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Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles. Nat Commun 2022; 13:757. [PMID: 35140210 PMCID: PMC8828778 DOI: 10.1038/s41467-022-28416-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Numerous intra- and inter-chromosomal contacts have been mapped in eukaryotic genomes, but it remains challenging to link these 3D structures to their regulatory functions. To establish the causal relationships between chromosome conformation and genome functions, we develop a method, Chemically Induced Chromosomal Interaction (CICI), to selectively perturb the chromosome conformation at targeted loci. Using this method, long-distance chromosomal interactions can be induced dynamically between intra- or inter-chromosomal loci pairs, including the ones with very low Hi-C contact frequencies. Measurement of CICI formation time allows us to probe chromosome encounter dynamics between different loci pairs across the cell cycle. We also conduct two functional tests of CICI. We perturb the chromosome conformation near a DNA double-strand break and observe altered donor preference in homologous recombination; we force interactions between early and late-firing DNA replication origins and find no significant changes in replication timing. These results suggest that chromosome conformation plays a deterministic role in homology-directed DNA repair, but not in the establishment of replication timing. Overall, our study demonstrates that CICI is a powerful tool to study chromosome dynamics and 3D genome function. Methods to selectively manipulate specific long-distance chromosomal interactions are limited. Here the authors develop a method called Chemically Induced Chromosomal Interaction (CICI) to engineer interactions and demonstrate that 3D conformation plays a causal role in establishing donor DNA preference during DNA repair.
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2
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Estrem C, Moore JK. Astral microtubule forces alter nuclear organization and inhibit DNA repair in budding yeast. Mol Biol Cell 2019; 30:2000-2013. [PMID: 31067146 PMCID: PMC6727761 DOI: 10.1091/mbc.e18-12-0808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Dividing cells must balance the maintenance of genome integrity with the generation of cytoskeletal forces that control chromosome position. In this study, we investigate how forces on astral microtubules impact the genome during cell division by using live-cell imaging of the cytoskeleton, chromatin, and DNA damage repair in budding yeast. Our results demonstrate that dynein-dependent forces on astral microtubules are propagated through the spindle during nuclear migration and when in excess can increase the frequency of double-stranded breaks (DSBs). Under these conditions, we find that homology-directed repair of DSBs is delayed, indicating antagonism between nuclear migration and the mechanism of homology-directed repair. These effects are partially rescued by mutants that weaken pericentric cohesion or mutants that decrease constriction on the nucleus as it moves through the bud neck. We propose that minimizing nuclear movement aids in finding a donor strand for homologous recombination.
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Affiliation(s)
- Cassi Estrem
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
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3
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Guirouilh-Barbat J, Lambert S, Bertrand P, Lopez BS. Is homologous recombination really an error-free process? Front Genet 2014; 5:175. [PMID: 24966870 PMCID: PMC4052342 DOI: 10.3389/fgene.2014.00175] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/23/2014] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR. First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO) and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here. We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic) or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be "Dr. Jekyll" in maintaining genome stability/variability and "Mr. Hyde" in jeopardizing genome integrity.
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Affiliation(s)
- Josée Guirouilh-Barbat
- CNRS, UMR 8200, Institut de Cancérologie Gustave Roussy, Équipe Labélisée, Université Paris-Sud, «LIGUE 2014» Villejuif, France
| | | | - Pascale Bertrand
- CEA DSV, UMR 967 CEA-INSERM-Université Paris Diderot-Université Paris Sud, Institut de Radiobiologie Cellulaire et Moléculaire Fontenay-aux-Roses, France
| | - Bernard S Lopez
- CNRS, UMR 8200, Institut de Cancérologie Gustave Roussy, Équipe Labélisée, Université Paris-Sud, «LIGUE 2014» Villejuif, France
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4
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Abstract
Mating type in Saccharomyces cerevisiae is determined by two nonhomologous alleles, MATa and MATα. These sequences encode regulators of the two different haploid mating types and of the diploids formed by their conjugation. Analysis of the MATa1, MATα1, and MATα2 alleles provided one of the earliest models of cell-type specification by transcriptional activators and repressors. Remarkably, homothallic yeast cells can switch their mating type as often as every generation by a highly choreographed, site-specific homologous recombination event that replaces one MAT allele with different DNA sequences encoding the opposite MAT allele. This replacement process involves the participation of two intact but unexpressed copies of mating-type information at the heterochromatic loci, HMLα and HMRa, which are located at opposite ends of the same chromosome-encoding MAT. The study of MAT switching has yielded important insights into the control of cell lineage, the silencing of gene expression, the formation of heterochromatin, and the regulation of accessibility of the donor sequences. Real-time analysis of MAT switching has provided the most detailed description of the molecular events that occur during the homologous recombinational repair of a programmed double-strand chromosome break.
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Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. PLoS Genet 2010; 6:e1001228. [PMID: 21151956 PMCID: PMC2996329 DOI: 10.1371/journal.pgen.1001228] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 10/29/2010] [Indexed: 01/11/2023] Open
Abstract
Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR–dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR–dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer. The human genome is structurally dynamic, frequently undergoing loss, duplication, and rearrangement of large chromosome segments. These structural changes occur both in normal and in cancerous cells and are thought to cause both benign and deleterious changes in cell function. Many of these structural alterations are generated when two dispersed repeated DNA sequences at non-allelic sites recombine during non-allelic homologous recombination (NAHR). Here we study NAHR on a genome-wide scale using the experimentally tractable budding yeast as a eukaryotic model genome with its fully sequenced family of repeated DNA elements, the Ty retrotransposons. With our novel system, we simultaneously measure the effects of known recombination parameters on the frequency of NAHR to understand which parameters most influence the occurrence of rearrangements between repetitive sequences. These findings provide a basic framework for interpreting how structural changes observed in the human genome may have arisen.
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Affiliation(s)
- Margaret L. Hoang
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Frederick J. Tan
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
| | - David C. Lai
- Baltimore Polytechnic Institute, Ingenuity Program, Baltimore, Maryland, United States of America
| | - Sue E. Celniker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Roger A. Hoskins
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yixian Zheng
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
| | - Douglas Koshland
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
- * E-mail:
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6
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Cross FR, Pecani K. Efficient and rapid exact gene replacement without selection. Yeast 2010; 28:167-79. [PMID: 21246629 DOI: 10.1002/yea.1822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 08/24/2010] [Indexed: 12/11/2022] Open
Abstract
We describe a highly efficient method for exact gene replacement in budding yeast. Induction of rapid and efficient recombination in an entire cell population results in at least 50% of the recombinants undergoing a switch of the endogenous copy to a specific mutated allele, with no remaining markers or remnant of foreign DNA, without selection. To accomplish this, a partial copy of the replacement allele, followed by an HO cut site, is installed adjacent to the wild-type locus, in a GAL-HO MATa-inc background. HO induction results in near-quantitative site cleavage and recombination/gene conversion, resulting in either regeneration of wild-type or switch of the endogenous allele to the mutant, with accompanying deletion of intervening marker sequences, yielding an exact replacement. Eliminating the need for selection (over days) of rare recombinants removes concerns about second-site suppressor mutations and also allows direct phenotypic analysis, even of lethal gene replacements, without the need of a method to make the lethality conditional or to employ regulated promoters of unknown strength compared to the endogenous promoter. To test this method, we tried two known lethal gene replacements, substituting the non-essential CDH1 gene with a dominantly lethal version mutated for its Cdk phosphorylation sites and substituting the essential CDC28 gene with two recessively lethal versions, one containing an early stop codon and another inactivating Cdc28 kinase activity. We also tested a gene replacement of unknown phenotypic consequences: replacing the non-essential CLB3 B-type cyclin with a version lacking its destruction box.
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7
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Abstract
Initial events in double-strand break repair by homologous recombination in vivo involve homology searching, 3' strand invasion, and new DNA synthesis. While studies in yeast have contributed much to our knowledge of these processes, in comparison, little is known of the early events in the integrated mammalian system. In this study, a sensitive PCR procedure was developed to detect the new DNA synthesis that accompanies mammalian homologous recombination. The test system exploits a well-characterized gene targeting assay in which the transfected vector bears a gap in the region of homology to the single-copy chromosomal immunoglobulin mu heavy chain gene in mouse hybridoma cells. New DNA synthesis primed by invading 3' vector ends copies chromosomal mu-gene template sequences excluded by the vector-borne double-stranded gap. Following electroporation, specific 3' extension products from each vector end are detected with rapid kinetics: they appear after 0.5 hr, peak at 3-6 hr, and then decline, likely as a result of the combined effects of susceptibility to degradation and cell division. New DNA synthesis from each vector 3' end extends at least approximately 1000 nucleotides into the gapped region, but the efficiency declines markedly within the first approximately 200 nucleotides. Over this short distance, an average frequency of 3' extension for the two invading vector ends is approximately 0.007 events/vector backbone. DNA sequencing reveals precise copying of the cognate chromosomal mu-gene template. In unsynchronized cells, 3' extension is sensitive to aphidicolin supporting involvement of a replicative polymerase. Analysis suggests that the vast majority of 3' extensions reside on linear plasmid molecules.
