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Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics

Nature Genetics volume 46, pages 1072–1080 (2014)Cite this article

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Abstract

The ability to examine all chromatids from a single meiosis in yeast tetrads has been indispensable for defining the mechanisms of homologous recombination initiated by DNA double-strand breaks (DSBs). Using a broadly applicable strategy for the analysis of chromatids from a single meiosis at two recombination hotspots in mouse oocytes and spermatocytes, we demonstrate here the unidirectional transfer of information—gene conversion—in both crossovers and noncrossovers. Whereas gene conversion in crossovers is associated with reciprocal exchange, the unbroken chromatid is not altered in noncrossover gene conversion events, providing strong evidence that noncrossovers arise from a distinct pathway. Gene conversion frequently spares the binding site of the hotspot-specifying protein PRDM9, with the result that erosion of the hotspot is slowed. Thus, mouse tetrad analysis demonstrates how unique aspects of mammalian recombination mechanisms shape hotspot evolutionary dynamics.

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Figure 1: Mouse oocyte tetrad analysis provides direct evidence for meiotic gene conversion.
Figure 2: Mouse spermatocyte tetrads demonstrate that noncrossovers result from the unidirectional transfer of information.
Figure 3: PRDM9 binds to the center of the A3 hotspot.
Figure 4: Models of recombination and hotspot loss.

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Acknowledgements

We thank members of the Jasin, Keeney and de Massy laboratories, especially J. Lange, E. de Boer, S. Tischfield, S. Yamada and S. Peterson. We also thank P. Hunt (Washington State University) for encouraging the oocyte experiments, A. Gabow (Memorial Sloan Kettering Cancer Center) and Y. Lu (University of Texas MD Anderson Cancer Center) for fixation calculations, and the Réseau des Animaleries de Montpellier (RAM) and D. Haddou for management of mice. This work was supported by R.L. Kirschstein National Research Service Award F32HD51392 (F.C.) and Cancer Prevention and Research Institute of Texas award R1213 (F.C.), the Centre National de la Recherche Scientifique (F.B., C.G. and B.d.M.), the Agence Nationale pour la Recherche (program ANR-09-BLAN-0269-01 to B.d.M.), the Association pour la Recherche contre le Cancer (B.d.M.) and US National Institutes of Health grants R01GM105421 (M.J. and S.K.) and R01HD53855 (S.K. and M.J.). This paper is dedicated to the memory of our colleague Jérôme Buard.

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Author notes

  1. Francesca Cole and Frédéric Baudat: These authors contributed equally to this work.

Authors and Affiliations

  1. Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Francesca Cole & Maria Jasin

  2. Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA

    Francesca Cole

  3. Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France

    Frédéric Baudat, Corinne Grey & Bernard de Massy

  4. Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Scott Keeney

  5. Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Scott Keeney

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Contributions

F.C., F.B., S.K., B.d.M. and M.J. conceived the study, interpreted the data and wrote the manuscript. F.C. and F.B. performed the spermatocyte and oocyte (and associated) recombination experiments, respectively. F.B. and C.G. performed the southwestern blotting. F.C., M.J. and S.K. estimated the fixation rates.

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Correspondence to Scott Keeney, Bernard de Massy or Maria Jasin.

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Integrated supplementary information

Supplementary Figure 1 Noncrossovers at the Psmb9 hotspot in B10.A × SGR hybrids determined by analysis of DNA isolated from ovaries and sperm, respectively.

Noncrossovers were identified on the B10.A chromosome at the seven queried polymorphisms (asterisks) in pooled ovaries (a) and sperm (b) as described23. See Supplementary Table 1 for detailed results. Once a noncrossover was identified at the queried polymorphism, the extent of gene conversion was assessed by sequencing the PCR product. For pooled ovaries, DNA was extracted from the ovaries of 2 newborn litters (6 and 5 females, respectively), and an estimated ∼4,739 genomes from oocytes were tested. For sperm, ∼8,981 genomes from a single 4-month-old mouse were tested for the –87 polymorphism and ∼15,739 genomes were tested for the other 6 polymorphisms. The polymorphisms known to affect PRDM9 binding are 70 and, to a lesser extent, 87, which are located 17 bp apart (red arrowhead32). The mean minimal and maximal gene conversion tracts are as indicated. In these particular experiments, the overall frequencies of detected noncrossovers (on the B10.A chromosome; representing >90% of noncrossover events in this hybrid) and crossovers (SGR-B10.A orientation only), respectively, were 0.89% and 0.40% in oocytes and 0.45% and 0.16% in sperm.

Supplementary Figure 2 Noncrossovers from sperm DNA at the A3 hotspot in A/J × DBA/2J hybrids.

(a) Noncrossovers were identified using established methods36 on the DBA/2J chromosome in sperm DNA isolated from the same mice used for tetrad analysis. The mean minimal and maximal gene conversion tracts are as indicated. A nearly identical frequency (Table 1) and similar distribution of noncrossovers were obtained. Co-conversions were observed at a lower frequency in spermatocytes (6 of 111 noncrossovers) than in sperm (13 of 78 noncrossovers; P = 0.0142), although whether this difference reflects a biological distinction between the cell types is unclear. (b) For each polymorphism, the frequency and distribution of noncrossovers on the DBA/2J chromosome was compared between tetrad analysis (top; the same data as shown in Fig. 2e) to sperm (bottom). Polymorphisms analyzed with oligonucleotide probes new to this study are indicated by dots.

Supplementary Figure 3 Single-chromatid analysis cannot distinguish recombination mechanisms because gene conversion tracts are not identified.

(a) Examples of two possible crossovers initiated by a DSB on the frequently cleaved chromosome. In the example on the left, the crossover breakpoints flank the site of the DSB such that the gene conversion tract encompasses the center of the hotspot. In the example on the right, both crossover breakpoints occur to one side of the DSB, such that the conversion tract does not overlap the center of the hotspot. (b) Example of a crossover initiated by a DSB on the infrequently cleaved chromosome in which the crossover breakpoints flank the site of the DSB. Note that the breakpoint on the lower chromosome (breakpoint 3b) is similar to that from the off-center conversion in a (breakpoint 2b). (c) Distribution of crossover breakpoints at the A3 hotspot from A/J × DBA/2J mice previously determined from sperm analysis18. The A/J to DBA/2J (top) and DBA/2J to A/J (bottom) breakpoints are shifted relative to each other (asymmetric), consistent with substantially more frequent initiation on the DBA/2J chromosome. Vertical lines represent the midpoint for each orientation. The intervals in which the crossover breakpoints from a and b occur are indicated. (d) Southwestern analysis of the PRDM9wm7 protein for the A3 hotspot. The horizontal bars represent the positions of the eight overlapping ∼250-bp DNA probes generated for the A/J and DBA/2J genotype. Representative southwesterns for each probe against His-tagged PRDM9wm7 are shown along with a loading control (probed with antibody to His) on the far right.

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Cole, F., Baudat, F., Grey, C. et al. Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet 46, 1072–1080 (2014). https://doi.org/10.1038/ng.3068

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