Physical monitoring of meiotic recombination in Saccharomyces cerevisiae

Meiosis: Dances Between Homologs

The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.

A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation

The development of streamlined and high-throughput sample processing workflows is important for capitalizing on emerging advances and innovations in mass spectrometry-based applications. While the adaptation of new technologies and improved methodologies is fast paced, automation of upstream sample processing often lags. Here we have developed and implemented a semiautomated paramagnetic bead-based platform for isobaric tag sample preparation. We benchmarked the robot-assisted platform by comparing the protein abundance profiles of six common parental laboratory yeast strains in triplicate TMTpro16-plex experiments against an identical set of experiments in which the samples were manually processed. Both sets of experiments quantified similar numbers of proteins and peptides with good reproducibility. Using these data, we constructed an interactive website to explore the proteome profiles of six yeast strains. We also provide the community with open-source templates for automating routine proteomics workflows on an opentrons OT-2 liquid handler. The robot-assisted platform offers a versatile and affordable option for reproducible sample processing for a wide range of protein profiling applications.

Modification of meiotic recombination by natural variation in plants

Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.

Integration of new alternative reference strain genome sequences into the Saccharomyces genome database

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.

Database URL:www.yeastgenome.org

Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae

The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

Tetrad, random spore, and molecular analysis of meiotic segregation and recombination

The power of Saccharomyces cerevisiae as an experimental organism derives from its genetic tractability. Mutant variants can be isolated or constructed and phenotypically characterized with relative ease. In addition, the ability to recover and characterize all four products of meiosis, as haploid spores in a tetrad ascus, greatly facilitates determining the allelic composition of variants, measuring linkage relationships between alleles, and constructing new allele combinations for the analysis of genetic interactions. Saccharomyces cerevisiae also is a preeminent model organism for the study of meiotic recombination, by analysis of tetrads, by analysis of populations of single spores (often called random spore analysis), and by direct monitoring of recombination at the DNA level. This chapter contains methods for tetrad dissection, for random spore preparation, and for preparing DNA for molecular analysis from liquid cultures undergoing synchronous meiosis.

Real-time analysis of double-strand DNA break repair by homologous recombination

The ability to induce synchronously a single site-specific double-strand break (DSB) in a budding yeast chromosome has made it possible to monitor the kinetics and genetic requirements of many molecular steps during DSB repair. Special attention has been paid to the switching of mating-type genes in Saccharomyces cerevisiae, a process initiated by the HO endonuclease by cleaving the MAT locus. A DSB in MATa is repaired by homologous recombination--specifically, by gene conversion--using a heterochromatic donor, HMLα. Repair results in the replacement of the a-specific sequences (Ya) by Yα and switching from MATa to MATα. We report that MAT switching requires the DNA replication factor Dpb11, although it does not require the Cdc7-Dbf4 kinase or the Mcm and Cdc45 helicase components. Using Southern blot, PCR, and ChIP analysis of samples collected every 10 min, we extend previous studies of this process to identify the times for the loading of Rad51 recombinase protein onto the DSB ends at MAT, the subsequent strand invasion by the Rad51 nucleoprotein filament into the donor sequences, the initiation of new DNA synthesis, and the removal of the nonhomologous Y sequences. In addition we report evidence for the transient displacement of well-positioned nucleosomes in the HML donor locus during strand invasion.

Interaction of genetic and environmental factors in Saccharomyces cerevisiae meiosis: the devil is in the details

One of the most important principles of scientific endeavour is that the results be reproducible from lab to lab. Although research groups rarely redo the published experiments of their colleagues, research plans almost always rely on the work of someone else. The assumption is that if the same experiment were repeated in another lab, results would be so similar that the same interpretation would be favoured. This notion allows one researcher to compare his/her own results to earlier work from other labs. An essential prerequisite for this is that the experiments are done in identical conditions and therefore the methodology must be clearly stated. While this may be scientific common sense, adherence is difficult because "standard" methods vary from one laboratory to another in subtle ways that are often not reported. More importantly, for many years the field ofyeast meiotic recombination considered typical differences to be innocuous. This chapter will highlight the documented environmental and genetic variables that are known to influence meiotic recombination in Saccharomyces cerevisiae. Other potential methodological sources of variation in meiotic experiments are also discussed. A careful assessment of the effects of these variables, has led to insights into our understanding of the control of recombination and meiosis.

Minisatellite variants generated in yeast meiosis involve DNA removal during gene conversion

Two yeast minisatellite alleles were cloned and inserted into a genetically defined interval in Saccharomyces cerevisiae. Analysis of flanking markers in combination with sequencing allowed the determination of the meiotic events that produced minisatellites with altered lengths. Tetrad analysis revealed that gene conversions, deletions, or complex combinations of both were involved in producing minisatellite variants. Similar changes were obtained following selection for nearby gene conversions or crossovers among random spores. The largest class of events involving the minisatellite was a 3:1 segregation of parental-size alleles, a class that would have been missed in all previous studies of minisatellites. Comparison of the sequences of the parental and novel alleles revealed that DNA must have been removed from the recipient array while a newly synthesized copy of donor array sequences was inserted. The length of inserted sequences did not appear to be constrained by the length of DNA that was removed. In cases where one or both sides of the insertion could be determined, the insertion endpoints were consistent with the suggestion that the event was mediated by alignment of homologous stretches of donor/recipient DNA.

Restriction of ectopic recombination by interhomolog interactions during Saccharomyces cerevisiae meiosis

In Saccharomyces cerevisiae meiosis, recombination occurs frequently between sequences at the same location on homologs (allelic recombination) and can take place between dispersed homologous sequences (ectopic recombination). Ectopic recombination occurs less often than does allelic, especially when homologous sequences are on heterologous chromosomes. To account for this, it has been suggested that homolog pairing (homolog colocalization and alignment) either promotes allelic recombination or restricts ectopic recombination. The latter suggestion was tested by examining ectopic recombination in two cases where normal interhomolog relationships are disrupted. In the first case, one member of a homolog pair was replaced by a homologous (related but not identical) chromosome that has diverged sufficiently to prevent allelic recombination. In the second case, ndj1 mutants were used to delay homolog pairing and synapsis. Both circumstances resulted in a substantial increase in the frequency of ectopic recombination between arg4-containing plasmid inserts located on heterologous chromosomes. These findings suggest that, during normal yeast meiosis, progressive homolog colocalization, alignment, synapsis, and allelic recombination restrict the ability of ectopically located sequences to find each other and recombine. In the absence of such restrictions, the meiotic homology search may encompass the entire genome.

Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae

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.

The leptotene-zygotene transition of meiosis

The leptotene/zygotene transition of meiosis, as defined by classical cytological studies, is the period when homologous chromosomes, already being discernible individualized entities, begin to be close together or touching over portions of their lengths. This period also includes the bouquet stage: Chromosome ends, which have already become integral components of the inner nuclear membrane, move into a polarized configuration, along with other nuclear envelope components. Chromosome movements, active or passive, also occur. The detailed nature of interhomologue interactions during this period, with special emphasis on the involvement of chromosome ends, and the overall role for meiosis and recombination of chromosome movement and, especially, the bouquet stage are discussed.

Crossover and noncrossover recombination during meiosis: timing and pathway relationships

During meiosis, crossovers occur at a high level, but the level of noncrossover recombinants is even higher. The biological rationale for the existence of the latter events is not known. It has been suggested that a noncrossover-specific pathway exists specifically to mediate chromosome pairing. Using a physical assay that monitors both crossovers and noncrossovers in cultures of yeast undergoing synchronous meiosis, we find that both types of products appear at essentially the same time, after chromosomes are fully synapsed at pachytene. We have also analyzed a situation in which commitment to meiotic recombination and formation of the synaptonemal complex are coordinately suppressed (mer1 versus mer1 MER2++). We find that suppression is due primarily to restoration of meiosis-specific double-strand breaks, a characteristic of the major meiotic recombination pathway. Taken together, the observations presented suggest that there probably is no noncrossover-specific pathway and that restoration of intermediate events in a single pairing/recombination pathway promotes synaptonemal complex formation. The biological significant of noncrossover recombination remains to be determined, however.

