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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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2
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Prada-Luengo I, Møller HD, Henriksen RA, Gao Q, Larsen C, Alizadeh S, Maretty L, Houseley J, Regenberg B. Replicative aging is associated with loss of genetic heterogeneity from extrachromosomal circular DNA in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:7883-7898. [PMID: 32609810 PMCID: PMC7430651 DOI: 10.1093/nar/gkaa545] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 05/28/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular DNA in Saccharomyces cerevisiae populations sampled when young and after extensive aging. Young cells possessed highly diverse circular DNA populations but 94% of the circular DNA were lost after ∼15 divisions, whereas rDNA circles underwent massive accumulation to >95% of circular DNA. Circles present in both young and old cells were characterized by replication origins including circles from unique regions of the genome and repetitive regions: rDNA and telomeric Y' regions. We further observed that circles can have flexible inheritance patterns: [HXT6/7circle] normally segregates to mother cells but in low glucose is present in up to 50% of cells, the majority of which must have inherited this circle from their mother. Interestingly, [HXT6/7circle] cells are eventually replaced by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting circular DNAs are intermediates in chromosomal amplifications. In conclusion, the heterogeneity of circular DNA offers flexibility in adaptation, but this heterogeneity is remarkably diminished with age.
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Affiliation(s)
- Iñigo Prada-Luengo
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Henrik D Møller
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zurich CH-8093, Switzerland
| | - Rasmus A Henriksen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Qian Gao
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge CB22 3-AT, UK
- Adaptimmune Ltd, Oxfordshire OX14 4RX, UK
| | - Camilla Eggert Larsen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Sefa Alizadeh
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Jonathan Houseley
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge CB22 3-AT, UK
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
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3
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Mehanna P, Gagné V, Lajoie M, Spinella JF, St-Onge P, Sinnett D, Brukner I, Krajinovic M. Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines. PLoS One 2017; 12:e0184365. [PMID: 28877255 PMCID: PMC5587290 DOI: 10.1371/journal.pone.0184365] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified. They are on average 100 to 400 bp long and are derived from unique non-repetitive genomic regions with high gene density. MicroDNAs are thought to arise from DNA breaks associated with RNA metabolism or replication slippage. Given the paucity of information on this entirely novel phenomenon, we aimed to get an additional insight into microDNA features by performing the microDNA analysis in 20 independent human lymphoblastoid cell lines (LCLs) prior and after treatment with chemotherapeutic drugs. The results showed non-random genesis of microDNA clusters from the active regions of the genome. The size periodicity of 190 bp was observed, which matches DNA fragmentation typical for apoptotic cells. The chemotherapeutic drug-induced apoptosis of LCLs increased both number and size of clusters further suggesting that part of microDNAs could result from the programmed cell death. Interestingly, proportion of identified microDNA sequences has common loci of origin when compared between cell line experiments. While compatible with the original observation that microDNAs originate from a normal physiological process, obtained results imply complementary source of its production. Furthermore, non-random genesis of microDNAs depicted by redundancy between samples makes these entities possible candidates for new biomarker generation.
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Affiliation(s)
- Pamela Mehanna
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Vincent Gagné
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Mathieu Lajoie
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | | | - Pascal St-Onge
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
| | - Ivan Brukner
- Molecular Diagnostics Laboratory, Jewish General Hospital, McGill University, Montreal, Montreal, Qc, Canada
| | - Maja Krajinovic
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- * E-mail:
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4
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Abstract
DNA repair is essential to maintain genomic integrity and initiate genetic diversity. While gene conversion and classical nonhomologous end-joining are the most physiologically predominant forms of DNA repair mechanisms, emerging lines of evidence suggest the usage of several noncanonical homology-directed repair (HDR) pathways in both prokaryotes and eukaryotes in different contexts. Here we review how these alternative HDR pathways are executed, specifically focusing on the determinants that dictate competition between them and their relevance to cancers that display complex genomic rearrangements or maintain their telomeres by homology-directed DNA synthesis.
