during maturation of the meiosis-specific presynaptic complex. EMBO J 2018; 37:embj.201798728. [PMID: 29444896 DOI: 10.15252/embj.201798728] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/03/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Most eukaryotes have two Rad51/RecA family recombinases, Rad51, which promotes recombination during mitotic double-strand break (DSB) repair, and the meiosis-specific recombinase Dmc1. During meiosis, the strand exchange activity of Rad51 is downregulated through interactions with the meiosis-specific protein Hed1, which helps ensure that strand exchange is driven by Dmc1 instead of Rad51. Hed1 acts by preventing Rad51 from interacting with Rad54, a cofactor required for promoting strand exchange during homologous recombination. However, we have a poor quantitative understanding of the regulatory interplay between these proteins. Here, we use real-time single-molecule imaging to probe how the Hed1- and Rad54-mediated regulatory network contributes to the identity of mitotic and meiotic presynaptic complexes. Based on our findings, we define a model in which kinetic competition between Hed1 and Rad54 helps define the functional identity of the presynaptic complex as cells undergo the transition from mitotic to meiotic repair.
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Affiliation(s)
- J Brooks Crickard
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kyle Kaniecki
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
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10
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Villa M, Bonetti D, Carraro M, Longhese MP. Rad9/53BP1 protects stalled replication forks from degradation in Mec1/ATR-defective cells. EMBO Rep 2018; 19:351-367. [PMID: 29301856 PMCID: PMC5797966 DOI: 10.15252/embr.201744910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Nucleolytic processing by nucleases can be a relevant mechanism to allow repair/restart of stalled replication forks. However, nuclease action needs to be controlled to prevent overprocessing of damaged replication forks that can be detrimental to genome stability. The checkpoint protein Rad9/53BP1 is known to limit nucleolytic degradation (resection) of DNA double-strand breaks (DSBs) in both yeast and mammals. Here, we show that loss of the inhibition that Rad9 exerts on resection exacerbates the sensitivity to replication stress of Mec1/ATR-defective yeast cells by exposing stalled replication forks to Dna2-dependent degradation. This Rad9 protective function is independent of checkpoint activation and relies mainly on Rad9-Dpb11 interaction. We propose that Rad9/53BP1 supports cell viability by protecting stalled replication forks from extensive resection when the intra-S checkpoint is not fully functional.
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Affiliation(s)
- Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Massimo Carraro
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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11
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Lafuente-Barquero J, Luke-Glaser S, Graf M, Silva S, Gómez-González B, Lockhart A, Lisby M, Aguilera A, Luke B. The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage. PLoS Genet 2017; 13:e1007136. [PMID: 29281624 PMCID: PMC5760084 DOI: 10.1371/journal.pgen.1007136] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 01/09/2018] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery. In the absence of RNase H enzymes, RNA-DNA hybrids accumulate, resulting in replication stress, DNA damage and compromised genomic integrity. We demonstrate that Mph1, the yeast homolog of Fanconi anemia protein M (FANCM), is required for cell viability in the absence of RNase H enzymes. The integrity of the Mph1 helicase domain is crucial to prevent the accumulation of RNA-DNA hybrids and RNA-DNA hybrid-dependent DNA damage, as determined by Rad52 foci. Mph1 forms foci when RNA-DNA hybrids accumulate, e.g. in RNase H or THO-complex mutants and at short telomeres. Mph1, however is a double-edged sword, whose action at hybrids must be regulated by the Smc5/6 complex. This is underlined by the observation that simultaneous inactivation of RNase H2 and Smc5/6 results in Mph1-dependent synthetic lethality, which is likely due to an accumulation of toxic recombination intermediates. The data presented here support a model, where Mph1’s helicase activity plays a crucial role in responding to persistent RNA-DNA hybrids. DNA damage can either occur exogenously through DNA damaging agents such as UV light and exposure to chemotherapeutics, or endogenously via metabolic, cellular processes. The RNA product of transcription, for example, can engage in the formation of RNA-DNA hybrids. Such RNA-DNA hybrids can impede replication fork progression and cause genomic instability, a hallmark of cancer. The misregulation of RNA-DNA hybrids has also been implicated in several neurological disorders. Recently, it has become evident that RNA-DNA hybrids may also have beneficial roles and therefore, these structures have to be tightly controlled. We found that Mph1 (mutator phenotype 1), the budding yeast homolog of Fanconi Anemia protein M, counteracts the accumulation of RNA-DNA hybrids. The inactivation of MPH1 results in a severe growth defect when combined with mutations in the well-characterized RNase H enzymes, that degrade the RNA moiety of an RNA-DNA hybrid. Based on the data presented here, we propose a model, where Mph1 itself has to be kept in check by the SMC (structural maintenance of chromosome) 5/6 complex at replication forks stalled by RNA-DNA hybrids. Mph1 acts as a double-edged sword, as both its deletion and the inability to control its helicase activity cause DNA damage and growth arrest when RNA-DNA hybrids accumulate.
