Structured Abstract

Introduction The dramatic events of meiotic recombination culminate in the exchange of genetic information between parental chromosomes and ensure the production of genetically distinct gametes. Recombination is initiated by the formation of programmed DNA double-strand breaks (DSBs), and most DSBs occur at discrete hotspots defined by the DNA binding specificity of the PRDM9 protein. The tandem array of PRDM9 zinc fingers that binds DNA is highly polymorphic, and different variants have different DNA binding preferences. Subsequent to binding, PRDM9 is thought to modify the local chromatin environment and to recruit SPO11 for DSB formation. Meiotic DSBs are predominantly repaired through homologous recombination, giving rise to either genetic crossovers, where a reciprocal genetic exchange occurs between homologous chromosomes, or noncrossovers.

Meiotic DSB maps in human male individuals. In meiotic cells, the formation of programmed meiotic DSBs facilitates the subsequent exchange of genetic material between parental homologous chromosomes. All current methods to study the sites of meiotic recombination rely on detection of these genetic exchanges. The DMC1 protein binds to DNA around meiotic DSBs, and in this work, we used testis biopsies from individual males to pull down the DNA bound by the DMC1 protein. We thus identified the sites of meiotic DSBs in five individual males. Analysis and comparison of the resultant PRDM9-specific, personal genome-wide maps offers insights into the mechanisms that initiate meiosis, genome evolution, crossover formation, human population structure, and predisposition to genomic disorders.

Rationale Despite recent progress in our understanding of recombination hotspot formation, the initiation of recombination remains poorly understood. Current approaches to study the early steps of meiotic recombination in humans primarily detect genetic crossovers, only one of the possible outcomes of DSB repair. Furthermore, these methods are limited by resolution, by sex and population averaging, or by an inability to extend the analysis genome-wide. To overcome these limitations, we built and analyzed high-resolution, individual-specific maps of meiotic DSBs in the human genome.

Results We report the maps of meiotic DSBs in five males: two homozygous for the most common PRDM9 allele (PRDM9 A ) and three heterozygous for the PRDM9 A allele and for the less frequent PRDM9 B or PRDM9 C alleles. We find that PRDM9 A and PRDM9 B define similar DSB hotspots, whereas the PRDM9 C allele has a distinct specificity. A comparison of DSB hotspot maps with linkage disequilibrium (LD)–based estimates of recombination rates in the human population indicates that the LD map is a superimposition of PRDM9 allele-specific DSB maps and that the contribution of individual maps is proportional to the PRDM9 allele frequency in modern Africans. In individuals with identical PRDM9 alleles, over 5% of DSB hotspots vary in strength, yet less than half of this variation could be explained by sequence variation at putative PRDM9 binding sites. We also find that PRDM9 heterozygosity affects hotspot strength. In human males, DSBs, like crossovers, occur more frequently at subtelomeric regions, and the crossover rate is directly proportional to our estimate of DSB frequency. This indicates that DSB initiation frequency is a major driver of the crossover rate in human males. We detect distinct signatures of GC-biased gene conversion and of recombination-coupled mutagenesis at DSB hotspots. In addition, DSB hotspots are enriched at the breakpoints of copy number variants that arise via homology-mediated mechanisms. Such variants may give rise to genomic disorders, and indeed, we find that meiotic DSBs defined by PRDM9 A often coincide with disease-associated chromosomal breakpoints.