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5
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Mourier T. Transposable elements and circular DNAs. Mob Genet Elements 2016; 6:e1240748. [PMID: 28090380 PMCID: PMC5173269 DOI: 10.1080/2159256x.2016.1240748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 01/06/2023] Open
Abstract
Circular DNAs are extra-chromosomal fragments that become circularized by genomic recombination events. We have recently shown that yeast LTR elements generate circular DNAs through recombination events between their flanking long terminal repeats (LTRs). Similarly, circular DNAs can be generated by recombination between LTRs residing at different genomic loci, in which case the circular DNA will contain the intervening sequence. In yeast, this can result in gene copy number variations when circles contain genes and origins of replication. Here, I speculate on the potential and implications of circular DNAs generated through recombination between human transposable elements.
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Affiliation(s)
- Tobias Mourier
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
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6
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Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2015; 6:453-62. [PMID: 26681518 PMCID: PMC4751563 DOI: 10.1534/g3.115.025858] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extrachromosomal linear DNA during the transpositional life cycle of retrotransposons, or from circularization of genomic Ty DNA. Circularization may happen through nonhomologous end-joining (NHEJ) of long terminal repeats (LTRs) flanking Ty elements, by Ty autointegration, or by LTR–LTR recombination. By performing an in-depth investigation of sequence reads stemming from Ty eccDNAs obtained from populations of Saccharomyces cerevisiae S288c, we find that eccDNAs predominantly correspond to full-length Ty1 elements. Analyses of sequence junctions reveal no signs of NHEJ or autointegration events. We detect recombination junctions that are consistent with yeast Ty eccDNAs being generated through recombination events within the genome. This opens the possibility that retrotransposable elements could move around in the genome without an RNA intermediate directly through DNA circularization.
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7
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Morrish TA, Bekbolysnov D, Velliquette D, Morgan M, Ross B, Wang Y, Chaney B, McQuigg J, Fager N, Maine IP. Multiple Mechanisms Contribute To Telomere Maintenance. JOURNAL OF CANCER BIOLOGY & RESEARCH 2013; 1:1012. [PMID: 25285314 PMCID: PMC4181876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The unlimited growth potential of tumors depends on telomere maintenance and typically depends on telomerase, an RNA-dependent DNA polymerase, which reverse transcribes the telomerase RNA template, synthesizing telomere repeats at the ends of chromosomes. Studies in various model organisms genetically deleted for telomerase indicate that several recombination-based mechanisms also contribute to telomere maintenance. Understanding the molecular basis of these mechanisms is critical since some human tumors form without telomerase, yet the sequence is maintained at the telomeres. Recombination-based mechanisms also likely contribute at some frequency to telomere maintenance in tumors expressing telomerase. Preventing telomere maintenance is predicted to impact tumor growth, yet inhibiting telomerase may select for the recombination-based mechanisms. Telomere recombination mechanisms likely involve altered or unregulated pathways of DNA repair. The use of some DNA damaging agents may encourage the use of these unregulated pathways of DNA repair to be utilized and may allow some tumors to generate resistance to these agents depending on which repair pathways are altered in the tumors. This review will discuss the various telomere recombination mechanisms and will provide rationale regarding the possibility that L1 retrotransposition may contribute to telomere maintenance in tumors lacking telomerase.
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Affiliation(s)
- Tammy A. Morrish
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Dulat Bekbolysnov
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
- Graduate Program in Microbiology and Immunology, University of Toledo, Toledo, OH 43614 USA
| | - David Velliquette
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Michelle Morgan
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Bryan Ross
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Yongheng Wang
- Department of Biological Sciences, University of Toledo, OH 43614, USA
| | - Benjamin Chaney
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Jessica McQuigg
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Nathan Fager
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
| | - Ira P. Maine
- Department of Biochemistry and Cancer Biology, University of Toledo, Toledo, OH 43614, USA
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8
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Galeote V, Bigey F, Beyne E, Novo M, Legras JL, Casaregola S, Dequin S. Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation. PLoS One 2011; 6:e17872. [PMID: 21423766 PMCID: PMC3053389 DOI: 10.1371/journal.pone.0017872] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/11/2011] [Indexed: 11/18/2022] Open
Abstract
We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Chromosome Breakpoints
- Chromosomes, Fungal/genetics
- DNA, Circular/genetics
- DNA, Fungal/genetics
- Diploidy
- Electrophoresis, Gel, Pulsed-Field
- Evolution, Molecular
- Extrachromosomal Inheritance/genetics
- Gene Amplification/genetics
- Gene Dosage/genetics
- Genetic Variation
- Genome, Fungal/genetics
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Insertional/genetics
- Saccharomyces cerevisiae/genetics
- Wine/microbiology
- Zygosaccharomyces/genetics
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Affiliation(s)
| | - Frédéric Bigey
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
| | | | - Maite Novo
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
| | | | - Serge Casaregola
- CIRM-Levures, INRA, UMR1319 Micalis, AgroParisTech, Thiverval-Grignon, France
| | - Sylvie Dequin
- INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France
- * E-mail:
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9
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Abstract
When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a "roll and spread" mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.
