We previously proposed a "counting model" for meiotic crossover interference, in which double-strand breaks occur independently and a fixed number of noncrossovers occur between neighboring crossovers. Whereas in some organisms (group I) this simple model alone describes the crossover distribution, in other organisms (group II) an additional assumption-that some crossovers lack interference-improves the fit. Other differences exist between the groups: Group II needs double-strand breaks and some repair functions to achieve synapsis, while repair in group I generally occurs after synapsis is achieved; group II, but not group I, has recombination proteins Dmc1, Mnd1, and Hop2. Here we report experiments in msh4 mutants that are designed to test predictions of the revised model in a group II organism. Further, we interpret these experiments, the above-mentioned differences between group I and II meiosis, and other data to yield the following proposal: Group II organisms use the repair of leptotene breaks to promote synapsis by generating double-Holliday-junction intermediates that lock homologs together (pairing pathway). The possible crossover or noncrossover resolution products of these structures lack interference. In contrast, for both group I and group II, repair during pachytene (disjunction pathway) is associated with interference and generates only two resolution types, whose structures suggest that the Holliday junctions of the repair intermediates are unligated. A crossover arises when such an intermediate is stabilized by a protein that prevents its default resolution to a noncrossover. The protein-binding pattern required for interference depends on clustering of sites that have received, or are normally about to receive, meiotic double-strand breaks.A key feature of meiosis in most organisms is crossing map) and still beguiles geneticists, microscopists, and mathematicians alike. over, the process in which homologous chromosomes exchange segments during the repair of programmed A mathematical model that effectively describes linkage data from the X chromosome of Drosophila (McPeek and double-strand breaks (DSBs) in their DNA. The frequencies of crossing over provide the basis for genetic Speed 1995; Zhao et al. 1995) was put forth by Cobbs (1978) and Stam (1979). Their model, notable for its linkage mapping (Sturtevant 1913), in which the dissimplicity and mathematical tractability, was foreshadtance between genes (in morgans) is defined as the owed by several others (reviewed in Bailey 1961). It average number of points of crossing over in the interval describes the probability distribution for the linkage that separates the genes (Haldane 1919). Sturtevant distances (in morgans) between adjacent crossovers as (1915) and Muller (1916) noted that crossovers occura scaled chi-square probability distribution with an even ring during Drosophila melanogaster oogenesis show a kind number of degrees of freedom. Such a distribution of territoriality-a relatively equitable, nonrandom disgained biolog...

The function and regulation of DNA methylation in eukaryotes remain unclear. Genes affecting methylation were identified in the fungus Neurospora crassa. A mutation in one gene, dim-2, resulted in the loss of all detectable DNA methylation. Abnormal segregation of the methylation defects in crosses led to the discovery that the methylation mutants frequently generate strains with extra chromosomes or chromosomal parts. Starvation for S-adenosylmethionine, the presumed methyl group donor for DNA methylation, also produced aneuploidy. These results suggest that DNA methylation plays a role in the normal control of chromosome behavior.

