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Cebrián J, Martínez V, Hernández P, Krimer DB, Martínez-Robles ML, Schvartzman JB, Fernández-Nestosa MJ. Electrophoretic Mobility Assay to Separate Supercoiled, Catenated, and Knotted DNA Molecules. Bio Protoc 2024; 14:e4983. [PMID: 38737504 PMCID: PMC11082789 DOI: 10.21769/bioprotoc.4983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024] Open
Abstract
Two-dimensional (2D) agarose gel electrophoresis is the method of choice to analyze DNA topology. The possibility to use E. coli strains with different genetic backgrounds in combination with nicking enzymes and different concentrations of norfloxacin improves the resolution of 2D gels to study the electrophoretic behavior of three different families of DNA topoisomers: supercoiled DNA molecules, post-replicative catenanes, and knotted DNA molecules. Here, we describe the materials and procedures required to optimize their separation by 2D gels. Understanding the differences in their electrophoretic behavior can help explain some important physical characteristics of these different types of DNA topoisomers. Key features • Preparative method to enrich DNA samples of supercoiled, catenated, and knotted families of topoisomers, later analyzed by 2D gels (or other techniques, e.g., microscopy). • 2D gels facilitate the separation of the topoisomers of any given circular DNA molecule. • Separation of DNA molecules with the same molecular masses but different shapes can be optimized by modifying the conditions of 2D gels. • Evaluating the roles of electric field and agarose concentration on the electrophoretic mobility of DNA topoisomers sheds light on their physical characteristics.
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Affiliation(s)
- Jorge Cebrián
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research (CSIC), Madrid, Spain
| | - Victor Martínez
- Polytechnic School, National University of Asuncion, San Lorenzo, Paraguay
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research (CSIC), Madrid, Spain
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research (CSIC), Madrid, Spain
| | - María-Luisa Martínez-Robles
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research (CSIC), Madrid, Spain
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research (CSIC), Madrid, Spain
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Cebrián J, Martínez V, Hernández P, Krimer DB, Fernández-Nestosa MJ, Schvartzman JB. Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates. BIOLOGY 2021; 10:biology10111195. [PMID: 34827187 PMCID: PMC8615216 DOI: 10.3390/biology10111195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary During replication, DNA molecules undergo topological changes that affect supercoiling, catenation and knotting. To better understand this process and the role of topoisomerases, the enzymes that control DNA topology in in vivo, two-dimensional agarose gel electrophoresis were used to investigate the efficiency of three type II DNA topoisomerases, the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α, on partially replicated bacterial plasmids containing replication forks stalled at specific sites. The results obtained revealed that despite the fact these DNA topoisomerases may have evolved to accomplish specific tasks, they share abilities. To our knowledge, this is the first time two-dimensional agarose gel electrophoresis have been used to examine the ability of these topoisomerases to relax supercoiling in the un-replicated region and unlink pre-catenanes in the replicated one of partially replicated molecules in vitro. The methodology described here can be used to study the role of different topoisomerases in partially replicated molecules. Abstract DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-TerE@AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli: DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro.
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Affiliation(s)
- Jorge Cebrián
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón, CIBERCV, 28040 Madrid, Spain
| | - Victor Martínez
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - María-José Fernández-Nestosa
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
- Correspondence:
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
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Tian T, Bu M, Chen X, Ding L, Yang Y, Han J, Feng XH, Xu P, Liu T, Ying S, Lei Y, Li Q, Huang J. The ZATT-TOP2A-PICH Axis Drives Extensive Replication Fork Reversal to Promote Genome Stability. Mol Cell 2020; 81:198-211.e6. [PMID: 33296677 DOI: 10.1016/j.molcel.2020.11.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/03/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
Replication fork reversal is a global response to replication stress in mammalian cells, but precisely how it occurs remains poorly understood. Here, we show that, upon replication stress, DNA topoisomerase IIalpha (TOP2A) is recruited to stalled forks in a manner dependent on the SNF2-family DNA translocases HLTF, ZRANB3, and SMARCAL1. This is accompanied by an increase in TOP2A SUMOylation mediated by the SUMO E3 ligase ZATT and followed by recruitment of a SUMO-targeted DNA translocase, PICH. Disruption of the ZATT-TOP2A-PICH axis results in accumulation of partially reversed forks and enhanced genome instability. These results suggest that fork reversal occurs via a sequential two-step process. First, HLTF, ZRANB3, and SMARCAL1 initiate limited fork reversal, creating superhelical strain in the newly replicated sister chromatids. Second, TOP2A drives extensive fork reversal by resolving the resulting topological barriers and via its role in recruiting PICH to stalled forks.
