Physical mapping of genes and sequences at the end of the human X chromosome short arm

Mental retardation in a boy with an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1: implication for the MRX locus

Although genotype-phenotype correlations in male patients with various types of nullisomy for Xp22.3 have assigned a locus for X-linked mental retardation (MRX) to an approximately 3-Mb region between DXS31 and STS, the precise location has not been determined. In this paper, we describe a 14 7/12 year old Japanese boy with mental retardation and an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1, and compare the deletion map with that of previously reported three familial male patients with low-normal intelligence and a similar interstitial deletion at Xp22.3. The results suggest that the MRX gene is further localized to the roughly 1.5-Mb region between DXS1060 and DXS1139.

A human pseudoautosomal gene, ADP/ATP translocase, escapes X-inactivation whereas a homologue on Xq is subject to X-inactivation

We report the cloning of a highly conserved pseudoautosomal gene on the human sex chromosomes. A cDNA clone was selected by crosshybridization with a microdissected clone from the chromosomal subregion Xp22.3. It encodes a previously characterized member of the ADP/ATP translocase family and plays a fundamental role in cellular energy metabolism. This gene, ANT3, is located approximately 1,300 kilobases from the telomere, proximal to the pseudoautosomal gene CSF2RA, and escapes X-inactivation. Interestingly, a homologue of ANT3, ANT2, maps to Xq and is subject to X-inactivation. These genes provide the first evidence of two closely related X-chromosomal genes, which show striking differences in their X-inactivation behaviour.

Characterization of a deleted Y chromosome in a male with Turner stigmata

A 46,X,+mar karyotype was detected in an 11-year-old male with a clinical picture characterized by obesity, short stature, bilateral cryptorchidism and coarctation of the aorta. The presence of ZFY and SRY genes was demonstrated by PCR amplification, and the origin of the marker chromosome from a deleted Y chromosome was analyzed by in situ hybridization. The proximal limits of a deletion in Yq were defined by the absence of Southern blot hybridization signals upon probing with Yq11 markers. Cytogenetics and molecular methods taken together indicate a deletion in q11.21. In addition, the loss of Yp subtelomeric sequences was suggested by the analysis of Southern blots hybridized with a 29A24 (DXYS14) probe and by the presence of coarctation of the aorta tentatively localized in Yp. The karyotype of the patient was suggested to be: 46,X,del (Y) (p11.3-q11.21).

Kallmann syndrome due to a translocation resulting in an X/Y fusion gene

The X-linked Kallmann syndrome gene was recently cloned and homologous sequences of unknown functional significance identified on the Y chromosome. We now describe a patient with Kallmann syndrome carrying an X;Y translocation resulting from abnormal pairing and precise recombination between the X-linked Kallmann syndrome gene and its homologue on the Y. The translocation created a recombinant, non-functional Kallmann syndrome gene identical to the normal X-linked gene with the exception of the 3' end which is derived from the Y. Our findings indicate that the 3' portion of the Kallmann syndrome gene is essential for its function and cannot be substituted by the Y-derived homologous region, although a 'position' effect remains a formal possibility.

Long-range restriction map of the terminal part of the short arm of the human X chromosome

The terminal part of the short arm of the human X chromosome has been mapped by pulsed-field gel electrophoresis (PFGE). The map, representing the distal two-thirds of Xp22.3 spans a total of 10,000 kilobases (kb) from Xpter to the DXS143 locus. A comparison with linkage data indicates that 1 centimorgan (cM) in this region corresponds to about 600 kb. CpG islands were essentially concentrated in the 1500 kb immediately proximal to the pseudoautosomal boundary. Several loci, including the gene encoding steroid sulfatase (STS) and the loci for the X-linked recessive form of chondrodysplasia punctata (CDPX) and for Kallmann syndrome (KAL) have been placed relative to the Xp telomere. CDPX is located between 2650 and 5550 kb from Xpter, and STS is located between 7250 and 7830 kb from Xpter. KAL maps to an interval of 350 kb between 8600 and 8950 kb from the telomere. The X-chromosomal breakpoints of a high proportion of XX males resulting from X-Y interchange cluster to a 920-kb region proximal and close to the pseudoautosomal boundary.

Long-range physical mapping around the human steroid sulfatase locus

The region of the human X chromosome containing the steroid sulfatase locus was analyzed by pulsed-field gel electrophoresis. Restriction site maps were generated for the X chromosome in the blood of a normal male individual and that in the mouse-human hybrid cell line ThyB-X; these maps extend over approximately 4.3 Mb of DNA of the former, and 3.2 Mb of the latter. Physical linkage was defined between the STS locus and sequences detected by the probes GMGX9 (DXS237), GMGXY19 (DYS74), CRI-S232 (DXS278), and dic56 (DXS143), and the order telomere--(STS, DYS74)--DXS237--DXS278--DXS143--centromere was deduced. The pulsed-field maps were used to demonstrate a deletion of 180 kb of DNA from the X chromosome of an individual with X-linked ichthyosis. Also, possible locations for the Kallmann syndrome gene were revealed, and the distance between the steroid sulfatase locus and the pseudoautosomal region was estimated to be at least 4 Mb.

