Effect of donor copy number on the rate of gene conversion in the yeast Saccharomyces cerevisiae

Melamed, C; Kupiec, Martin

doi:10.1007/bf00286186

Cited by 17 publications

(11 citation statements)

References 18 publications

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“…A previous study revealed that recombination events promoted by the HO endonuclease occur with similar frequency regardless of the location of the recombining sequences within the genome, consistent with the idea that a homology search mechanism may facilitate such events (Haber and Leung, 1996). It has also been demonstrated that increasing the copy number of a sequence can increase the likelihood a sequence will undergo recombination, suggesting that recombination is stimulated by increasing the frequency with which sequences interact (Melamed and Kupiec, 1992). Collision frequency may play a greater role in promoting recombinational repair of a broken dicentric chromosome, where each half of the broken chromosome is actively separated from the other, than it does in repair of other types of DSBs.…”

Section: Discussionsupporting

confidence: 62%

Nuclear oscillations and nuclear filament formation accompany single-strand annealing repair of a dicentric chromosome in Saccharomyces cerevisiae

Thrower

Yeh

Bloom

2003

Journal of Cell Science

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IntroductionThe study of DNA repair mechanisms has been aided by the development of experimental systems that generate DNA double-strand breaks (DSBs) at specific chromosomal locations and during defined periods of the cell cycle. One such system is the budding yeast conditional dicentric chromosome (Hill and Bloom, 1989). This inducible dicentric chromosome was constructed by inserting a second copy of centromere 3 (CEN3) into chromosome III, approximately 45 kb upstream of the endogenous centromere 3 (Fig. 1A). The inserted centromere is under control of the GAL1 promoter, allowing for the reversible inactivation of this centromere when cells are grown in the presence of galactose. Studies utilizing dicentric chromosomes are unique in that DSBs are generated by mitotic pulling forces when centromeres on the same sister chromatid are aligned to opposite spindle poles during mitosis. Previous work showed that efficient healing of a broken dicentric chromosome in Saccharomyces cerevisiae requires RAD52, indicating that repair occurs primarily through homologous recombination . In cells lacking RAD52, infrequent dicentric chromosome repair events occur through non-homologous end joining (Kramer et al., 1994).Resolution of a conditional dicentric chromosome is accompanied by the deletion of one centromere and the intervening DNA. These events were initially thought to result from gene conversion (GC) accompanied by crossover (Jager and Philippsen, 1989). However, other studies of direct repeat recombination have shown that deletions commonly occur without generating the circular product predicted to form through a crossover event (Fishman-Lobell et al., 1992). Moreover, many deletion events are dependent on RAD1 and RAD10 (Klein, 1988;Schiestl and Prakash, 1990;Ivanov and Haber, 1995). The Rad1 and Rad10 proteins form a structurespecific endonuclease that generates 5′ single-stranded ends (Siede et al., 1993). These genes function in a recombination pathway known as single-strand annealing (SSA) (Sugawara and Haber, 1992;Sung et al., 1993;Ivanov and Haber, 1995). The recognition of SSA as a major pathway for direct repeat recombination suggests that this mechanism plays a role in the repair of a dicentric chromosome.Previous studies have shown that recombination frequency is primarily governed by the degree of sequence homology rather than the location of the recombining sequences within the genome (Haber and Leung, 1996). This implies the existence of a homology search mechanism as part of the recombination process. The integration of E. coli lacO and tetO sequences into chromosomes of yeast strains encoding lac repressor-GFP and tet repressor-GFP fusion proteins has recently provided visual evidence of long-distance interactions between like sequences (Aragon- Alcaide and Strunnikov, 2000). Such interactions may represent a constitutive homology search process. The mechanisms that bring homologous sequences into close association are unknown. Efficient meiotic recombination in the fission yeast Schizosaccharomyce...

