XY chromosome behaviour in the germ-line of the human male: a FISH analysis of spatial orientation, chromatin condensation and pairing

A major recombination hotspot in the XqYq pseudoautosomal region gives new insight into processing of human gene conversion events

Recombination plays a fundamental role in meiosis. Non-exchange gene conversion (non-crossover, NCO) may facilitate homologue pairing, while reciprocal crossover (CO) physically connects homologues so they orientate appropriately on the meiotic spindle. In males, X-Y homologous pairing and exchange occurs within the two pseudoautosomal regions (PARs) together comprising <5% of the human sex chromosomes. Successful meiosis depends on an obligatory CO within PAR1, while the nature and role of exchange within PAR2 is unclear. Here, we describe the identification and characterization of a typical ~1 kb wide recombination hotspot within PAR2. We find that both COs and NCOs are strongly modulated in trans by the presumed chromatin remodelling protein PRDM9, and in cis by a single nucleotide polymorphism (SNP) located at the hotspot centre that appears to influence recombination initiation and which causes biased gene conversion in SNP heterozygotes. This, the largest survey to date of human NCOs reveals for the first time substantial inter-individual variation in the NCO:CO ratio. Although the extent of biased transmission at the central marker in COs is similar across men, it is highly variable among NCO recombinants. This suggests that cis-effects are mediated not only through recombination initiation frequencies varying between haplotypes but also through subsequent processing, with the potential to significantly intensify meiotic drive of hotspot-suppressing alleles. The NCO:CO ratio and extent of transmission distortion among NCOs appear to be inter-related, suggesting the existence of two NCO pathways in humans.

Dynamic gene order on the Silene latifolia Y chromosome

Dioecious Silene latifolia evolved heteromorphic sex chromosomes within the last ten million years, making it a species of choice for studies of the early stages of sex chromosome evolution in plants. About a dozen genes have been isolated from its sex chromosomes and basic genetic and deletion maps exist for the X and Y chromosomes. However, discrepancies between Y chromosome maps led to the proposal that individual Y chromosomes may differ in gene order. Here, we use an alternative approach, with fluorescence in situ hybridization (FISH), to locate individual genes on S. latifolia sex chromosomes. We demonstrate that gene order on the Y chromosome differs between plants from two populations. We suggest that dynamic gene order may be a general property of Y chromosomes in species with XY systems, in view of recent work demonstrating that the gene order on the Y chromosomes of humans and chimpanzees are dramatically different.

The AZF proteins

The azoospermia factor (AZF) locus in Yq11 is now functionally subdivided in three distinct spermatogenesis loci: AZFa, AZFb and AZFc. After knowledge of the complete genomic Y sequence in Yq11, 14 Y genes encoding putatively functional proteins and expressed in human testis are found to be located in one of the three AZF intervals. Therefore, a major question for each infertility clinic performing molecular screening for AZF deletions has now raised concerning the functional contribution of the encoded AZF proteins to human spermatogenesis. Additionally, it has been shown that distinct chromatin regions in Yq11 overlapping with the genomic AZFb and AZFc intervals are probably involved in the pre-meiotic X and Y chromosome pairing process. An old hypothesis on the germ line function of AZF becomes therefore revitalized. It proposed a specific chromatin folding code in Yq11, which controls the condensation cycle of the Y chromosome in the male germ line. Thus, with the exception of AZF proteins functionally expressed during the pre-meiotic differentiation and proliferation of spermatogonia, the need for AZF proteins functionally expressed at meiosis or during the post-meiotic spermatid maturation process is difficult to assess before the identification of specific mutations in the corresponding AZF gene causing male infertility.

Studying meiosis: a review of FISH and M-FISH techniques used in the analysis of meiotic processes in humans

It is well known that chromosome in situ hybridization allows the unequivocal identification of targeted human somatic chromosomes. Different fluorescent in situ hybridization (FISH) techniques have been developed throughout the years and, following the mitotic studies, meiotic analyses have been performed using these different techniques. The introduction of M-FISH techniques to the analysis of meiotic cells has allowed the study of meiotic processes for every individual human chromosome. In this paper, we review the different FISH and M-FISH techniques that have been used on human meiotic cells in both men and women.

The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture

Genomes are housed within cell nuclei as individual chromosome territories. Nuclei contain several architectural structures that interact and influence the genome. In this review, we discuss how the genome may be organised within its nuclear environment with the position of chromosomes inside nuclei being either influenced by gene density or by chromosomes size. We compare interphase genome organisation in diverse species and reveal similarities and differences between evolutionary divergent organisms. Genome organisation is also discussed with relevance to regulation of gene expression, development and differentiation and asks whether large movements of whole chromosomes are really observed during differentiation. Literature and data describing alterations to genome organisation in disease are also discussed. Further, the nuclear structures that are involved in genome function are described, with reference to what happens to the genome when these structures contain protein from mutant genes as in the laminopathies.

AZF deletions and Y chromosomal haplogroups: history and update based on sequence

AZF deletions are genomic deletions in the euchromatic part of the long arm of the human Y chromosome (Yq11) associated with azoospermia or severe oligozoospermia. Consequently, it can be assumed that these deletions remove Y chromosomal genes required for spermatogenesis. However, these 'classical' or 'complete' AZF deletions, AZFa, AZFb and AZFc, represent only a subset of rearrangements in Yq11. With the benefit of the Y chromosome sequence, more rearrangements (deletions, duplications, inversions) inside and outside the classical AZF deletion intervals have been elucidated and intra-chromosomal non-allelic homologous recombinations (NAHRs) of repetitive sequence blocks have been identified as their major cause. These include duplications in AZFa, AZFb and AZFc and the partial AZFb and AZFc deletions of which some were summarized under the pseudonym 'gr/gr' deletions. At least some of these rearrangements are associated with distinct Y chromosomal haplogroups and are present with similar frequencies in fertile and infertile men. This suggests a functional redundancy of the AZFb/AZFc multi-copy genes. Alternatively, the functional contribution(s) of these genes to human spermatogenesis might be different in men of different Y haplogroups. That raises the question whether, the frequency of Y haplogroups with different AZF gene contents in distinct human populations leads to a male fertility status that varies between populations or whether, the presence of the multiple Y haplogroups implies a balancing selection via genomic deletion/amplification mechanisms.

Homologous pairing and chromosome dynamics in meiosis and mitosis

Pairing of homologous chromosomes is an essential feature of meiosis, acting to promote high levels of recombination and to ensure segregation of homologs. However, homologous pairing also occurs in somatic cells, most regularly in Dipterans such as Drosophila, but also to a lesser extent in other organisms, and it is not known how mitotic and meiotic pairing relate to each other. In this article, I summarize results of recent molecular studies of pairing in both mitosis and meiosis, focusing especially on studies using fluorescent in situ hybridization (FISH) and GFP-tagging of single loci, which have allowed investigators to assay the pairing status of chromosomes directly. These approaches have permitted the demonstration that pairing occurs throughout the cell cycle in mitotic cells in Drosophila, and that the transition from mitotic to meiotic pairing in spermatogenesis is accompanied by a dramatic increase in pairing frequency. Similar approaches in mammals, plants and fungi have established that with few exceptions, chromosomes enter meiosis unpaired and that chromosome movements involving the telomeric, and sometimes centromeric, regions often precede the onset of meiotic pairing. The possible roles of proteins involved in homologous recombination, synapsis and sister chromatid cohesion in homolog pairing are discussed with an emphasis on those for which mutant phenotypes have permitted an assessment of effects on homolog pairing. Finally, I consider the question of the distribution and identity of chromosomal pairing sites, using recent data to evaluate possible relationships between pairing sites and other chromosomal sites, such as centromeres, telomeres, promoters and heterochromatin. I cite evidence that may point to a relationship between matrix attachment sites and homologous pairing sites.

Meiosis, recombination and chromosomes: a review of gene isolation and fluorescent in situ hybridization data in plants

Evidence is now increasing that many functions and processes of meiotic genes are similar in yeast and higher eukaryotes. However, there are significant differences and, most notably, yeast has considerably higher recombination frequencies than higher eukaryotes, different cross-over interference and possibly more than one pathway for recombination, one late and one early. Other significant events are the timing of double-strand breaks (induced by Spo11) that could be either cause or consequence of homologous chromosome synapsis and SC formation depending on the organisms, yeast plants and mammals versus Drosophila melanogaster and Caenorhabditis elegans. Many plant homologues and heterologues to meiotic genes of yeast and other organisms have now been isolated, in particular in Arabidopsis thaliana, showing that overall recombination genes are very conserved while synaptonemal complex and cohesion proteins are not. In addition to the importance of unravelling the meiotic processes by gene discovery, this review discusses the significance of chromatin packaging, genome organization, and distribution of specific repeated DNA sequences for homologous chromosome cognition and pairing, and the distribution of recombination events along the chromosomes.

Meiotic sex chromosome inactivation in male mice with targeted disruptions of Xist

X chromosome inactivation occurs twice during the life cycle of placental mammals. In normal females, one X chromosome in each cell is inactivated early in embryogenesis, while in the male, the X chromosome is inactivated together with the Y chromosome in spermatogenic cells shortly before or during early meiotic prophase. Inactivation of one X chromosome in somatic cells of females serves to equalise X-linked gene dosage between males and females, but the role of male meiotic sex chromosome inactivation (MSCI) is unknown. The inactive X-chromosome of somatic cells and male meiotic cells share similar properties such as late replication and enrichment for histone macroH2A1.2, suggesting a common mechanism of inactivation. This possibility is supported by the fact that Xist RNA that mediates somatic X-inactivation is expressed in the testis of male mice and humans. In the present study we show that both Xist RNA and Tsix RNA, an antisense RNA that controls Xist function in the soma, are expressed in the testis in a germ-cell-dependent manner. However, our finding that MSCI and sex-body formation are unaltered in mice with targeted mutations of Xist that prevent somatic X inactivation suggests that somatic X-inactivation and MSCI occur by fundamentally different mechanisms.

Asynchronous chromosome pairing in male meiosis of the rat (Rattus norvegicus)

Premeiotic and meiotic chromosome distribution was studied in rat testes suspensions by a triple-color fluorescent staining protocol which allows simultaneous visual inspection of two chromosomal targets highlighted by FISH together with immunostained SCP3 synaptonemal complex (SC) proteins which are marked by a third, composite color. Triple labeling with rat chromosome (RNO) 4q and 19p specific probes and SCP3 staining disclosed that homologs are separated in premeiotic and leptotene nuclei. Pairing of homologous chromosome regions commenced during early zygotene, with pairing of the small metacentric chromosomes 19 preceding that of the distal region of the long arm of RNO4. Our results show that homolog association occurs during zygotene of rat spermatogenesis, with small and large chromosomes showing a considerable asynchrony. Comparison with pairing progression in meiosis of other mammals suggests that asynchronous chromosome pairing reflects size differences within a complement.

Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana

The intranuclear arrangements of centromeres and telomeres during meiotic interphase and early prophase I of meiosis in Arabidopsis thaliana were analysed by fluorescent in situ hybridisation to spread pollen mother cells and embryo-sac mother cells. Meiocyte identification, staging and progression were established by spreading and sectioning techniques, including various staining procedures and bromodeoxyuridine labeling of replicating DNA.

Centromere regions of Arabidopsis are unpaired, widely dispersed and peripherally located in nuclei during meiotic interphase, and they remain unpaired and unassociated throughout leptotene. Eventually they associate pairwise during zygotene, as part of the nucleus-wide synapsis of homologous chromosomes.

Telomeres, by contrast, show a persistent association with the nucleolus throughout meiotic interphase. Variation in telomere signal number indicates that telomeres undergo pairing during this interval, preceding the onset of general chromosome synapsis. During leptotene the paired telomeres lose their association with the nucleolus and become widely dispersed. As the chromosomes synapse during zygotene, the telomeres reveal a loose clustering within one hemisphere, which may represent a degenerate or relic bouquet configuration. We propose that in Arabidopsis the classical leptotene/zygotene bouquet is absent and is replaced functionally by nucleolus-associated telomere clustering.

