Comprehensive, Fine-Scale Dissection of Homologous Recombination Outcomes at a Hot Spot in Mouse Meiosis

Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
Molecular cell (Impact Factor: 14.02). 09/2010; 39(5):700-10. DOI: 10.1016/j.molcel.2010.08.017
Source: PubMed


In mammalian meiosis, only a small fraction of programmed DNA double-strand breaks are repaired as interhomolog crossovers (COs). To analyze another product of meiotic recombination, interhomolog noncrossovers (NCOs), we performed high-resolution mapping of recombination events at an intensely active mouse hot spot in F1 hybrids derived from inbred mouse strains. We provide direct evidence that the vast majority of repair events are interhomolog NCOs, consistent with models in which frequent interhomolog interactions promote accurate chromosome pairing. NCOs peaked at the center of the hot spot but were also broadly distributed throughout. In some hybrid strains, localized zones within the hot spot were highly refractory to COs and showed elevated frequency of coconversion of adjacent polymorphisms in NCOs, raising the possibility of double-strand gap repair. Transmission distortion was observed in one hybrid, with NCOs providing a significant contribution. Thus, NCO recombination events play a substantial role in mammalian meiosis and genome evolution.

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Available from: Francesca Cole, Jul 27, 2015
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    • "How this happens is not understood. The capacity of certain pachytene arrested mutants (e.g., ndt80D) to continue DSB formation (Xu and Kleckner 1995), and also the late persistence of Spo11 and other DSB proteins along the chromosomes after DSB formation (Arora et al. 2004; Cole et al. 2010; Gray et al. 2013), are puzzling observations that call to further integrate the connection of DSB formation and repair with changes in chromosome structures and movements and explore the underlying signaling pathway(s) in connection to the meiotic cell-cycle progression. Another important DSB control can be called " DSB compensation " to denote the homeostatic process that is able to redistribute DSBs along the chromosomes (Fig. 2C). "
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    ABSTRACT: Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs) catalyzed by the evolutionary conserved Spo11 protein and accessory factors. DSBs are nonrandomly distributed along the chromosomes displaying a significant (~400-fold) variation of frequencies, which ultimately establishes local and long-range “hot” and “cold” domains for recombination initiation. This remarkable patterning is set up within the chromatin context, involving multiple layers of biochemical activity. Predisposed chromatin accessibility, but also a range of transcription factors, chromatin remodelers, and histone modifiers likely promote local recruitment of DSB proteins, as well as mobilization, sliding, and eviction of nucleosomes before and after the occurrence of meiotic DSBs. Here, we assess our understanding of meiotic DSB formation and methods to change its patterning. We also synthesize current heterogeneous knowledge on how histone modifications and chromatin remodeling may impact this decisive step in meiotic recombination. © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.
    Cold Spring Harbor perspectives in biology 05/2015; 7(5):a016527. DOI:10.1101/cshperspect.a016527 · 8.68 Impact Factor
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    • "It was somewhat surprising to find that PRDM9 binding sites are not uniformly positioned in relation to hotspot centers. One possible explanation for this asymmetry could be the presence of crossover refractory zones created by the nature of adjoining DNA sequences that create directionality in the spreading of the Holliday junctions away from initiation sites [30]. However, our genetic data point to a more likely alternative. "
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    ABSTRACT: Background Meiotic recombination ensures proper segregation of homologous chromosomes and creates genetic variation. In many organisms, recombination occurs at limited sites, termed 'hotspots', whose positions in mammals are determined by PR domain member 9 (PRDM9), a long-array zinc-finger and chromatin-modifier protein. Determining the rules governing the DNA binding of PRDM9 is a major issue in understanding how it functions. Results Mouse PRDM9 protein variants bind to hotspot DNA sequences in a manner that is specific for both PRDM9 and DNA haplotypes, and that in vitro binding parallels its in vivo biological activity. Examining four hotspots, three activated by Prdm9Cst and one activated by Prdm9Dom2, we found that all binding sites required the full array of 11 or 12 contiguous fingers, depending on the allele, and that there was little sequence similarity between the binding sites of the three Prdm9Cst activated hotspots. The binding specificity of each position in the Hlx1 binding site, activated by Prdm9Cst, was tested by mutating each nucleotide to its three alternatives. The 31 positions along the binding site varied considerably in the ability of alternative bases to support binding, which also implicates a role for additional binding to the DNA phosphate backbone. Conclusions These results, which provide the first detailed mapping of PRDM9 binding to DNA and, to our knowledge, the most detailed analysis yet of DNA binding by a long zinc-finger array, make clear that the binding specificities of PRDM9, and possibly other long-array zinc-finger proteins, are unusually complex.
    Genome biology 04/2013; 14(4):R35. DOI:10.1186/gb-2013-14-4-r35 · 10.81 Impact Factor
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    • "For example, mouse spermatocytes are estimated to make ;200–250 DSBs on average, based on numbers of chromosome-associated foci of the strand exchange proteins RAD51 and DMC1. Of this number, only approximately one-tenth is matured into crossovers; analysis of individual recombination hot spots suggests that a large fraction of the remaining DSBs mature into noncrossovers (Cole et al. 2010; F Baudat and B de Massy, unpubl.; E de Boer, M Jasin and S Keeney, unpubl.), "
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    ABSTRACT: Different organisms display widely different numbers of the programmed double-strand breaks (DSBs) that initiate meiotic recombination (e.g., hundreds per meiocyte in mice and humans vs. dozens in nematodes), but little is known about what drives these species-specific DSB set points or the regulatory pathways that control them. Here we examine male mice with a lowered dosage of SPO11, the meiotic DSB catalyst, to gain insight into the effect of reduced DSB numbers on mammalian chromosome dynamics. An approximately twofold DSB reduction was associated with the reduced ability of homologs to synapse along their lengths, provoking prophase arrest and, ultimately, sterility. In many spermatocytes, chromosome subsets displayed a mix of synaptic failure and synapsis with both homologous and nonhomologous partners ("chromosome tangles"). The X chromosome was nearly always involved in tangles, and small autosomes were involved more often than large ones. We conclude that homolog pairing requirements dictate DSB set points during meiosis. Importantly, our results reveal that karyotype is a key factor: Smaller autosomes and heteromorphic sex chromosomes become weak links when DSBs are reduced below a critical threshold. Unexpectedly, unsynapsed chromosome segments trapped in tangles displayed an elevated density of DSB markers later in meiotic prophase. The unsynapsed portion of the X chromosome in wild-type males also showed evidence that DSB numbers increased as prophase progressed. These findings point to the existence of a feedback mechanism that links DSB number and distribution with interhomolog interactions.
    Genes & development 04/2013; 27(8). DOI:10.1101/gad.213652.113 · 10.80 Impact Factor
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