Reduced Mismatch Repair of Heteroduplexes Reveals “Non”-interfering Crossing Over in Wild-Type Saccharomyces cerevisiae

Abstract

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...

Hot Regions of Noninterfering Crossovers Coexist with a Nonuniformly Interfering Pathway inArabidopsis thaliana

“…Indeed, one already knows that double-strand breaks mature into crossovers or into noncrossovers in proportions depending on the locus (Mancera et al 2008); such a propensity may extend to the choice of using one CO pathway rather than the other. Differences in the treatment of double-strand breaks may in fact tie in with the different mechanisms that are used for mis-match repair in the two pathways of CO formation (Getz et al 2008).…”

Serendipity and the times

“…My genetic studies with T4, 7,8 were complemented by a bit of kibitzing, 9 followed by studies with Lambda 10,12 and then with yeast. [13][14][15][16][17] Throughout, I had the privilege of teaching courses in genetics and the pleasure of deeply rewarding sabbatical leaves in Cambridge UK (with Sidney Brenner and Francis Crick), 18 Edinburgh (with Noreen and Ken Murray), Jerusalem (with Giora Simchen), and Cambridge MA (with Maury Fox and David Botstein). Teaching lab courses in bacteriophage (Cold Spring Harbor, Naples and Bombay) sometimes started me smoking again.…”

On Spo16 and the Coefficient of Coincidence

“…Zalevsky et al (1999) proposed that these crossovers represent a class of crossovers in wild-type yeast that serve to promote chromosome pairing. That proposal has received its most direct support from the observation of a class of crossovers in wild-type yeast, identifiable by their frequent evasion of mismatch repair, that lack positive interference and have a frequency that is independent of Msh4 (Getz et al 2008).…”

“…Because the two-pathway interpretation restricts interference to the disjunction phase [ignoring the possibility of negative interference between interfering and noninterfering crossovers (Getz et al 2008)], the observed frequency of double crossovers becomes…”

“…Values of the ratio of interfering to noninterfering crossovers, needed to evaluate Equation 3, may be obtained from data on zmm mutants such as msh4, and presumably zip1, where the density of residual crossovers reflects the density of noninterfering crossovers (Getz et al 2008). According to the zip1 data of Shinohara et al (2008) and the msh4 data of Stahl et al (2004), the relative densities of the two types of crossovers on chromosome III appear to be close to 1/1, perhaps varying among intervals over a range from 1/3 to 3/1.…”