Contiguous gene syndromes due to deletions in the distal short arm of the human X chromosome

Mendelian inherited disorders due to deletions of adjacent genes on a chromosome have been described as "contiguous gene syndromes." Short stature, chondrodysplasia punctata, mental retardation, steroid sulfatase deficiency, and Kallmann syndrome have been found as isolated entities or associated in various combinations in 27 patients with interstitial and terminal deletions involving the distal short arm of the X chromosome. The use of cDNA and genomic probes from the Xp22-pter region allowed us to identify 12 different deletion intervals and to confirm, and further refine, the chromosomal assignment of X-linked recessive chondrodysplasia punctata and Kallmann syndrome genes. A putative pseudoautosomal gene affecting height and an X-linked non-specific mental retardation gene have been tentatively assigned to specific intervals. The deletion panel described is a useful tool for mapping new sequences and orienting chromosome walks in the region.

Chromosome maps of man and mouse. IV

Current knowledge of man-mouse genetic homology is presented in the form of chromosomal displays, tables and a grid, which show locations of the 322 loci now assigned to chromosomes in both species, as well as 12 DNA segments not yet associated with gene loci. At least 50 conserved autosomal segments with two or more loci have been identified, twelve of which are over 20 cM long in the mouse, as well as five conserved segments on the X chromosome. All human and mouse chromosomes now have conserved regions; human 17 still shows the least evidence of rearrangement, with a single long conserved segment which apparently spans the centromere. The loci include 102 which are known to be associated with human hereditary disease; these are listed separately. Human parental effects which may well be the result of genomic imprinting are reviewed and the location of the factors concerned displayed in relation to mouse chromosomal regions which have been implicated in imprinting phenomena.

An extremely polymorphic locus on the short arm of the human X chromosome with homology to the long arm of the Y chromosome

A genomic DNA clone named CRI-S232 reveals an array of highly polymorphic restriction fragments on the X chromosome as well as a set of non-polymorphic fragments on the Y chromosome. Every individual has multiple bands, highly variable in length, in every restriction enzyme digest tested. One set of bands is found in all males, and co-segregates with the Y chromosome in families. These sequences have been regionally localized by deletion mapping to the long arm of the Y chromosome. Segregation analysis in families shows that all of the remaining fragments co-segregate as a single locus on the X chromosome, each haplotype consisting of three or more polymorphic fragments. This locus (designated DXS278) is linked to several markers on Xp, the closest being dic56 (DXS143) at a distance of 2 cM. Although it is outside the pseudoautosomal region, the S232 X chromosome locus shows linkage to pseudoautosomal markers in female meiosis. In determining the X chromosome S232 haplotypes of 138 offspring among 19 families, we observed three non-parental haplotypes. Two were recombinant haplotypes, consistent with a cross-over among the S232-hybridizing fragments in maternal meiosis. The third was a mutant haplotype arising on a paternal X chromosome. The locus identified by CRI-S232 may therefore be a recombination and mutation hotspot.

Molecular characterization of human X/Y translocations suggests their aetiology through aberrant exchange between homologous sequences on Xp and Yq

Several DNA sequences from two homologous regions, localized on the distal part of the human X chromosome short arm and on the long arm of the Y chromosome, have been hybridized to DNAs from seven human-rodent hybrids containing human X; Y translocation chromosomes. Molecular characterization of the translocated chromosomes has revealed, in all but one case, transfer of the Y cluster of sequences and complete deletion of the corresponding X-chromosomal sequences. The possible role of X/Y homology in the aetiology of X; Y translocations is proposed.

X/Y translocation in a family with X-linked ichthyosis, chondrodysplasia punctata, and mental retardation: DNA analysis reveals deletion of the steroid sulphatase gene and translocation of its Y pseudogene

We describe a family with two male members showing an X/Y translocation (karyotype: 46,Y,der(X)t(X;Y)(p22;q11]. At physical examination both patients showed ichthyosis, mental retardation and dysmorphic features. Chondrodysplasia punctata and short stature were present in one case. Direct DNA analysis, using a steroid sulphatase cDNA probe, was performed in one patient, his mother and sister, both carriers of the translocation. We found that the translocated region of the Y chromosome includes the steroid sulphatase pseudogene. These results suggest that in our patients the X/Y translocation may be derived from a recombinational event between homologous regions located on the short arm of the X chromosome and the long arm of the Y chromosome. Clinical and molecular studies on the present family add further information for the construction of a tentative physical map of the distal Xp.

A long range restriction map of the pseudoautosomal region by partial digest PFGE analysis from the telomere

The analysis of partial digestion products extending from the telomere of the human X and Y chromosomes, visualised by hybridisation to a probe located close to the telomere, was used to establish a restriction map of the pseudoautosomal region. In this highly polymorphic region with a 10-fold elevated recombination frequency in males we identified site or methylation differences between 7 different in male and female cell lines and tissues, and derived an estimate of the size of the pseudoautosomal region of approximately 3 Megabases by comparing X and Y chromosomes. This size correlates well with previous estimates based on genetic arguments and argues against a strongly enhanced rate of exchange near telomeres in general. We identified a CpG rich and hypomethylated region within 500 kbp from the telomere, which might reflect structural features of mammalian telomeres, and a small number of (additional) CpG islands, which might represent candidate genes for the Turner phenotype in XO females.