Mms4 chromosomal association reveals functional relationships between meiotic crossover pathways in budding yeast

Meiotic crossovers are generated from the repair of programmed DNA double-strand breaks (DSBs). In the budding yeast Saccharomyces cerevisiae and mammals, most crossovers are generated through the Class I pathway, involving the mismatch-repair related complex Msh4-Msh5, while a smaller fraction is produced by the Mms4-Mus81 endonuclease (Class II pathway). We present the first report on the genome-wide localization of the Mms4 protein during meiosis in S. cerevisiae. Surprisingly, Mms4 localization showed a trend towards weak DSB sites, unlike the localization of the Class I crossover protein -Msh5, which is biased towards strong DSB sites. This preference for weaker DSB hotspots was retained in a msh5∆ mutant, arguing against competitive models of Mms4 and Msh5 association on meiotic chromosomes. The chromosomal association of Mms4 does not require the formation of meiotic DNA breaks but is facilitated by chromosome axis assembly. These results suggest Mms4 is primarily associated with chromosomal axis regions positioned near recombination intermediates. Mms4 binding is also largely insensitive to heterozygosity, unlike Msh5, consistent with its independence from recombination for localization. Together, these findings support a model in which Mms4-Mus81 enhances the robustness of meiotic recombination with a trend towards binding DSB hotspots that are weaker or are located in regions with sequence divergence that may be processed less efficiently by the Class I pathway.