Localisation of the Becker muscular dystrophy gene on the short arm of the X chromosome by linkage to cloned DNA sequences

Summary A linkage study in 30 Becker muscular dystrophy (BMD) kindreds using three cloned DNA sequences from the X chromosome which demonstrate restriction fragment length polymorphisms (RFLPs), suggests that the BMD gene is located on the short arm of the X chromosome, in the p21 region. The genes for Becker and Duchenne dystrophies must therefore be closely linked, if not allelic, and any future DNA probes found to be of practical use in one disorder should be equally applicable to the other. The linkage analysis also provides data on the frequency of recombination along the short arm of the X chromosome, and across the centromeric region.     

Choroideremia-locus maps between DXS3 and DXS11 on Xq

Summary Choroideremia is a progressive tapetochoroidal dystrophy with X-linked transmission leading frequently to blindness in affected males. The choroideremia-locus (TCD) has recently been assigned to the long arm of the X chromosome by linkage to polymorphic DNA markers. In order to further define the location of the gene defect, two families segregating for choroideremia were examined for DNA restriction fragment length polymorphisms. A search was undertaken for linkage with cloned DNA probes from the proximal short and long arm as well as from the mid-portion of the long arm of the X chromosome. Our data suggest that the most plausible gene order on the Xq is: Xcen-DXYS1-DXS3-TCD-DXS11-Xqter.     

Mapping of the Menkes locus to Xq13.3 distal to the X-inactivation center by an intrachromosomal insertion of the segment Xq13.3-q21.2

Summary During a systematic chromosomal survey of 167 unrelated boys with the X-linked recessive Menkes disease (MIM 309400), a unique rearrangement of the X chromosome was detected, involving an insertion of the long arm segment Xq13.3-q21.2 into the short arm at band Xp11.4, giving the karyotype 46,XY,ins(X) (p11.4q13.3q21.2). The same rearranged X chromosome was present de novo in the subject's phenotypically normal mother, where it was preferentially inactivated. The restriction fragment length polymorphism and methylation patterns at DXS255 indicated that the rearrangement originated from the maternal grandfather. Together with a previously described X;autosomal translocation in a female Menkes patient, the present finding supports the localization of the Menkes locus (MNK) to Xq13, with a suggested fine mapping to sub-band Xq13.3. This localization is compatible with linkage data in both man and mouse. The chromosomal bend associated with the X-inactivation center (XIC) was present on the proximal long arm of the rearranged X chromosome, in line with a location of XIC proximal to MNK. Combined data suggest the following order: Xcen-XIST(XIC), DXS128-DXS171, DXS56-MNK-PGK1-Xqter.     

Toward a complete linkage map of the human X chromosome: regional assignment of 16 cloned single-copy DNA sequences employing a panel of somatic cell hybrids.

Closely linked restriction fragment length polymorphisms (RFLPs) are potentially useful as diagnostic markers of genetic defects, and, in principle, RFLPs can be employed to construct a complete linkage map of the human genome. On the X chromosome, linkage studies are particularly rewarding because in man more than 120 X-linked genes are known. Thus, it is probable that each X-specific RFLP will be of use as a genetic marker of one or several X-linked disorders. To facilitate the search for closely linked RFLPs, we have regionally assigned 16 cloned DNA sequences to various portions of the human X chromosome, employing a large panel of somatic cell hybrids. These probes have been used to correlate genetic and physical distances on Xp, and it can be extrapolated from these data that the number and distribution of available Xq sequences will also suffice to span the long arm of the X chromosome.     

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.     

Linkage analysis of two cloned DNA sequences flanking the Duchenne muscular dystrophy locus on the short arm of the human X chromosome.

The inheritance of two restriction fragment length polymorphisms (RFLPs) on the short arm of the human X chromosome has been studied relative to Duchenne muscular dystrophy. This provides a partial genetic map of the short arm of the human X chromosome between Xp110 and Xp223. The data were derived from the segregation between a RFLP located at Xp21-Xp223, the DMD locus, and a RFLP located at Xp110-Xp113. The genetic distance from Xp110 to Xp223 was found to be approximately 40 centimorgans (cM). This provides experimental confirmation that 1cM corresponds to approximately 1,000 kilobase pairs of DNA for this region of the human X chromosome. Our data confirm that the DMD mutation lies between Xp223 and Xp110. The availability of flanking probes surrounding the DMD locus will assist in the ordering of further DNA sequences relative to the mutation.     