Meiosis-specific arrest revealed in DNA topoisomerase II mutants

Although the processes of mitosis and meiosis are similar, there is evidence for fundamental regulatory differences between the two. To examine these differences, we have compared the meiotic phenotype of DNA topoisomerase II mutants with their previously described mitotic phenotype (C. Holm, T. Goto, J. Wang, and D. Botstein, Cell 41:553-563, 1985). top2 mutants in meiosis show no defects in the latest detectable stages of recombination, yet they arrest prior to spindle establishment at meiosis I. Fluorescence and electron microscopy reveal that top2 mutants exhibit wild-type levels of meiotic chromosome condensation and form morphologically normal synaptonemal complex but are delayed in the exit from pachytene. Arrested cells retain viability and form colonies if transferred to mitotic medium. Our results suggest that the top2 meiotic arrest is regulatory in nature. This arrest may have evolved to ensure the resolution of fortuitous tangles between nonhomologous chromosomes.

Meiosis-specific arrest revealed in DNA topoisomerase II mutants

Although the processes of mitosis and meiosis are similar, there is evidence for fundamental regulatory differences between the two. To examine these differences, we have compared the meiotic phenotype of DNA topoisomerase II mutants with their previously described mitotic phenotype (C. Holm, T. Goto, J. Wang, and D. Botstein, Cell 41:553-563, 1985). top2 mutants in meiosis show no defects in the latest detectable stages of recombination, yet they arrest prior to spindle establishment at meiosis I. Fluorescence and electron microscopy reveal that top2 mutants exhibit wild-type levels of meiotic chromosome condensation and form morphologically normal synaptonemal complex but are delayed in the exit from pachytene. Arrested cells retain viability and form colonies if transferred to mitotic medium. Our results suggest that the top2 meiotic arrest is regulatory in nature. This arrest may have evolved to ensure the resolution of fortuitous tangles between nonhomologous chromosomes.

A promoter deletion reduces the rate of mitotic, but not meiotic, recombination at the HIS4 locus in yeast

Several investigators have reported that transcription stimulates some types of mitotic recombination in the yeast Saccharomyces cerevisiae. We find that mutations that reduce the rate of transcription of the yeast HIS4 gene in vegetative cells reduce the frequency of mitotic, but not meiotic, recombination events.

Pulsed-field gel analysis of the pattern of DNA double-strand breaks in the Saccharomyces genome during meiosis

Pulsed-field gel electrophoresis (PFGE) has been used to study the timing, frequency, and distribution of double-strand breaks (DSBs) in chromosomal-sized DNA during meiosis in yeast. It has previously been shown that DSBs are associated with some genetic hotspots during recombination, and it is important to know whether meiotic recombination events routinely initiate via DSBs. Two strains have been studied here--a high-sporulating homothallic wild type and a congenic mutant strain carrying a rad50S mutation. This mutant has previously been reported to accumulate broken molecules in meiosis to much higher frequencies than wild type and to abolish the characteristic wild-type processing of DNA that has been observed at the break sites. When whole chromosomes are resolved by PFGE, both strains show some broken molecules starting at the time that cells commit to genetic recombination. Breakage has been assessed primarily on Chromosome III and Chr. XV, using Southern hybridization to identify these chromosomes and their fragments. At any one time, break frequency in wild type is much lower than the cumulative frequency of recombination events that occur during meiosis. However, there is suggestive evidence that each break is short-lived, and it is therefore difficult to estimate the total number of breaks that may occur. In rad50S, chromosome breaks accumulate to much higher levels, which are probably broadly consistent with the estimated number of recombination events in wild type. However, since rad50S is substantially defective in completing recombination, it is not known for certain if it initiates events at wild-type frequencies. A surprising feature of the data is that a strong banding pattern is observed in the fragment distribution from broken chromosomes in both strains, implying that at least much of the breakage occurs at specific sites or within short regions. However, with the exception of the rDNA region on Chr. XII, assessment of the genetic map indicates that recombination can occur almost anywhere in the genome, although some regions are much hotter than others. Possible reasons for this apparent paradox are discussed. It may in part result from breakage levels too low for adequate detection in cold regions but may also imply that recombination events are localized more than previously realized. Alternatively, there may be a more indirect relationship between break sites and the associated recombination events.

