PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans

Journal name:
Nature Genetics
Year published:
Published online

PRDM9 has recently been identified as a likely trans regulator of meiotic recombination hot spots in humans and mice1, 2, 3. PRDM9 contains a zinc finger array that, in humans, can recognize a short sequence motif associated with hot spots4, with binding to this motif possibly triggering hot-spot activity via chromatin remodeling5. We now report that human genetic variation at the PRDM9 locus has a strong effect on sperm hot-spot activity, even at hot spots lacking the sequence motif. Subtle changes within the zinc finger array can create hot-spot nonactivating or enhancing variants and can even trigger the appearance of a new hot spot, suggesting that PRDM9 is a major global regulator of hot spots in humans. Variation at the PRDM9 locus also influences aspects of genome instability—specifically, a megabase-scale rearrangement underlying two genomic disorders6 as well as minisatellite instability7—implicating PRDM9 as a risk factor for some pathological genome rearrangements.

At a glance


  1. PRDM9 ZnF variants and crossover hot-spot activity in sperm.
    Figure 1: PRDM9 ZnF variants and crossover hot-spot activity in sperm.

    (a) Examples of tandem repeats encoding the ZnF array with variant repeat units colored differently. The predicted DNA binding sequence is shown below, with dots indicating weakly predicted bases and uppercase letters indicating the most strongly predicted bases, and aligned with the hot-spot motif CCNCCNTNNCCNC (ref. 4). The binding sequence for allele A matches all eight specified bases in the motif, while allele L1 matches at best only six of the eight bases. (b) PRDM9 ZnF array diversity in Europeans and Africans, with alleles classified either by structure or by the strength of the predicted match with the motif (details of alleles are provided in Supplementary Fig. 1). (c) Variation between men in sperm crossover activity in hot spots, named above each panel, containing a central hot-spot motif. Different sets of men informative for the SNPs required for crossover detection were analyzed at each hot spot (Supplementary Table 1). Men carrying two PRDM9 A alleles (A/A, shown in black), one A allele (A/N, shown in blue) or two non-A alleles (N/N, shown in red) were grouped separately in ascending order. Confidence intervals for each estimate of recombination frequency are shown, and median recombination frequencies within each group are indicated by dotted lines. Mann-Whitney test results for the significance of differences between the A/A group and the A/N or N/N groups are given at the top right (ns, not significant, P > 0.05; *P < 0.05; **P < 0.01; ***P < 0.001). (d) Corresponding analyses of hot spots lacking an obvious hot-spot motif (Supplementary Fig. 2).

  2. Activating and nonactivating PRDM9 alleles.
    Figure 2: Activating and nonactivating PRDM9 alleles.

    Nonactivating alleles at each hot spot were defined as alleles present in N/N men who showed <5% of the median recombination frequency seen in A/A men. Allele structures are coded as in Supplementary Figure 1, with predicted DNA binding sequences and best motif matches shown as in Figure 1. Data for each hot spot give the number of specific N alleles detected in suppressed men; for example, five such men typed at hot spot F carried the C allele. Evidence that the B allele is active is based on a B/L6 heterozygote assayable only at hot spot CG who showed crossovers at 40% of the median frequency seen in A/A homozygotes. Because allele L6 is a nonactivator at CG, this implies that allele B is similar in activity to allele A.

  3. PRDM9 variation influences crossover activity at hot spots MSTM1a and MSTM1b.
    Figure 3: PRDM9 variation influences crossover activity at hot spots MSTM1a and MSTM1b.

    (a) Variant alleles present in men previously typed for sperm crossovers at these hot spots16; all other men were A/A homozygotes. Recombination frequencies at each hot spot are shown with 95% CIs. Note that alleles L9 and L24 associate not only with MSTM1a activity but also apparently with elevated recombination frequency at MSTM1b (P = 0.035). (b) DNA sequence structures of these alleles, colored as in Figure 2, plus amino acid sequence changes relative to allele A, with locations given with respect to the main ZnF DNA-contact residues (−1, 2, 3 and 6)15.

  4. Influence of PRDM9 variation on minisatellite instability in sperm.
    Figure 4: Influence of PRDM9 variation on minisatellite instability in sperm.

    (a) Minisatellite repeat units, with the best matches to the hot-spot motif indicated. Minisatellites MS1 and CEB1 both contain perfect matches. Two contiguous repeats are shown for MS1. (b) Representative small-pool PCR results for minisatellite CEB1, for a PRDM9 A/A homozygote and a C/L16 heterozygote. (c) Mutation frequencies in A/A (black), A/N (blue) and N/N (red) men, with CIs, median values per group, and Mann-Whitney test results indicated as in Figure 1 (ns, not significant, P > 0.05; *P < 0.05).

  5. PRDM9 variation and de novo HNPP/CMT1A rearrangements in sperm DNA.
    Figure 5: PRDM9 variation and de novo HNPP/CMT1A rearrangements in sperm DNA.

    (a) Detection of HNPP deletion junctions in sperm DNA from a PRDM9 A/A homozygote and a C/L14 heterozygote with 40 ng DNA input per PCR reaction. (b) Rearrangement frequencies in A/A (black), A/N (blue) and N/N (red) men for HNPP deletions and CMT1A duplications, with CIs, median values per group, and Mann-Whitney test results shown as in Figure 1 (*P < 0.05; **P < 0.01). The same men were analyzed for both rearrangements, but not all men were typed for duplications, which arise at a lower frequency than deletions6. Rearrangements in blood were rare6 (frequency of < 2.2 × 10−6 for deletions and < 1.3 × 10−6 for duplications; P > 0.95).

  6. PRDM9 variation and t(11;22) translocation frequencies.
    Figure 6: PRDM9 variation and t(11;22) translocation frequencies.

