Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes

Author summaryMeiosis is the specialized cell cycle used to generate genetic diversity and reduce the genome copy number in gametes. Successful meiosis requires homologous chromosomes to pair and recombine to form crossovers, which are necessary for proper chromosome segregation. However, chromosome rearrangements called inversions that reverse the order of genes on one of the homologous chromosomes suppress crossovers. While this phenomenon has been studied for 100 years, much is still unknown about the mechanisms that prevent crossovers from occurring. In our current work, we show that these heterozygous inversions suppress crossovers nearby but outside of the rearrangement boundaries by altering the regulation of recombination. Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.