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Affiliation(s)
- Juan Lafuente-Barquero
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | - Sarah Luke-Glaser
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marco Graf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sonia Silva
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Belén Gómez-González
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | | | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Andrés Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- * E-mail: (BL); (AA)
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Institute of Neurobiology and Developmental Biology, JGU Mainz, Mainz, Germany
- * E-mail: (BL); (AA)
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12
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Leshets M, Ramamurthy D, Lisby M, Lehming N, Pines O. Fumarase is involved in DNA double-strand break resection through a functional interaction with Sae2. Curr Genet 2017; 64:697-712. [DOI: 10.1007/s00294-017-0786-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/19/2017] [Accepted: 11/22/2017] [Indexed: 11/28/2022]
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13
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Cesena D, Cassani C, Rizzo E, Lisby M, Bonetti D, Longhese MP. Regulation of telomere metabolism by the RNA processing protein Xrn1. Nucleic Acids Res 2017; 45:3860-3874. [PMID: 28160602 PMCID: PMC5397203 DOI: 10.1093/nar/gkx072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/19/2022] Open
Abstract
Telomeric DNA consists of repetitive G-rich sequences that terminate with a 3΄-ended single stranded overhang (G-tail), which is important for telomere extension by telomerase. Several proteins, including the CST complex, are necessary to maintain telomere structure and length in both yeast and mammals. Emerging evidence indicates that RNA processing factors play critical, yet poorly understood, roles in telomere metabolism. Here, we show that the lack of the RNA processing proteins Xrn1 or Rrp6 partially bypasses the requirement for the CST component Cdc13 in telomere protection by attenuating the activation of the DNA damage checkpoint. Xrn1 is necessary for checkpoint activation upon telomere uncapping because it promotes the generation of single-stranded DNA. Moreover, Xrn1 maintains telomere length by promoting the association of Cdc13 to telomeres independently of ssDNA generation and exerts this function by downregulating the transcript encoding the telomerase inhibitor Rif1. These findings reveal novel roles for RNA processing proteins in the regulation of telomere metabolism with implications for genome stability in eukaryotes.
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Affiliation(s)
- Daniele Cesena
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Emanuela Rizzo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
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14
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Churikov D, Charifi F, Eckert-Boulet N, Silva S, Simon MN, Lisby M, Géli V. SUMO-Dependent Relocalization of Eroded Telomeres to Nuclear Pore Complexes Controls Telomere Recombination. Cell Rep 2016; 15:1242-53. [PMID: 27134164 DOI: 10.1016/j.celrep.2016.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 02/05/2023] Open
Abstract
In budding yeast, inactivation of telomerase and ensuing telomere erosion cause relocalization of telomeres to nuclear pore complexes (NPCs). However, neither the mechanism of such relocalization nor its significance are understood. We report that proteins bound to eroded telomeres are recognized by the SUMO (small ubiquitin-like modifier)-targeted ubiquitin ligase (STUbL) Slx5-Slx8 and become increasingly SUMOylated. Recruitment of Slx5-Slx8 to eroded telomeres facilitates telomere relocalization to NPCs and type II telomere recombination, a counterpart of mammalian alternative lengthening of telomeres (ALT). Moreover, artificial tethering of a telomere to a NPC promotes type II telomere recombination but cannot bypass the lack of Slx5-Slx8 in this process. Together, our results indicate that SUMOylation positively contributes to telomere relocalization to the NPC, where poly-SUMOylated proteins that accumulated over time have to be removed. We propose that STUbL-dependent relocalization of telomeres to NPCs constitutes a pathway in which excessively SUMOylated proteins are removed from "congested" intermediates to ensure unconventional recombination.
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Affiliation(s)
- Dmitri Churikov
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France
| | - Ferose Charifi
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France
| | | | - Sonia Silva
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France.
| | - Michael Lisby
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France.