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9
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Nakahara M, Sonoda E, Nojima K, Sale JE, Takenaka K, Kikuchi K, Taniguchi Y, Nakamura K, Sumitomo Y, Bree RT, Lowndes NF, Takeda S. Genetic evidence for single-strand lesions initiating Nbs1-dependent homologous recombination in diversification of Ig v in chicken B lymphocytes. PLoS Genet 2009; 5:e1000356. [PMID: 19180185 PMCID: PMC2625440 DOI: 10.1371/journal.pgen.1000356] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 12/23/2008] [Indexed: 11/18/2022] Open
Abstract
Homologous recombination (HR) is initiated by DNA double-strand breaks (DSB). However, it remains unclear whether single-strand lesions also initiate HR in genomic DNA. Chicken B lymphocytes diversify their Immunoglobulin (Ig) V genes through HR (Ig gene conversion) and non-templated hypermutation. Both types of Ig V diversification are initiated by AID-dependent abasic-site formation. Abasic sites stall replication, resulting in the formation of single-stranded gaps. These gaps can be filled by error-prone DNA polymerases, resulting in hypermutation. However, it is unclear whether these single-strand gaps can also initiate Ig gene conversion without being first converted to DSBs. The Mre11-Rad50-Nbs1 (MRN) complex, which produces 3′ single-strand overhangs, promotes the initiation of DSB-induced HR in yeast. We show that a DT40 line expressing only a truncated form of Nbs1 (Nbs1p70) exhibits defective HR-dependent DSB repair, and a significant reduction in the rate—though not the fidelity—of Ig gene conversion. Interestingly, this defective gene conversion was restored to wild type levels by overproduction of Escherichia coli SbcB, a 3′ to 5′ single-strand–specific exonuclease, without affecting DSB repair. Conversely, overexpression of chicken Exo1 increased the efficiency of DSB-induced gene-targeting more than 10-fold, with no effect on Ig gene conversion. These results suggest that Ig gene conversion may be initiated by single-strand gaps rather than by DSBs, and, like SbcB, the MRN complex in DT40 may convert AID-induced lesions into single-strand gaps suitable for triggering HR. In summary, Ig gene conversion and hypermutation may share a common substrate—single-stranded gaps. Genetic analysis of the two types of Ig V diversification in DT40 provides a unique opportunity to gain insight into the molecular mechanisms underlying the filling of gaps that arise as a consequence of replication blocks at abasic sites, by HR and error-prone polymerases. An important class of chemotherapeutic drugs used in the treatment of cancer induces DNA damage that interferes with DNA replication. The resulting block to replication results in the formation of single-strand gaps in DNA. These gaps can be filled by specialized DNA polymerases, a process associated with the introduction of mutations or by recombination with an undamaged segment of DNA with an identical or similar sequence. Our work shows that diversification of the antibody genes in the chicken B cell line DT40, which is initiated by localized replication-stalling DNA damage, proceeds by formation of a single-strand intermediate. These gaps are generated by the action of a specific nuclease complex, comprising the Mre11, Rad50, and Nbs1 proteins, which have previously been implicated in the initiation of homologous recombination from double-strand breaks. However, in this context, their dysfunction can be reversed by the expression of a bacterial single-strand–specific nuclease, SbcB. Antibody diversification in DT40 thus provides an excellent model for studying the process of replication-stalling DNA damage and will allow a more detailed understanding of the mechanisms underlying gap repair and cellular tolerance of chemotherapeutic agents.
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Affiliation(s)
- Makoto Nakahara
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eiichiro Sonoda
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | - Kuniharu Nojima
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | - Julian E. Sale
- Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Cambridge, United Kingdom
| | - Katsuya Takenaka
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | - Koji Kikuchi
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | | | - Kyoko Nakamura
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshiki Sumitomo
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
| | - Ronan T. Bree
- Genome Stability Laboratory, Department of Biochemistry, National University of Ireland-Galway, Galway, Ireland
- National Centre for Biomedical Engineering Science, National University of Ireland-Galway, Galway, Ireland
| | - Noel F. Lowndes
- Genome Stability Laboratory, Department of Biochemistry, National University of Ireland-Galway, Galway, Ireland
- National Centre for Biomedical Engineering Science, National University of Ireland-Galway, Galway, Ireland
| | - Shunichi Takeda
- CREST Research Project, Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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10
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Chromatin assembly factors Asf1 and CAF-1 have overlapping roles in deactivating the DNA damage checkpoint when DNA repair is complete. Proc Natl Acad Sci U S A 2009; 106:1151-6. [PMID: 19164567 DOI: 10.1073/pnas.0812578106] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to a DNA double-strand break (DSB), chromatin is rapidly modified by the damage dependent checkpoint kinases. Also, disassembly of chromatin occurs at the break site. The damage-induced modification of chromatin structure is involved in the maintenance of the checkpoint. However, it has not been determined how chromatin is restored to its undamaged state when DSB repair is complete. Here, we show the involvement of two chromatin assembly factors (CAFs), Asf1 and CAF-1, in turning off the DNA damage checkpoint in budding yeast. DSB repair or formation of gamma-H2AX does not depend on either the CAF-1 protein, Cac1, or Asf1. Absence of these proteins does not impair the ability of cells to resume cell cycle progression in the presence of an unrepaired DSB (adaptation). However, recovery from cell cycle checkpoint arrest when the DSB is repaired by gene conversion is substantially defective in the absence of both CAF-1 and Asf1, whereas deleting CAC1 or ASF1 individually had little effect. We suggest that CAF-1 and Asf1 function redundantly to deactivate the checkpoint by restoring chromatin structure on the completion of DSB repair.
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11
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Abstract
Trinucleotide repeat expansions are an important cause of inherited neurodegenerative disease. The expanded repeats are unstable, changing in size when transmitted from parents to offspring (intergenerational instability, "meiotic instability") and often showing size variation within the tissues of an affected individual (somatic mosaicism, "mitotic instability"). Repeat instability is a clinically important phenomenon, as increasing repeat lengths correlate with an earlier age of onset and a more severe disease phenotype. The tendency of expanded trinucleotide repeats to increase in length during their transmission from parent to offspring in these diseases provides a molecular explanation for anticipation (increasing disease severity in successive affected generations). In this review, I explore the genetic and molecular basis of trinucleotide repeat instability. Studies of patients and families with trinucleotide repeat disorders have revealed a number of factors that determine the rate and magnitude of trinucleotide repeat change. Analysis of trinucleotide repeat instability in bacteria, yeast, and mice has yielded additional insights. Despite these advances, the pathways and mechanisms underlying trinucleotide repeat instability in humans remain largely unknown. There are many reasons to suspect that this uniquely human phenomenon will significantly impact upon our understanding of development, differentiation and neurobiology.
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Affiliation(s)
- A R La Spada
- Department of Laboratory Medicine and Pharmacology, University of Washington Medical Center, Seattle 98195, USA.