    (a) Detection of de novo der(22) translocation junctions by nested PCR amplification29 of multiple 150 ng aliquots of blood and sperm DNA. Minor variation in junction size resulted from differences in translocation breakpoint locations within the PATRR24. (b) der(22) translocation frequencies, with CIs, in sperm DNA in PRDM9 A/A, A/N and N/N men, with identities of the N alleles shown above. The median frequency per group, similar to previously reported translocation frequencies24, is indicated by a dotted line. There was no significant difference in translocation frequency between the groups (Kruskal-Wallis test, P = 0.98). No de novo translocations were seen in blood DNA tested from four different men (frequency < 5 × 10−7, P > 0.95).

Accession codes

Referenced accessions

NCBI Reference Sequence


  1. Baudat, F. et al. PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327, 836840 (2010).
  2. Myers, S. et al. Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327, 876879 (2010).
  3. Parvanov, E.D., Petkov, P.M. & Paigen, K. Prdm9 controls activation of mammalian recombination hotspots. Science 327, 835 (2010).
  4. Myers, S., Freeman, C., Auton, A., Donnelly, P. & McVean, G. A common sequence motif associated with recombination hot spots and genome instability in humans. Nat. Genet. 40, 11241129 (2008).
  5. Paigen, K. & Petkov, P. Mammalian recombination hot spots: properties, control and evolution. Nat. Rev. Genet. 11, 221233 (2010).
  6. Turner, D.J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 9095 (2008).
  7. Jeffreys, A.J. et al. Complex gene conversion events in germline mutation at human minisatellites. Nat. Genet. 6, 136145 (1994).
  8. Hayashi, K., Yoshida, K. & Matsui, Y. A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 438, 374378 (2005).
  9. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851861 (2007).
  10. Webb, A.J., Berg, I.L. & Jeffreys, A. Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association. Proc. Natl. Acad. Sci. USA 105, 1047110476 (2008).
  11. Jeffreys, A.J. & Neumann, R. The rise and fall of a human recombination hot spot. Nat. Genet. 41, 625629 (2009).
  12. Jeffreys, A.J., Ritchie, A. & Neumann, R. High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Hum. Mol. Genet. 9, 725733 (2000).
  13. Jeffreys, A.J. & Neumann, R. Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat. Genet. 31, 267271 (2002).
  14. Jeffreys, A.J. & Neumann, R. Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot. Hum. Mol. Genet. 14, 22772287 (2005).
  15. Wolfe, S.A., Nekludova, L. & Pabo, C.O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183212 (2000).
  16. Neumann, R. & Jeffreys, A.J. Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation. Hum. Mol. Genet. 15, 14011411 (2006).
  17. Buard, J., Bourdet, A., Yardley, J., Dubrova, Y. & Jeffreys, A.J. Influences of array size and homogeneity on minisatellite mutation. EMBO J. 17, 34953502 (1998).
  18. Tamaki, K., May, C.A., Dubrova, Y.E. & Jeffreys, A.J. Extremely complex repeat shuffling during germline mutation at human minisatellite B6.7. Hum. Mol. Genet. 8, 879888 (1999).
  19. Berg, I., Neumann, R., Cederberg, H., Rannug, U. & Jeffreys, A.J. Two modes of germline instability at human minisatellite MS1 (locus D1S7): complex rearrangements and paradoxical hyperdeletion. Am. J. Hum. Genet. 72, 14361447 (2003).
  20. Jeffreys, A.J., Murray, J. & Neumann, R. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol. Cell 2, 267273 (1998).
  21. Conrad, D.F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704712 (2010).
  22. Pentao, L., Wise, C.A., Chinault, A.C., Patel, P.I. & Lupski, J.R. Charcot-Marie-Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit. Nat. Genet. 2, 292300 (1992).
  23. Lindsay, S.J., Khajavi, M., Lupski, J.R. & Hurles, M.E. A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am. J. Hum. Genet. 79, 890902 (2006).
  24. Kurahashi, H. & Emanuel, B.S. Unexpectedly high rate of de novo constitutional t(11;22) translocations in sperm from normal males. Nat. Genet. 29, 139140 (2001).
  25. Kato, T. et al. Genetic variation affects de novo translocation frequency. Science 311, 971 (2006).
  26. Reich, D.E. et al. Linkage disequilibrium in the human genome. Nature 411, 199204 (2001).
  27. Kong, A. et al. Sequence variants in the RNF212 gene associate with genome-wide recombination rate. Science 319, 13981401 (2008).
  28. Chowdhury, R. et al. Genetic analysis of variation in human meiotic recombination. PLoS Genet. 5, e1000648 (2009).
  29. Kurahashi, H. et al. Tightly clustered 11q23 and 22q11 breakpoints permit PCR-based detection of the recurrent constitutional t(11;22). Am. J. Hum. Genet. 67, 763768 (2000).
  30. Monckton, D.G. et al. Minisatellite mutation rate variation associated with a flanking DNA sequence polymorphism. Nat. Genet. 8, 162170 (1994).

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Author information


  1. Department of Genetics, University of Leicester, Leicester, UK.

    • Ingrid L Berg,
    • Rita Neumann,
    • Kwan-Wood G Lam,
    • Shriparna Sarbajna,
    • Linda Odenthal-Hesse,
    • Celia A May &
    • Alec J Jeffreys


I.L.B., R.N., K.-W.G.L., S.S., L.O.-H., C.A.M. and A.J.J. all contributed to designing aspects of the study. I.L.B., R.N. and A.J.J. characterized PRDM9 alleles, I.L.B., S.S., L.O.-H. and A.J.J. analyzed hot spots, R.N. surveyed minisatellite instability, K.-W.G.L. characterized genome rearrangements and A.J.J. analyzed translocations. A.J.J. wrote the paper.

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