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10
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Larrivée M, Wellinger RJ. Telomerase- and capping-independent yeast survivors with alternate telomere states. Nat Cell Biol 2006; 8:741-7. [PMID: 16767083 DOI: 10.1038/ncb1429] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Accepted: 05/11/2006] [Indexed: 11/09/2022]
Abstract
Maintaining telomeric DNA at chromosome ends is essential for genome stability. In virtually all organisms the telomerase enzyme provides this function; however, telomerase-independent mechanisms also exist. These latter mechanisms rely on recombination pathways to replenish telomeric DNA and extrachromosomal DNA may also be implicated. Here, we report that in Saccharomyces cerevisiae cells, extrachromosomal circular DNA occurs for both subtypes of telomerase-independent telomere-maintenance mechanisms. This DNA consists of circular molecules of full-length subtelomeric repeat elements in type I cells, and very heterogeneously sized circles of telomeric repeat DNA in type II cells that are at least partially single stranded. Surprisingly, both type I and type II cells can adapt to a loss of the normally essential telomere-capping protein Cdc13p by inducing an alternate and reversible state of chromosome ends. Chromosome capping, therefore, is not strictly dependent on canonical capping proteins, such as Cdc13p, but can be achieved by alternate mechanisms.
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Affiliation(s)
- Michel Larrivée
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
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11
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Nosek J, Tomáška Ľ, Kucejová B. The chromosome end replication: lessons from mitochondrial genetics. J Appl Biomed 2004. [DOI: 10.32725/jab.2004.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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12
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Tomaska L, McEachern MJ, Nosek J. Alternatives to telomerase: keeping linear chromosomes via telomeric circles. FEBS Lett 2004; 567:142-6. [PMID: 15165907 DOI: 10.1016/j.febslet.2004.04.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 04/15/2004] [Accepted: 04/19/2004] [Indexed: 11/16/2022]
Abstract
Recombination is often capable of lengthening telomeres in situations where telomerase is absent. This recombinational telomere maintenance is often accompanied by telomeric instability including the accumulation of extrachromosomal telomeric circles (t-circles). Recent results of in vivo and in vitro experiments have suggested that t-circles can lead to the production of extended stretches of telomeric DNA by serving as templates for rolling-circle synthesis. This implies that t-circles can provide an efficient means of telomere elongation. The existence of t-circles in both nuclear and mitochondrial compartments of distantly related species suggests that they may be important contributors to an evolutionary conserved telomerase-independent mechanism of maintenance of telomeric tandem arrays.
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Affiliation(s)
- Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina B-1, 84215 Bratislava, Slovakia.
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13
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Bechter OE, Zou Y, Shay JW, Wright WE. Homologous recombination in human telomerase-positive and ALT cells occurs with the same frequency. EMBO Rep 2003; 4:1138-43. [PMID: 14618159 PMCID: PMC1326419 DOI: 10.1038/sj.embor.7400027] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 09/24/2003] [Accepted: 09/23/2003] [Indexed: 11/09/2022] Open
Abstract
Homologous recombination is thought to be the molecular mechanism for maintaining telomere length in alternative lengthening of telomeres (ALT) cells. We used a recombination reporter system to show that the frequency of homologous recombination is the same for ALT- and telomerase-positive cells, suggesting that if ALT cells have a recombination defect it specifically involves telomeric sequences. We compared internal and telomere-adjacent positions of our reporter construct to investigate if telomeric sequences near an induced double-strand break alter the frequency of recombination between nontelomeric sequences, and found no differences among the different cell lines analysed. Our results indicate that the underlying defect in homologous recombination in ALT cells does not affect sequences independent of their chromosomal location but is likely to be primarily a specific telomeric defect.
