High-resolution global recombination mapping in C. elegans reveals sexual dimorphisms shaped by meiotic chromosomal features and structures

Abstract

Crossover recombination events during meiosis repair double-strand DNA breaks and ensure accurate chromosome segregation in most organisms. For many species, the genomic distribution of crossovers is nonrandom and sexually dimorphic. While many species evolved kilobase-scale "hotspots" for crossover formation, the Caenorhabditis elegans genome lacks hotspots, and crossovers are enriched across megabase-scale domains. Further, genetic and cytological studies indicate the crossover frequency in C. elegans spermatogenesis is higher relative to oogenesis in many but not all genetic intervals. To determine the genomic features that contribute to the sexually dimorphic recombination landscape in the absence of hot spots, we defined and analyzed the recombination landscape across the whole genome in C. elegans using whole-genome sequencing and high-resolution recombination mapping in single worms bearing recombinant chromosomes from individual sperm and oocytes. We find that the spatial distribution of crossovers is sexually dimorphic on chromosomes I, II, and III, and that the global rate of double-crossover events is 4.7-fold higher in spermatocytes. Additionally, we find that pairing and synapsis may contribute to the sexually dimorphic crossover landscape. In comparison to the spermatocyte crossover landscape, a higher proportion of oocyte crossovers are formed in the domains directly adjacent to the pairing centers of each chromosome. Further, reducing the genetic dosage of the synaptonemal complex central region protein SYP-2, which is a meiotic chromosome structural protein required for homologous chromosome synapsis, reshapes the oocyte crossover landscape to resemble observations in wild-type spermatocytes. Finally, we found that spermatocyte crossovers are partially enriched in H3K36me3-marked euchromatic regions, while many oocyte crossovers are enriched in H3K27me3-marked heterochromatic regions. Taken together, our studies reveal how synaptonemal complex component dosage and local chromatin states influence crossover placement and the sex-specific regulation of meiotic recombination. Author SummaryProduction of viable eggs and sperm depends on accurate chromosome segregation during meiosis. Segregation of parental copies of homologous chromosomes requires the reciprocal exchange and physical linkage of DNA that arises through crossover recombination. Increasing evidence indicates the existence of sexual dimorphisms during meiotic recombination. In this study, we generated and analyzed high-resolution recombination maps specific to spermatogenesis and oogenesis in the nematode C. elegans, which reveals sex-specific crossover distributions and a higher rate of crossing over in sperm cells. Further, we indicate how specific chromosomal features and structures differentially affect the crossover landscape in eggs versus sperm. Our work highlights how, in a system absent of pre-defined "hotspots" for recombination, local chromatin structures, chromosomal pairing domains, and the abundance of synaptonemal complex proteins are potential drivers for establishing the observable sex differences in crossover recombination.