Organization of the X and Y chromosomes in human, chimpanzee and mouse pachytene nuclei using molecular cytogenetics and three-dimensional confocal analyses

We used multicolour fluorescence in-situ hybridization on air-dried pachytene nuclei to analyse the structural and functional domains of the sex vesicle (SV) in human, chimpanzee and mouse. The same technology associated with 3-dimensional analysis was then performed on human and mouse pachytene nuclei from cytospin preparations and tissue cryosections. The human and the chimpanzee SVs were very similar, with a consistently small size and a high degree of condensation. The mouse SV was most often seen to be large and poorly condensed, although it did undergo progressive condensation during pachynema. These results suggest that the condensation of the sex chromosomes is not a prerequisite for the formation of the mouse SV, and that a different specific mechanism could be responsible for its formation. We also found that the X and Y chromosomes are organized into two separate and non-entangled chromatin domains in the SV of the three species. In each species, telomeres of the X and Y chromosomes remain clustered in a small area of the SV, even those without a pseudoautosomal region. The possible mechanisms involved in the organization of the sex chromosomes and in SV formation are discussed.

Detection of aneuploidy in rodent and human sperm by multicolor FISH after chronic exposure to diazepam

Aneuploidy induction in male germ cells of mice and men after chronic exposure to diazepam (DZ; CAS 439-14-5; Valium was assessed by multicolor fluorescence in situ hybridization (FISH). DZ, a widely administered sedative and muscle relaxant, was proposed to act as an aneugen by disturbing spindle function in various assay systems. Male mice were treated by oral intubation with 3mg/kg DZ once or daily for 14 consecutive days. At 22 days after the last treatment, epididymal sperm were collected from the caudae epididymes. Evaluation of aneuploid and diploid sperm (10,000 sperm per animal) was performed by multicolor FISH employing DNA probes specific for chromosomes X, Y, and 8 simultaneously. We found a significant increase in the frequency of disomy 8 in subchronically DZ-treated mice when compared to the concurrent solvent control group (2.4-fold; P<0.01), while no increase was detected for sex-chromosome hyperhaploidies. No effect was seen when mice were treated with a single dose (3mg/kg DZ). In a parallel human approach, two men were evaluated who chronically ingested >0.3mg/kg/d DZ for more than 6 months. Multicolor FISH was applied to human sperm probing for chromosomes X, Y, and 13. Frequencies for sperm with disomy 13, disomy X, and total sex-chromosomal disomies were found to be elevated among the two subjects after chronic DZ-exposure compared to control subjects. In conclusion, the results indicate that diazepam acts as an aneugen during meiosis in male spermatogenesis, both in mice and humans. The quantitative comparison indicates that humans may be at least 10 times more sensitive than mice for aneuploidy induction by DZ during male meiosis.

Evaluation of meiotic impairment of azoospermic men by fluorescence in situ hybridization

OBJECTIVE

To identify predictive criteria for the existence of spermatogenesis in nonobstructive azoospermic men.

DESIGN

Prospective study.

SETTING

Andrology laboratory at a teaching hospital.

PATIENT(S)

Twenty-two azoospermic men were divided into three groups by qualitative testicular histopathology and the presence of spermatozoa in minced biopsies.

INTERVENTION(S)

Testicular biopsies evaluation.

MAIN OUTCOME MEASURE(S)

The presence of spermatozoa and/or mature spermatids, the percentage of sex vesicle formation (X and Y chromosomes in proximity), and the pairing of the two 18 homologous chromosomes.

RESULT(S)

Spermatozoa and mature spermatids were found in 17 study patients. Whenever few mature spermatids and/or spermatozoa were found, the rates of X-Y and 18 bivalents were significantly higher (mean +/- SD, 73% +/- 13. 3% and 91% +/- 7.1%) than those in cases of spermatocyte maturation arrest (23% +/- 8.0% and 60% +/- 11.8%, respectively).

CONCLUSION(S)

Pairing of chromosomes during meiosis is apparently related to the progression of spermatogenesis. Consequently, high rates of bivalent formation increase the prospect of focal spermatogenesis in the testis, despite the failure to identify mature spermatids in the specific testicular biopsy under examination.

Comparison of sex chromosome aneuploidy in spermatozoa of fertile men and those requiring ICSI treatment detected by fluorescence in situ hybridization

OBJECTIVE

To compare the frequencies of aneuploidy for chromosomes X, Y and 18 in spermatozoa of infertile and fertile males, using 3-color fluorescence in situ hybridization.

METHODS

Twelve infertile patients who underwent intracytoplasmic sperm injection treatment at Queen's Medical Centre, Nottingham were studied. Three fertile men served as controls. Aneuploidy frequencies in both groups were compared using 2-sample t-tests.

RESULTS

A total of 26,615 ad 93,649 cells were scored in the control and infertile groups respectively. The frequencies of diploidy, sex chromosome disomy and chromosome 18 disomy in the fertile (0.11, 0.28 and 0.11%) compared to the infertile males (0.05, 0.18 and 0.06%) were not statistically significantly different.

CONCLUSION

Our preliminary data do not indicate an increased risk from paternal origin sex chromosome aneuploidies in ICSI. However, we recommend further investigations of the cytogenetic constitution of spermatozoa from severe male factor patients.

A review of fluorescence in situ hybridization (FISH): current status and future prospects

Fluorescence in situ hybridization (FISH) is a powerful technique for detecting DNA or RNA sequences in cells, tissues and tumors. This molecular cytogenetic technique enables the localization of specific DNA sequences within interphase chromatin and metaphase chromosomes and the identification of both structural and numerical chromosome changes. FISH is quickly becoming one of the most extensively used cytochemical staining techniques owing to its sensitivity and versatility, and with the improvement of current technology and cost effectiveness, its use will surely continue to expand. Here we review the wide variety of current applications and future prospects of FISH technology.

Bouquet formation in budding yeast: initiation of recombination is not required for meiotic telomere clustering

Fluorescence in situ hybridization in combination with synaptonemal complex and spindle pole body immunostaining to both spread and structurally preserved nuclei from time course experiments disclosed prominent telomere clustering during meiotic prophase of the yeast Saccharomyces cerevisiae. It was found that centromere clustering, which dominates vegetative nuclear structure, is rapidly lost after induction of meiosis. Telomeres tightly clustered during leptotene/zygotene-equivalent stages in the vicinity of the spindle pole body, giving rise to a classical chromosomal bouquet arrangement. This arrangement dissolved later during prophase. Painting of chromosomes XI revealed that initially compacted chromosome territories adopt an outstretched morphology in bouquet nuclei. This conformational state was associated with alignment and pairing. Chromosome condensation during pachytene rendered condensed and compact bivalents, and dispersed telomeres. Both the spo11 and rad50S recombination mutants formed bouquets, demonstrating that bouquet formation is recombination and synapsis independent.

Aspects of three-dimensional chromosome reorganization during the onset of human male meiotic prophase

The three-dimensional morphology and distribution of human chromosomes 3 were studied in nuclei of spermatogonia and spermatocytes I from formaldehyde-fixed human testis sections. Chromosome arms, pericentromeres and telomeric regions were painted by a three-color, five-probe fluorescence in situ hybridization protocol. Light optical serial sections of premeiotic and meiotic nuclei obtained by confocal laser scanning microscopy revealed that premeiotic chromosomes 3 are separate from each other and occupy variably shaped territories, which are sectored in distinct 3 p- and q-arm domains. Three-dimensional reconstructions of the painted chromosome domains by a Voronoi tessellation approach showed that mean chromosome volumes did not differ significantly among the premeiotic and meiotic stages investigated. A significant increase in surface area and reduction of dimensionless ‘roundness factor’ estimates of arm domains indicated that the restructuring of spatially separate chromosome territories initiates during preleptotene. Telomeric regions, which in meiotic stem cells located predominantly in arm-domain chromatin, showed a redistribution towards the domain surface during this stage. At leptotene homologues were generally misaligned and displayed intimate intermingling of non-homologous chromatin. Pairing initiated at the ends of bent zygotene chromosomes, which displayed a complex surface structure with discernible sister chromatids. The results indicate that, in mammals, homology search is executed during leptotene, after remodeling of chromosome territories.