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Affiliation(s)
- Tian Tian
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Min Bu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xu Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Linli Ding
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinhua Han
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ting Liu
- Department of Cell Biology and Department of General Surgery of Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Lei
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qing Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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5
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Abstract
In all organisms, replication impairments are an important source of genome rearrangements, mainly because of the formation of double-stranded DNA (dsDNA) ends at inactivated replication forks. Three reactions for the formation of dsDNA ends at replication forks were originally described for Escherichia coli and became seminal models for all organisms: the encounter of replication forks with preexisting single-stranded DNA (ssDNA) interruptions, replication fork reversal, and head-to-tail collisions of successive replication rounds. Here, we first review the experimental evidence that now allows us to know when, where, and how these three different reactions occur in E. coli. Next, we recall our recent studies showing that in wild-type E. coli, spontaneous replication fork breakage occurs in 18% of cells at each generation. We propose that it results from the replication of preexisting nicks or gaps, since it does not involve replication fork reversal or head-to-tail fork collisions. In the recB mutant, deficient for double-strand break (DSB) repair, fork breakage triggers DSBs in the chromosome terminus during cell division, a reaction that is heritable for several generations. Finally, we recapitulate several observations suggesting that restart from intact inactivated replication forks and restart from recombination intermediates require different sets of enzymatic activities. The finding that 18% of cells suffer replication fork breakage suggests that DNA remains intact at most inactivated forks. Similarly, only 18% of cells need the helicase loader for replication restart, which leads us to speculate that the replicative helicase remains on DNA at intact inactivated replication forks and is reactivated by the replication restart proteins.
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Cebrián J, Castán A, Martínez V, Kadomatsu-Hermosa MJ, Parra C, Fernández-Nestosa MJ, Schaerer C, Hernández P, Krimer DB, Schvartzman JB. Direct Evidence for the Formation of Precatenanes during DNA Replication. J Biol Chem 2015; 290:13725-35. [PMID: 25829493 PMCID: PMC4447951 DOI: 10.1074/jbc.m115.642272] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
The dynamics of DNA topology during replication are still poorly understood. Bacterial plasmids are negatively supercoiled. This underwinding facilitates strand separation of the DNA duplex during replication. Leading the replisome, a DNA helicase separates the parental strands that are to be used as templates. This strand separation causes overwinding of the duplex ahead. If this overwinding persists, it would eventually impede fork progression. In bacteria, DNA gyrase and topoisomerase IV act ahead of the fork to keep DNA underwound. However, the processivity of the DNA helicase might overcome DNA gyrase and topoisomerase IV. It was proposed that the overwinding that builds up ahead of the fork could force it to swivel and diffuse this positive supercoiling behind the fork where topoisomerase IV would also act to maintain replicating the DNA underwound. Putative intertwining of sister duplexes in the replicated region are called precatenanes. Fork swiveling and the formation of precatenanes, however, are still questioned. Here, we used classical genetics and high resolution two-dimensional agarose gel electrophoresis to examine the torsional tension of replication intermediates of three bacterial plasmids with the fork stalled at different sites before termination. The results obtained indicated that precatenanes do form as replication progresses before termination.