The TSM1 gene of Saccharomyces cerevisiae overlaps the MAT locus

We have cloned the region from MAT to THR4 on chromosome III of Saccharomyces cerevisiae. Although the region is only 15 kb, the two loci are genetically separated by 22 cM. This is in sharp contrast to the very low level of recombination (2 cM in 22 kb) that is observed in the adjacent CRY1-MAT interval, and suggests that there may be a "hot spot" for recombination in the MAT-THR4 region. The DNA sequence of the first 4.4 kb distal to MAT reveals an open reading frame that we have identified as the essential gene, TSM1. Surprisingly, the TSM1 open reading frame of 1,410 amino acids extends into the MAT locus, such that the 3'-end of the MAT alpha 1 transcript ends 15 bp from the 3'-end of the TSM1 open reading frame.

Synchronized meiosis and recombination in fission yeast: observations with pat1-114 diploid cells

The mutation pat1-114 has been used to synchronize meiosis in the fission yeast Schizosaccharomyces pombe. We have investigated several aspects of such synchronized meiotic cultures. In both pat1-114 and pat1+ diploids, meiotic landmark events are initiated at the same time after meiosis induction, but synchrony is much more pronounced in the pat1-114-driven meiosis. Commitment to recombination and to meiosis have been timed at 2 h after meiotic induction. Due to a seven-fold reduction of intragenic recombination frequency in the ade6 region of pat1-114 diploids, physical analysis of recombination has not been possible. We have distinguished three factors that influence intragenic recombination frequencies: temperature, azygotic versus zygotic meiosis, and the nature of the pat1 allele. Differences and similarities in the timing of meiotic landmarks in S. cerevisiae and S. pombe are discussed.

The frequency of meiotic recombination in yeast is independent of the number and position of homologous donor sequences: implications for chromosome pairing

We constructed diploids of Saccharomyces cerevisiae homozygous for LEU2 and carrying one, two, or four copies of leu2 at ectopic locations and determined the frequency of 3+:1- (LEU2:leu2) meiotic tetrads. Gene conversion between a LEU2 recipient and a leu2 ectopic donor occurred at the same frequency as did gene conversion between allelic copies of LEU2 and leu2. An increase in the number of possible ectopic donor loci did not lead to a proportional increase in the level of ectopic gene conversion. We suggest that the limiting step in meiotic recombination is the activation of a locus to become a recipient in recombination and that once activated, a locus can search the entire genome for a homologous partner with which to recombine. In this respect, this search for a homologous partner resembles the efficient premeiotic methylation/inactivation of duplicated sequences in Ascobolus and Neurospora. These observations support models in which strand exchange serves to align homologous chromosomes prior to their becoming much more fully synapsed by the elaboration of the synaptonemal complex.

Unequal crossing-over and gene conversion at the amplified CUP1 locus of yeast

Meiotic recombination was analyzed between two twelve-copy arrays of a gene amplification at the CUP1 locus of Saccharomyces cerevisiae. Utilizing Southern analysis to identify spores with non-parental repeat arrays, we find that approximately 11% of a sample with 202 unselected tetrads possess at least one nonparental spore array. Both reciprocal and non-reciprocal changes are observed. The data suggest a model in which frequent mispairing among identical copies of the 2.0 kb repeat unit leads to the formation of unpaired loops containing integral numbers of repeat units. In this model, conversions involving the loops lead to non-reciprocal changes in arrays: about half are associated with reciprocal exchange, and net increases in repeat unit numbers occur about as frequently as net decreases. Thus, the known properties of gene conversion can account for all the segregations we observe.

Double-strand breaks at an initiation site for meiotic gene conversion

It has been proposed that the initiation of meiotic recombination involves either single-strand or double-strand breaks in DNA. It is difficult to distinguish between these on the basis of genetic evidence because they give rise to similar predictions. All models invoke initiation at specific sites to explain polarity, which is a gradient in gene conversion frequency from one end of a gene to the other. In the accompanying paper we describe the localization of an initiation site for gene conversion to the promoter region of the ARG4 gene of the yeast Saccharomyces cerevisiae. Here, we show that a double-strand break appears at the ARG4 recombination initiation site at the time of recombination, and that the broken DNA molecules end in long single-stranded tails.