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15
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Weninger A, Killinger M, Vogl T. Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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16
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Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p. Nat Commun 2015; 6:7726. [PMID: 26158509 PMCID: PMC4510963 DOI: 10.1038/ncomms8726] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 06/04/2015] [Indexed: 01/23/2023] Open
Abstract
The essential vitamin biotin is a covalent and tenaciously attached prosthetic group in several carboxylases that play important roles in the regulation of energy metabolism. Here we describe increased acetyl-CoA levels and mitochondrial hyperacetylation as downstream metabolic effects of biotin deficiency. Upregulated mitochondrial acetylation sites correlate with the cellular deficiency of the Hst4p deacetylase, and a biotin-starvation-induced accumulation of Hst4p in mitochondria supports a role for Hst4p in lowering mitochondrial acetylation. We show that biotin starvation and knockout of Hst4p cause alterations in cellular respiration and an increase in reactive oxygen species (ROS). These results suggest that Hst4p plays a pivotal role in biotin metabolism and cellular energy homeostasis, and supports that Hst4p is a functional yeast homologue of the sirtuin deacetylase SIRT3. With biotin deficiency being involved in various metabolic disorders, this study provides valuable insight into the metabolic effects biotin exerts on eukaryotic cells.
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17
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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18
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Chavdarova M, Marini V, Sisakova A, Sedlackova H, Vigasova D, Brill SJ, Lisby M, Krejci L. Srs2 promotes Mus81-Mms4-mediated resolution of recombination intermediates. Nucleic Acids Res 2015; 43:3626-42. [PMID: 25765656 PMCID: PMC4402524 DOI: 10.1093/nar/gkv198] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/26/2015] [Indexed: 11/26/2022] Open
Abstract
A variety of DNA lesions, secondary DNA structures or topological stress within the DNA template may lead to stalling of the replication fork. Recovery of such forks is essential for the maintenance of genomic stability. The structure-specific endonuclease Mus81–Mms4 has been implicated in processing DNA intermediates that arise from collapsed forks and homologous recombination. According to previous genetic studies, the Srs2 helicase may play a role in the repair of double-strand breaks and ssDNA gaps together with Mus81–Mms4. In this study, we show that the Srs2 and Mus81–Mms4 proteins physically interact in vitro and in vivo and we map the interaction domains within the Srs2 and Mus81 proteins. Further, we show that Srs2 plays a dual role in the stimulation of the Mus81–Mms4 nuclease activity on a variety of DNA substrates. First, Srs2 directly stimulates Mus81–Mms4 nuclease activity independent of its helicase activity. Second, Srs2 removes Rad51 from DNA to allow access of Mus81–Mms4 to cleave DNA. Concomitantly, Mus81–Mms4 inhibits the helicase activity of Srs2. Taken together, our data point to a coordinated role of Mus81–Mms4 and Srs2 in processing of recombination as well as replication intermediates.
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Affiliation(s)
- Melita Chavdarova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic
| | - Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic
| | - Alexandra Sisakova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Hana Sedlackova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic
| | - Dana Vigasova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Steven J Brill
- Department of Genetics, Cancer Research Institute, Vlarska 7, 833 91 Bratislava, Slovakia
| | - Michael Lisby
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
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19
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Fallet E, Jolivet P, Soudet J, Lisby M, Gilson E, Teixeira MT. Length-dependent processing of telomeres in the absence of telomerase. Nucleic Acids Res 2014; 42:3648-65. [PMID: 24393774 PMCID: PMC3973311 DOI: 10.1093/nar/gkt1328] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the absence of telomerase, telomeres progressively shorten with every round of DNA replication, leading to replicative senescence. In telomerase-deficient Saccharomyces cerevisiae, the shortest telomere triggers the onset of senescence by activating the DNA damage checkpoint and recruiting homologous recombination (HR) factors. Yet, the molecular structures that trigger this checkpoint and the mechanisms of repair have remained elusive. By tracking individual telomeres, we show that telomeres are subjected to different pathways depending on their length. We first demonstrate a progressive accumulation of subtelomeric single-stranded DNA (ssDNA) through 5'-3' resection as telomeres shorten. Thus, exposure of subtelomeric ssDNA could be the signal for cell cycle arrest in senescence. Strikingly, early after loss of telomerase, HR counteracts subtelomeric ssDNA accumulation rather than elongates telomeres. We then asked whether replication repair pathways contribute to this mechanism. We uncovered that Rad5, a DNA helicase/Ubiquitin ligase of the error-free branch of the DNA damage tolerance (DDT) pathway, associates with native telomeres and cooperates with HR in senescent cells. We propose that DDT acts in a length-independent manner, whereas an HR-based repair using the sister chromatid as a template buffers precocious 5'-3' resection at the shortest telomeres.