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Affiliation(s)
- Jorge Cebrián
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Alicia Castán
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Víctor Martínez
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Maridian J Kadomatsu-Hermosa
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Cristina Parra
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - María José Fernández-Nestosa
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Christian Schaerer
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Pablo Hernández
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Dora B Krimer
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Jorge B Schvartzman
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
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7
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Replication forks reverse at high frequency upon replication stress in Physarum polycephalum. Chromosoma 2014; 123:577-85. [PMID: 24951952 DOI: 10.1007/s00412-014-0471-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/24/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
The addition of hydroxyurea after the onset of S phase allows replication to start and permits the successive detecting of replication-dependent joint DNA molecules and chicken foot structures in the synchronous nuclei of Physarum polycephalum. We find evidence for a very high frequency of reversed replication forks upon replication stress. The formation of these reversed forks is dependent on the presence of joint DNA molecules, the impediment of the replication fork progression by hydroxyurea, and likely on the propensity of some replication origins to reinitiate replication to counteract the action of this compound. As hydroxyurea treatment enables us to successively detect the appearance of joint DNA molecules and then of reversed replication forks, we propose that chicken foot structures are formed both from the regression of hydroxyurea-frozen joint DNA molecules and from hydroxyurea-stalled replication forks. These experiments underscore the transient nature of replication fork regression, which becomes detectable due to the hydroxyurea-induced slowing down of replication fork progression.
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8
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Abstract
DNA topology changes dynamically during DNA replication. Supercoiling, precatenation, catenation and knotting interplay throughout the process that is finely regulated by DNA topoisomerases. In the present article, we provide an overview of theoretical and experimental approaches to understand the interplay between various manifestations of topological constraints acting on replicating DNA molecules. Data discussed reveal that DNA entanglements (supercoils and catenanes) play an active role in preventing the formation of deleterious knots.
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9
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Sinha AK, Pavankumar TL, Kamisetty S, Mittal P, Ray MK. Replication arrest is a major threat to growth at low temperature in Antarctic Pseudomonas syringae Lz4W. Mol Microbiol 2013; 89:792-810. [PMID: 23815755 DOI: 10.1111/mmi.12315] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
Abstract
Chromosomal damage was detected previously in the recBCD mutants of the Antarctic bacterium Pseudomonas syringae Lz4W, which accumulated linear chromosomal DNA leading to cell death and growth inhibition at 4°C. RecBCD protein generally repairs DNA double-strand breaks by RecA-dependent homologous recombination pathway. Here we show that ΔrecA mutant of P. syringae is not cold-sensitive. Significantly, inactivation of additional DNA repair genes ruvAB rescued the cold-sensitive phenotype of ΔrecBCD mutant. The ΔrecA and ΔruvAB mutants were UV-sensitive as expected. We propose that, at low temperature DNA replication encounters barriers leading to frequent replication fork (RF) arrest and fork reversal. RuvAB binds to the reversed RFs (RRFs) having Holliday junction-like structures and resolves them upon association with RuvC nuclease to cause linearization of the chromosome, a threat to cell survival. RecBCD prevents this by degrading the RRFs, and facilitates replication re-initiation. This model is consistent with our observation that low temperature-induced DNA lesions do not evoke SOS response in P. syringae. Additional studies show that two other repair genes, radA (encoding a RecA paralogue) and recF are not involved in providing cold resistance to the Antarctic bacterium.
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Affiliation(s)
- Anurag K Sinha
- Centre for Cellular and Molecular Biology Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, India
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10
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Abstract
Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single-molecule field have led to the development of techniques that add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study that would be well suited for analysis with torsional measurement techniques.
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Affiliation(s)
- Scott Forth
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York 10065, USA.