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Affiliation(s)
- Oliver E Bechter
- Department of Cell Biology, Southwestern Medical
Center, The University of Texas, Dallas, Texas,
USA
- Department of Cell Biology, Southwestern Medical
Center, The University of Texas, 5323 Harry Hines Blvd,
Dallas, Texas 75390-9039, USA
| | - Ying Zou
- Department of Cell Biology, Southwestern Medical
Center, The University of Texas, Dallas, Texas,
USA
| | - Jerry W Shay
- Department of Cell Biology, Southwestern Medical
Center, The University of Texas, Dallas, Texas,
USA
| | - Woodring E Wright
- Department of Cell Biology, Southwestern Medical
Center, The University of Texas, Dallas, Texas,
USA
- Tel: +1 214 648 8694; Fax: +1 214 648 8694; E-mail:
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14
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Curcio MJ, Derbyshire KM. The outs and ins of transposition: from Mu to Kangaroo. Nat Rev Mol Cell Biol 2003; 4:865-77. [PMID: 14682279 DOI: 10.1038/nrm1241] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M Joan Curcio
- Laboratory of Developmental Genetics, Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University of New York at Albany, 12201-2002, USA
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15
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Abstract
Instability and plasticity of telomeric DNA, which includes extrachromosomal DNA, are usually correlated with the absence of telomerase and with abnormal growth of mammalian cells. Here, we show the formation of extrachromosomal circular DNA of telomeric repeats (tel-eccDNA) during the development of Xenopus laevis. Tel-eccDNA is double-stranded relaxed circles composed of the vertebrate consensus telomeric repeats [TTAGGG](n). Its size varies from <2 to >20 kb and it comprises up to 10% of the total cellular telomere content of the early embryo (pre-MBT stage). The amount of tel-eccDNA is reduced in later developmental stages and in adult tissues. Using a cell-free system derived from Xenopus egg extracts, we show that tel-eccDNA can be formed de novo from the telomere chromosomal tracts of sperm nuclei and naked DNA in a replication-independent manner. These results reveal an unusual plasticity of telomeric DNA during normal development of Xenopus.
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Affiliation(s)
- Sarit Cohen
- Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France
- Present address: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcel Méchali
- Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France
- Tel: +33 (4) 99 61 99 17; Fax: +33 (4) 99 61 99 20;
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16
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Fu G, Melville SE. Polymorphism in the subtelomeric regions of chromosomes of Kinetoplastida. Trans R Soc Trop Med Hyg 2002; 96 Suppl 1:S31-40. [PMID: 12055849 DOI: 10.1016/s0035-9203(02)90049-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Leishmania spp. and the related kinetoplastid Trypanosoma brucei are single-celled parasites. In Leishmania, the nuclear genome comprises 36 diploid chromosomes and occasional amplified minichromosomes, while the T. brucei nucleus contains 11 larger diploid chromosomes and a variable number of intermediate-sized and minichromosomes. This paper primarily describes the subtelomeric structure of the larger diploid chromosomes of L. major and T. brucei, although some aspects may also apply to smaller chromosomes. The diploid chromosomes contain most protein-coding genes and vary in size. The telomeric sequence is common to both species, but adjacent subtelomeric repeats vary between species and chromosomes. It is possible that some of the complex repeats described here play a role in stabilizing replication and copy number of the chromosomes. The subtelomeric regions of T. brucei chromosomes differ from those of other protozoan parasites, as they are dedicated to expression sites for variant surface glycoprotein genes, used by the parasite to evade immune destruction by antigenic variation. Variation in these sites creates segmental aneuploidy in many T. brucei chromosomes.