A method for fluorescence in situ hybridization against synaptonemal complex-associated chromatin of plant meiocytes

An improved method of preparing two-dimensional surface spreads of plant synaptonemal complexes (SCs) associated with fluorescent in situ hybridization is described. This technique produces clear preparations of SCs and, in addition, consistently reveals the organization and location of different repetitive DNA sequences in plant meiotic prophase chromosomes.

Combined immunocytogenetic and molecular cytogenetic analysis of meiosis I human spermatocytes

We have used a combination of immunocytogenetic and molecular cytogenetic technology on human spermatocytes to investigate (1) meiosis I chromosome pairing, and (2) organization of synaptonemal complex (SC)-associated chromatin with respect to whole chromosome paints, unique DNA sequences and repetitive DNA of heterochromatic blocks, centromeres and telomeres. It is evident that synapsis normally starts at the termini of homologues. In general, synapsis proceeds synchronously from termini towards the centre of bivalents without any indication of interstitial initiation. Some aberrant meiosis I spermatocytes showed asynchronous pairing, demonstrating not only large differences in the degree of SC formation between bivalents, but also chromosome alignment without synapsis as well as clear interstitial synaptic initiation. It may be the case that alignment normally takes place along the entire length of homologues before synapsis occurs and that the potential for synaptic initiation exists along the length of chromosomes. Telomeric sequences were seen tightly associated with the SCs, as might be expected considering their kinetic properties in relation to the nuclear membrane. Other repetitive DNA, i.e. centromeric alpha-satellites and classical satellites of the heterochromatic blocks 1qh and 9qh, were all found to form loops that are associated with SCs only at their bases. A unique DNA cosmid probe (21q22.3) was found to produce a hybridization pattern consisting of spots located outside SC. The fluorescence in situ hybridization (FISH) signals of these spread DNA sequences have a granular appearance, probably reflecting the pattern of coiling and chromatin condensation of the target DNAs.

Centromere and telomere movements during early meiotic prophase of mouse and man are associated with the onset of chromosome pairing

The preconditions and early steps of meiotic chromosome pairing were studied by fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes to mouse and human testis tissue sections. Premeiotic pairing of homologous chromosomes was not detected in spermatogonia of the two species. FISH with centromere- and telomere-specific DNA probes in combination with immunostaining (IS) of synaptonemal complex (SC) proteins to testis sections of prepuberal mice at days 4-12 post partum was performed to study sequentially the meiotic pairing process. Movements of centromeres and then telomeres to the nuclear envelope, and of telomeres along the nuclear envelope leading to the formation of a chromosomal bouquet were detected during mouse prophase. At the bouquet stage, pairing of a mouse chromosome-8-specific probe was observed. SC-IS and simultaneous telomere FISH revealed that axial element proteins appear as large aggregates in mouse meiocytes when telomeres are attached to the nuclear envelope. Axial element formation initiates during tight telomere clustering and transverse filament-IS indicated the initiation of synapsis during this stage. Comparison of telomere and centromere distribution patterns of mouse and human meiocytes revealed movements of centromeres and then telomeres to the nuclear envelope and subsequent bouquet formation as conserved motifs of the pairing process. Chromosome painting in human spermatogonia revealed compacted, largely mutually exclusive chromosome territories. The territories developed into long, thin threads at the onset of meiotic prophase. Based on these results a unified model of the pairing process is proposed.

An Mr 51,000 protein of mammalian spermatogenic cells that is common to the whole XY body and centromeric heterochromatin of autosomes

During mammalian male meiotic prophase the sex chromosomes form a structure called the XY body or sex vesicle. This structure is characterized by differential condensation of chromatin and transcriptional inactivity. The reasons and mechanisms for the allocyclic behaviour of sex chromosomes with respect to autosomes are largely unknown. In order to gain insight into the process of XY-body formation we are involved in the characterization of proteins associated with meiotic sex chromosomes by immunological approaches. Here we report on the identification of an Mr 51,000 protein (p51) that is homogeneously distributed in the XY body of rodents as shown by immunocytochemistry with the novel monoclonal antibody 4EC. Interestingly, in germ line cells the antibody also labelled the centromeric heterochromatin of autosomes. We speculate that p51 may be a component of the mechanisms that lead to wide chromosome regions becoming inaccessible for transcription and/or recombination events.