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12
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Egel R, Penny D. On the Origin of Meiosis in Eukaryotic Evolution: Coevolution of Meiosis and Mitosis from Feeble Beginnings. RECOMBINATION AND MEIOSIS 2007. [DOI: 10.1007/7050_2007_036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Herrmann G, Kais S, Hoffbauer J, Shah-Hosseini K, Brüggenolte N, Schober H, Fäsi M, Schär P. Conserved interactions of the splicing factor Ntr1/Spp382 with proteins involved in DNA double-strand break repair and telomere metabolism. Nucleic Acids Res 2007; 35:2321-32. [PMID: 17389648 PMCID: PMC1874655 DOI: 10.1093/nar/gkm127] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 02/14/2007] [Accepted: 02/15/2007] [Indexed: 11/25/2022] Open
Abstract
The ligation of DNA double-strand breaks in the process of non-homologous end-joining (NHEJ) is accomplished by a heterodimeric enzyme complex consisting of DNA ligase IV and an associated non-catalytic factor. This DNA ligase also accounts for the fatal joining of unprotected telomere ends. Hence, its activity must be tightly controlled. Here, we describe interactions of the DNA ligase IV-associated proteins Lif1p and XRCC4 of yeast and human with the putatively orthologous G-patch proteins Ntr1p/Spp382p and NTR1/TFIP11 that have recently been implicated in mRNA splicing. These conserved interactions occupy the DNA ligase IV-binding sites of Lif1p and XRCC4, thus preventing the formation of an active enzyme complex. Consistently, an excess of Ntr1p in yeast reduces NHEJ efficiency in a plasmid ligation assay as well as in a chromosomal double-strand break repair (DSBR) assay. Both yeast and human NTR1 also interact with PinX1, another G-patch protein that has dual functions in the regulation of telomerase activity and telomere stability, and in RNA processing. Like PinX1, NTR1 localizes to telomeres and associates with nucleoli in yeast and human cells, suggesting a function in localized control of DSBR.
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Affiliation(s)
- Gernot Herrmann
- Department of Dermatology, University of Cologne, Cologne, Germany.
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14
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Lettier G, Feng Q, de Mayolo AA, Erdeniz N, Reid RJD, Lisby M, Mortensen UH, Rothstein R. The role of DNA double-strand breaks in spontaneous homologous recombination in S. cerevisiae. PLoS Genet 2006; 2:e194. [PMID: 17096599 PMCID: PMC1635536 DOI: 10.1371/journal.pgen.0020194] [Citation(s) in RCA: 78] [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: 02/03/2006] [Accepted: 10/04/2006] [Indexed: 11/18/2022] Open
Abstract
Homologous recombination (HR) is a source of genomic instability and the loss of heterozygosity in mitotic cells. Since these events pose a severe health risk, it is important to understand the molecular events that cause spontaneous HR. In eukaryotes, high levels of HR are a normal feature of meiosis and result from the induction of a large number of DNA double-strand breaks (DSBs). By analogy, it is generally believed that the rare spontaneous mitotic HR events are due to repair of DNA DSBs that accidentally occur during mitotic growth. Here we provide the first direct evidence that most spontaneous mitotic HR in Saccharomyces cerevisiae is initiated by DNA lesions other than DSBs. Specifically, we describe a class of rad52 mutants that are fully proficient in inter- and intra-chromosomal mitotic HR, yet at the same time fail to repair DNA DSBs. The conclusions are drawn from genetic analyses, evaluation of the consequences of DSB repair failure at the DNA level, and examination of the cellular re-localization of Rad51 and mutant Rad52 proteins after introduction of specific DSBs. In further support of our conclusions, we show that, as in wild-type strains, UV-irradiation induces HR in these rad52 mutants, supporting the view that DNA nicks and single-stranded gaps, rather than DSBs, are major sources of spontaneous HR in mitotic yeast cells.
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Affiliation(s)
- Gaëlle Lettier
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
| | - Qi Feng
- Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of America
| | - Adriana Antúnez de Mayolo
- Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of America
| | - Naz Erdeniz
- Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of America
| | - Robert J. D Reid
- Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of America
| | - Michael Lisby
- Department of Genetics, Institute of Molecular Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe H Mortensen
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of America
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15
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Douglas NL, Dozier SK, Donato JJ. Dual roles for Mcm10 in DNA replication initiation and silencing at the mating-type loci. Mol Biol Rep 2006; 32:197-204. [PMID: 16328881 DOI: 10.1007/s11033-005-2312-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2005] [Indexed: 11/30/2022]
Abstract
Recent studies linking DNA replication proteins to transcriptional silencing suggest that some of the same mechanisms that facilitate the initiation of replication at origins might be involved in establishing repressed chromatin at silencer elements. Our ongoing studies of several mutants of the replication initiation factor Mcm10 of budding yeast revealed an associated defect in the production of mating type pheromones. This observation prompted us to look more directly at the effect of MCM10 mutations on the expression of a reporter gene in the mating type locus and to assay for physical interactions between Mcm10 and known silencing factors. Our findings, that Mcm10 mutants disrupt mating loci silencing and that Mcm10 interacts with Sir2 and Sir3, suggest that Mcm10 also plays an essential, and separable role in transcriptional silencing.
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Affiliation(s)
- Nancy L Douglas
- Department of Molecular Biology and Genetics, Cornell University, 327 Biotechnology Building, Ithaca, NY 14853-2703, USA.
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16
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Kawamoto T, Araki K, Sonoda E, Yamashita YM, Harada K, Kikuchi K, Masutani C, Hanaoka F, Nozaki K, Hashimoto N, Takeda S. Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis. Mol Cell 2006; 20:793-9. [PMID: 16337602 DOI: 10.1016/j.molcel.2005.10.016] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 09/30/2005] [Accepted: 10/12/2005] [Indexed: 01/26/2023]
Abstract
Chicken B lymphocyte precursors and DT40 cells diversify their immunoglobulin-variable (IgV) genes through homologous recombination (HR)-mediated Ig gene conversion. To identify DNA polymerases that are involved in Ig gene conversion, we created DT40 clones deficient in DNA polymerase eta (poleta), which, in humans, is defective in the variant form of xeroderma pigmentosum (XP-V). Poleta is an error-prone translesion DNA synthesis polymerase that can bypass UV damage-induced lesions and is involved in IgV hypermutation. Like XP-V cells, poleta-disrupted (poleta) clones exhibited hypersensitivity to UV. Remarkably, poleta cells showed a significant decrease in the frequency of both Ig gene conversion and double-strand break-induced HR when compared to wild-type cells, and these defects were reversed by complementation with human poleta. Our findings identify a DNA polymerase that carries out DNA synthesis for physiological HR and provides evidence that a single DNA polymerase can play multiple cellular roles.
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Affiliation(s)
- Takuo Kawamoto
- CREST, Japan Science and Technology Agency, Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Japan
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17
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Law GL, Bickel KS, MacKay VL, Morris DR. The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders. Genome Biol 2006; 6:R111. [PMID: 16420678 PMCID: PMC1414110 DOI: 10.1186/gb-2005-6-13-r111] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 10/17/2005] [Accepted: 11/21/2005] [Indexed: 11/21/2022] Open
Abstract
Eight per cent of yeast transcripts, mostly involved in responses to stress or external stimuli, were found to be under-loaded with ribosomes, and most of them exhibited structural changes in their 5’ transcript leaders in response to the environmental signal. Background Translational efficiencies in Saccharomyces cerevisiae vary from transcript to transcript by approximately two orders of magnitude. Many of the poorly translated transcripts were found to respond to the appropriate external stimulus by recruiting ribosomes. Unexpectedly, a high frequency of these transcripts showed the appearance of altered 5' leaders that coincide with increased ribosome loading. Results Of the detectable transcripts in S. cerevisiae, 8% were found to be underloaded with ribosomes. Gene ontology categories of responses to stress or external stimuli were overrepresented in this population of transcripts. Seventeen poorly loaded transcripts involved in responses to pheromone, nitrogen starvation, and osmotic stress were selected for detailed study and were found to respond to the appropriate environmental signal with increased ribosome loading. Twelve of these regulated transcripts exhibited structural changes in their 5' transcript leaders in response to the environmental signal. In many of these the coding region remained intact, whereas regulated shortening of the 5' end truncated the open reading frame in others. Colinearity between the gene and transcript sequences eliminated regulated splicing as a mechanism for these alterations in structure. Conclusion Frequent occurrence of coordinated changes in transcript structure and translation efficiency, in at least three different gene regulatory networks, suggests a widespread phenomenon. It is likely that many of these altered 5' leaders arose from changes in promoter usage. We speculate that production of translationally silenced transcripts may be one mechanism for allowing low-level transcription activity necessary for maintaining an open chromatin structure while not allowing inappropriate protein production.