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Affiliation(s)
- Guoliang Fu
- Imperial College School of Medicine, Hammersmith Hospital, London, W12 0NN, UK
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17
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Abstract
Recombination-dependent maintenance of telomeres, first discovered in budding yeast, has revealed an alternative pathway for telomere maintenance that does not require the enzyme telomerase. Experiments conducted in two budding yeasts, S. cerevisiae and K. lactis, have shown recombination can replenish terminal G-rich telomeric tracts that would otherwise shorten in the absence of telomerase, as well as disperse and amplify sub-telomeric repeat elements. Investigation of the genetic requirements for this process have revealed that at least two different recombination pathways, defined by RAD50 and RAD51, can promote telomere maintenance. Although critically short telomeres are very recombinogenic, recombination among telomeres that have only partially shortened in the absence of telomerase can also contribute to telomerase-independent survival. These observations provide new insights into the mechanism(s) by which recombination can restore telomere function in yeast, and suggest future experiments for the investigation of potentially similar pathways in human cells.
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Affiliation(s)
- Victoria Lundblad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, TX 77030, USA.
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18
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Abstract
Telomeres are DNA and protein structures that form complexes protecting the ends of chromosomes. Understanding of the mechanisms maintaining telomeres and insights into their function have advanced considerably in recent years. This review summarizes the currently known components of the telomere/telomerase functional complex, and focuses on how they act in the control of processes occurring at telomeres. These include processes acting on the telomeric DNA and on telomeric proteins. Key among them are DNA replication and elongation of one telomeric DNA strand by telomerase. In some situations, homologous recombination of telomeric and subtelomeric DNA is induced. All these processes act to replenish or restore telomeres. Conversely, degradative processes that shorten telomeric DNA, and nonhomologous end-joining of telomeric DNA, can lead to loss of telomere function and genomic instability. Hence they too must normally be tightly controlled.
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Affiliation(s)
- M J McEachern
- University of Georgia, Department of Genetics, Athens, Georgia, 30602, USA.
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19
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Abstract
Although many cellular and organismal changes have been described in aging individuals, a precise, molecular cause of aging has yet to be found. A prior study of aging yeast mother cells showed a progressive enlargement and fragmentation of the nucleolus. Here we show that these nucleolar changes are likely due to the accumulation of extrachromosomal rDNA circles (ERCs) in old cells and that, in fact, ERCs cause aging. Mutants for sgs1, the yeast homolog of the Werner's syndrome gene, accumulate ERCs more rapidly, leading to premature aging and a shorter life span. We speculate on the generality of this molecular cause of aging in higher species, including mammals.
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Affiliation(s)
- D A Sinclair
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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20
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Nosek J, Dinouël N, Kovac L, Fukuhara H. Linear mitochondrial DNAs from yeasts: telomeres with large tandem repetitions. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:61-72. [PMID: 7715605 DOI: 10.1007/bf00425822] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The terminal structure of the linear mitochondrial DNA (mtDNA) from the yeast Candida parapsilosis was investigated. This mtDNA, 30 kb long, has symmetrical ends forming inverted terminal repeats. These repeats are made up of a variable number of tandemly repeating units of 738 bp each; the terminal nucleotide corresponds to a precise position within the last repeat unit sequence. The ends had an open structure accessible to enzymes, with a 5' single-stranded extension of about 110 nucleotides. No circular forms were detected in the DNA preparations. Two other unrelated species, Pichia philodendra and Candida salmanticensis also appear to have a linear mtDNA of similar organization. These linear DNAs (which we name Type 2 linear mtDNAs) are distinct from the previously described linear mtDNAs of yeasts whose termini are formed by a closed hairpin loop (Type 1 linear mtDNA). The terminal structure of C. parapsilosis mtDNA is reminiscent of the linear mitochondrial genomes of the ciliate Tetrahymena although, in the latter, the telomeric tandem repeat unit is considerably shorter.
