Linkage, physical mapping, and DNA sequence analysis of pseudoautosomal loci on the human X and Y chromosomes

The pseudoautosomal region of the human X and Y chromosomes is subject to frequent X-Y recombination during male meiosis. We report the finding of two pseudoautosomal loci, DXYS20 and DXYS28, characterized by highly informative restriction fragment length polymorphisms (RFLPs). The pseudoautosomal character of DXYS20 and DXYS28 was formally demonstrated by comparing their transmission to 45,X and to normal individuals. Studies of the inheritance of these loci reveal that the pseudoautosomal region, though highly recombinogenic, is subject to marked recombinational interference in male meiosis; no double recombinants were observed in 143 triply informative meioses, and the coefficient of coincidence is likely less than 0.45. In female meiosis, linkage of these pseudoautosomal RFLPs to strictly sex-linked RFLPs on the short arm of the X is readily detected; the genetic length of the pseudoautosomal region in female meiosis is at least 4 cM but not more than 18 cM. The genetic map of the human X chromosome is now defined from near the short-arm telomere to band q28 on the long arm. Locus DXYS20, which maps near the X and Y short-arm telomeres, is composed of long tandem arrays of 61-bp repeats. Occasional, seemingly random base-pair substitutions within these arrays of 61-bp repeats, in combination with marked variation in the size of the array, generate the high degree of DNA polymorphism at DXYS20.     

The pseudoautosomal regions of the human sex chromosomes

In human females, both X chromosomes are equivalent in size and genetic content, and pairing and recombination can theoretically occur anywhere along their entire length. In human males, however, only small regions of sequence identity exist between the sex chromosomes. Recombination and genetic exchange is restricted to these regions of identity, which cover 2.6 and 0.4 Mbp, respectively, and are located at the tips of the short and the long arm of the X and Y chromosome. The unique biology of these regions has attracted considerable interest, and complete long-range restriction maps as well as comprehensive physical maps of overlapping YAC clones are already available. A dense genetic linkage map has disclosed a high rate of recombination at the short arm telomere. A consequence of the obligatory recombination within the pseudoautosomal region is that genes show only partial sex linkage. Pseudoautosomal genes are also predicted to escape X-inactivation, thus guaranteeing an equal dosage of expressed sequences between the X and Y chromosomes. Gene pairs that are active on the X and Y chromosomes are suggested as candidates for the phenotypes seen in numerical X chromosome disorders, such as Klinefelter's (47,XXY) and Turner's syndrome (45,X). Several new genes have been assigned to the Xp/Yp pseudoautosomal region. Potential associations with clinical disorders such as short stature, one of the Turner features, and psychiatric diseases are discussed. Genes in the Xq/Yq pseudoautosomal region have not been identified to date.     

Deletions within the pseudoautosomal region help map three new markers and indicate a possible role of this region in linear growth.

Short stature is consistently found in individuals with terminal deletions of Xp. In order to refine the localization of a putative locus affecting height, we analyzed two patients with a partial monosomy of the pseudoautosomal region at the molecular level. Eight pseudoautosomal probes were used for the genetic deletion analysis through dose evaluation. Three of them represent new markers (DXS415, DXS419, and DXS406) which were positioned on the pseudoautosomal map by pulsed field gel electrophoresis. Our data suggest that a locus affecting height maps in a region of about 1.5 Mbp, distal to the DXS406 locus and proximal to the DXS415 locus, a region which includes two CpG islands, and rule out an involvement of very distal sequences at the X/Y telomeres.     

A VNTR immediately adjacent to the human pseudoautosomal telomere.

The probe 29C1 detects a hypervariable locus 18kb from the telomere of the human X and Y chromosomes, in the pseudoautosomal region. Here we report that hypervariability of fragments containing this sequence in the human population arises by loss or gain of a 31 base pair GC rich repeat. Labelled 29C1 does not detect a DNA fingerprint at low stringency, though the consensus repeat sequence does show some similarity to previously reported minisatellites. Sequence within the repeat block has G and C rich strands, a feature associated with sequences at the telomeres of many higher organisms. The repeat block shows sequence characteristics normally associated with a low methylation island, though the locus is methylated and does not appear to be transcribed.     