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Affiliation(s)
- G Lynn Law
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kellie S Bickel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Vivian L MacKay
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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18
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Okada T, Sonoda E, Yoshimura M, Kawano Y, Saya H, Kohzaki M, Takeda S. Multiple roles of vertebrate REV genes in DNA repair and recombination. Mol Cell Biol 2005; 25:6103-11. [PMID: 15988022 PMCID: PMC1168817 DOI: 10.1128/mcb.25.14.6103-6111.2005] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In yeast, Rev1, Rev3, and Rev7 are involved in translesion synthesis over various kinds of DNA damage and spontaneous and UV-induced mutagenesis. Here, we disrupted Rev1, Rev3, and Rev7 in the chicken B-lymphocyte line DT40. REV1-/- REV3-/- REV7-/- cells showed spontaneous cell death, chromosomal instability/fragility, and hypersensitivity to various genotoxic treatments as observed in each of the single mutants. Surprisingly, the triple-knockout cells showed a suppressed level of sister chromatid exchanges (SCEs), which may reflect postreplication repair events mediated by homologous recombination, while each single mutant showed an elevated SCE level. Furthermore, REV1-/- cells as well as triple mutants showed a decreased level of immunoglobulin gene conversion, suggesting participation of Rev1 in a recombination-based pathway. The present study gives us a new insight into cooperative function of three Rev molecules and the Polzeta (Rev3-Rev7)-independent role of Rev1 in vertebrate cells.
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Affiliation(s)
- Takashi Okada
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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19
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Abstract
Exclusive gene expression, where only one member of a gene or gene cassette family is selected for expression, plays an important role in the establishment of cell identity in several biological systems. Here, we compare four such systems: mating-type switching in fission and budding yeast, where cells choose between expressing one of the two different mating-type cassettes, and immunoglobulin and odorant receptor gene expression in mammals, where the number of gene choices is substantially higher. The underlying mechanisms that establish this selective expression pattern in each system differ in almost every detail. In all four systems, once a successful gene activation event has taken place, a feedback mechanism affects the fate of the cell. In the mammalian systems, feedback is mediated by the expressed cell surface receptor to ensure monoallelic gene expression, whereas in the yeasts, the expressed gene cassette at the mating-type locus affects donor choice during the subsequent switching event.
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20
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Sun K, Coïc E, Zhou Z, Durrens P, Haber JE. Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer. Genes Dev 2002; 16:2085-96. [PMID: 12183363 PMCID: PMC186439 DOI: 10.1101/gad.994902] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Saccharomyces mating-type switching results from replacement by gene conversion of the MAT locus with sequences copied from one of two unexpressed donor loci, HML or HMR. MATa cells recombine with HMLalpha approximately 90% of the time, whereas MATalpha cells choose HMRa 80%-90% of the time. HML preference in MATa is controlled by the cis-acting recombination enhancer (RE) that regulates recombination along the entire left arm of chromosome III. Comparison of RE sequences between S. cerevisiae, S. carlsbergensis, and S. bayanus defines four highly conserved regions (A, B, C, and D) within a 270-bp minimum RE. An adjacent E region enhances RE activity. Multimers of region A, D, or E are sufficient to promote selective use of HML. Regions A, D, and E each bind in vivo the transcription activator forkhead proteins Fkh1p and Fkh2p and their associated Ndd1p, although there are no adjacent open reading frames (ORFs). Deletion of FKH1 significantly reduces MATa's use of HML, as does mutation of the Fkh1/Fkh2-binding sites in a multimer of region A. We conclude that Fkh1p regulates MATa donor preference through direct interaction with RE.
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Affiliation(s)
- Kaiming Sun
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9910, USA
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21
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Lisby M, Rothstein R, Mortensen UH. Rad52 forms DNA repair and recombination centers during S phase. Proc Natl Acad Sci U S A 2001; 98:8276-82. [PMID: 11459964 PMCID: PMC37432 DOI: 10.1073/pnas.121006298] [Citation(s) in RCA: 359] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maintenance of genomic integrity and stable transmission of genetic information depend on a number of DNA repair processes. Failure to faithfully perform these processes can result in genetic alterations and subsequent development of cancer and other genetic diseases. In the eukaryote Saccharomyces cerevisiae, homologous recombination is the major pathway for repairing DNA double-strand breaks. The key role played by Rad52 in this pathway has been attributed to its ability to seek out and mediate annealing of homologous DNA strands. In this study, we find that S. cerevisiae Rad52 fused to green fluorescent protein (GFP) is fully functional in DNA repair and recombination. After induction of DNA double-strand breaks by gamma-irradiation, meiosis, or the HO endonuclease, Rad52-GFP relocalizes from a diffuse nuclear distribution to distinct foci. Interestingly, Rad52 foci are formed almost exclusively during the S phase of mitotic cells, consistent with coordination between recombinational repair and DNA replication. This notion is further strengthened by the dramatic increase in the frequency of Rad52 focus formation observed in a pol12-100 replication mutant and a mec1 DNA damage checkpoint mutant. Furthermore, our data indicate that each Rad52 focus represents a center of recombinational repair capable of processing multiple DNA lesions.
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Affiliation(s)
- M Lisby
- Department of Genetics and Development, Columbia University, College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032-2704, USA
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22
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Tremblay A, Jasin M, Chartrand P. A double-strand break in a chromosomal LINE element can be repaired by gene conversion with various endogenous LINE elements in mouse cells. Mol Cell Biol 2000; 20:54-60. [PMID: 10594008 PMCID: PMC85044 DOI: 10.1128/mcb.20.1.54-60.2000] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A double-strand break (DSB) in the mammalian genome has been shown to be a very potent signal for the cell to activate repair processes. Two different types of repair have been identified in mammalian cells. Broken ends can be rejoined with or without loss or addition of DNA or, alternatively, a homologous template can be used to repair the break. For most genomic sequences the latter event would involve allelic sequences present on the sister chromatid or homologous chromosome. However, since more than 30% of our genome consists of repetitive sequences, these would have the option of using nonallelic sequences for homologous repair. This could have an impact on the evolution of these sequences and of the genome itself. We have designed an assay to look at the repair of DSBs in LINE-1 (L1) elements which number 10(5) copies distributed throughout the genome of all mammals. We introduced into the genome of mouse epithelial cells an L1 element with an I-SceI endonuclease site. We induced DSBs at the I-SceI site and determined their mechanism of repair. We found that in over 95% of cases, the DSBs were repaired by an end-joining process. However, in almost 1% of cases, we found strong evidence for repair involving gene conversion with various endogenous L1 elements, with some being used preferentially. In particular, the T(F) family and the L1Md-A2 subfamily, which are the most active in retrotransposition, appeared to be contributing the most in this process. The degree of homology did not seem to be a determining factor in the selection of the endogenous elements used for repair but may be based instead on accessibility. Considering their abundance and dispersion, gene conversion between repetitive elements may be occurring frequently enough to be playing a role in their evolution.
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Affiliation(s)
- A Tremblay
- Molecular Biology Program, University of Montreal, Montreal, Quebec, Canada
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23
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Semionov A, Cournoyer D, Chow TY. Inhibition of poly(ADP-ribose)polymerase stimulates extrachromosomal homologous recombination in mouse Ltk-fibroblasts. Nucleic Acids Res 1999; 27:4526-31. [PMID: 10536164 PMCID: PMC148738 DOI: 10.1093/nar/27.22.4526] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Poly(ADP-ribose)polymerase (PARP) is an abundant nuclear enzyme activated by DNA breaks. PARP is generally believed to play a role in maintaining the integrity of the genome in eukaryote cells via anti-recombinogenic activity by preventing inappropriate homologous recombination reactions at DNA double-strand breaks. While inhibition of PARP reduces non-homologous recombination, at the same time it stimulates sister chromatid exchange and intrachromosomal homologous recombination. Here we report that the inhibition of PARP with 100 microg/ml (0.622 mM) 1,5-isoquinolinediol results in an average 4.6-fold increase in the frequency of extrachromosomal homologous recombination between two linearized plasmids carrying herpes simplex virus thymidine kinase genes inactivated by non-overlapping mutations, in mouse Ltk-fibroblasts. These results are in disagreement with the previously reported observation that PARP inhibition had no effect on extrachromosomal homologous recombination in Ltk-cells.