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Affiliation(s)
- Emilie Fallet
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, FRE3354, 75005 Paris, France, Laboratoire de Biologie Moléculaire de la Cellule, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Université de Lyon 1, UMR5239, 69364 Lyon Cedex 07, France, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark, Institute for Research on Cancer and Aging, Nice (IRCAN), University of Nice Sophia-Antipolis, CNRS UMR7284/INSERM U1081, Faculty of Medicine, Nice F-06107, France and Department of Medical Genetics, CHU Nice, 06202 Nice cedex 3, France
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20
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Germann SM, Schramke V, Pedersen RT, Gallina I, Eckert-Boulet N, Oestergaard VH, Lisby M. TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability. ACTA ACUST UNITED AC 2013; 204:45-59. [PMID: 24379413 PMCID: PMC3882784 DOI: 10.1083/jcb.201305157] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
TopBP1/Dpb11 prevents accumulation of anaphase chromatin bridges by stimulating the Mec1/ATR kinase and suppressing homologous recombination. DNA anaphase bridges are a potential source of genome instability that may lead to chromosome breakage or nondisjunction during mitosis. Two classes of anaphase bridges can be distinguished: DAPI-positive chromatin bridges and DAPI-negative ultrafine DNA bridges (UFBs). Here, we establish budding yeast Saccharomyces cerevisiae and the avian DT40 cell line as model systems for studying DNA anaphase bridges and show that TopBP1/Dpb11 plays an evolutionarily conserved role in their metabolism. Together with the single-stranded DNA binding protein RPA, TopBP1/Dpb11 binds to UFBs, and depletion of TopBP1/Dpb11 led to an accumulation of chromatin bridges. Importantly, the NoCut checkpoint that delays progression from anaphase to abscission in yeast was activated by both UFBs and chromatin bridges independently of Dpb11, and disruption of the NoCut checkpoint in Dpb11-depleted cells led to genome instability. In conclusion, we propose that TopBP1/Dpb11 prevents accumulation of anaphase bridges via stimulation of the Mec1/ATR kinase and suppression of homologous recombination.
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Affiliation(s)
- Susanne M Germann
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, DK-2200 Copenhagen N, Denmark
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21
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Sander AF, Lavstsen T, Rask TS, Lisby M, Salanti A, Fordyce SL, Jespersen JS, Carter R, Deitsch KW, Theander TG, Pedersen AG, Arnot DE. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families. Nucleic Acids Res 2013; 42:2270-81. [PMID: 24253306 PMCID: PMC3936766 DOI: 10.1093/nar/gkt1174] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens.
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Affiliation(s)
- Adam F Sander
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, Building 22 & 23, PO Box 2099, 1014 Copenhagen K, Denmark, Centre for Medical Parasitology, Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen K, Denmark, Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark, Institute of Infection and Immunology Research, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, UK and Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
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22
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Mathiasen DP, Gallina I, Germann SM, Hamou W, Eléouët M, Thodberg S, Eckert-Boulet N, Game J, Lisby M. Physical mapping and cloning of RAD56. Gene X 2013; 519:182-6. [DOI: 10.1016/j.gene.2013.01.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/16/2022] Open
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23
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Silva S, Gallina I, Eckert-Boulet N, Lisby M. Live cell microscopy of DNA damage response in Saccharomyces cerevisiae. Methods Mol Biol 2012; 920:433-443. [PMID: 22941621 DOI: 10.1007/978-1-61779-998-3_30] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescence microscopy of the DNA damage response in living cells stands out from many other DNA repair assays by its ability to monitor the response to individual DNA lesions in single cells. This is particularly true in yeast, where the frequency of spontaneous DNA lesions is relatively low compared to organisms with much larger genomes such as mammalian cells. Single cell analysis of individual DNA lesions allows specific events in the DNA damage response to be correlated with cell morphology, cell cycle phase, and other specific characteristics of a particular cell. Moreover, fluorescence live cell imaging allows for multiple cellular markers to be monitored over several hours. This chapter reviews useful fluorescent markers and genotoxic agents for studying the DNA damage response in living cells and provides protocols for live cell imaging, time-lapse microscopy, and for induction of site-specific DNA lesions.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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