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Affiliation(s)
- J Nosek
- Institut Curie, Section de Biologie, Centre universitaire Paris XI, Orsay, France
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21
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Abstract
Extensive genome plasticity in Plasmodium involves frequent loss of dispensable functions under non-selective conditions, polymorphisms in subtelomeric repetitive regions, as well as rapid and apparently concerted variation in the intra-genic repetitive arrays that are typical of plasmodial antigen genes. As an example of the latter type of variation, the region of the merozoite surface antigen gene MSA-1 of Plasmodium falciparum, which encodes a tri-peptide repeat, is analysed in detail. The example illustrates how evasion of the immune defenses of the vertebrate host can be achieved through repeat homogenization mechanisms, acting at the DNA level, and leading to rapid fixation of variant epitopes. The remarkable ability of Plasmodia to utilize mechanisms which operate on its own nuclear DNA in the course of mitotic multiplication is discussed against the need of life cycle closure as a haploid unicellular. The possibility is suggested that active genomic diversification in a (clonal) multicellular population evolved as an adaptive tool.
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Affiliation(s)
- C Frontali
- Laboratorio di Biologia Cellulare, Istituto Superiore di Sanità, Rome, Italy
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22
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Abstract
Yeast cells lacking a functional EST1 gene show progressive shortening of the terminal G1-3T telomeric repeats and a parallel increase in the frequency of cell death. Although the majority of the cells in an est1- culture die, a minor subpopulation survives the potentially lethal consequences of the est1 mutation. We show that these est1- survivors arise as a result of the amplification and acquisition of subtelomeric elements (and their deletion derivatives) by a large number of telomeres. Hence, even when the primary pathway for telomere replication is defective, an alternative backup pathway can restore telomere function and keep the cell alive.
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Affiliation(s)
- V Lundblad
- Department of Microbiology and Immunology University of California, San Francisco 94143-0414
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23
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Abstract
The advent of pulsed field electrophoresis has allowed a direct approach to the karyotype of Leishmania. The molecular karyotype thus obtained is a stable characteristic of a given strain, although minor modifications may occur during in vitro maintenance. Between 20 and 28 chromosomal bands can be resolved depending on the strain, ranging in size from approximately 250 to 2600 kb. The technique has revealed a striking degree of polymorphism in the size and number of the chromosomal bands between different strains, and this seems independent of the category (species, zymodeme, population) to which the strains belong. It appears that only certain strains originating from the same geographic area may share extensive similarities. This polymorphism can largely be accounted for by chromosome size variations, which can involve up to 25% of the chromosome length. As a result, homologous chromosomes can exist in versions of markedly different size within the same strain. When this occurs with several different chromosomes, the interpretation of PFE patterns appears difficult without prior identification of the size-variable chromosomes and of the chromosome homologies. DNA deletions and amplifications have been shown to account for some of these size modifications, but other mechanisms are probably involved; nevertheless, interchromosomal exchange does not seem to play a major role in these polymorphisms. These chromosomal rearrangements, yet in an early stage of characterization, exhibit two relevant features: they seem (1) to affect essentially the subtelomeric regions and (2) to occur in a recurrent nonrandom manner. Chromosomal rearrangements sharing the same characteristics have been identified in yeast and other protozoa such as Trypanosoma and Plasmodium. The significance of this hypervariability for the biology of the parasite remains unknown, but it can be expected that such mechanisms have been maintained for some purpose; genes specifically located near chromosome ends might benefit from rapid sequence change, alternating activation, or polymorphism of expression. The chromosomal plasticity could represent a general mode of mutation in these parasites, in parallel with genetic exchange which may be uncommon in nature. The molecular characterization of these rearrangements, the identification of each chromosome with the help of physical restriction maps and linkage maps, and the collation of such data on a number of strains and species should allow a significant progress in the understanding of the genetics of Leishmania, in particular as regards ploidy, generation of phenotypic diversity, and genome evolution. Finally, like other models, this is susceptible to improve our knowledge of DNA-DNA interactions and of the chromosome functional structure and dynamics.
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Affiliation(s)
- P Bastien
- Laboratoire d'Ecologie Médicale et Pathologie Parasitaire, Annexe de la Faculté de Médecine, Montpellier, France
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24
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Abstract
The DNA of telomeres--the terminal DNA-protein complexes of chromosomes--differs notably from other DNA sequences in both structure and function. Recent work has highlighted its remarkable mode of synthesis by the ribonucleoprotein reverse transcriptase, telomerase, as well as its ability to form unusual structures in vitro. Moreover, telomere synthesis by telomerase has been shown to be essential for telomere maintenance and long-term viability.