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Affiliation(s)
- A Semionov
- Departments of Oncology and Medicine, Faculty of Medicine, McGill University and Montreal General Hospital, 1650 Avenue Cedar, Montreal, Quebec H3G 1A4, Canada
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24
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Lewis LK, Westmoreland JW, Resnick MA. Repair of endonuclease-induced double-strand breaks in Saccharomyces cerevisiae: essential role for genes associated with nonhomologous end-joining. Genetics 1999; 152:1513-29. [PMID: 10430580 PMCID: PMC1460701 DOI: 10.1093/genetics/152.4.1513] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Repair of double-strand breaks (DSBs) in chromosomal DNA by nonhomologous end-joining (NHEJ) is not well characterized in the yeast Saccharomyces cerevisiae. Here we demonstrate that several genes associated with NHEJ perform essential functions in the repair of endonuclease-induced DSBs in vivo. Galactose-induced expression of EcoRI endonuclease in rad50, mre11, or xrs2 mutants, which are deficient in plasmid DSB end-joining and some forms of recombination, resulted in G2 arrest and rapid cell killing. Endonuclease synthesis also produced moderate cell killing in sir4 strains. In contrast, EcoRI caused prolonged cell-cycle arrest of recombination-defective rad51, rad52, rad54, rad55, and rad57 mutants, but cells remained viable. Cell-cycle progression was inhibited in excision repair-defective rad1 mutants, but not in rad2 cells, indicating a role for Rad1 processing of the DSB ends. Phenotypic responses of additional mutants, including exo1, srs2, rad5, and rdh54 strains, suggest roles in recombinational repair, but not in NHEJ. Interestingly, the rapid cell killing in haploid rad50 and mre11 strains was largely eliminated in diploids, suggesting that the cohesive-ended DSBs could be efficiently repaired by homologous recombination throughout the cell cycle in the diploid mutants. These results demonstrate essential but separable roles for NHEJ pathway genes in the repair of chromosomal DSBs that are structurally similar to those occurring during cellular development.
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Affiliation(s)
- L K Lewis
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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25
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Pâques F, Haber JE. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 1999; 63:349-404. [PMID: 10357855 PMCID: PMC98970 DOI: 10.1128/mmbr.63.2.349-404.1999] [Citation(s) in RCA: 1649] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been the principal organism used in experiments to examine genetic recombination in eukaryotes. Studies over the past decade have shown that meiotic recombination and probably most mitotic recombination arise from the repair of double-strand breaks (DSBs). There are multiple pathways by which such DSBs can be repaired, including several homologous recombination pathways and still other nonhomologous mechanisms. Our understanding has also been greatly enriched by the characterization of many proteins involved in recombination and by insights that link aspects of DNA repair to chromosome replication. New molecular models of DSB-induced gene conversion are presented. This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.
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Affiliation(s)
- F Pâques
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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26
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Abstract
The yeast Saccharomyces can switch its mating type by a highly choreographed recombination event in which 'a' or 'alpha' sequences at the mating-type (MAT) locus are replaced by opposite mating-type sequences copied from one of two donors, HML and HMR, located near the two ends of the same chromosome III. MAT alpha cells 'know' to choose HML, while MAT alpha cells preferentially recombine with HMR. Donor preference is regulated by a 250 bp recombination enhancer, that controls recombination of the entire left arm of chromosome III. Recent studies have shown how this locus-control region is turned on and off.
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Affiliation(s)
- J E Haber
- Rosenstiel Center, Keck Institute for Cellular Visualization, Brandeis University, Waltham, MA 02254, USA.
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27
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Wu C, Weiss K, Yang C, Harris MA, Tye BK, Newlon CS, Simpson RT, Haber JE. Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching. Genes Dev 1998; 12:1726-37. [PMID: 9620858 PMCID: PMC316872 DOI: 10.1101/gad.12.11.1726] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/1998] [Accepted: 04/01/1998] [Indexed: 02/07/2023]
Abstract
Switching of Saccharomyces mating type by replacement of sequences at the MAT locus involves a choice between two donors, HML and HMR. MATalpha cells inhibit recombination along the entire left arm of chromosome III, including HML, whereas MATa cells activate this same region. MATa-dependent activation of HML depends on a small, cis-acting DNA sequence designated the recombination enhancer (RE), located 17 kb centromere-proximal to HML. A comparison of RE sequences interchangeable between Saccharomyces cerevisiae and Saccharomyces carlsbergensis defines a minimum RE of 244 bp. RE activity is repressed in MATalpha cells by binding of the Matalpha2-Mcm1 corepressor to a site within the RE. Mutation of the two Matalpha2 binding sites removes most, but not all, of this repression, and RE chromatin structure in MATalpha cells becomes indistinguishable from that seen in MATa. Surprisingly, a 2-bp mutation in the Mcm1 binding site completely abolishes RE activity in MATa cells; moreover, RE chromatin structure in the MATa mutant becomes very similar to that seen in MATalpha cells with a normal RE, displaying highly ordered nucleosomes despite the absence of Matalpha2. Further, a mutation that alters the ability of Mcm1 to act with Matalpha2 in repressing a-specific genes also alters donor preference in either mating type. Thus, Mcm1 is critically responsible for the activation as well as the Matalpha2-Mcm1-mediated repression of RE activity.
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Affiliation(s)
- C Wu
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110 USA
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28
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Lewis LK, Kirchner JM, Resnick MA. Requirement for end-joining and checkpoint functions, but not RAD52-mediated recombination, after EcoRI endonuclease cleavage of Saccharomyces cerevisiae DNA. Mol Cell Biol 1998; 18:1891-902. [PMID: 9528760 PMCID: PMC121418 DOI: 10.1128/mcb.18.4.1891] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RAD52 and RAD9 are required for the repair of double-strand breaks (DSBs) induced by physical and chemical DNA-damaging agents in Saccharomyces cerevisiae. Analysis of EcoRI endonuclease expression in vivo revealed that, in contrast to DSBs containing damaged or modified termini, chromosomal DSBs retaining complementary ends could be repaired in rad52 mutants and in G1-phase Rad+ cells. Continuous EcoRI-induced scission of chromosomal DNA blocked the growth of rad52 mutants, with most cells arrested in G2 phase. Surprisingly, rad52 mutants were not more sensitive to EcoRI-induced cell killing than wild-type strains. In contrast, endonuclease expression was lethal in cells deficient in Ku-mediated end joining. Checkpoint-defective rad9 mutants did not arrest cell cycling and lost viability rapidly when EcoRI was expressed. Synthesis of the endonuclease produced extensive breakage of nuclear DNA and stimulated interchromosomal recombination. These results and those of additional experiments indicate that cohesive ended DSBs in chromosomal DNA can be accurately repaired by RAD52-mediated recombination and by recombination-independent complementary end joining in yeast cells.
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Affiliation(s)
- L K Lewis
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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29
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Osman F, Subramani S. Double-strand break-induced recombination in eukaryotes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 58:263-99. [PMID: 9308369 DOI: 10.1016/s0079-6603(08)60039-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genetic recombination is of fundamental importance for a wide variety of biological processes in eukaryotic cells. One of the major questions in recombination relates to the mechanism by which the exchange of genetic information is initiated. In recent years, DNA double strand breaks (DSBs) have emerged as an important lesion that can initiate and stimulate meiotic and mitotic homologous recombination. In this review, we examine the models by which DSBs induce recombination, describe the types of recombination events that DSBs stimulate, and compare the genetic control of DSB-induced mitotic recombination in budding and fission yeasts.
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Affiliation(s)
- F Osman
- Department of Biochemistry, University of Oxford, United Kingdom
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30
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Abstract
Homing endonucleases are rare-cutting enzymes encoded by introns and inteins. They have striking structural and functional properties that distinguish them from restriction enzymes. Nomenclature conventions analogous to those for restriction enzymes have been developed for the homing endonucleases. Recent progress in understanding the structure and function of the four families of homing enzymes is reviewed. Of particular interest are the first reported structures of homing endonucleases of the LAGLIDADG family. The exploitation of the homing enzymes in genome analysis and recombination research is also summarized. Finally, the evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.
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Affiliation(s)
- M Belfort
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and School of Public Health, State University of New York at Albany, PO Box 22002, Albany, New York 12201-2002, USA.
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31
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Schär P, Herrmann G, Daly G, Lindahl T. A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks. Genes Dev 1997; 11:1912-24. [PMID: 9271115 PMCID: PMC316416 DOI: 10.1101/gad.11.15.1912] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Eukaryotic DNA ligases are ATP-dependent DNA strand-joining enzymes that participate in DNA replication, repair, and recombination. Whereas mammalian cells contain several different DNA ligases, encoded by at least three distinct genes, only one DNA ligase has been detected previously in either budding yeast or fission yeast. Here, we describe a newly identified nonessential Saccharomyces cerevisiae gene that encodes a DNA ligase distinct from the CDC9 gene product. This DNA ligase shares significant amino acid sequence homology with human DNA ligase IV; accordingly, we designate the yeast gene LIG4. Recombinant LIG4 protein forms a covalent enzyme-AMP complex and can join a DNA single-strand break in a DNA/RNA hybrid duplex, the preferred substrate in vitro. Disruption of the LIG4 gene causes only marginally increased cellular sensitivity to several DNA damaging agents, and does not further sensitize cdc9 or rad52 mutant cells. In contrast, lig4 mutant cells have a 1000-fold reduced capacity for correct recircularization of linearized plasmids by illegitimate end-joining after transformation. Moreover, homozygous lig4 mutant diploids sporulate less efficiently than isogenic wild-type cells, and show retarded progression through meiotic prophase I. Spore viability is normal, but lig4 mutants appear to produce a higher proportion of tetrads with only three viable spores. The mutant phenotypes are consistent with functions of LIG4 in an illegitimate DNA end-joining pathway and ensuring efficient meiosis.
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Affiliation(s)
- P Schär
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, UK
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32
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Abstract
Transposable elements are discrete mobile DNA segments that can insert into non-homologous target sites. Diverse patterns of target site selectivity are observed: Some elements display considerable target site selectivity and others display little obvious selectivity, although none appears to be truly "random." A variety of mechanisms for target site selection are used: Some elements use direct interactions between the recombinase and target DNA whereas other elements depend upon interactions with accessory proteins that communicate both with the target DNA and the recombinase. The study of target site selectivity is useful in probing recombination mechanisms, in studying genome structure and function, and also in providing tools for genome manipulation.
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Affiliation(s)
- N L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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33
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Richard M, Gusew N, Belmaaza A, Chartrand P. Homologous junctions formed between a vector and human genomic repetitive LINE-1 elements as a result of one-sided invasion. SOMATIC CELL AND MOLECULAR GENETICS 1997; 23:75-81. [PMID: 9218003 DOI: 10.1007/bf02679957] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Studies on homologous recombination in mammalian cells between an exogenous DNA molecule containing a double-strand break and a homologous genomic sequence have indicated that there were at least two distinct types of homologous recombination processes, one that involved the formation of two homologous junctions and another that involved the formation of one homologous junction and one illegitimate junction. Both types of events are produced in gene targeting experiments. We have proposed a model to account for the later process called one-sided invasion. One-sided invasion has now been reported in numerous species belonging to different phyla and appears to be a universal mechanism. It has also been observed in normal human germ cells. The role of one-sided invasion is still unknown. Using a recombination assay between LINE-1 elements from the human genome and exogenous LINE-1 sequences, we have characterized the process of homologous junction formation in one-sided invasion. We found that at each of the homologous junctions, variable lengths of the vector L1 sequences had been replaced by genomic L1 sequences. We also found a homologous junction that involved three partners, suggesting that the homologous end could be released and become available for a second round of interaction.
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Affiliation(s)
- M Richard
- Institut du cancer de Montréal, Quebec, Canada
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34
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Lim DS, Hasty P. A mutation in mouse rad51 results in an early embryonic lethal that is suppressed by a mutation in p53. Mol Cell Biol 1996; 16:7133-43. [PMID: 8943369 PMCID: PMC231717 DOI: 10.1128/mcb.16.12.7133] [Citation(s) in RCA: 555] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
RecA in Escherichia coli and its homolog, ScRad51 in Saccharomyces cerevisiae, are known to be essential for recombinational repair. The homolog of RecA and ScRad51 in mice, MmRad51, was mutated to determine its function. Mutant embryos arrested early during development. A decrease in cell proliferation, followed by programmed cell death and chromosome loss, was observed. Radiation sensitivity was demonstrated in trophectoderm-derived cells. Interestingly, embryonic development progressed further in a p53 null background; however, fibroblasts derived from double-mutant embryos failed to proliferate in tissue culture.
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Affiliation(s)
- D S Lim
- Department of Biochemistry and Molecular Biology, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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35
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Puchta H, Dujon B, Hohn B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci U S A 1996; 93:5055-60. [PMID: 8643528 PMCID: PMC39405 DOI: 10.1073/pnas.93.10.5055] [Citation(s) in RCA: 249] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Genomic double-strand breaks (DSBs) are key intermediates in recombination reactions of living organisms. We studied the repair of genomic DSBs by homologous sequences in plants. Tobacco plants containing a site for the highly specific restriction enzyme I-Sce I were cotransformed with Agrobacterium strains carrying sequences homologous to the transgene locus and, separately, containing the gene coding for the enzyme. We show that the induction of a DSB can increase the frequency of homologous recombination at a specific locus by up to two orders of magnitude. Analysis of the recombination products demonstrates that a DSB can be repaired via homologous recombination by at least two different but related pathways. In the major pathway, homologies on both sides of the DSB are used, analogous to the conservative DSB repair model originally proposed for meiotic recombination in yeast. Homologous recombination of the minor pathway is restricted to one side of the DSB as described by the nonconservative one-sided invasion model. The sequence of the recombination partners was absolutely conserved in two cases, whereas in a third case, a deletion of 14 bp had occurred, probably due to DNA polymerase slippage during the copy process. The induction of DSB breaks to enhance homologous recombination can be applied for a variety of approaches of plant genome manipulation.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA Damage
- DNA Repair/genetics
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Gene Targeting
- Genome, Plant
- Models, Genetic
- Molecular Sequence Data
- Plants/genetics
- Plants/metabolism
- Plants/microbiology
- Plants, Genetically Modified
- Plants, Toxic
- Polymerase Chain Reaction
- Recombination, Genetic
- Rhizobium/genetics
- Saccharomyces cerevisiae Proteins
- Sequence Deletion
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/microbiology
- Transformation, Genetic
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Affiliation(s)
- H Puchta
- Friedrich Miescher-Institut, Basel, Switzerland
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36
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Moore JK, Haber JE. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 1996; 16:2164-73. [PMID: 8628283 PMCID: PMC231204 DOI: 10.1128/mcb.16.5.2164] [Citation(s) in RCA: 563] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In Saccharomyces cerevisiae, an HO endonuclease-induced double-strand break can be repaired by at least two pathways of nonhomologous end joining (NHEJ) that closely resemble events in mammalian cells. In one pathway the chromosome ends are degraded to yield deletions with different sizes whose endpoints have 1 to 6 bp of homology. Alternatively, the 4-bp overhanging 3' ends of HO-cut DNA (5'-AACA-3') are not degraded but can be base paired in misalignment to produce +CA and +ACA insertions. When HO was expressed throughout the cell cycle, the efficiency of NHEJ repair was 30 times higher than when HO was expressed only in G1. The types of repair events were also very different when HO was expressed throughout the cell cycle; 78% of survivors had small insertions, while almost none had large deletions. When HO expression was confined to the G1 phase, only 21% were insertions and 38% had large deletions. These results suggest that there are distinct mechanisms of NHEJ repair producing either insertions or deletions and that these two pathways are differently affected by the time in the cell cycle when HO is expressed. The frequency of NHEJ is unaltered in strains from which RAD1, RAD2, RAD51, RAD52, RAD54, or RAD57 is deleted; however, deletions of RAD50, XRS2, or MRE11 reduced NHEJ by more than 70-fold when HO was not cell cycle regulated. Moreover, mutations in these three genes markedly reduced +CA insertions, while significantly increasing the proportion of both small (-ACA) and larger deletion events. In contrast, the rad5O mutation had little effect on the viability of G1-induced cells but significantly reduced the frequency of both +CA insertions and -ACA deletions in favor of larger deletions. Thus, RAD50 (and by extension XRS2 and MRE11) exerts a much more important role in the insertion-producing pathway of NHEJ repair found in S and/or G2 than in the less frequent deletion events that predominate when HO is expressed only in G1.