Using small palindromes to monitor meiotic double-strand-break-repair (DSBr) events, we demonstrate that two distinct classes of crossovers occur during meiosis in wild-type yeast. We found that crossovers accompanying 5:3 segregation of a palindrome show no conventional (i.e., positive) interference, while crossovers with 6:2 or normal 4:4 segregation for the same palindrome, in the same cross, do manifest interference. Our observations support the concept of a ''non''-interference class and an interference class of meiotic double-strand-break-repair events, each with its own rules for mismatch repair of heteroduplexes. We further show that deletion of MSH4 reduces crossover tetrads with 6:2 or normal 4:4 segregation more than it does those with 5:3 segregation, consistent with Msh4p specifically promoting formation of crossovers in the interference class. Additionally, we present evidence that an ndj1 mutation causes a shift of noncrossovers to crossovers specifically within the ''non''-interference class of DSBr events. We use these and other data in support of a model in which meiotic recombination occurs in two phases-one specializing in homolog pairing, the other in disjunction-and each producing both noncrossovers and crossovers. I N yeast, deletion of the meiosis-specific gene MSH4, which, despite its name, is said to have no involvement in mismatch repair (Ross-Macdonald and Roeder 1994), usually leaves residual crossovers, and these crossovers have reduced interference (Novak et al. 2001). In Caenorhabditis elegans, however, which is characterized by strong crossover interference as well as by cis-acting ''pairing centers'' that promote synapsis of homologous chromosomes (Dernburg et al. 1998;MacQueen et al. 2005;Phillips and Dernburg 2006), deletion of him-14, a homolog of MSH4, eliminates essentially all crossing over while apparently leaving intact the ability to repair meiotic double-strand breaks (Zalevsky et al. 1999). On the basis of these data, Zalevsky et al. (1999) suggested that yeast, and other creatures lacking pairing centers, have two kinds of crossing over, one of which is Msh4 independent, has little or no crossover interference, and serves to establish effective pairing of homologous chromosomes. Stahl et al. (2004) noted that the concept of two kinds of crossing over provides an explanation for the apparent correlation between the strength of interference and the fraction of crossovers that are Msh4 dependent in a given interval. Furthermore, Malkova et al. (2004), using a statistical analysis, which in the light of information presented here appears oversimplified, reported that the distribution of crossovers along the left arm of chromosome VII in wild-type yeast was better described by a two-kinds-of-crossover model than by the simple ''counting model'' for interference (Foss et al. 1993). More compelling support came from the phenotype of mms4 and mus81 deletions. Each of these mutations caused a reduction in crossing over but not in interference, while deletion of MMS4 a...

Be that as it may, Duesberg's rejoinders to all objections reminded me of the old story of the man who complained to a psychiatrist that he thought he was dead. The psychiatrist then asked whether dead men bleed, and on receiving a negative answer, took out a lancet and stuck the patient's finger. The man stared at his bleeding finger for a moment and then said, "Well, I guess dead men do bleed."

Several apparently paradoxical observations regarding meiotic crossing over and gene conversion are readily resolved in a framework that recognizes the existence of two recombination pathways that differ in mismatch repair, structures of intermediates, crossover interference, and the generation of noncrossovers. One manifestation of these differences is that simultaneous gene conversion on both sides of a recombination-initiating DNA double-strand break (''two-sidedness'') characterizes only one of the two pathways and is promoted by mismatch repair. Data from previous work are analyzed quantitatively within this framework, and a molecular model for meiotic double-strand break repair based on the concept of sliding D-loops is offered as an efficient scheme for visualizing the salient results from studies of crossing over and gene conversion, the molecular structures of recombination intermediates, and the biochemical competencies of the proteins involved. E UKARYOTES transit from the diplophase to the haplophase via meiosis, which is associated with a number of interrelated processes, including crossing over and gene conversion. These processes involve meiosisspecific, programmed DNA double-strand breaks (DSBs) and their repair (DSBr). DSBr, in turn, is associated with mismatched base pairs and their rectification, referred to as ''mismatch repair '' or MMR (Bishop et al. 1987). Current efforts to accommodate both the genetic and molecular phenomena associated with meiotic DSBr in yeast (Saccharomyces cerevisiae) have been thoroughly reviewed (e.g., Hollingsworth and Brill 2004;Hoffmann and Borts 2004;Surtees et al. 2004;Hunter 2007;Berchowitz and Copenhaver 2010), but none of the reviews commits to an overall picture with quantitative predictions. This work aims to remedy that lack. Specifically, we have made use of salient published studies to develop, step-by-step, a comprehensive model of meiotic DSBr and MMR. The main features of this model are summarized in Table 1. RESULTSFor readers who are unfamiliar with yeast genetics and/or the known details of MMR, we begin by reviewing (1) the basic principles and vocabulary of tetrad analysis in yeast, which expose the products of individual acts of meiosis, (2) the DSBr model of Szostak et al. (1983) as modified by Sun et al. (1991), which has provided a basic molecular interpretation of meiotic recombination, and (3) the known roles of mismatchrepair proteins such as Msh2 and Mlh1.Relative frequencies of tetrad types provide measures of linkage distance and crossover interference: Consider a population of diploid yeast cells heterozygous for two linked sites, A/a and D/d. When meiosis proceeds without a hitch, the resulting tetrads each contain four viable haploid spores. Because the genotypes of the spores are identifiable by the phenotypes of the colonies they give rise to, each spore in the tetrad can be characterized as a crossover or a noncrossover with respect to sites A/a and D/d. When the A/a and D/d sites are closely linked, the most frequent ...