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25
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Gottschling DE, Aparicio OM, Billington BL, Zakian VA. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 1990; 63:751-62. [PMID: 2225075 DOI: 10.1016/0092-8674(90)90141-z] [Citation(s) in RCA: 1064] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
S. cerevisiae chromosomes end with the telomeric repeat (TG1-3)n. When any of four Pol II genes was placed immediately adjacent to the telomeric repeats, expression of the gene was reversibly repressed as demonstrated by phenotype and mRNA analyses. For example, cells bearing a telomere-linked copy of ADE2 produced predominantly red colonies (a phenotype characteristic of ade2- cells) containing white sectors (characteristic of ADE2+ cells). Repression was due to proximity to the telomere itself since an 81 bp tract of (TG1-3)n positioned downstream of URA3 when URA3 was approximately 20 kb from the end of chromosome VII did not alter expression of the gene. However, this internal tract of (TG1-3)n could spontaneously become telomeric, in which case expression of the URA3 gene was repressed. These data demonstrate that yeast telomeres exert a position effect on the transcription of nearby genes, an effect that is under epigenetic control.
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Affiliation(s)
- D E Gottschling
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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26
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Biessmann H, Mason JM, Ferry K, d'Hulst M, Valgeirsdottir K, Traverse KL, Pardue ML. Addition of telomere-associated HeT DNA sequences "heals" broken chromosome ends in Drosophila. Cell 1990; 61:663-73. [PMID: 2111731 DOI: 10.1016/0092-8674(90)90478-w] [Citation(s) in RCA: 203] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Stocks of D. melanogaster X chromosomes carrying terminal deletions (RT chromosomes) have been maintained for several years. Some of the chromosomes are slowly losing DNA from the broken ends (as expected if replication is incomplete) and show no telomere-associated DNA added to the receding ends. Two stocks carry chromosomes that have become "healed" and are no longer losing DNA. In both stocks the broken chromosome end has acquired a segment of HeT DNA, a family of complex repeats found only at telomeres and in pericentric heterochromatin. Although the HeT family is complex, the HeT sequence joined to the broken chromosome end is the same in both stocks. In contrast, the two chromosomes are broken in different places and have no detectable sequence similarity at the junction with the new DNA. Sequence analysis suggests that the new telomere sequences have been added by a specific mechanism that does not involve homologous recombination.
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Affiliation(s)
- H Biessmann
- Developmental Biology Center, University of California, Irvine 92717
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27
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Dore E, Pace T, Ponzi M, Picci L, Frontali C. Organization of subtelomeric repeats in Plasmodium berghei. Mol Cell Biol 1990; 10:2423-7. [PMID: 2183034 PMCID: PMC360592 DOI: 10.1128/mcb.10.5.2423-2427.1990] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several (but not all) Plasmodium berghei chromosomes bear in the subtelomeric position a cluster of 2.3-kilobase (kb) tandem repeats. The 2.3-kb unit contains 160 base pairs of telomeric sequence. The resulting subtelomeric structure is one in which stretches of telomeric sequences are periodically spaced by a 2.1-kb reiterated sequence. This periodic organization of internal telomeric sequences might be related to chromosome-size polymorphisms involving the loss or addition of subtelomeric 2.3-kb units.
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Affiliation(s)
- E Dore
- Laboratory of Cell Biology, Istituto Superiore di Sanità, Rome, Italy
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28
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Constable A, Feipeng L, Walmsley RM. Yeast telomere length varies in response to changes in the amount of polyC1-3A in the cell. MOLECULAR & GENERAL GENETICS : MGG 1990; 221:280-2. [PMID: 2196434 DOI: 10.1007/bf00261732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Yeast chromosomes terminate in a GC-rich tail of DNA. Previous investigations have shown that the length of this tail can change in response to genetic variation. Here we present data that show that the length can also alter in response to changes in the amount of the GC-rich DNA found elsewhere in the nucleus.