Linkage relationships between retinoschisis,Xg, and a cloned DNA sequence from the distal short arm of the X chromosome

Summary A cloned DNA sequence, RC8, from the short arm of the X chromosome which is linked to the Duchenne muscular dystrophy (DMD) gene has been employed to study linkage relationships with the Xg-linked retinoschisis (RS) locus. Results of three point linkage analyses in two families suggest that the gene order on Xp is Xg-RS-RC8. Moreover, it can be inferred from these data that the genetic distance between Xg and DMD is approximately 55 cM.     

A linkage map of sheep chromosome X (OARX) aligned to human chromosome X (HSAX)

We have constructed a genetic linkage map of the sheep X chromosome (OARX) containing 22 new gene loci from across the human X chromosome (HSAX). The female OARX linkage map has a total length of 152.6 cM with average gene spacing of 5.5 cM. Comparison with HSAX confirms one previously reported major breakpoint and inversion, and other minor rearrangements between OARX and HSAX. Comparison of the linkage map with sheep sequence data OAR 1.0 reveals a different arrangement of markers on the q arm, which may more accurately reflect the genuine arrangement of this region.     

Genetic Analysis of a Kindred With X-linked Mental Handicap and Retinitis Pigmentosa

A kindred is described in which X-linked nonspecific mental handicap segregates together with retinitis pigmentosa. Carrier females are mentally normal but may show signs of the X-linked retinitis pigmentosa carrier state and become symptomatic in their later years. Analysis of polymorphic DNA markers at nine loci on the short arm of the X chromosome shows that no crossing-over occurs between the disease and Xp11 markers DXS255, TIMP, DXS426, MAOA, and DXS228. The 90% confidence limits show that the locus is in the Xp21-q21 region. Haplotype analysis is consistent with the causal gene being located proximal to the Xp21 loci DXS538 and 5'-dystrophin on the short arm of the X chromosome. The posterior probability of linkage to the RP2 region of the X chromosome short arm (Xp11.4-p11.23) is .727, suggesting the possibility of a contiguous-gene-deletion syndrome. No cytogenetic abnormality has been identified.     

A locus for X-linked congenital stationary night blindness is located on the proximal portion of the short arm of the X chromosome

Summary Linkage between X-linked congenital stationary night blindness (CSNB1) and seven markers on the X chromosome was investigated in a large four-generation Albertan kindred. We detected significant linkage between the CSNB1 locus and the locus DXS255 (maximum lod score = 6.73 at a recombination fraction of 6%; confidence interval of 1% to 18%), which anchors the CSNB1 locus to the proximal region near p11.22 on the short arm of the X chromosome.     

An alpha satellite DNA polymorphism specific for the centromeric region of chromosome 13

Alpha satellite DNA is composed of variants of a short consensus sequence that are repeated in tandem arrays in the centromeric heterochromatin of each human chromosome. To define centromeric markers for linkage studies, we screened human genomic DNA for restriction fragment length polymorphisms using a probe detecting alphoid sequences on chromosomes 13 and 21. We describe one such DNA polymorphism. Analysis of linkage of this DNA marker to other polymorphic markers in the CEPH pedigrees demonstrates linkage to markers on the proximal long arm of chromosome 13 and defines the centromeric end of the linkage map of this chromosome.     

Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome.

There are several copies of related sequences on the distal short arm of the human X chromosome and the proximal long arm of the Y chromosome which were originally detected by cross hybridization with a genomic DNA clone, CRI-S232. Recombination between two S232-like sequences flanking the steroid sulfatase locus has been shown to cause frequent deletions in the X chromosome short arm, resulting in steroid sulfatase deficiency. We now report the characterization of several S232-like sequences. Restriction mapping and sequence analysis show that each S232 unit contains 5 kb of unique sequence in addition to two elements, RU1 and RU2, composed of a variable number of tandem repeats. RU1 consists of 30 bp repeating units and its length shows minimal variation between individuals. The RU2 elements in the hypervariable S232 loci on the X chromosome consist of repeating sequences which are highly asymmetric, with about 90% purines and no C's on one strand. The X-derived RU2 elements range from 0.6 kb to over 23 kb among different individuals, accounting entirely for the observed polymorphism at the S232 loci. Although the repeating units of the RU2 elements in the nonpolymorphic S232 loci on the Y chromosome share high sequence homology with those on the X chromosome, they exhibit much higher intrarepeat sequence variation. S232 homologous sequences are found in great apes, old world and new world monkeys. In chimpanzees and gorillas the S232-like sequences are polymorphic in length.     

