Cytological studies of recombination in rhesus males

Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta)

Meiotic recombination landscapes differ greatly between distantly and closely related taxa, populations, individuals, sexes, and even within genomes; however, the factors driving this variation are yet to be well elucidated. Here, we directly estimate contemporary crossover rates and, for the first time, noncrossover rates in rhesus macaques (Macaca mulatta) from four three-generation pedigrees comprising 32 individuals. We further compare these results with historical, demography-aware, linkage disequilibrium-based recombination rate estimates. From paternal meioses in the pedigrees, 165 crossover events with a median resolution of 22.3 kb were observed, corresponding to a male autosomal map length of 2,357 cM-approximately 15% longer than an existing linkage map based on human microsatellite loci. In addition, 85 noncrossover events with a mean tract length of 155 bp were identified-similar to the tract lengths observed in the only other two primates in which noncrossovers have been studied to date, humans and baboons. Consistent with observations in other placental mammals with PRDM9-directed recombination, crossover (and to a lesser extent noncrossover) events in rhesus macaques clustered in intergenic regions and toward the chromosomal ends in males-a pattern in broad agreement with the historical, sex-averaged recombination rate estimates-and evidence of GC-biased gene conversion was observed at noncrossover sites.

Aneuploidy and DNA Methylation as Mirrored Features of Early Human Embryo Development

Genome stability is an integral feature of all living organisms. Aneuploidy is the most common cause of fetal death in humans. The timing of bursts in increased aneuploidy frequency coincides with the waves of global epigenetic reprogramming in mammals. During gametogenesis and early embryogenesis, parental genomes undergo two waves of DNA methylation reprogramming. Failure of these processes can critically affect genome stability, including chromosome segregation during cell division. Abnormal methylation due to errors in the reprogramming process can potentially lead to aneuploidy. On the other hand, the presence of an entire additional chromosome, or chromosome loss, can affect the global genome methylation level. The associations of these two phenomena are well studied in the context of carcinogenesis, but here, we consider the relationship of DNA methylation and aneuploidy in early human and mammalian ontogenesis. In this review, we link these two phenomena and highlight the critical ontogenesis periods and genome regions that play a significant role in human reproduction and in the formation of pathological phenotypes in newborns with chromosomal aneuploidy.

Tet1 Deficiency Leads to Premature Reproductive Aging by Reducing Spermatogonia Stem Cells and Germ Cell Differentiation

Ten-eleven translocation (Tet) enzymes are involved in DNA demethylation, important in regulating embryo development, stem cell pluripotency and tumorigenesis. Alterations of DNA methylation with age have been shown in various somatic cell types. We investigated whether Tet1 and Tet2 regulate aging. We showed that Tet1-deficient mice undergo a progressive reduction of spermatogonia stem cells and spermatogenesis and thus accelerated infertility with age. Tet1 deficiency decreases 5hmC levels in spermatogonia and downregulates a subset of genes important for cell cycle, germ cell differentiation, meiosis and reproduction, such as Ccna1 and Spo11, resulting in premature reproductive aging. Moreover, Tet1 and 5hmC both regulate signaling pathways key for stem cell development, including Wnt and PI3K-Akt, autophagy and stress response genes. In contrast, effect of Tet2 deficiency on male reproductive aging is minor. Hence, Tet1 maintains spermatogonia stem cells with age, revealing an important role of Tet1 in regulating stem cell aging.

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Tet1 regulates stem cell aging and differentiation

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Tet1 plays an important role in maintaining spermatogonial stem cells

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Loss of Tet1 results in exhaustion of spermatogonia and premature reproductive aging

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Effect of Tet2 deficiency on reproductive aging in males is minor

Meiotic Recombination Differences in Rams from Three Breeds of Sheep in the US

Meiotic recombination is an important contributor to genetic variation and ensures proper chromosome segregation during gametogenesis. Previous studies suggest that at least 1 crossover (CO) per chromosome arm is important to avoid mis-segregation. While the total number of COs per spermatocyte is known to differ in mice, this is only beginning to be evaluated in sheep. This study used a cytogenetic approach to quantify and compare the number of COs per spermatocyte in rams from 3 breeds of sheep: Suffolk, Icelandic, and Targhee. In total, 2,758 spermatocytes and over 170,000 COs were examined. Suffolk rams exhibited the lowest mean number of COs (61.1 ± 0.15) compared to Icelandic (63.5 ± 0.27) and Targhee (65.9 ± 0.26) rams. Significant differences in the number of COs per spermatocyte were observed between Suffolk, Icelandic, and Targhee breeds as well as within each breed. Additionally, the number and location of COs were characterized for homologous chromosomes in a subset of spermatocytes for each ram. A positive correlation was identified between the number of COs and the length of the homologous chromosome pair. Suffolk and Icelandic rams exhibited up to 7 COs per chromosome, while Targhee rams exhibited up to 9. Further, distinct CO location preferences on homologous chromosome pairs with 1, 2, 3, and 4 COs were observed in all 3 breeds. These data in sheep will aid in elucidating the mechanism of mammalian meiotic recombination, an important contributor to genetic diversity.

Connecting theory and data to understand recombination rate evolution

Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.

Recombination correlates with synaptonemal complex length and chromatin loop size in bovids-insights into mammalian meiotic chromosomal organization

Homologous chromosomes exchange genetic information through recombination during meiosis, a process that increases genetic diversity, and is fundamental to sexual reproduction. In an attempt to shed light on the dynamics of mammalian recombination and its implications for genome organization, we have studied the recombination characteristics of 112 individuals belonging to 28 different species in the family Bovidae. In particular, we analyzed the distribution of RAD51 and MLH1 foci during the meiotic prophase I that serve, respectively, as proxies for double-strand breaks (DSBs) which form in early stages of meiosis and for crossovers. In addition, synaptonemal complex length and meiotic DNA loop size were estimated to explore how genome organization determines DSBs and crossover patterns. We show that although the number of meiotic DSBs per cell and recombination rates observed vary between individuals of the same species, these are correlated with diploid number as well as with synaptonemal complex and DNA loop sizes. Our results illustrate that genome packaging, DSB frequencies, and crossover rates tend to be correlated, while meiotic chromosomal axis length and DNA loop size are inversely correlated in mammals. Moreover, axis length, DSB frequency, and crossover frequencies all covary, suggesting that these correlations are established in the early stages of meiosis.

Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals

The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals.

Effect of species-specific differences in chromosome morphology on chromatin compaction and the frequency and distribution of RAD51 and MLH1 foci in two bovid species: cattle (Bos taurus) and the common eland (Taurotragus oryx)

Meiotic recombination between homologous chromosomes is crucial for their correct segregation into gametes and for generating diversity. We compared the frequency and distribution of MLH1 foci and RAD51 foci, synaptonemal complex (SC) length and DNA loop size in two related Bovidae species that share chromosome arm homology but show an extreme difference in their diploid chromosome number: cattle (Bos taurus, 2n = 60) and the common eland (Taurotragus oryx, 2nmale = 31). Compared to cattle, significantly fewer MLH1 foci per cell were observed in the common eland, which can be attributed to the lower number of initial double-strand breaks (DSBs) detected as RAD51 foci in leptonema. Despite the significantly shorter total autosomal SC length and longer DNA loop size of the common eland bi-armed chromosomes compared to those of bovine acrocentrics, the overall crossover density in the common eland was still lower than in cattle, probably due to the reduction in the number of MLH1 foci in the proximal regions of the bi-armed chromosomes. The formation of centric fusions during karyotype evolution of the common eland accompanied by meiotic chromatin compaction has greater implications in the reduction in the number of DSBs in leptonema than in the decrease of MLH1 foci number in pachynema.

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

BACKGROUND

By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.

RESULTS

We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.

CONCLUSIONS

Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage.

Variation in genome-wide levels of meiotic recombination is established at the onset of prophase in mammalian males

Segregation of chromosomes during the first meiotic division relies on crossovers established during prophase. Although crossovers are strictly regulated so that at least one occurs per chromosome, individual variation in crossover levels is not uncommon. In an analysis of different inbred strains of male mice, we identified among-strain variation in the number of foci for the crossover-associated protein MLH1. We report studies of strains with “low” (CAST/EiJ), “medium” (C3H/HeJ), and “high” (C57BL/6J) genome-wide MLH1 values to define factors responsible for this variation. We utilized immunofluorescence to analyze the number and distribution of proteins that function at different stages in the recombination pathway: RAD51 and DMC1, strand invasion proteins acting shortly after double-strand break (DSB) formation, MSH4, part of the complex stabilizing double Holliday junctions, and the Bloom helicase BLM, thought to have anti-crossover activity. For each protein, we identified strain-specific differences that mirrored the results for MLH1; i.e., CAST/EiJ mice had the lowest values, C3H/HeJ mice intermediate values, and C57BL/6J mice the highest values. This indicates that differences in the numbers of DSBs (as identified by RAD51 and DMC1) are translated into differences in the number of crossovers, suggesting that variation in crossover levels is established by the time of DSB formation. However, DSBs per se are unlikely to be the primary determinant, since allelic variation for the DSB-inducing locus Spo11 resulted in differences in the numbers of DSBs but not the number of MLH1 foci. Instead, chromatin conformation appears to be a more important contributor, since analysis of synaptonemal complex length and DNA loop size also identified consistent strain-specific differences; i.e., crossover frequency increased with synaptonemal complex length and was inversely related to chromatin loop size. This indicates a relationship between recombination and chromatin compaction that may develop as DSBs form or earlier during establishment of the meiotic axis.

During prophase of meiosis, homologous chromosomes exchange genetic material, in a process known as crossing-over. Crossovers are thought to be essential for proper separation of chromosomes during meiosis but, surprisingly, most mammalian species exhibit substantial individual variation in the number of crossovers per cell. We investigated the basis for this variation by examining localization patterns of crossover-associated proteins in inbred strains of male mice with differing average numbers of crossovers per spermatocyte. Our results indicate that the strain-specific variation is established early in meiotic prophase, possibly even before the DNA is broken in advance of subsequent exchanges between homologous chromosomes.

Cytological studies of human meiosis: sex-specific differences in recombination originate at, or prior to, establishment of double-strand breaks

Meiotic recombination is sexually dimorphic in most mammalian species, including humans, but the basis for the male:female differences remains unclear. In the present study, we used cytological methodology to directly compare recombination levels between human males and females, and to examine possible sex-specific differences in upstream events of double-strand break (DSB) formation and synaptic initiation. Specifically, we utilized the DNA mismatch repair protein MLH1 as a marker of recombination events, the RecA homologue RAD51 as a surrogate for DSBs, and the synaptonemal complex proteins SYCP3 and/or SYCP1 to examine synapsis between homologs. Consistent with linkage studies, genome-wide recombination levels were higher in females than in males, and the placement of exchanges varied between the sexes. Subsequent analyses of DSBs and synaptic initiation sites indicated similar male:female differences, providing strong evidence that sex-specific differences in recombination rates are established at or before the formation of meiotic DSBs. We then asked whether these differences might be linked to variation in the organization of the meiotic axis and/or axis-associated DNA and, indeed, we observed striking male:female differences in synaptonemal complex (SC) length and DNA loop size. Taken together, our observations suggest that sex specific differences in recombination in humans may derive from chromatin differences established prior to the onset of the recombination pathway.

A comparative study of meiotic recombination in cattle (Bos taurus) and three wildebeest species (Connochaetes gnou, C. taurinus taurinus and C. t. albojubatus)

The karyotypic evolution in the family Bovidae is based on centric fusions of ancestral acrocentric chromosomes. Here, the frequency and distribution of meiotic recombination was analyzed in pachytene spermatocytes from Bos taurus (2n = 60) and 3 wildebeest species (Connochaetes gnou, C. taurinus taurinus and C. t. albojubatus) (2n = 58) using immunofluorescence and fluorescence in situ hybridization. Significant differences in mean numbers of recombination events per cell were observed between B. taurus and members of the genus Connochaetes (47.2 vs. 43.7, p < 0.001). The number of MLH1 foci was significantly correlated with the length of the autosomal synaptonemal complexes. The average interfocus distance was influenced by interference. The male recombination maps of bovine chromosomes 2 and 25 and of their fused homologues in wildebeests were constructed. A significant reduction of recombination in the fused chromosome BTA25 was observed in wildebeests (p = 0.005). This was probably caused by interference acting across the centromere, which was significantly stronger than the intra-arm interference. This comparative meiotic study showed significant differences among the species from the family Bovidae with the same fundamental number of autosomal arms (FNa = 29) which differ by a single centric fusion.

Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes

GC-biased gene conversion (gBGC) is a major evolutionary force shaping genomic nucleotide landscapes, distorting the estimation of the strength of selection, and having potentially deleterious effects on genome-wide fitness. Yet, a global quantitative picture, at large evolutionary scale, of the relative strength of gBGC compared with selection and random drift is still lacking. Furthermore, owing to its dependence on the local recombination rate, gBGC results in modulations of the substitution patterns along genomes and across time which, if correctly interpreted, may yield quantitative insights into the long-term evolutionary dynamics of recombination landscapes. Deriving a model of the substitution process at putatively neutral nucleotide positions from population-genetics arguments, and accounting for among-lineage and among-gene effects, we propose a reconstruction of the variation in gBGC intensity at the scale of placental mammals, and of its scaling with body-size and karyotypic traits. Our results are compatible with a simple population genetics model relating gBGC to effective population size and recombination rate. In addition, among-gene variation and phylogenetic patterns of exon-specific levels of gBGC reveal the presence of rugged recombination landscapes, and suggest that short-lived recombination hot-spots are a general feature of placentals. Across placental mammals, variation in gBGC strength spans two orders of magnitude, at its lowest in apes, strongest in lagomorphs, microbats or tenrecs, and near or above the nearly neutral threshold in most other lineages. Combined with among-gene variation, such high levels of biased gene conversion are likely to significantly impact midly selected positions, and to represent a substantial mutation load. Altogether, our analysis suggests a more important role of gBGC in placental genome evolution, compared with what could have been anticipated from studies conducted in anthropoid primates.

A comparative study of the recombination pattern in three species of Platyrrhini monkeys (primates)

Homologous chromosomes exchange genetic information through recombination during meiotic synapsis, a process that increases genetic diversity and is fundamental to sexual reproduction. Meiotic studies in mammalian species are scarce and mainly focused on human and mouse. Here, the meiotic recombination events were determined in three species of Platyrrhini monkeys (Cebus libidinosus, Cebus nigritus and Alouatta caraya) by analysing the distribution of MLH1 foci at the stage of pachytene. Moreover, the combination of immunofluorescence and fluorescent in situ hybridisation has enabled us to construct recombination maps of primate chromosomes that are homologous to human chromosomes 13 and 21. Our results show that (a) the overall number of MLH1 foci varies among all three species, (b) the presence of heterochromatin blocks does not have a major influence on the distribution of MLH1 foci and (c) the distribution of crossovers in the homologous chromosomes to human chromosomes 13 and 21 are conserved between species of the same genus (C. libidinosus and C. nigritus) but are significantly different between Cebus and Alouatta. This heterogeneity in recombination behaviour among Ceboidea species may reflect differences in genetic diversity and genome composition.

On the origin of crossover interference: A chromosome oscillatory movement (COM) model

BACKGROUND

It is now nearly a century since it was first discovered that crossovers between homologous parental chromosomes, originating at the Prophase stage of Meiosis I, are not randomly placed. In fact, the number and distribution of crossovers are strictly regulated with crossovers/chiasmata formed in optimal positions along the length of individual chromosomes, facilitating regular chromosome segregation at the first meiotic division. In spite of much research addressing this question, the underlying mechanism(s) for the phenomenon called crossover/chiasma interference is/are still unknown; and this constitutes an outstanding biological enigma.

RESULTS

The Chromosome Oscillatory Movement (COM) model for crossover/chiasma interference implies that, during Prophase of Meiosis I, oscillatory movements of the telomeres (attached to the nuclear membrane) and the kinetochores (within the centromeres) create waves along the length of chromosome pairs (bivalents) so that crossing-over and chiasma formation is facilitated by the proximity of parental homologs induced at the nodal regions of the waves thus created. This model adequately explains the salient features of crossover/chiasma interference, where (1) there is normally at least one crossover/chiasma per bivalent, (2) the number is correlated to bivalent length, (3) the positions are dependent on the number per bivalent, (4) interference distances are on average longer over the centromere than along chromosome arms, and (5) there are significant changes in carriers of structural chromosome rearrangements.

CONCLUSIONS

The crossover/chiasma frequency distribution in humans and mice with normal karyotypes as well as in carriers of structural chromosome rearrangements are those expected on the COM model. Further studies are underway to analyze mechanical/mathematical aspects of this model for the origin of crossover/chiasma interference, using string replicas of the homologous chromosomes at the Prophase stage of Meiosis I. The parameters to vary in this type of experiment will include: (1) the mitotic karyotype, i.e. ranked length and centromere index of the chromosomes involved, (2) the specific bivalent/multivalent length and flexibility, dependent on the way this structure is positioned within the nucleus and the size of the respective meiocyte nuclei, (3) the frequency characteristics of the oscillatory movements at respectively the telomeres and the kinetochores.

Evolution of the genomic recombination rate in murid rodents

Although very closely related species can differ in their fine-scale patterns of recombination hotspots, variation in the average genomic recombination rate among recently diverged taxa has rarely been surveyed. We measured recombination rates in eight species that collectively represent several temporal scales of divergence within a single rodent family, Muridae. We used a cytological approach that enables in situ visualization of crossovers at meiosis to quantify recombination rates in multiple males from each rodent group. We uncovered large differences in genomic recombination rate between rodent species, which were independent of karyotypic variation. The divergence in genomic recombination rate that we document is not proportional to DNA sequence divergence, suggesting that recombination has evolved at variable rates along the murid phylogeny. Additionally, we document significant variation in genomic recombination rate both within and between subspecies of house mice. Recombination rates estimated in F(1) hybrids reveal evidence for sex-linked loci contributing to the evolution of recombination in house mice. Our results provide one of the first detailed portraits of genomic-scale recombination rate variation within a single mammalian family and demonstrate that the low recombination rates in laboratory mice and rats reflect a more general reduction in recombination rate across murid rodents.

Broad-scale recombination patterns underlying proper disjunction in humans

Although recombination is essential to the successful completion of human meiosis, it remains unclear how tightly the process is regulated and over what scale. To assess the nature and stringency of constraints on human recombination, we examined crossover patterns in transmissions to viable, non-trisomic offspring, using dense genotyping data collected in a large set of pedigrees. Our analysis supports a requirement for one chiasma per chromosome rather than per arm to ensure proper disjunction, with additional chiasmata occurring in proportion to physical length. The requirement is not absolute, however, as chromosome 21 seems to be frequently transmitted properly in the absence of a chiasma in females, a finding that raises the possibility of a back-up mechanism aiding in its correct segregation. We also found a set of double crossovers in surprisingly close proximity, as expected from a second pathway that is not subject to crossover interference. These findings point to multiple mechanisms that shape the distribution of crossovers, influencing proper disjunction in humans.

In humans, as in most sexually reproducing organisms, recombination plays a fundamental role in meiosis, helping to align chromosomes and to ensure their proper segregation. Recombination events are tightly regulated both in terms of their minimum number (the rule of “crossover assurance”) and placement (due to “crossover interference”). Accumulating evidence, however, suggests that recombination patterns are highly variable among humans, raising numerous questions about the nature and stringency of crossover assurance and interference. We took a first step towards answering these questions by examining patterns of recombination in gametes inherited by viable, non-trisomic offspring. We found that the minimum number of crossovers is tightly regulated at the level of a chromosome (rather than chromosome arm), but with a notable exception: in females, chromosome 21 appears to frequently segregate properly in the absence of a crossover. We also found a set of double recombination events in surprisingly close proximity, consistent with a pathway not subject to crossover interference. These findings suggest that there are multiple mechanisms of recombination in human meiosis, which may buffer the effects of inter-individual variation in rates.