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Affiliation(s)
- A Constable
- Department of Biochemistry and Applied Molecular Biology, University of Manchester, England
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29
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Louis EJ, Haber JE. The subtelomeric Y' repeat family in Saccharomyces cerevisiae: an experimental system for repeated sequence evolution. Genetics 1990; 124:533-45. [PMID: 2179052 PMCID: PMC1203947 DOI: 10.1093/genetics/124.3.533] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The subtelomeric Y' repeated sequence families in two divergent strains of the yeast Saccharomyces cerevisiae have been characterized in terms of copy number, location and restriction site differences. The strain YP1 has 26 to 30 Y's that fall into two previously described, long (6.7 kb) and short (5.2 kb), size classes. These Y's reside at 19 of the 32 chromosome ends and are concentrated in the higher molecular weight chromosomes. Five ends contain tandem arrays, each of which has only one size class of Y's. There is restriction site homogeneity among the Y's of YP1 even between size classes. The Y's of strain Y55 contrast sharply with the Y's of YP1 in terms of copy number, location and sequence differences. There are 14 to 16 Y's, both long and short, most of which are found at different chromosome ends than those of YP1. None of these are tandemly arrayed. Four to six of the Y's appear degenerate in that they have homology with a telomere distal end Y' probe but no homology with sequences at the telomere proximal end. The majority of the Y55 Y's have the same restriction sites as in YP1. Despite the conservation of restriction sites among Y's, a great deal of restriction fragment length heterogeneity between the strains is observed. The characterized Y' repeated sequence families provide an experimental system in which repeated sequence interactions and subsequent evolution can be studied.
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Affiliation(s)
- E J Louis
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110
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30
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Louis EJ, Haber JE. Mitotic recombination among subtelomeric Y' repeats in Saccharomyces cerevisiae. Genetics 1990; 124:547-59. [PMID: 2179053 PMCID: PMC1203948 DOI: 10.1093/genetics/124.3.547] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Y's are a dispersed family of repeats that vary in copy number, location and restriction fragment lengths between strains but exhibit within-strain homogeneity. We have studied mitotic recombination between members of the subtelomeric Y' repeated sequence family of Saccharomyces cerevisiae. Individual copies of Y's were marked with SUP11 and URA3 which allowed for the selection of duplications and losses of the marked Y's. Duplications occurred by ectopic recombinational interactions between Y's at different chromosome ends as well as by unequal sister chromatid exchange. Several of the ectopic duplications resulted in an originally Y'-less chromosome end acquiring a marked Y'. Among losses, most resulted from ectopic exchange or conversion in which only the marker sequence was lost. In some losses, the chromosome end became Y'-less. Although the two subsets of Y's, Y'-longs (6.7 kb) and Y'-shorts (5.2 kb), share extensive sequence homology, a marked Y' recombines highly preferentially within its own subset. These mitotic interactions can in part explain the maintenance of Y's and their subsets, the homogeneity among Y's within a strain, as well as diversity between strains.
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Affiliation(s)
- E J Louis
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254
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31
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Vanoni M, Sollitti P, Goldenthal M, Marmur J. Structure and regulation of the multigene family controlling maltose fermentation in budding yeast. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:281-322. [PMID: 2672110 DOI: 10.1016/s0079-6603(08)60701-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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33
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Affiliation(s)
- R M Walmsley
- Department of Biochemistry and Applied Molecular Biology, University of Manchester Institute of Science and Technology, U.K
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34
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Morin GB, Cech TR. The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats. Cell 1986; 46:873-83. [PMID: 3019555 DOI: 10.1016/0092-8674(86)90069-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 +/- 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination.
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35
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Zakian VA, Blanton HM, Wetzel L. Distribution of telomere-associated sequences in yeast. BASIC LIFE SCIENCES 1986; 40:493-8. [PMID: 3551920 DOI: 10.1007/978-1-4684-5251-8_37] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two middle repetitive DNA sequences called X and Y' are found near the telomeres of many chromosomes in Saccharomyces cerevisiae. Orthogonal field gel electrophoresis (OFAGE) was used to examine the distribution of X and Y' on different yeast chromosomes. Although the distribution of X and Y' varies among different laboratory strains of yeast, most yeast chromosomes in four different strains carry both X and Y'. However, at least one chromosome in each strain lacks the Y' element. This result indicates that Y' is not essential for replication or segregation of at least some yeast chromosomes.
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