Recombination initiation maps of individual human genomes

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 (PRDM9A) and three heterozygous for the PRDM9A allele and for the less frequent PRDM9B or PRDM9C alleles. We find that PRDM9A and PRDM9B define similar DSB hotspots, whereas the PRDM9C 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 PRDM9A often coincide with disease-associated chromosomal breakpoints. Conclusions Our genome-wide recombination initiation maps in individual human males offer unprecedented resolution of recombination initiation sites defined by specific alleles of the PRDM9 protein. Our analysis indicates that DSB frequency is a primary determinant of crossover frequency, and that factors other than PRDM9 modulate the frequency of recombination initiation. We also find that meiotic DSB repair and subsequent recombination affect the genome sequence both locally and at the level of structural rearrangements. Taken together, these data provide a foundation for future studies of genetic recombination, meiosis, and genome stability. DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here, we present high-resolution maps of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors may dictate the efficiency of DSB formation. We find evidence for both GC-biased gene conversion and mutagenesis around meiotic DSB hotspots, while frequent colocalization of DSB hotspots with chromosome rearrangement breakpoints implicates the aberrant repair of meiotic DSBs in genomic disorders. Furthermore, our data indicate that DSB frequency is a major determinant of crossover rate. These maps provide new insights into the regulation of meiotic recombination and the impact of meiotic recombination on genome function. Mapping human male meiotic recombination sites reveals their influence on genome evolution and genetic disease. [Also see Perspective by de Massy] Mapping recombination in individual human males Sperm and eggs form from diploid cells that contain two copies of our genomic DNA. The haploid germ cells must undergo a special cell division, meiosis, which halves their DNA content. Meiosis involves a DNA recombination step between parental chromosomes. Recombination is initiated by a DNA double-strand break, which can exchange DNA between the chromosomes, a process that drives human genetic variation. Pratto et al. mapped meiotic recombination sites in individual human males (see the Perspective by de Massy). Recombination hotspots were influenced by variants of the histone-lysine N-methyltransferase protein, PRDM9, as well as by other factors. The recombination sites also influence genome evolution and the incidence of genetic disease. Science, this issue 10.1126/science.1256442; see also p. 808