Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

Center for Genome Dynamics The Jackson Laboratory Bar Harbor Maine United States of America

Laboratory of Germ Cell Development Division BIOCEV Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic v v i Prague Czech Republic

See more in PubMed

Baudat F, Imai Y, de Massy B (2013) Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14: 794–806. 10.1038/nrg3573 PubMed DOI

Paigen K, Petkov P (2010) Mammalian recombination hot spots: properties, control and evolution. Nat Rev Genet 11: 221–233. 10.1038/nrg2712 PubMed DOI PMC

Axelsson E, Webster MT, Ratnakumar A, Ponting CP, Lindblad-Toh K (2012) Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res 22: 51–63. 10.1101/gr.124123.111 PubMed DOI PMC

Munoz-Fuentes V, Di Rienzo A, Vila C (2011) Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes. PLoS One 6: e25498 10.1371/journal.pone.0025498 PubMed DOI PMC

Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836–840. 10.1126/science.1183439 PubMed DOI PMC

Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, et al. (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876–879. 10.1126/science.1182363 PubMed DOI PMC

Parvanov ED, Petkov PM, Paigen K (2010) Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835 10.1126/science.1181495 PubMed DOI PMC

Buard J, Barthes P, Grey C, de Massy B (2009) Distinct histone modifications define initiation and repair of meiotic recombination in the mouse. EMBO J 28: 2616–2624. 10.1038/emboj.2009.207 PubMed DOI PMC

Baker CL, Kajita S, Walker M, Petkov PM, Paigen K (2014) PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration. Genome Res 24: 724–732. 10.1101/gr.170167.113 PubMed DOI PMC

Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV (2012) Genetic recombination is directed away from functional genomic elements in mice. Nature 485: 642–645. 10.1038/nature11089 PubMed DOI PMC

Smagulova F, Gregoretti IV, Brick K, Khil P, Camerini-Otero RD, et al. (2011) Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 472: 375–378. 10.1038/nature09869 PubMed DOI PMC

Keeney S (2008) Spo11 and the Formation of DNA Double-Strand Breaks in Meiosis. Genome dynamics and stability 2: 81–123. PubMed PMC

Hayashi K, Yoshida K, Matsui Y (2005) A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 438: 374–378. PubMed

Irie S, Tsujimura A, Miyagawa Y, Ueda T, Matsuoka Y, et al. (2009) Single-nucleotide polymorphisms of the PRDM9 (MEISETZ) gene in patients with nonobstructive azoospermia. J Androl 30: 426–431. 10.2164/jandrol.108.006262 PubMed DOI

Miyamoto T, Koh E, Sakugawa N, Sato H, Hayashi H, et al. (2008) Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. J Assist Reprod Genet 25: 553–557. 10.1007/s10815-008-9270-x PubMed DOI PMC

Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323: 373–375. 10.1126/science.1163601 PubMed DOI

Berg IL, Neumann R, Lam KW, Sarbajna S, Odenthal-Hesse L, et al. (2010) PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. Nat Genet 42: 859–863. 10.1038/ng.658 PubMed DOI PMC

Berg IL, Neumann R, Sarbajna S, Odenthal-Hesse L, Butler NJ, et al. (2011) Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Proc Natl Acad Sci U S A 108: 12378–12383. 10.1073/pnas.1109531108 PubMed DOI PMC

Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, et al. (2011) The landscape of recombination in African Americans. Nature 476: 170–175. 10.1038/nature10336 PubMed DOI PMC

Grey C, Barthes P, Chauveau-Le Friec G, Langa F, Baudat F, et al. (2011) Mouse PRDM9 DNA-binding specificity determines sites of histone H3 lysine 4 trimethylation for initiation of meiotic recombination. PLoS Biol 9: e1001176 10.1371/journal.pbio.1001176 PubMed DOI PMC

Groeneveld LF, Atencia R, Garriga RM, Vigilant L (2012) High diversity at PRDM9 in chimpanzees and bonobos. PLoS One 7: e39064 10.1371/journal.pone.0039064 PubMed DOI PMC

Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L, et al. (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336: 193–198. 10.1126/science.1216872 PubMed DOI PMC

Schwartz JJ, Roach DJ, Thomas JH, Shendure J (2014) Primate evolution of the recombination regulator PRDM9. Nat Commun 5: 4370 10.1038/ncomms5370 PubMed DOI PMC

Sandor C, Li W, Coppieters W, Druet T, Charlier C, et al. (2012) Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genet 8: e1002854 10.1371/journal.pgen.1002854 PubMed DOI PMC

Steiner CC, Ryder OA (2013) Characterization of Prdm9 in equids and sterility in mules. PLoS One 8: e61746 10.1371/journal.pone.0061746 PubMed DOI PMC

Parvanov ED, Ng SH, Petkov PM, Paigen K (2009) Trans-regulation of mouse meiotic recombination hotspots by Rcr1. PLoS Biol 7: e36 10.1371/journal.pbio.1000036 PubMed DOI PMC

Neumann R, Jeffreys AJ (2006) Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation. Hum Mol Genet 15: 1401–1411. PubMed

Pratto F, Brick K, Khil P, Smagulova F, Petukhova GV, et al. (2014) DNA recombination. Recombination initiation maps of individual human genomes. Science 346: 1256442 10.1126/science.1256442 PubMed DOI PMC

Segurel L, Leffler EM, Przeworski M (2011) The case of the fickle fingers: how the PRDM9 zinc finger protein specifies meiotic recombination hotspots in humans. PLoS Biol 9: e1001211 10.1371/journal.pbio.1001211 PubMed DOI PMC