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Affiliation(s)
- J K Moore
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-09110, USA
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37
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Zou S, Ke N, Kim JM, Voytas DF. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev 1996; 10:634-45. [PMID: 8598292 DOI: 10.1101/gad.10.5.634] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The nonrandom integration of retrotransposons and retroviruses suggests that chromatin influences target choice. Targeted integration, in turn, likely affects genome organization. In Saccharomyces, native Ty5 retrotransposons are located near telomeres and the silent mating locus HMR. To determine whether this distribution is a consequence of targeted integration, we isolated a transposition-competent Ty5 element from S. paradoxus, a species closely related to S. cerevisiae. This Ty5 element was used to develop a transposition assay in S. cerevisiae to investigate target preference of de novo transposition events. Of 87 independent Ty5 insertions, approximately 30% were located on chromosome III, indicating this small chromosome (approximately 1/40 of the yeast genome) is a highly preferred target. Mapping of the exact location of 19 chromosome III insertions showed that 18 were within or adjacent to transcriptional silencers flanking HML and HMR or the type X subtelomeric repeat. We predict Ty5 target preference is attributable to interactions between transposition intermediates and constituents of silent chromatin assembled at these sites. Ty5 target preference extends the link between telomere structure and reverse transcription as carried out by telomerase and Drosophila retrotransposons.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Chromatin/genetics
- Chromosome Mapping
- Chromosomes, Fungal
- Gene Expression Regulation, Fungal
- Mating Factor
- Models, Genetic
- Molecular Sequence Data
- Peptides/genetics
- RNA, Fungal/analysis
- RNA, Messenger/analysis
- Repetitive Sequences, Nucleic Acid
- Retroelements/genetics
- Saccharomyces/genetics
- Saccharomyces cerevisiae/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Species Specificity
- Telomere/genetics
- Transcription, Genetic
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Affiliation(s)
- S Zou
- Department of Zoology and Genetics, Iowa State University, Ames, 50011, USA
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38
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Wu X, Moore JK, Haber JE. Mechanism of MAT alpha donor preference during mating-type switching of Saccharomyces cerevisiae. Mol Cell Biol 1996; 16:657-68. [PMID: 8552094 PMCID: PMC231045 DOI: 10.1128/mcb.16.2.657] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
During homothallic switching of the mating-type (MAT) gene in Saccharomyces cerevisiae, a- or alpha-specific sequences are replaced by opposite mating-type sequences copied from one of two silent donor loci, HML alpha or HMRa. The two donors lie at opposite ends of chromosome III, approximately 190 and 90 kb, respectively, from MAT. MAT alpha cells preferentially recombine with HMR, while MATa cells select HML. The mechanisms of donor selection are different for the two mating types. MATa cells, deleted for the preferred HML gene, efficiently use HMR as a donor. However, in MAT alpha cells, HML is not an efficient donor when HMR is deleted; consequently, approximately one-third of HO HML alpha MAT alpha hmr delta cells die because they fail to repair the HO endonuclease-induced double-strand break at MAT. MAT alpha donor preference depends not on the sequence differences between HML and HMR or their surrounding regions but on their chromosomal locations. Cloned HMR donors placed at three other locations to the left of MAT, on either side of the centromere, all fail to act as efficient donors. When the donor is placed 37 kb to the left of MAT, its proximity overcomes normal donor preference, but this position is again inefficiently used when additional DNA is inserted in between the donor and MAT to increase the distance to 62 kb. Donors placed to the right of MAT are efficiently recruited, and in fact a donor situated 16 kb proximal to HMR is used in preference to HMR. The cis-acting chromosomal determinants of MAT alpha preference are not influenced by the chromosomal orientation of MAT or by sequences as far as 6 kb from HMR. These data argue that there is an alpha-specific mechanism to inhibit the use of donors to the left of MAT alpha, causing the cell to recombine most often with donors to the right of MAT alpha.
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MESH Headings
- Base Sequence
- Centromere/genetics
- Chromosome Inversion
- Chromosomes, Fungal
- Cloning, Molecular
- Crosses, Genetic
- DNA Repair
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Gene Conversion
- Genes, Fungal
- Genes, Mating Type, Fungal
- Genes, Switch
- Mating Factor
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Insertional
- Peptides/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Sequence Deletion
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Affiliation(s)
- X Wu
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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39
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Mueller JE, Clyman J, Huang YJ, Parker MM, Belfort M. Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways. Genes Dev 1996; 10:351-64. [PMID: 8595885 DOI: 10.1101/gad.10.3.351] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Numerous group I introns in both prokaryotes and eukaryotes behave as mobile genetic elements. The functional requirements for intron mobility were determined in the T4 phage system using an in vivo assay to measure intron homing with wild-type and mutant derivatives. Thus, it was demonstrated that intron mobility occurs in the context of phage recombination-dependent replication, a pathway that uses overlapping subsets of replication and recombination functions. The functional requirements for intron homing and the nature of recombinant products are only partially consistent with the accepted double-strand-break repair (DSBR) model for intron inheritance, and implicate additional homing pathways. Whereas ambiguities in resolvase requirements and underrepresentation of crossover recombination products are difficult to rationalize strictly by DSBR, these properties are most readily consistent with a synthesis-dependent strand annealing (SDSA) pathway. These pathways share common features in the strand invasion steps, but differ in subsequent repair synthesis and resolution steps, influencing the genetic consequences of the intron transfer event.
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Affiliation(s)
- J E Mueller
- Molecular Genetics Program, State University of New York at Albany 12201-2002 USA
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40
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Birdsell J, Wills C. Significant competitive advantage conferred by meiosis and syngamy in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1996; 93:908-12. [PMID: 8570658 PMCID: PMC40157 DOI: 10.1073/pnas.93.2.908] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The presumed advantages of genetic recombinations are difficult to demonstrate directly. To investigate the effects of recombination and background heterozygosity on competitive ability, we have performed serial-transfer competition experiments between isogenic sexual and asexual strains of the yeast Saccharomyces cerevisiae. The members of these diploid pairs of strains differed only in being heterozygous (sexual) or homozygous (asexual) at the mating type or MAT locus. Competing pairs had either a completely homozygous or a heterozygous genetic background, the latter being heterozygous at many different loci throughout the genome. A round of meiotic recombination (automixis) conferred a large and statistically significant enhancement of competitive ability on sexual strains with a heterozygous genetic background. By contrast, in homozygous background competitions, meiosis decreased the sexual strains' initial relative competitive ability. In all cases, however, the sexual strains outcompeted their isogenic asexual counterparts, whether meiotic recombination had occurred or not. In some genetic backgrounds, this was due in part to an overdominance effect on competitive advantage of heterozygosity at the MAT locus. The advantage of the sexual strains also increased significantly during the course of the homozygous background competitions, particularly when meiosis had occurred. This latter effect either did not occur or was very weak in heterozygous background competitions. Overall, sexual strains with heterozygous genetic backgrounds had a significantly higher initial relative competitive ability than those with homozygous backgrounds. The advantage of mating type heterozygosity in this organism extends far beyond the ability to recombine meiotically.
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Affiliation(s)
- J Birdsell
- Department of Biology, University of California, San Diego, La Jolla 92093-0116, USA
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41
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Affiliation(s)
- C W Anderson
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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42
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Garvik B, Carson M, Hartwell L. Single-stranded DNA arising at telomeres in cdc13 mutants may constitute a specific signal for the RAD9 checkpoint. Mol Cell Biol 1995; 15:6128-38. [PMID: 7565765 PMCID: PMC230864 DOI: 10.1128/mcb.15.11.6128] [Citation(s) in RCA: 517] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A cdc13 temperature-sensitive mutant of Saccharomyces cerevisiae arrests in the G2 phase of the cell cycle at the restrictive temperature as a result of DNA damage that activates the RAD9 checkpoint. The DNA lesions present after a failure of Cdc13p function appear to be located almost exclusively in telomere-proximal regions, on the basis of the profile of induced mitotic recombination. cdc13 rad9 cells dividing at the restrictive temperature contain single-stranded DNA corresponding to telomeric and telomere-proximal DNA sequences and eventually lose telomere-associated sequences. These results suggest that the CDC13 product functions in telomere metabolism, either in the replication of telomeric DNA or in protecting telomeres from the double-strand break repair system. Moreover, since cdc13 rad9 cells divide at a wild-type rate for several divisions at the restrictive temperature while cdc13 RAD9 cells arrest in G2, these results also suggest that single-stranded DNA may be a specific signal for the RAD9 checkpoint.
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Affiliation(s)
- B Garvik
- Department of Genetics, University of Washington, Seattle 98195, USA
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43
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Abstract
Double-strand breaks (DSBs) and single-strand gaps in damaged DNA are efficiently repaired by mechanisms associated with recombination. Recombination is a series of complex biochemical reactions, requiring at least 20 gene products, even in Escherichia coli. Genes homologous to bacterial and yeast recombination genes have been cloned in higher eukaryotes, suggesting there might be a common fundamental mechanism of recombination among a wide variety of species. In eukaryotes, protein-protein interactions play important roles in recombination: by interacting with a specific protein(s), the complex involved in repair of DSBs is modified to carry out specialized cellular functions, such as meiotic recombination and switching of mating types in yeast.