Linkage of the murine steroid sulfatase locus, Sts, to sex reversed, Sxr: a genetic and molecular analysis.

We present genetic and molecular data demonstrating linkage of the gene for steroid sulfatase (Sts) to the mutation sex reversed (Sxr) definitively showing the existance of a functional allele for Sts mapping to the pseudoautosomal region of the mouse Y chromosome. Thus, in mouse, functional Sts genes are present in the pseudoautosomal region of both the X and Y chromosomes. This is in contrast to man where Sts has been mapped to the short arm of the X just centromeric to the pseudoautosomal region. Only a single recombinant separating Sts and Sxr was found out of 103 male meioses analyzed; double recombinants were not found between sex (Tdy), Sts and Sxr. If the rate of recombination in the pseudoautosomal region in male mice is equivalent to that in man and thus 7-10X higher than normal, then our data suggest that the distance between Sts and Sxr (or the telomere of the Y) is approximately 100-200 kb in length. Our data is in contrast to a recent report of a recombination frequency separating Sts and Sxr of as high as 6.2-9.8%.     

Synapsis and obligate recombination between the sex chromosomes of male laboratory mice carrying the Y* rearrangement.

The synaptic and recombinational behavior of the sex chromosomes in male laboratory mice carrying the Y* rearrangement was analyzed by light and electron microscopy. Examination of zygotene and pachytene X-Y* configurations revealed a surprising paucity of the staggered pairing configuration predicted from the distal position of the X pseudoautosomal region and the subcentromeric position of the Y* pseudoautosomal region. When paired at pachynema, the X and Y* chromosomes usually assumed configurations similar to those of typical sex bivalents from normal male laboratory mice. The X and Y* chromosomes were present as univalents in more than half of the early- and mid-pachytene nuclei, presumably as a result of steric difficulties associated with homologous alignment of the pseudoautosomal regions. When paired at diakinesis and metaphase I, the X and Y* chromosomes exhibited an asymmetrical chiasmatic association indicative of recombination within the staggered synaptic configuration. Both pairing disruption and recombinational failure apparently contribute to diakinesis/metaphase I sex-chromosome univalency, as most cells at these stages possessed X and Y* univalents lacking evidence of prior recombination. Recombinant X or Y* chromosomes were detected in all metaphase II complements examined, thus substantiating the hypothesis that X-Y recombination is a prerequisite for the normal progression of male meiosis.     

Shared DNA sequences between the X and Y chromosomes in the tammar wallaby – evidence for independent additions to eutherian and marsupial sex chromosomes

Marsupial sex chromosomes are smaller than their eutherian counterparts and are thought to reflect an ancestral mammalian X and Y. The gene content of this original X is represented largely by the long arm of the human X chromosome. Genes on the short arm of the human X are autosomal in marsupials and monotremes, and represent a recent addition to the eutherian X and Y. The marsupial X and Y apparently lack a pseudoautosomal region and show only end-to-end pairing at meiosis. However, the sex chromosomes of macropodid marsupials (kangaroos and wallabies) are larger than the sex chromosomes of other groups, and a nucleolus organizer is present on the X and occasionally the Y. Chromosome painting using DNA from sorted and microdissected wallaby X and Y chromosomes reveals homologous sequences on the tammar X and Y chromosomes, concentrated on the long arm of the Y chromosome and short arm of the X. Ribosomal DNA sequences were detected by fluorescence in situ hybridization on the wallaby Xp but not the Y. Since no chiasmata have been observed in marsupial sex chromosomes, it is unlikely that these shared sequences act as a pseudoautosomal region within which crossing over may occur, but they may be required for end-to-end associations. The shared region of wallaby X and Y chromosomes bears no homology with the recently added region of the eutherian sex chromosomes, so we conclude that independent additions occurred to both sex chromosomes in a eutherian and macropodid ancestor, as predicted by the addition-attrition hypothesis of sex chromosome evolution. Received: 18 October 1996 / Accepted: 21 February 1997     

The mammalian pseudoautosomal region

Despite being morphologically dissimilar, mammalian sex chromosomes pair in male meiosis. Molecular studies of the X and Y chromosomes in humans and mice have identified the pseudoautosomal region, a genetically unique region of shared, recombining sequences that fall within the meiotic pairing region. Complete meiotic and physical maps of the human pseudoautosomal region have been produced and the pseudoautosomal boundary has been cloned and sequenced. These studies have provided clues to mammalian sex chromosome function and evolution.     

Analysis of methylation of a human X located gene which escapes X inactivation.

The gene MIC2 is located in the pseudoautosomal region at the ends of the short arms of the X and Y chromosomes. In females MIC2 escapes X inactivation. We have analyzed the methylation pattern of MIC2 on the active X, the inactive X chromosomes, and the Y chromosome. The 5' end of the gene contains a GC rich region which is unmethylated on the active X, the inactive X and on the Y. The body of the gene is characterized by variable methylation.     

The mouse Y* chromosome involves a complex rearrangement, including interstitial positioning of the pseudoautosomal region.

Cytological analysis of the mouse Y* chromosome revealed a complex rearrangement involving acquisition of a functional centromere and centromeric heterochromatin and attachment of this chromosomal segment to the distal end of a normal Y* chromosome. This rearrangement positioned the Y* short-arm region at the distal end of the Y* chromosome and the pseudoautosomal region interstitially, just distal to the newly acquired centromere. In addition, the majority of the pseudoautosomal region was inverted. Recombination between the X and the Y* chromosomes generates two new sex chromosomes: (1) a large chromosome comprised of the X chromosome attached at its distal end to all of the Y* chromosome but missing the centromeric region (XY*) and (2) a small chromosome containing the centromeric portion of the Y* chromosome attached to G-band-negative material from the X chromosome (YX). Mice that inherit the XY* chromosome develop as sterile males, whereas mice that inherit the Y*X chromosome develop as fertile females. Recovery of equal numbers of recombinant and nonrecombinant offspring from XY* males supports the hypothesis that recombination between the mammalian X and Y chromosomes is necessary for primary spermatocytes to successfully complete spermatogenesis and form functional sperm.     

Strong linkage disequilibrium between the XY274 polymorphism and the pseudoautosomal boundary.

The pseudoautosomal boundary is defined by an Alu repeat element on the Y chromosome. The Alu element is found on all Y chromosomes and on no X chromosomes, establishing it as part of Y-specific sequences. Distal to the Alu element, sequences from the X and Y are strictly homologous, suggesting that the boundary is formed by an abrupt break in sequence homology. Further investigation of the function of the boundary has been undertaken by examining the population structure of an MspI restriction-site polymorphism (XY274), which is located 274 bp distal to the Alu insertion site. Southern blot and polymerase chain reaction analysis demonstrate fixation of the high allele (noncutting or AT base pair) of XY274 on the Y chromosome in most populations, while a full range of high allele frequencies is found on the X chromosomes of different populations. Two exceptions to fixation on the Y chromosome were found in African populations. The level of linkage disequilibrium suggests that the first few hundred base pairs of the pseudoautosomal region on the Y chromosome share a single common origin more recent than the origin of the species.     

The human X-linked steroid sulfatase gene and a Y-encoded pseudogene: evidence for an inversion of the Y chromosome during primate evolution

The mammalian X and Y chromosomes are thought to have evolved from a common, nearly homologous chromosome pair. Although there is little sequence similarity between the mouse or the human X and Y, there are several regions in which moderate to extensive sequence homologies have been found, including, but not limited to, the so-called pseudoautosomal segment, in which X-Y pairing and recombination take place. The steroid sulfatase gene is in the pseudoautosomal region of the mouse, but not in man. We have cloned and characterized the human STS X-encoded locus and a pseudogene that is present on the long arm of the Y chromosome. Our data in humans and other primates suggest that there has been a pericentric inversion of the Y chromosome during primate evolution that has disrupted the former pseudoautosomal arrangement of these genes. These results provide additional insight into the evolution of the sex chromosomes and into the nature of this interesting portion of the human genome.     

Structure and chromosomal mapping of a highly polymorphic repetitive DNA sequence from the pseudoautosomal region of the mouse sex chromosomes

The pseudoautosomal region of the Mov15 mouse strain is marked by a Moloney murine leukemia provirus. The sequences flanking the Mov15 provirus were molecularly cloned and shown to consist of a tandemly repeated sequence of 31 nucleotides. Copy number variation of this repeat most likely accounts for the polymorphism in the mouse pseudoautosomal region detected with a probe from the flanking sequences. In situ hybridization to metaphase chromosomes showed heavy labeling of the pairing region of the X and Y chromosomes. The repetitive sequence was also found at the subtelomeric region of three autosomes. A similar level of amplification as the one seen on the sex chromosomes seems to be present on chromosomes 9 and 13. Lower copy number appear to be present on chromosome 4.     

Gene Conversion between the X Chromosome and the Male-Specific Region of the Y Chromosome at a Translocation Hotspot

Outside the pseudoautosomal regions, the mammalian sex chromosomes are thought to have been genetically isolated for up to 350 million years. However, in humans pathogenic XY translocations occur in XY-homologous (gametologous) regions, causing sex-reversal and infertility. Gene conversion might accompany recombination intermediates that resolve without translocation and persist in the population. We resequenced X and Y copies of a translocation hotspot adjacent to the PRKX and PRKY genes and found evidence of historical exchange between the male-specific region of the human Y and the X in patchy flanking gene-conversion tracts on both chromosomes. The rate of X-to-Y conversion (per base per generation) is four to five orders of magnitude more rapid than the rate of Y-chromosomal base-substitution mutation, and given assumptions about the recombination history of the X locus, tract lengths have an overall average length of ∼100 bp. Sequence exchange outside the pseudoautosomal regions could play a role in protecting the Y-linked copies of gametologous genes from degeneration.     

Elevated DNA sequence diversity in the genomic region of the phosphatase PPP2R3L gene in the human pseudoautosomal region

The evolution, inheritance and recombination rate of genes located in the pseudoautosomal region 1 (PAR1) is exceptional within the human genome. Pseudoautosomal genes are identical on X and Y chromosomes and are not inherited in a sex linked manner. Due to an obligatory recombination event in male meiosis, pseudoautosomal genes are exchanged frequently between X and Y chromosomes. During the isolation, characterization and sequencing of a novel gene PPP2R3L, which was classified by sequence homology as a novel member of the protein phosphatase regulatory subunit families, it became apparent that cosmids of different origin harboring this gene are highly polymorphic between individuals, both at the nucleotide level and in the number.     

The minimal mammalian Y chromosome - the marsupial Y as a model system

The mammalian X and Y chromosomes are very different in size and gene content. The Y chromosome is much smaller than the X and consists largely of highly repeated non-coding DNA, containing few active genes. The 65-Mb human Y is homologous to the X over two small pseudoautosomal regions which together contain 13 active genes. The heterochromatic distal half of the human Yq is entirely composed of highly repeated non-coding DNA, and even the euchromatic portion of the differential region is largely composed of non-coding repeated sequences, amongst which about 30 active genes are located. The basic marsupial Y chromosome (about 10 Mb) is much smaller than that of humans or other eutherian mammals. It appears to include no PAR, since it does not undergo homologous pairing, synaptonemal complex formation or recombination with the X. We show here that the tiny dunnart Y chromosome does not share cytogenetically detectable sequences with any other chromosome, suggesting that it contains many fewer repetitive DNA sequences than the human or mouse Y chromosomes. However, it shares several genes with the human and/or mouse Y chromosome, including the sex determining gene SRY and the candidate spermatogenesis gene RBMY, implying that the marsupial and eutherian Y are monophyletic. This minimal mammalian Y chromosome might provide a good model Y in which to hunt for new mammalian Y specific genes.     

Studying the biological and technical sources of variation in telomere length of individual chromosomes.

