Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination

PRDM9 points the zinc finger at meiotic recombination hotspots

Recent work shows that the histone methyltransferase PRDM9 determines the nonrandom genomic distribution of meiotic recombination hotspots.

Meiotic recombination events are spread nonrandomly across eukaryotic genomes in 'hotspots'. Recent work shows that a unique histone methyltransferase, PRDM9, determines their distribution.

Genetics. Genetic control of hotspots

Both chromatin and DNA sequence account for individual differences in the location and frequency of genetic recombination.

Contrasting methods of quantifying fine structure of human recombination

There has been considerable excitement over the ability to construct linkage maps based only on genome-wide genotype data for single nucleotide polymorphic sites (SNPs) in a population sample. These maps, which are derived from estimates of linkage disequilibrium (LD), rely on population genetics theory to relate the decay of LD to the local rate of recombination, but other population processes also come into play. Here we contrast these LD maps to the classically derived, pedigree-based human recombination maps. The LD maps have a level of resolution greatly exceeding that of the pedigree maps, and at this fine scale, sperm typing allows a means of validation. While at a gross level both the pedigree maps and the sperm typing methods generally agree with LD maps, there are significant local differences between them, and the fact that these maps measure different genetic features should be remembered when using them for other genetic inferences.

PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice

Meiotic recombination events cluster into narrow segments of the genome, defined as hotspots. Here, we demonstrate that a major player for hotspot specification is the Prdm9 gene. First, two mouse strains that differ in hotspot usage are polymorphic for the zinc finger DNA binding array of PRDM9. Second, the human consensus PRDM9 allele is predicted to recognize the 13-mer motif enriched at human hotspots; this DNA binding specificity is verified by in vitro studies. Third, allelic variants of PRDM9 zinc fingers are significantly associated with variability in genome-wide hotspot usage among humans. Our results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome.