High-resolution crossover maps for each bivalent of Zea mays using recombination nodules

Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. Using the maize inbred line KYS, we prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4267 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. RN frequencies are closely correlated with both chiasma frequencies and SC length. The total length of the RN recombination map is about twofold shorter than that of most maize linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents.     

Solitary and synaptonemal complex-associated recombination nodules in pro-nurse cells during oogenesis in Drosophila melanogaster

An oocyte in Drosophila melanogaster originates from 1 of 16 cells comprising an ovarial syncytium. The two pro-oocytes proceed into the pachytene stage of meiosis, but only one develops further into a mature oocyte while the other reverts to a nurse cell. It is known that pro-nurse cells also enter meiosis, as they contain incomplete synaptonemal complexes (SCs). We now show that these cells also harbour recombination nodules (RNs). In cells that only occasionally contain SC segments, the RNs are typically not located close to distinct tripartite SC structures. Instead, these RNs are frequently associated with a spherical body of amorphous material and two to three, more or less parallel fibres, possibly representing SC material. The significance of the solitary RNs is discussed in relation to the present knowledge of the assembly and disassembly of the SC.     

Recombination nodules in coleopteran species: Palembus dermestoides (Tenebrionidae) and Epicauta atomaria (Meloidae)

This work describes the first report about the occurrence of recombination nodules (RNs) in spread pachytene cells of two species of Coleoptera: Palembus dermestoides (Tenebrionidae) and Epicauta atomaria (Meloidae). The RNs were observed in preparations contrasted with phosphotungstic acid. Considering RN morphology and its occurrence in pachytene bivalents (one per autosome bivalent) these structures were interpreted to be late RNs. P. dermestoides and E. atomaria have 2n = 20 chromosomes including an Xy(p) sex determination system. In spite of most frequently subtelocentric morphology observed in the autosomes of both species, the occurrence of RNs is limited only to the synaptonemal complex (SC) structure of the long arms. These findings are in agreement with those obtained using light microscopy analysis in which only one chiasma or terminalization event is observed per autosomal bivalent in early or late metaphase I cells. The RNs have the same average width of the SC of each analyzed species, a circular shape, strong electron density, and are observed mainly between the lateral elements of the SC. The RNs of P. dermestoides and E. atomaria have approximately the same average size (width), 180 +/- 20 nm and 160 +/- 80 nm, respectively. The absence of RNs in the short arms and its occurrence in the long arms are discussed considering the short arm pericentromeric and pro-centric heterochromatin.     

Two-dimensional spreads of synaptonemal complexes from solanaceous plants

By using serial sectioning and a new hypotonic bursting technique on primary microsporocytes of tomato (Lycopersicon esculentum), relatively large numbers of recombination nodules (RNs) are observed on the synaptonemal complexes forming during zygonema. In pachynema most, but not all, of these RNs are lost. If RNs represent sites of potential crossing over during zygonema and sites of actual crossing over during late pachynema, the observed temporal and spatial distribution of RNs may provide answers for some classic cytogenetic questions such as: how is at least one crossover per bivalent assured? How are crossovers localized? What is the basis for positive chiasma interference?     

The distribution of early recombination nodules on zygotene bivalents from plants.

Early recombination nodules (ENs) are protein complexes approximately 100 nm in diameter that are associated with forming synaptonemal complexes (SCs) during leptotene and zygotene of meiosis. Although their functions are not yet clear, ENs may have roles in synapsis and recombination. Here we report on the frequency and distribution of ENs in zygotene SC spreads from six plant species that include one lower vascular plant, two dicots, and three monocots. For each species, the number of ENs per unit length is higher for SC segments than for (asynapsed) axial elements (AEs). In addition, EN number is strongly correlated with SC segment length. There are statistically significant differences in EN frequencies on SCs between species, but these differences are not related to genome size, number of chromosomes, or phylogenetic class. There is no difference in the frequency of ENs per unit length of SC from early to late zygotene. The distribution of distances between adjacent ENs on SC segments is random for all six species, but ENs are found at synaptic forks more often than expected for a random distribution of ENs on SCs. From these observations, we conclude that in plants: (1) some ENs bind to AEs prior to synapsis, (2) most ENs bind to forming SCs at synaptic forks, and (3) ENs do not bind to already formed SCs.     

Integrating genetic linkage maps with pachytene chromosome structure in maize

Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1). all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2). each RN corresponds to one crossover, and (3). the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r(2) = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.     

Meiotic checkpoints and the interchromosomal effect on crossing over in Drosophila females

During prophase of meiosis I, genetic recombination is initiated with a Spo11-dependent DNA double-strand break (DSB). Repair of these DSBs can generate crossovers, which become chiasmata and are important for the process of chromosome segregation. To ensure at least one chiasma per homologous pair of chromosomes, the number and distribution of crossovers is regulated. One system contributing to the distribution of crossovers is the pachytene checkpoint, which requires the conserved gene pch2 that encodes an AAA+ATPase family member. Pch2-dependent pachytene checkpoint function causes delays in pachytene progression when there are defects in processes required for crossover formation, such as mutations in DSB-repair genes and when there are defects in the structure of the meiotic chromosome axis. Thus, the pachytene checkpoint appears to monitor events leading up to the generation of crossovers. Interestingly, heterozygous chromosome rearrangements cause Pch2-dependent pachytene delays and as little as two breaks in the continuity of the paired chromosome axes are sufficient to evoke checkpoint activity. These chromosome rearrangements also cause an interchromosomal effect on recombination whereby crossing over is suppressed between the affected chromosomes but is increased between the normal chromosome pairs. We have shown that this phenomenon is also due to pachytene checkpoint activity.     

Equal frequencies of recombination nodules in both sexes of the pigeon suggest a basic difference with eutherian mammals.

The total number of recombination nodules (RNs) in the autosomal synaptonemal complexes (SCs) is statistically equivalent in oocytes and spermatocytes from the domestic pigeon Columba livia. The distribution on RNs along the three longest autosomes is also equivalent in oocytes and spermatocytes. The numbers of RNs show a linear relationship when plotted against SC length both in oocytes and spermatocytes. On the other hand, the ZW pair shows a single and strictly localized RN near the synaptic termini, but the ZZ pair shows unrestricted location of RNs (average 3.8). The ZW and ZZ pairs of the pigeon are euchromatic and do not show specific chromatin packing at pachytene in either sex. The lack of sex-specific differences in the number and location of RNs in the autosomal bivalents of C. livia and previous data on the chicken, suggest that the regulation of crossing-over is basically different in birds and mammals.     

Crossing over during Caenorhabditis elegans meiosis requires a conserved MutS-based pathway that is partially dispensable in budding yeast.

Formation of crossovers between homologous chromosomes during Caenorhabditis elegans meiosis requires the him-14 gene. Loss of him-14 function severely reduces crossing over, resulting in lack of chiasmata between homologs and consequent missegregation. Cytological analysis showing that homologs are paired and aligned in him-14 pachytene nuclei, together with temperature-shift experiments showing that him-14 functions during the pachytene stage, indicate that him-14 is not needed to establish pairing or synapsis and likely has a more direct role in crossover formation. him-14 encodes a germline-specific member of the MutS family of DNA mismatch repair (MMR) proteins. him-14 has no apparent role in MMR, but like its Saccharomyces cerevisiae ortholog MSH4, has a specialized role in promoting crossing over during meiosis. Despite this conservation, worms and yeast differ significantly in their reliance on this pathway: whereas worms use this pathway to generate most, if not all, crossovers, yeast still form 30-50% of their normal number of crossovers when this pathway is absent. This differential reliance may reflect differential stability of crossover-competent recombination intermediates, or alternatively, the presence of two different pathways for crossover formation in yeast, only one of which predominates during nematode meiosis. We discuss a model in which HIM-14 promotes crossing over by interfering with Holliday junction branch migration.     

Meiotic checkpoints and the interchromosomal effect on crossing over in Drosophila females

During prophase of meiosis I, genetic recombination is initiated with a Spo11-dependent DNA double-strand break (DSB). Repair of these DSBs can generate crossovers, which become chiasmata and are important for the process of chromosome segregation. To ensure at least one chiasma per homologous pair of chromosomes, the number and distribution of crossovers is regulated. One system contributing to the distribution of crossovers is the pachytene checkpoint, which requires the conserved gene pch2 that encodes an AAA+ATPase family member. Pch2-dependent pachytene checkpoint function causes delays in pachytene progression when there are defects in processes required for crossover formation, such as mutations in DSB-repair genes and when there are defects in the structure of the meiotic chromosome axis. Thus, the pachytene checkpoint appears to monitor events leading up to the generation of crossovers. Interestingly, heterozygous chromosome rearrangements cause Pch2-dependent pachytene delays and as little as two breaks in the continuity of the paired chromosome axes are sufficient to evoke checkpoint activity. These chromosome rearrangements also cause an interchromosomal effect on recombination whereby crossing over is suppressed between the affected chromosomes but is increased between the normal chromosome pairs. We have shown that this phenomenon is also due to pachytene checkpoint activity.     

The coupling of crossing over and homologous synapsis in maize inversions

Because fresh initiations of synapsis must occur for homologous synapsis of internal heterozygously inverted chromosome segments, attention has been directed at homologous synapsis and crossing over in overlapping paracentric inversions in the long arm of chromosome 1 of maize. In an earlier study with a relatively short inversion (where double crossovers within the inversion were rare), a recombination nodule (RN) was generally found at pachytene in reverse paired (homologously synapsed) inverted regions. Crossover frequency within the inversion, which could be independently estimated from analysis of bridge and fragment frequency at anaphase I and II, closely corresponded to crossover frequency estimated from observed RN frequency in pachytene inversion loops. These findings were consistent with the interpretation that establishment of homologous synapsis in this case is generally coupled to crossing over. This coupling suggests that there is very early commitment to the form of resolution of recombination intermediates that results in reciprocal recombination events instead of conversion only or other noncrossover events. This study examines another, larger paracentric inversion in the long arm of chromosome 1 that completely overlaps the first inversion. It is sufficiently longer than the first inversion that double crossover events are found within it with substantial frequency and interference considerations are feasible. This study confers additional insight into the interrelationships of synapsis and crossing over and the probable sequence in which the various involved processes usually occur. It raises the strong possibility that crossovers can be initiated during the alignment phase that precedes synapsis.     

Mammalian meiotic recombination: a reexamination

Recombination nodules (RNs) are small electron-dense structures associated with the synaptonemal complex. Two types have been identified: early RNs present during zygonema-early pachynema, which are thought to be involved in gene conversion and synaptic initiation, and late RNs present during mid-to-late pachynema, which are thought to be involved in reciprocal recombination leading to chiasma formation. In organisms as diverse as Sodaria, Drosophila, and plants there is indeed a close correlation between the observed number of late RNs and crossovers, or their cytogenetic manifestation, chiasmata. However, as this reexamination of the human data shows, there is not a similar correlation in mammals. Instead, there is a severe deficiency in RNs in eutherian males and marsupial females near chromosome ends and other recombinational hot spots (defined genetically), or localized chiasmata (defined cytogenetically). Many of these sites of hyper-recombination correspond to sites of telomere or telomere-associated sequences. Together these observations suggest the possibility of a second, mechanistically different, recombination pathway that does not involve RNs, but may directly involve telomere or telomere-associated sequences. This pathway may be responsible for sex-specific hot-spots of recombination observed at highly localized sites throughout the genome.     

BRC-1 acts in the inter-sister pathway of meiotic double-strand break repair

The breast and ovarian cancer susceptibility protein BRCA1 is evolutionarily conserved and functions in DNA double-strand break (DSB) repair through homologous recombination, but its role in meiosis is poorly understood. By using genetic analysis, we investigated the role of the Caenorhabditis elegans BRCA1 orthologue (brc-1) during meiotic prophase. The null mutant in the brc-1 gene is viable, fertile and shows the wild-type complement of six bivalents in most diakinetic nuclei, which is indicative of successful crossover recombination. However, brc-1 mutants show an abnormal increase in apoptosis and RAD-51 foci at pachytene that are abolished by loss of spo-11 function, suggesting a defect in meiosis rather than during premeiotic DNA replication. In genetic backgrounds in which chiasma formation is abrogated, such as him-14/MSH4 and syp-2, loss of brc-1 leads to chromosome fragmentation suggesting that brc-1 is dispensable for crossing over but essential for DSB repair through inter-sister recombination.     

NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae.

We describe the identification of a new meiosis-specific gene of Saccharomyces cerevisiae, NDT80. The ndt80 null and point mutants arrest at the pachytene stage of meiosis, with homologs connected by full-length synaptonemal complexes and spindle pole bodies duplicated but unseparated. Meiotic recombination in an ndt80 delta mutant is relatively normal, although commitment to heteroallelic recombination is elevated two- to threefold and crossing over is decreased twofold compared with those of the wild type. ndt80 arrest is not alleviated by mutations in early recombination genes, e.g., SPO11 or RAD50, and thus cannot be attributed to an intermediate block in prophase chromosome metabolism like that observed in several other mutants. The ndt80 mutant phenotype during meiosis most closely resembles that of a cdc28 mutant, which contains a thermolabile p34, the catalytic subunit of maturation-promoting factor. Cloning and molecular analysis reveal that the NDT80 gene maps on the right arm of chromosome VIII between EPT1 and a Phe-tRNA gene, encodes a 627-amino-acid protein which exhibits no significant homology to other known proteins, and is transcribed specifically during middle meiotic prophase. The NDT80 gene product could be a component of the cell cycle regulatory machinery involved in the transition out of pachytene, a participant in an unknown aspect of meiosis sensed by a pachytene checkpoint, or a SPO11- and RAD50-independent component of meiotic chromosomes that is the target of cell cycle signaling.     

The Relationship of Homologous Synapsis and Crossing over in a Maize Inversion

Frequency of homologous synapsis at pachytene for a relatively short heterozygous inversion was compared to the frequency of crossover occurrence within the inversion and to the frequency of the presence of a recombination nodule within the homologously synapsed inverted region. Crossover frequencies were estimated from bridge-fragment frequencies at anaphase I and anaphase II. Recombination nodules (RNs) were observed in electron micrographs. Results show very similar frequencies of homologous synapsis and the occurrence of reciprocal recombination within the inverted region, consistent with the interpretation that establishment of homologous synapsis in this case is related to at least commitment to the form of resolution of crossover intermediates which gives rise to reciprocal recombination, not conversion only, events. An RN was generally found at pachytene in homologously synapsed inverted regions.     

Two kinds of "recombination nodules" in Neurospora crassa

Two morphological types of recombination nodules, termed early and late, are recognized in Neurospora crassa. Eighty nuclei at different substages were used to determine numbers of nodules per nucleus, distribution of nodules along the nucleolus-organizing chromosome, and distribution of nodules among the two largest chromosomes. Early nodules appear at the synaptonemal complex at early zygotene and increase in number during zygotene until a dramatic reduction occurs at zygotene-pachytene transition. Thereafter early nodules are steadily eliminated until they disappear by diplotene. Late nodules are also present during zygotene. Their number doubles at the zygotene-pachytene transition and stays at this level until diplotene. The total number of nodules is rather constant through zygotene and pachytene. Distribution of bivalents with 0, 1, 2, etc. nodules follows a Poisson distribution at zygotene, but not at pachytene, where variance is less than the mean, indicating positive interference. Nodules are distributed nonrandomly along the nucleolus-organizer bivalent. The pattern differs slightly in nuclei of different origin. Nuclei with unusual synaptonemal complexes sustain normal levels of recombination by having the same amount of nodules as normal nuclei. In abnormal nuclei nodules are preferentially associated with normal segments. It is proposed that early nodules do not participate in any form of recombination but have a role in finding an appropriate site for a crossing-over event. Morphological change to the late type indicates that the site has been reached and the exchange event can be mediated by the late nodule.     

Differential immunolocalization of a putative Rec8p in meiotic autosomes and sex chromosomes of triatomine bugs

Hemipteran chromosomes are holocentric and show regular, special behavior at meiosis. While the autosomes pair at pachytene, have synaptonemal complexes (SCs) and recombination nodules (RNs) and segregate at anaphase I, the sex chromosomes do not form an SC or RNs, divide equationally at anaphase I, and their chromatids segregate at anaphase II. Here we show that this behavior is shared by the X and Y chromosomes of Triatoma infestans and the X(1)X(2)Y chromosomes of Triatoma pallidipennis. As Rec8p is a widely occurring component of meiotic cohesin, involved in meiotic homolog segregation, we used an antibody against Rec8p of Caenorhabditis elegans for immunolocalization in these triatomines. We show that while Rec8p is colocalized with SCs in the autosomes, no Rec8p can be found by immunolabeling in the sex chromosomes at any stage of meiosis. Furthermore, Rec8p labeling is lost from autosomal bivalents prior to metaphase I. In both triatomine species the sex chromosomes conjoin with each other during prophase I, and lack any SC, but they form "fuzzy cores", which are observed with silver staining and with light and electron microscopy during pachytene. Thin, serial sectioning and electron microscopy of spermatocytes at metaphases I and II reveals differential behavior of the sex chromosomes. At metaphase I the sex chromosomes form separate entities, each surrounded by a membranous sheath. On the other hand, at metaphase II the sex chromatids are closely tied and surrounded by a shared membranous sheath. The peculiar features of meiosis in these hemipterans suggest that they depart from the standard meiotic mechanisms proposed for other organisms.     

Cytological analysis of MRE11 protein during early meiotic prophase I in Arabidopsis and tomato

Early recombination nodules (ENs) are multiprotein complexes that are thought to be involved in synapsis and recombination, but little is known about their components or how they may be involved in these events. In this study, we describe the cytological behavior of a possible EN component, MRE11, a protein that is important for the repair of the numerous, programmed deoxyribonucleic acid double-strand breaks (DSBs) that occur early in the meiotic prophase. By immunofluorescence, many MRE11 foci were associated with chromosomal axes during early prophase I in both wild-type Arabidopsis and tomato primary microsporocytes. Similar patterns of MRE11 foci were observed in two Arabidopsis mutants (Atspo11-1 and Atprd1) that are defective in DSB formation and synapsis. In tomato chromosomes, MRE11 foci were more common in distal euchromatin than in proximal heterochromatin, consistent with known EN patterns. However, electron microscopic immunogold localization demonstrated that only about 10% of ENs were labeled, and most MRE11 label was associated with synaptonemal complex components. Thus, in plants, MRE11 foci are not dependent on DSB formation, and most MRE11 foci do not correspond to ENs. More generally, our results show that the simple presence of large numbers of fluorescent foci associated with synapsing chromosomes is insufficient evidence to equate these foci with ENs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Leslie D. Lohmiller and Arnaud De Muyt contributed equally.     

Enhanced Gene Conversion and Postmeiotic Segregation in Pachytene-Arrested SACCHAROMYCES CEREVISIAE

Previous study has demonstrated that incubation of yeast cells of strain AP-1 in sporulation medium at 36° permits them to begin meiosis but that they become arrested at pachytene and undergo enhanced intragenic recombination between ade2 heteroalleles. Tetrad analysis was undertaken to characterize the altered program of meiotic recombination more widely. In one set of experiments, pachytene-arrested cells were permitted to resume sporulation upon transfer to the permissive temperature. In the resulting asci, both postmeiotic segregation and gene conversion were increased several-fold at a number of loci relative to unarrested controls, whereas reciprocal recombination increased two- to threefold. Another set of experiments analyzed the genetic consequences of inducing the pachytene-arrested cells to revert directly to mitotic growth without completion of meiosis. The appearance of homozygous sectors from heterozygous markers revealed that these cells had become committed to appreciable recombination but that reciprocal exchange was less frequent than in normal asci. Taken together, the data indicate that pachytene arrest rendered the cells committed to enhanced recombination upon resumption of sporulation but that most of the crossing over did not occur until release from the arrest. —The genetic basis of pachytene arrest by AP-1 was investigated by mating each of its parents with progeny of strain Y55, which is able to sporulate at 36°. Both of these diploids sporulated at 36°, and asci from the one studied further exhibited 2:2 segregation of the sporulation defect, indicating that pachytene arrest is dependent on a recessive, temperature-sensitive allele at a chromosomal locus.