BACKGROUND: Consistent average length differences between species and chromosome arm differences within species indicate that telomere length is genetically determined. This seems to contradict an observed large variation in lengths of the same human telomere between metaphases of the same individual. We examined the extent to which the variation in the telomeres of the human X and Y chromosomes is heritable, induced, or technical in origin. METHODS: Metaphase chromosomes were stained by fluorescence in situ hybridization with a telomere repeat-specific probe, and fluorescence intensities of the X and Y chromosomes were measured. If telomere length variation is predominantly genetically determined and a 50% probability of meiotic recombination between the pseudo-autosomal regions of Yp and Xp in the father is taken into account, one expects an equal chance that the Yp telomere of a son is derived from his father's Xp or Yp telomere. This implies that the Yp/Yq telomere ratios in fathers and sons will be identical in the absence of paternal meiotic recombination and different when recombination occurs. RESULTS: Among five father-son pairs, four showed similar Yp/Yq ratios (P > 0.05), whereas one pair exhibited a large difference in the Yp/Yq ratio that was attributable to a significantly longer Xp than Yp telomere in the father and a presumptive meiotic exchange between X and Y during paternal meiosis. Further, the Xq telomere exhibited a generally shorter telomere length than the others. CONCLUSIONS: The high variation in telomere length appeared to be intracellular (between sister chromatids) and, hence, technical in nature. We found no measurable induced variation in the cells studied, implying that, if induced variation exists, it is small compared with the technical variation.     

Sex chromosome polymorphism in guppies

Sex chromosomes differ from autosomes by dissimilar gene content and, at a more advanced stage of their evolution, also in structure and size. This is driven by the divergence of the Y or W from their counterparts, X and Z, due to reduced recombination and the resulting degeneration as well as the accumulation of sex-specific and sexually antagonistic genes. A paradigmatic example for Y-chromosome evolution is found in guppies. In these fishes, conflicting data exist for a morphological and molecular differentiation of sex chromosomes. Using molecular probes and the previously established linkage map, we performed a cytogenetic analysis of sex chromosomes. We show that the Y chromosome has a very large pseudoautosomal region, which is followed by a heterochromatin block (HCY) separating the subtelomeric male-specific region from the rest of the chromosome. Interestingly, the size of the HCY is highly variable between individuals from different population. The largest HCY was found in one population of Poecilia wingei, making the Y almost double the size of the X and the largest chromosome of the complement. Comparative analysis revealed that the Y chromosomes of different guppy species are homologous and share the same structure and organization. The observed size differences are explained by an expansion of the HCY, which is due to increased amounts of repetitive DNA. In one population, we observed also a polymorphism of the X chromosome. We suggest that sex chromosome-linked color patterns and other sexually selected genes are important for maintaining the observed structural polymorphism of sex chromosomes.     

Identification of the telomere in Trypanosoma cruzi reveals highly heterogeneous telomere lengths in different parasite strains.

Here we describe the cloning and characterisation of the Trypanosoma cruzi telomere. In the Y strain, it is formed by typical GGGTTA repeats with a mean size of approximately 500 bp. Adjacent to the telomere repeats we found a DNA sequence with significant homology to the T.cruzi 85 kDa surface antigen (gp85). Examination of the telomere in nine T.cruzi strains reveals differences in the organisation of chromosome ends. In one group of strains the size of the telomere repeat is relatively homogeneous and short (0.5-1.5 kb) as in the Y strain, while in the other, the length of the repeat is very heterogeneous and significantly longer, ranging in size from 1 to >10 kb. These different strains can be grouped similarly to previously existing classifications based on isoenzyme loci, rRNA genes, mini-exon gene sequences, randomly amplified polymorphic DNA and rRNA promoter sequences, suggesting that differential control of telomere length and organisation appeared as an early event in T. cruzi evolution. Two-dimensional pulsed field gel electrophoresis analysis shows that some chromosomes carry telomeres which are significantly larger than the mean telomere length. Importantly, the T.cruzi telomeres are organised in nucleosomal and non-nucleosomal chromatin.