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Section: Discussionsupporting

confidence: 62%

Nuclear oscillations and nuclear filament formation accompany single-strand annealing repair of a dicentric chromosome in Saccharomyces cerevisiae

Thrower

Yeh

Bloom

2003

Journal of Cell Science

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“…Although limited, these data are consistent with dependence of recombinational repair frequency on inter-locus collision rate. A similar conclusion was drawn from a third study in which the frequency of recombination between a chromosomal locus and an homologous sequence increased when an increased number of copies of the partner sequence were provided on a multicopy plasmid (Melamed and Kupiec 1992).…”

Section: Implications For Other Cellular Processes That Involve Intersupporting

confidence: 68%

Collisions between yeast chromosomal loci in vivo are governed by three layers of organization

Burgess

Kleckner

1999

Genes & Development

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The relative probabilities that different pairs of chromosomal loci will collide with one another in vegetatively growing diploid yeast cells have been assessed using a genetic assay for Cre/loxP site-specific recombination. Recombination rates have been determined for 18 different pairs of loxP sites representing diverse pairs of positions within the genome. Overall, relative collision probabilities vary over an eightfold range. Within this range, a hierarchy comprising three levels of organization can be discerned. First, collisions between loci on nonhomologous chromosomes are governed by nonspecific centromere clustering. Second, a sequence is closer to allelic or nearby sequences on its homolog than to sequences on nonhomologous chromosomes, an effect most simply attributed to homolog pairing. Third, a sequence can be closer to other sequences nearby on the same chromosome than to sequences on other chromosomes. These findings provide a framework for assessing the role of chromosome disposition in cellular processes such as DNA repair and gene expression. Also the possibility is raised that genome-wide coalignment of homologs is not the fundamental raison d'etre of the somatic pairing process. We suggest instead that pairing may exist to promote juxtaposition of homologous regions within irregular genome complements. Chromosome organization, disposition, and behavior have been investigated by many experimental approaches. A handful of studies have used site-specific recombination reactions to probe chromosome status in living cells. In bacteria, the phage Int reaction has been used to assess in vivo supercoiling levels (Bliska and Cozzarelli 1987); the bacteriophage P1 Cre/loxP recombination reaction has been used to assess effective DNA concentration (Hildebrandt and Cozzarelli 1995); and the ␥-␦ resolvase reaction has been used to probe for domainal organization of chromosomes (e.g., Staczek and Higgins 1998). Also, in Drosophila, the yeast Flp/frt recombination reaction has been used to assess the effect of chromosomal inversions on pairing of allelic regions lying distal to the rearrangement breakpoints (Golic and Golic 1996b) and to compare intrachromosomal versus interchromosomal recombination rates (Golic and Golic 1996a).The current study exploits Cre/loxP site-specific recombination to examine chromosome status in vegetatively growing diploid budding yeast cells. A genetic assay for Cre/loxP recombination in yeast has been developed and used to determine in vivo recombination rates for 18 different pairs of loxP inserts representing various pairs of positions within the genome. The goal of this study was to assess the relative probabilities with which different regions of the genome collide with one another. Cre/loxP recombination seemed to be an appropriate tool for such analysis because the amount of product formed depends on the square of the loxP concentration in vitro and retains its dependence on loxP concentration in vivo in Escherichia coli (Hildebrandt and Cozzarelli 1995). Thus, the relat...

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“…It has been shown that the rate of gene conversion for a given gene increases in proportion to the number of available, identical donor sequences (Melamed and Kupiec 1992). By extension, one might assume that the larger the multigene family to which a gene belongs, the more likely it would be to undergo gene conversion.…”

Section: Discussionmentioning

confidence: 99%

“…This reflects increasing sequence divergence between members of larger families due to the ''single-link'' method of constructing multigene families. Melamed and Kupiec (1992) have demonstrated that for a given yeast gene, the frequency of gene conversion is proportional to the number of homologous sequences available for conversion. This effect might have been evident as a positive correlation between gene conversion frequency and the number of BLASTP hits for the genes in the present data.…”

Section: Gene Conversionmentioning

confidence: 99%

Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

1999

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A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only 2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative rates of duplication and deletion may contribute to the compactness of the C. elegans genome.

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Effect of donor copy number on the rate of gene conversion in the yeast Saccharomyces cerevisiae

Cited by 17 publications

References 18 publications

Nuclear oscillations and nuclear filament formation accompany single-strand annealing repair of a dicentric chromosome in Saccharomyces cerevisiae

Nuclear oscillations and nuclear filament formation accompany single-strand annealing repair of a dicentric chromosome in Saccharomyces cerevisiae

Collisions between yeast chromosomal loci in vivo are governed by three layers of organization

Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

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