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Affiliation(s)
- A Shinohara
- Department of Biology, Faculty of Science, Osaka University, Japan
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44
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Wu X, Haber JE. MATa donor preference in yeast mating-type switching: activation of a large chromosomal region for recombination. Genes Dev 1995; 9:1922-32. [PMID: 7649475 DOI: 10.1101/gad.9.15.1922] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
During mating-type gene switching in Saccharomyces cerevisiae, DNA at the MAT locus is replaced by sequences copied from one of two unexpressed donor loci, HML or HMR, located near the two ends of the same chromosome and > or = 90 kb from MAT. MATa cells recombine nearly 90% of the time with HML, whereas MAT alpha cells select HMR. MATa donor preference was examined by deleting HML and inserting a donor at other chromosome III locations. MATa activated a large (> or = 40 kb) region near the left end of chromosome III, such that a donor placed at several sites within this domain was strongly preferred over HMR. When inserted outside of this domain, the donor was used equally with HMR. MATa donor preference for HML was abolished by the expression of the negative regulator, MAT alpha 2; however, HML regained its preferred status when the donor was unsilenced. Mating-type-dependent activation of the left end of the chromosome is also observed for other types of recombination that do not involve MAT switching. Spontaneous recombination between two leu2 alleles is 20-30 times higher in MATa than in MAT alpha when one of the leu2 alleles is inserted in place of HML. Transcription in this donor activation region is not affected by mating type. We conclude that MATa donor preference involves a mating-type-regulated change in the accessibility of a large chromosomal domain for recombination.
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Affiliation(s)
- X Wu
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110, USA
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45
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Haber JE. In vivo biochemistry: physical monitoring of recombination induced by site-specific endonucleases. Bioessays 1995; 17:609-20. [PMID: 7646483 DOI: 10.1002/bies.950170707] [Citation(s) in RCA: 162] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The recombinational repair of chromosomal double-strand breaks (DSBs) is of critical importance to all organisms, who devote considerable genetic resources to ensuring such repair is accomplished. In Saccharomyces cerevisiae, DSB-mediated recombination can be initiated synchronously by the conditional expression of two site-specific endonucleases, HO or I-Scel. DNA undergoing recombination can then be extracted at intervals and analyzed. Recombination initiated by meiotic-specific DSBs can be followed in a similar fashion. This type of 'in vivo biochemistry' has been used to describe several discrete steps in two different homologous recombination pathways: gene conversion and single-strand annealing. The roles of specific proteins during recombination can be established by examining DNA in strains deleted for the corresponding gene. These same approaches are now becoming available for the study of recombination in both higher plants and animals. Physical monitoring can also be used to analyze nonhomologous recombination events, whose mechanisms appear to be conserved from yeast to mammals.
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Affiliation(s)
- J E Haber
- Rosenstiel Center, Brandeis University, Waltham, MA 02254-9110, USA
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46
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Higuchi I, Kanemura Y, Shimizu H, Urushihara H. Self- and non-self-recognition in bisexual mating of Dictyostelium discoideum. Dev Growth Differ 1995. [DOI: 10.1046/j.1440-169x.1995.t01-2-00009.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Eggleston AK, O'Neill TE, Bradbury EM, Kowalczykowski SC. Unwinding of nucleosomal DNA by a DNA helicase. J Biol Chem 1995; 270:2024-31. [PMID: 7836428 DOI: 10.1074/jbc.270.5.2024] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have asked whether a DNA helicase can unwind DNA contained within both isolated native chromatin and reconstituted chromatin containing regularly spaced arrays of nucleosome cores on a linear tandem repeat sequence. We find that Escherichia coli recBCD enzyme is capable of unwinding these DNA substrates and displacing the nucleosomes, although both the rate and the processivity of enzymatic unwinding are inhibited (a maximum of 3- and > 25-fold, respectively) as the nucleosome density on the template is increased. The observed rate of unwinding is not affected if the histone octamer is chemically cross-linked; thus, dissociation, or splitting, of the histone octamer is not required for unwinding to occur. The unwinding of native chromatin isolated from HeLa cell nuclei occurs both in the absence and in the presence of linker histone H1. These results suggest that as helicases unwind DNA, they facilitate nuclear processes by acting to clear DNA of histones or DNA-binding proteins in general.
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Affiliation(s)
- A K Eggleston
- Section of Microbiology, University of California, Davis 95616
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48
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Carrasco CD, Buettner JA, Golden JW. Programmed DNA rearrangement of a cyanobacterial hupL gene in heterocysts. Proc Natl Acad Sci U S A 1995; 92:791-5. [PMID: 7846053 PMCID: PMC42706 DOI: 10.1073/pnas.92.3.791] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Programmed DNA rearrangements that occur during cellular differentiation are uncommon and have been described in only two prokaryotic organisms. Here, we identify the developmentally regulated rearrangement of a hydrogenase gene in heterocysts of the cyanobacterium Anabaena sp. strain PCC 7120. Heterocysts are terminally differentiated cells specialized for nitrogen fixation. Late during heterocyst differentiation, a 10.5-kb DNA element is excised from within the hupL gene by site-specific recombination between 16-bp direct repeats that flank the element. The predicted HupL polypeptide is homologous to the large subunit of [NiFe] uptake hydrogenases. hupL is expressed similarly to the nitrogen-fixation genes; hupL message was detected only during the late stages of heterocyst development. An open reading frame, named xisC, identified near one end of the hupL DNA element is presumed to encode the element's site-specific recombinase. The predicted XisC polypeptide is homologous with the Anabaena sp. strain PCC 7120 site-specific recombinase XisA. Neither XisC nor XisA shows sequence similarity to other proteins, suggesting that they represent a different class of site-specific recombinase.
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MESH Headings
- Amino Acid Sequence
- Anabaena/genetics
- Anabaena/growth & development
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Base Sequence
- Cloning, Molecular
- DNA Nucleotidyltransferases/genetics
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Developmental
- Gene Rearrangement
- Genes, Bacterial/genetics
- Integrases
- Molecular Sequence Data
- Oxidoreductases
- RNA, Messenger/biosynthesis
- Recombinases
- Recombination, Genetic/genetics
- Restriction Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- C D Carrasco
- Department of Biology, Texas A&M University, College Station 77843-3258
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49
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Sugawara N, Ivanov EL, Fishman-Lobell J, Ray BL, Wu X, Haber JE. DNA structure-dependent requirements for yeast RAD genes in gene conversion. Nature 1995; 373:84-6. [PMID: 7800045 DOI: 10.1038/373084a0] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In Saccharomyces cerevisiae, HO endonuclease-induced mating-type (MAT) switching is a specialized mitotic recombination event in which MAT sequences are replaced by those copied from a distant, unexpressed donor (HML or HMR). The donors have a chromatin structure inaccessible for both transcription and HO cleavage. Here we use physical monitoring of DNA to show that MAT switching is completely blocked at an early step in recombination in strains deleted for the DNA repair genes RAD51, RAD52, RAD54, RAD55 or RAD57. We find, however, that only RAD52 is required when the donor sequence is simultaneously not silenced and located on a plasmid. RAD51, RAD54, RAD55 and RAD57 are still required when the same transcribed donor is on the chromosome. We conclude that recombination in vivo occurs between DNA molecules in chromatin, whose structure significantly influences the outcome. RAD51, RAD54, RAD55 and RAD57 are all required to facilitate strand invasion into otherwise inaccessible donor sequences.
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Affiliation(s)
- N Sugawara
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110
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50
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Ross-Macdonald P, Roeder GS. Mutation of a meiosis-specific MutS homolog decreases crossing over but not mismatch correction. Cell 1994; 79:1069-80. [PMID: 8001134 DOI: 10.1016/0092-8674(94)90037-x] [Citation(s) in RCA: 298] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MSH4 is a novel meiosis-specific gene required for wild-type levels of spore viability in S. cerevisiae. The predicted product of the MSH4 gene is homologous to the MutS family of proteins; however, msh4-null mutants have no apparent defect in mismatch repair. msh4 mutant strains display wild-type levels of gene conversion and postmeiotic segregation, but they show a reduction in crossing over and a resultant increase in nondisjunction of homologous chromosomes at meiosis I. Immunofluorescence experiments demonstrate that the Msh4 protein is localized to discrete sites on pachytene chromosomes. We propose that Msh4 interacts with a recombination intermediate to influence its resolution.
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Affiliation(s)
- P Ross-Macdonald
- Department of Biology, Yale University, New Haven, Connecticut 06520-8103
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