A DNA sequence conferring high postmeiotic segregation frequency to heterozygous deletions in Saccharomyces cerevisiae is related to sequences associated with eucaryotic recombination hotspots

The meiotic behavior of two graded series of deletion mutations in the ADE8 gene in Saccharomyces cerevisiae was analyzed to investigate the molecular basis of meiotic recombination. Postmeiotic segregation (PMS) was observed for a subset of the deletion heterozygosities, including deletions of 38 to 93 base pairs. There was no clear relationship between deletion length and PMS frequency. A common sequence characterized the novel joint region in the alleles which displayed PMS. This sequence is related to repeated sequences recently identified in association with recombination hotspots in the human and mouse genomes. We propose that these particular deletion heterozygosities escape heteroduplex DNA repair because of fortuitous homology to a binding site for a protein.

A DNA sequence conferring high postmeiotic segregation frequency to heterozygous deletions in Saccharomyces cerevisiae is related to sequences associated with eucaryotic recombination hotspots

The meiotic behavior of two graded series of deletion mutations in the ADE8 gene in Saccharomyces cerevisiae was analyzed to investigate the molecular basis of meiotic recombination. Postmeiotic segregation (PMS) was observed for a subset of the deletion heterozygosities, including deletions of 38 to 93 base pairs. There was no clear relationship between deletion length and PMS frequency. A common sequence characterized the novel joint region in the alleles which displayed PMS. This sequence is related to repeated sequences recently identified in association with recombination hotspots in the human and mouse genomes. We propose that these particular deletion heterozygosities escape heteroduplex DNA repair because of fortuitous homology to a binding site for a protein.

Meiotic recombination in yeast: alteration by multiple heterozygosities

Although meiotic gene conversion has long been known to be accompanied by crossing-over, a direct test of the converse has not been possible. An experiment was designed to determine whether crossing-over is accompanied by gene conversion in Saccharomyces cerevisiae. Nine restriction site heterologies were introduced into a 9-kilobase chromosomal interval that exhibits 22 percent crossing-over. Of all the exchange events that occurred, at least 59 percent of meiotic crossovers are accompanied by gene conversion of one or more of the restriction site heterologies. The average gene conversion tract length was 1.5 kilobases. An unexpected result was that the introduction of as few as seven heterozygosities significantly altered the outcome of recombination events, reducing the frequency of crossovers by 50 percent and increasing the number of exceptional tetrads. This alteration results from a second recombination event induced by repair of heteroduplex DNA containing multiple mismatched base pairs.

Gene conversion, unequal crossing-over and mispairing at a non-tandem duplication during meiosis of Saccharomyces cerevisiae

We have developed a novel system to examine conversion, exchange and mispairing involving a non-tandem duplication of the ade8 locus in yeast by monitoring the segregation of heterozygous markers between the duplicated sequence. Plasmid Yrp17 carries the yeast selectable markers URA3+ and TRP1+. Yrp17 derivatives with a 4 kb insert carrying ade8-18 were used to clone the mutations trp1-1 and ura3-1 by gap repair. Integrants of the resulting plasmids at the Ade8 locus were crossed to yield diploid hybrids with a non-tandem duplication of Ade8 and heterozygosity for the plasmid markers between the duplicated sequences. 1192 complete, unselected asci were analyzed and 270 exhibiting recombination of the markers contributed by the plasmid were analyzed by Southern transfers to detect changes in plasmid sequences. Twenty-seven tetrads had unequal homologous exchanges and five had unequal sister-chromatid exchanges. Seven tetrads carry an additional copy of the integrated plasmid and ten are missing one. We propose that these two classes represent conversions of the entire 11 kb plasmid, which occur after misalignment and formation of an unpaired loop. Mispairing is a frequent event, and occurs in approximately fifty percent of all meioses. The system described provides a means to determine the meiotic rules of conversion, exchange and pairing for duplicated DNA sequences.

