Formation of circular amplifications inSaccharomyces cerevisiae by a breakage-fusion-bridge mechanism

Moore, Irene K.; Martin, Michael P.; Dorsey, Michael J.; Paquin, Charlotte E.

doi:10.1002/1098-2280(2000)36:2<113::aid-em5>3.0.co;2-t

Cited by 14 publications

(8 citation statements)

References 28 publications

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“…1A; Carson and Hartwell 1985;Weinert and Hartwell 1990;Moore et al 2000;Galgoczy and Toczyski 2001;Ivessa et al 2003). One of the ChrVII homologs contains a copy of the CAN1 gene inserted 25 kb from the left telomere, and the normal CAN1 gene on Chromosome V (ChrV) was mutated to an inactive form.…”

Section: The Chrvii Assaymentioning

confidence: 99%

Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast

Admire¹,

Shanks²,

Danzl³

et al. 2005

Genes Dev.

128

163

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We report here that a normal budding yeast chromosome (ChrVII) can undergo remarkable cycles of chromosome instability. The events associated with cycles of instability caused a distinctive "sectoring" of colonies on selective agar plates. We found that instability initiated at any of several sites on ChrVII, and was sharply increased by the disruption of DNA replication or by defects in checkpoint controls. We studied in detail the cycles of instability associated with one particular chromosomal site (the "403 site"). This site contained multiple tRNA genes known to stall replication forks, and when deleted, the overall frequency of sectoring was reduced. Instability of the 403 site involved multiple nonallelic recombination events that led to the formation of a monocentric translocation. This translocation remained unstable, frequently undergoing either loss or recombination events linked to the translocation junction. These results suggest a model in which instability initiates at specific chromosomal sites that stall replication forks. Forks not stabilized by checkpoint proteins break and undergo multiple rounds of nonallelic recombination to form translocations. Some translocations remain unstable because they join two "incompatible" chromosomal regions. Cycles of instability of this normal yeast chromosome may be relevant to chromosome instability of mammalian fragile sites and of chromosomes in cancer cells.[Keywords: Chromosome instability; checkpoints; fragile sites] Supplemental material is available at http://www.genesdev.org.

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Section: The Chrvii Assaymentioning

confidence: 99%

Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast

Admire¹,

Shanks²,

Danzl³

et al. 2005

Genes Dev.

128

163

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“…These methods provide little or no information about the sequence of the circular DNA. Targeted techniques such as Southern blotting 6,7 , inverse PCR 8 , or fluorescence in situ hybridization 9 provide evidence only about specific eccDNA elements. None of these methods provide the sequence of all existing eccDNA types in a cell population.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Møller

Bojsen

Tachibana

et al. 2016

JoVE

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Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10 10 cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.

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“…Earlier attempts to characterize gene duplication were mainly based on the yeast CUP1 gene dosage selection system, and different mechanisms of primary gene amplification, such as aneuploidization, extrachromosomal amplification or cycle of breakage–fusion–bridge, were described (Whittaker et al , 1988; Spector and Fogel, 1992; Dorsey et al , 1993; Moore et al , 2000). Some DNA content variations of large chromosomal regions were reported as potential large segmental duplications in the Saccharomyces cerevisiae genome (Bach et al , 1995; Roelants et al , 1995; Hughes et al , 2000).…”

Section: Introductionmentioning

confidence: 99%

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments

Koszul

Caburet

Dujon

et al. 2003

EMBO J

194

197

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There is growing evidence that duplications have played a major role in eucaryotic genome evolution. Sequencing data revealed the presence of large duplicated regions in the genomes of many eucaryotic organisms, and comparative studies have suggested that duplication of large DNA segments has been a continuing process during evolution. However, little experimental data have been produced regarding this issue. Using a gene dosage assay for growth recovery in Saccharomyces cerevisiae, we demonstrate that a majority of the revertant strains (58%) resulted from the spontaneous duplication of large DNA segments, either intra-or interchromosomally, ranging from 41 to 655 kb in size. These events result in the concomitant duplication of dozens of genes and in some cases in the formation of chimeric open reading frames at the junction of the duplicated blocks. The types of sequences at the breakpoints as well as their superposition with the replication map suggest that spontaneous large segmental duplications result from replication accidents. Aneuploidization events or suppressor mutations that do not involve largescale rearrangements accounted for the rest of the reversion events (in 26 and 16% of the strains, respectively).

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Formation of circular amplifications inSaccharomyces cerevisiae by a breakage-fusion-bridge mechanism

Cited by 14 publications

References 28 publications

Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast

Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments

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