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11
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Schvartzman JB, Martínez-Robles ML, Hernández P, Krimer DB. Plasmid DNA topology assayed by two-dimensional agarose gel electrophoresis. Methods Mol Biol 2013; 1054:121-132. [PMID: 23913288 DOI: 10.1007/978-1-62703-565-1_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two-dimensional (2D) agarose gel electrophoresis is nowadays one of the best methods available to analyze DNA molecules with different masses and shapes. The possibility to use nicking enzymes and intercalating agents to change the twist of DNA during only one or in both runs, improves the capacity of 2D gels to discern molecules that apparently may look alike. Here we present protocols where 2D gels are used to understand the structure of DNA molecules and its dynamics in living cells. This knowledge is essential to comprehend how DNA topology affects and is affected by all the essential functions that DNA is involved in: replication, transcription, repair and recombination.
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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12
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Lin YL, Pasero P. Interference between DNA replication and transcription as a cause of genomic instability. Curr Genomics 2012; 13:65-73. [PMID: 22942676 PMCID: PMC3269018 DOI: 10.2174/138920212799034767] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 11/22/2022] Open
Abstract
Replication and transcription are key aspects of DNA metabolism that take place on the same template and potentially interfere with each other. Conflicts between these two activities include head-on or co-directional collisions between DNA and RNA polymerases, which can lead to the formation of DNA breaks and chromosome rearrangements. To avoid these deleterious consequences and prevent genomic instability, cells have evolved multiple mechanisms preventing replication forks from colliding with the transcription machinery. Yet, recent reports indicate that interference between replication and transcription is not limited to physical interactions between polymerases and that other cotranscriptional processes can interfere with DNA replication. These include DNA-RNA hybrids that assemble behind elongating RNA polymerases, impede fork progression and promote homologous recombination. Here, we discuss recent evidence indicating that R-loops represent a major source of genomic instability in all organisms, from bacteria to human, and are potentially implicated in cancer development.
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Affiliation(s)
- Yea-Lih Lin
- Institute of Human Genetics, CNRS-UPR1142, Montpellier, France
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13
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López V, Martínez-Robles ML, Hernández P, Krimer DB, Schvartzman JB. Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication. Nucleic Acids Res 2011; 40:3563-73. [PMID: 22187153 PMCID: PMC3333868 DOI: 10.1093/nar/gkr1237] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA topology plays a crucial role in all living cells. In prokaryotes, negative supercoiling is required to initiate replication and either negative or positive supercoiling assists decatenation. The role of DNA knots, however, remains a mystery. Knots are very harmful for cells if not removed efficiently, but DNA molecules become knotted in vivo. If knots are deleterious, why then does DNA become knotted? Here, we used classical genetics, high-resolution 2D agarose gel electrophoresis and atomic force microscopy to show that topoisomerase IV (Topo IV), one of the two type-II DNA topoisomerases in bacteria, is responsible for the knotting and unknotting of sister duplexes during DNA replication. We propose that when progression of the replication forks is impaired, sister duplexes become loosely intertwined. Under these conditions, Topo IV inadvertently makes the strand passages that lead to the formation of knots and removes them later on to allow their correct segregation.
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Affiliation(s)
| | | | | | | | - Jorge B. Schvartzman
- *To whom correspondence should be addressed. Tel: +34 91 837 3112 (ext. 4232); Fax: +34 91 536 0432;
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14
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Abstract
DNA supercoiling plays essential role in maintaining proper chromosome structure, as well as the equilibrium between genome dynamics and stability under specific physicochemical and physiological conditions. In mesophilic organisms, DNA is negatively supercoiled and, until recently, positive supercoiling was considered a peculiar mark of (hyper)thermophilic archaea needed to survive high temperatures. However, several lines of evidence suggest that negative and positive supercoiling might coexist in both (hyper)thermophilic and mesophilic organisms, raising the possibility that positive supercoiling might serve as a regulator of various cellular events, such as chromosome condensation, gene expression, mitosis, sister chromatid cohesion, centromere identity and telomere homoeostasis.