Baker CL, Kajita S, Walker M, Saxl RL, Raghupathy N, et al. (2015) PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination. PLoS Genet 11: e1004916 10.1371/journal.pgen.1004916 PubMed DOI PMC

Billings T, Parvanov ED, Baker CL, Walker M, Paigen K, et al. (2013) DNA binding specificities of the long zinc-finger recombination protein PRDM9. Genome Biol 14: R35 10.1186/gb-2013-14-4-r35 PubMed DOI PMC

Hinch AG, Altemose N, Noor N, Donnelly P, Myers SR (2014) Recombination in the human Pseudoautosomal region PAR1. PLoS Genet 10: e1004503 10.1371/journal.pgen.1004503 PubMed DOI PMC

Eram MS, Bustos SP, Lima-Fernandes E, Siarheyeva A, Senisterra G, et al. (2014) Trimethylation of histone H3 lysine 36 by human methyltransferase PRDM9 protein. J Biol Chem 289: 12177–12188. 10.1074/jbc.M113.523183 PubMed DOI PMC

Sun F, Fujiwara Y, Reinholdt LG, Hu J, Saxl RL, et al. (2015) Nuclear localization of PRDM9 and its role in meiotic chromatin modifications and homologous synapsis. Chromosoma. PubMed PMC

Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, et al. (2011) Mutation discovery in mice by whole exome sequencing. Genome Biol 12: R86 10.1186/gb-2011-12-9-r86 PubMed DOI PMC

Flachs P, Mihola O, Simecek P, Gregorova S, Schimenti JC, et al. (2012) Interallelic and intergenic incompatibilities of the Prdm9 (Hst1) gene in mouse hybrid sterility. PLoS Genet 8: e1003044 10.1371/journal.pgen.1003044 PubMed DOI PMC

Weiss J, Hurley LA, Harris RM, Finlayson C, Tong M, et al. (2012) ENU mutagenesis in mice identifies candidate genes for hypogonadism. Mamm Genome 23: 346–355. 10.1007/s00335-011-9388-5 PubMed DOI PMC

Flachs P, Bhattacharyya T, Mihola O, Pialek J, Forejt J, et al. (2014) Prdm9 incompatibility controls oligospermia and delayed fertility but no selfish transmission in mouse intersubspecific hybrids. PLoS One 9: e95806 10.1371/journal.pone.0095806 PubMed DOI PMC

Dzur-Gejdosova M, Simecek P, Gregorova S, Bhattacharyya T, Forejt J (2012) Dissecting the genetic architecture of F1 hybrid sterility in house mice. Evolution 66: 3321–3335. 10.1111/j.1558-5646.2012.01684.x PubMed DOI

Bhattacharyya T, Gregorova S, Mihola O, Anger M, Sebestova J, et al. (2013) Mechanistic basis of infertility of mouse intersubspecific hybrids. Proc Natl Acad Sci U S A 110: E468–477. 10.1073/pnas.1219126110 PubMed DOI PMC

Fog CK, Galli GG, Lund AH (2012) PRDM proteins: important players in differentiation and disease. Bioessays 34: 50–60. 10.1002/bies.201100107 PubMed DOI

Hohenauer T, Moore AW (2012) The Prdm family: expanding roles in stem cells and development. Development 139: 2267–2282. 10.1242/dev.070110 PubMed DOI

Huang S, Shao G, Liu L (1998) The PR domain of the Rb-binding zinc finger protein RIZ1 is a protein binding interface and is related to the SET domain functioning in chromatin-mediated gene expression. J Biol Chem 273: 15933–15939. PubMed

Davis CA, Haberland M, Arnold MA, Sutherland LB, McDonald OG, et al. (2006) PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Molecular and cellular biology 26: 2626–2636. PubMed PMC

Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP, et al. (1996) KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes & development 10: 2067–2078. PubMed

Urrutia R (2003) KRAB-containing zinc-finger repressor proteins. Genome Biol 4: 231 PubMed PMC

Edelstein LC, Collins T (2005) The SCAN domain family of zinc finger transcription factors. Gene 359: 1–17. PubMed

Buard J, Rivals E, Dunoyer de Segonzac D, Garres C, Caminade P, et al. (2014) Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite. PLoS One 9: e85021 10.1371/journal.pone.0085021 PubMed DOI PMC

Kono H, Tamura M, Osada N, Suzuki H, Abe K, et al. (2014) Prdm9 polymorphism unveils mouse evolutionary tracks. DNA Res 21: 315–326. 10.1093/dnares/dst059 PubMed DOI PMC

Shultz KL, Donahue LR, Bouxsein ML, Baylink DJ, Rosen CJ, et al. (2003) Congenic strains of mice for verification and genetic decomposition of quantitative trait loci for femoral bone mineral density. J Bone Miner Res 18: 175–185. PubMed

Anderson LK, Reeves A, Webb LM, Ashley T (1999) Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein. Genetics 151: 1569–1579. PubMed PMC

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890. PubMed

Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103: 10352–10357. PubMed PMC

Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137 10.1186/gb-2008-9-9-r137 PubMed DOI PMC

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208. 10.1093/nar/gkp335 PubMed DOI PMC

Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, et al. (2012) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481: 389–393. 10.1038/nature10730 PubMed DOI PMC

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, et al. (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39: e35 10.1093/nar/gkq1287 PubMed DOI PMC

Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841–842. 10.1093/bioinformatics/btq033 PubMed DOI PMC

Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility

Histone methyltransferase PRDM9 is not essential for meiosis in male mice

Modulation of Prdm9-controlled meiotic chromosome asynapsis overrides hybrid sterility in mice

PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis