The heterogeneous nature of cell types in the testis and the absence of meiotic cell culture models have been significant hurdles to the study of the unique differentiation programs that are manifest during meiosis. Two principal methods have been developed to purify, to varying degrees, various meiotic fractions from both adult and immature animals: elutriation or Staput (sedimentation) using BSA and/or percoll gradients. Both of these methods rely on cell size and density to separate meiotic cells [1][2][3][4][5] . Overall, except for few cell populations 6 , these protocols fail to yield sufficient purity of the numerous meiotic cell populations that are necessary for detailed molecular analyses. Moreover, with such methods usually one type of meiotic cells can be purified at a given time, which adds an extra level of complexity regarding the reproducibility and homogeneity when comparing meiotic cell samples.Here, we describe a refined method that allows one to easily visualize, identify, and purify meiotic cells, from germ cells to round spermatids, using FACS combined with Hoechst 33342 staining 7,8 . This method provides an overall snapshot of the entire meiotic process and allows one to highly purify viable cells from most stage of meiosis. These purified cells can then be analyzed in detail for molecular changes that accompany progression through meiosis, for example changes in gene expression 9,10 and the dynamics of nucleosome occupancy at hotspots of meiotic recombination 11 . ProtocolThis protocol can be separated in two major steps: (1) the dissociation and Hoechst 33342 staining of mouse testis cells followed by, if necessary, (2) FACS sorting of the relevant meiotic fractions, including all stages of meiosis, from germ cells to round spermatids. Once collected, these highly enriched meiotic populations can be used for a wide range of analysis. This protocol describes the dissociation of one adult testis; volumes can be adapted accordingly for juveniles or for additional testes.

During meiosis, paternal and maternal homologous chromosomes recombine at specific recombination sites named hotspots. What renders 2% of the mammalian genomes permissive to meiotic recombination by allowing Spo11 endonuclease to initiate double-strand breaks is largely unknown. Work in yeast has shown that chromatin accessibility seems to be important for this activity. Here, we define nucleosome profiles and dynamics at four mouse recombination hotspots by purifying highly enriched fractions of meiotic cells. We found that nucleosome occupancy is generally stable during meiosis progression. Interestingly, the cores of recombination hotspots have largely open chromatin structure, and the localization of the few nucleosomes present in these cores correlates precisely with the crossover-free zones in recombinogenic domains. Collectively, these high-resolution studies suggest that nucleosome occupancy seems to direct, at least in part, how meiotic recombination events are processed.

Male spermatogenesis is an essential and complex process necessary to gain totipotency and allow a whole new organism to develop upon fertilization. While single-gene based studies have provided insights into the mechanisms underlying spermatogenesis, detailed global profiling of all the key meiotic stages is required to fully define these processes. Here, by isolating highly enriched mouse meiotic cell populations, we have generated a comprehensive gene expression atlas of mammalian meiosis. Our data define unique signatures for the specific stages of meiosis, including global chromosome X inactivation and reactivation. The data also reveal profound switches in global gene expression at the initiation of pachynema that are reminiscent of the commitment to meiosis observed in budding yeast. Overall, this meiotic atlas provides an exhaustive blueprint and resource for mammalian gametogenesis and meiosis.

Genome-wide analyses have suggested thousands of meiotic recombination hot spots across mammalian genomes. However, very few hot spots have been directly analyzed at a sub-kb scale for crossover (CO) activity. Using recombinant inbred strains as a CO library, here we report the identification and detailed characterization of seven new meiotic hot spots on mouse chromosome 19, more than doubling the number of currently available mouse hot spots. Although a shared feature is the narrow 1.5–2.5-kb width of these recombinogenic sites, these analyses revealed that hot spots have diverse sequence attributes and distinct symmetric and asymmetric CO profiles. Interestingly, CO molecules with discontinuous conversion tracts are commonly observed, contrasting with those found in human. Furthermore, unlike human hot spots, those present in the mouse do not necessarily have a quasi-normal CO distribution but harbor CO repulsion zones within recombinogenic cores. We propose a model where local chromatin landscape directs these repulsion zones.

Meiotic recombination initiates following the formation of DNA doublestrand breaks (DSBs) by the Spo11 endonuclease early in prophase I, at discrete regions in the genome coined "hot spots." In mammals, meiotic DSB site selection is directed in part by sequence-specific binding of PRDM9, a polymorphic histone H3 (H3K4Me3) methyltransferase. However, other chromatin features needed for meiotic hot spot specification are largely unknown. Here we show that the recombinogenic cores of active hot spots in mice harbor several histone H3 and H4 acetylation and methylation marks that are typical of open, active chromatin. Further, deposition of these open chromatin-associated histone marks is dynamic and is manifest at spermatogonia and/or pre-leptotene-stage cells, which facilitates PRDM9 binding and access for Spo11 to direct the formation of DSBs, which are initiated at the leptotene stage. Importantly, manipulating histone acetylase and deacetylase activities established that histone acetylation marks are necessary for both hot spot activity and crossover resolution. We conclude that there are functional roles for histone acetylation marks at mammalian meiotic recombination hot spots.KEYWORDS crossover, double-strand break initiation, histone acetylation, meiotic recombination, mouse meiosis M eiotic recombination commences only following the double-stranded cleavage of DNA by the meiosis-specific Spo11 endonuclease in leptotene to early zygotene meiosis I cells (1-4), at discrete regions of the genome coined meiotic recombination "hot spots" (5, 6). Meiotic DNA double-strand breaks (DSBs) are then repaired by homologous recombination (HR) pathways, mediated by the meiosis-specific Rad51 and DMC1 repair proteins in mid-and late-zygotene-stage cells (4,7,8). The chromatin features, regulatory factors, and histone modifications that contribute to the control of mammalian meiotic DSB site selection by Spo11 and to the initiation, crossover (CO) activity, and resolution of meiotic recombination events are generally poorly understood.In mice and humans, one key regulator of DSB site selection is PRDM9 (5, 9-13), a polymorphic histone H3 methyltransferase that binds in a sequence-specific fashion to polymorphic sequences that are present in nearly 90% of hot spot cores (14) and that generates the trimethylated histone H3 lysine 4 (H3K4Me3) mark that is a hallmark of open chromatin (15,16). However, in addition to the known role for the H3K4Me3 mark at hot spot cores, an emerging body of evidence suggests that several histone modifications associated with open chromatin, including acetylation, methylation, and