The evolutionarily conserved repetitive sequence d(TG.AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis

We have studied the genetic behavior of the alternating copolymer d(TG.AC)n inserted into a defined position in the genome of the yeast Saccharomyces cerevisiae. When d(TG.AC)n sequences were present at the HIS3 locus on homologous chromosomes, diploid cells undergoing meiosis generated an excess of tetrads containing reciprocally recombined products with crossover points close to the repetitive DNA insert. Most of these tetrads exhibited gene conversion of a d(TG.AC)n insert. However, the insertion of d(TG.AC)n sequences had no effect on the frequency of gene conversion of closely linked marker genes. Surprisingly, when d(TG.AC)n sequences were present on only one homolog at the HIS3 locus, one-half of the tetrads exhibiting nonparental segregation for marker genes that flanked the repetitive DNA insert were very unusual and appeared to have arisen by multiple recombination events in the vicinity of the d(TG.AC)n insert. Similar multiply recombinant tetrads were seen in crosses in which d(TG.AC)n sequences were present on both homologs. Combined, the data strongly suggest that d(TG.AC)n sequences significantly enhance reciprocal meiotic recombination and may be important in causing multiple recombination events to occur within a relatively small region of the yeast chromosome. Molecular evidence is presented that clearly documents the postmeiotic segregation of an 80-base stretch of d(TG.AC)n.

The evolutionarily conserved repetitive sequence d(TG.AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis

We have studied the genetic behavior of the alternating copolymer d(TG.AC)n inserted into a defined position in the genome of the yeast Saccharomyces cerevisiae. When d(TG.AC)n sequences were present at the HIS3 locus on homologous chromosomes, diploid cells undergoing meiosis generated an excess of tetrads containing reciprocally recombined products with crossover points close to the repetitive DNA insert. Most of these tetrads exhibited gene conversion of a d(TG.AC)n insert. However, the insertion of d(TG.AC)n sequences had no effect on the frequency of gene conversion of closely linked marker genes. Surprisingly, when d(TG.AC)n sequences were present on only one homolog at the HIS3 locus, one-half of the tetrads exhibiting nonparental segregation for marker genes that flanked the repetitive DNA insert were very unusual and appeared to have arisen by multiple recombination events in the vicinity of the d(TG.AC)n insert. Similar multiply recombinant tetrads were seen in crosses in which d(TG.AC)n sequences were present on both homologs. Combined, the data strongly suggest that d(TG.AC)n sequences significantly enhance reciprocal meiotic recombination and may be important in causing multiple recombination events to occur within a relatively small region of the yeast chromosome. Molecular evidence is presented that clearly documents the postmeiotic segregation of an 80-base stretch of d(TG.AC)n.

Recombination hot spot in the human beta-globin gene cluster: meiotic recombination of human DNA fragments in Saccharomyces cerevisiae

We describe a novel system for the analysis of sequence-specific meiotic recombination in Saccharomyces cerevisiae. A comparison of three adjacent restriction fragments from the human beta-globin locus revealed that one of them, previously hypothesized to contain a relative hot spot for genetic recombination, engages in reciprocal exchange during yeast meiosis significantly more frequently than either of the other two fragments. Removal of the longest of four potential Z-DNA-forming regions from this fragment does not affect the high frequency of genetic recombination.

Properties of spontaneous mitotic recombination occurring in the presence of the rad52-1 mutation of Saccharomyces cerevisiae

All major recombination pathways in the yeastSaccharomyces cerevisiaerequire theRAD52gene product. We have examined the effect of therad52-1mutation on spontaneous mitotic recombination between heteroalleles, and found that prototrophs are produced at frequencies significantly above reversion. This residual recombination occurs at a relatively uniform level at all of the loci examined. To help understand the role thatRAD52plays in mitotic recombination, we examined recombination between all pairwise combinations of six mutant alleles of theLYS2gene. Therad52-1mutation decreased the variation in amount of recombination between the various pairwise combinations as well as lowering the overall frequency of recombination. The reduced variation results in a different pattern of recombination inrad52-1cells than in wild type. One interpretation of these results is that theRAD52gene product, directly or indirectly, plays a role in the formation or the resolution of mismatches in heteroduplex DNA.

Recombination hot spot in the human beta-globin gene cluster: meiotic recombination of human DNA fragments in Saccharomyces cerevisiae

We describe a novel system for the analysis of sequence-specific meiotic recombination in Saccharomyces cerevisiae. A comparison of three adjacent restriction fragments from the human beta-globin locus revealed that one of them, previously hypothesized to contain a relative hot spot for genetic recombination, engages in reciprocal exchange during yeast meiosis significantly more frequently than either of the other two fragments. Removal of the longest of four potential Z-DNA-forming regions from this fragment does not affect the high frequency of genetic recombination.