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15
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Branzei D, Foiani M. Maintaining genome stability at the replication fork. Nat Rev Mol Cell Biol 2010; 11:208-19. [PMID: 20177396 DOI: 10.1038/nrm2852] [Citation(s) in RCA: 610] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aberrant DNA replication is a major source of the mutations and chromosome rearrangements that are associated with pathological disorders. When replication is compromised, DNA becomes more prone to breakage. Secondary structures, highly transcribed DNA sequences and damaged DNA stall replication forks, which then require checkpoint factors and specialized enzymatic activities for their stabilization and subsequent advance. These mechanisms ensure that the local DNA damage response, which enables replication fork progression and DNA repair in S phase, is coupled with cell cycle transitions. The mechanisms that operate in eukaryotic cells to promote replication fork integrity and coordinate replication with other aspects of chromosome maintenance are becoming clear.
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Affiliation(s)
- Dana Branzei
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan, Italy.
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16
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Witz G, Stasiak A. DNA supercoiling and its role in DNA decatenation and unknotting. Nucleic Acids Res 2010; 38:2119-33. [PMID: 20026582 PMCID: PMC2853108 DOI: 10.1093/nar/gkp1161] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/17/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022] Open
Abstract
Chromosomal and plasmid DNA molecules in bacterial cells are maintained under torsional tension and are therefore supercoiled. With the exception of extreme thermophiles, supercoiling has a negative sign, which means that the torsional tension diminishes the DNA helicity and facilitates strand separation. In consequence, negative supercoiling aids such processes as DNA replication or transcription that require global- or local-strand separation. In extreme thermophiles, DNA is positively supercoiled which protects it from thermal denaturation. While the role of DNA supercoiling connected to the control of DNA stability, is thoroughly researched and subject of many reviews, a less known role of DNA supercoiling emerges and consists of aiding DNA topoisomerases in DNA decatenation and unknotting. Although DNA catenanes are natural intermediates in the process of DNA replication of circular DNA molecules, it is necessary that they become very efficiently decatenated, as otherwise the segregation of freshly replicated DNA molecules would be blocked. DNA knots arise as by-products of topoisomerase-mediated intramolecular passages that are needed to facilitate general DNA metabolism, including DNA replication, transcription or recombination. The formed knots are, however, very harmful for cells if not removed efficiently. Here, we overview the role of DNA supercoiling in DNA unknotting and decatenation.
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Affiliation(s)
- Guillaume Witz
- Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne and Laboratoire de Physique de la Matière Vivante, Faculté des Sciences de Base, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne and Laboratoire de Physique de la Matière Vivante, Faculté des Sciences de Base, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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Schvartzman JB, Martínez-Robles ML, Hernández P, Krimer DB. Plasmid DNA replication and topology as visualized by two-dimensional agarose gel electrophoresis. Plasmid 2009; 63:1-10. [PMID: 19925824 DOI: 10.1016/j.plasmid.2009.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/10/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022]
Abstract
During the last 20 years, two-dimensional agarose gel electrophoresis combined with other techniques such as Polymerase Chain Reaction, helicase assay and electron microscopy, helped to characterize plasmid DNA replication and topology. Here we describe some of the most important findings that were made using this method including the characterization of uni-directional replication, replication origin interference, DNA breakage at the forks, replication fork blockage, replication knotting, replication fork reversal, the interplay of supercoiling and catenation and other changes in DNA topology that take place as replication progresses.
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Affiliation(s)
- J B Schvartzman
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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18
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Hyrien O. Topological analysis of plasmid DNA replication intermediates using two-dimensional agarose gels. Methods Mol Biol 2009; 521:139-67. [PMID: 19563105 DOI: 10.1007/978-1-60327-815-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
A fundamental process in DNA replication is the disentangling of the two parental strands by DNA topoisomerases. In this chapter, I detail the topological analysis of plasmid replication intermediates using two-dimensional (2D) agarose gels. The method can resolve replication intermediates according to mass and topology, and can resolve unlinked monomeric circles from catenated dimers of varying topology. The method has been used, alone or in combination with a procedure for purifying covalent protein-DNA complexes, to analyse the effect oftopoisomerase inhibitors on the topology of replication intermediates, to map the location of drug-stabilized topoisomerase cleavage complexes with respect to replication forks and to detect the breakage and repair of replication forks following collision with cleavage complexes. Other applications include the detection of knots that form independently of, or concomitantly with, DNA replication.
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Affiliation(s)
- Olivier Hyrien
- Genetique Moleculaire, Ecole Normale Supérieure, Paris, France
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Martínez-Robles ML, Witz G, Hernández P, Schvartzman JB, Stasiak A, Krimer DB. Interplay of DNA supercoiling and catenation during the segregation of sister duplexes. Nucleic Acids Res 2009; 37:5126-37. [PMID: 19553196 PMCID: PMC2731910 DOI: 10.1093/nar/gkp530] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as a result of DNA replication in Escherichia coli cells whose topoisomerase IV activity was inhibited. We combined high-resolution two-dimensional agarose gel electrophoresis with numerical simulations in order to better understand the relationship between the negative supercoiling of DNA generated by DNA gyrase and the DNA interlinking resulting from replication of circular DNA molecules. We showed that in those replication intermediates formed in vivo, catenation and negative supercoiling compete with each other. In interlinked molecules with high catenation numbers negative supercoiling is greatly limited. However, when interlinking decreases, as required for the segregation of newly replicated sister duplexes, their negative supercoiling increases. This observation indicates that negative supercoiling plays an active role during progressive decatenation of newly replicated DNA molecules in vivo.
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Affiliation(s)
- María Luisa Martínez-Robles
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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20
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SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet repeats by restraining recombination. Nat Struct Mol Biol 2009; 16:159-67. [PMID: 19136956 DOI: 10.1038/nsmb.1544] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 12/04/2008] [Indexed: 01/30/2023]
Abstract
Several molecular mechanisms have been proposed to explain trinucleotide repeat expansions. Here we show that in yeast srs2Delta cells, CTG repeats undergo both expansions and contractions, and they show increased chromosomal fragility. Deletion of RAD52 or RAD51 suppresses these phenotypes, suggesting that recombination triggers trinucleotide repeat instability in srs2Delta cells. In sgs1Delta cells, CTG repeats undergo contractions and increased fragility by a mechanism partially dependent on RAD52 and RAD51. Analysis of replication intermediates revealed abundant joint molecules at the CTG repeats during S phase. These molecules migrate similarly to reversed replication forks, and their presence is dependent on SRS2 and SGS1 but not RAD51. Our results suggest that Srs2 promotes fork reversal in repetitive sequences, preventing repeat instability and fragility. In the absence of Srs2 or Sgs1, DNA damage accumulates and is processed by homologous recombination, triggering repeat rearrangements.
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21
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 334] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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Fierro-Fernández M, Hernández P, Krimer DB, Schvartzman JB. Replication fork reversal occurs spontaneously after digestion but is constrained in supercoiled domains. J Biol Chem 2007; 282:18190-18196. [PMID: 17456472 DOI: 10.1074/jbc.m701559200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication fork reversal was investigated in undigested and linearized replication intermediates of bacterial DNA plasmids containing a stalled fork. Two-dimensional agarose gel electrophoresis, a branch migration and extrusion assay, electron microscopy, and DNA-psoralen cross-linking were used to show that extensive replication fork reversal and extrusion of the nascent-nascent duplex occurs spontaneously after DNA nicking and restriction enzyme digestion but that fork retreat is severely limited in covalently closed supercoiled domains.
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Affiliation(s)
- Marta Fierro-Fernández
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Hernández
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Dora B Krimer
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge B Schvartzman
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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