Genetic linkage relationships between the Xg blood group system and two X chromosome DNA polymorphisms in families with Duchenne and Becker muscular dystrophy

The existence of linkage has been investigated between the Xg blood group system, two DNA restriction fragment length polymorphisms (RFLPs) located on the short arm of the X chromosome, Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). No linkage was found between the Xg locus and the more proximal RFLP (L 1.28); close linkage between Xg and the more distal RFLP (lambda RC8) was also excluded. Both RFLPs show linkage with DMD but are not closely linked with each other. Analyses of 11 families with DMD and ten with BMD, informative for the Xg blood group, reinforce the conclusions of others that there is no measurable linkage between the loci for Xg and for the X-linked forms of muscular dystrophy.     

Probable linkage between the human galactose-1-P uridyl transferase locus and 9qh.

Evaluation of a family in which electrophoretic variants of the eznyme galactose-1-phosphate uridyl transferase (GALT) and 9qh variants occur demonstrates close linkage between these two traits: lod score of 3.67 at theta = 0. Taken with information indicating GALT is on the short arm of chromosome 9, these linkage data suggest that this locus is close to the centromere on the short arm of chromosome 9.     

X-linked hypohidrotic ectodermal dysplasia: DNA probe linkage analysis and gene localization

Summary A linkage study of 24 families with hypohidrotic (anhidrotic) ectodermal dysplasia (HED) has been performed. The previously suggested linkage to DXYS1 has been confirmed, and linkage to probes DXS14 and DXS3 has been established. We suggest that the HED locus lies in the centromeric region between DXYS1 on the long arm and DXS14 on the short arm of the X chromosome, probably on proximal Xq.     

X-linked dominant Charcot-Marie-Tooth disease: Suggestion of linkage with a cloned DNA sequence from the proximal Xq

Summary A large kindred with the X-linked dominant form of peroneal muscular atrophy (Charcot-Marie-Tooth disease) was analyzed for individual variation in the length of DNA fragments after restriction endonuclease digestion. A systematic search was performed for linkage with a series of cloned single-copy DNA sequences of known regional assignment to the human X chromosome. Close linkage was found with the pDP34 probe (DXYS1 locus, Xq13-q21), suggesting that the gene responsible for the disease is located on the proximal long arm of the X chromosome.     

Linkage studies in a family with X-linked recessive ichthyosis employing a cloned DNA sequence from the distal short arm of the X chromosome

Recently linkage has been described between the Duchenne muscular dystrophy (DMD) gene and a cloned DNA sequence, RC8, that detects restriction fragment length polymorphism and is derived from the distal short arm of the X chromosome. Positive lod scores between RC8 and Xg prompted us to examine the linkage relationship of RC8 to the steroid sulfatase-X-linked recessive ichthyosis (XRI) locus which is situated 15 cM proximal from Xg in the subtelomeric region of Xp. Unexpectedly, at least two crossovers were found among nine informative meioses of an informative family, suggesting that RC8 and XRI may be about 25 cM apart. This implies that the genetic distance between the Xg locus and the DMD locus may exceed 50 cM.     

A DNA fragment from the human X chromosome short arm which detects a partially homologous sequence on the Y chromosomes long arm.

An X linked human DNA fragment (named DXS31 ) which detects partially homologous sequences on the Y chromosome has been isolated. Regional localisation of the two sex linked sequences was determined using a panel of rodent-human somatic cell hybrids. The X specific sequence is located at the tip of the short arm ( Xp22 .3-pter), i.e. within or close to the region which pairs with the Y chromosome short arm at meiosis. However the Y specific sequence is located in the heterochromatic region of the long arm ( Yq11 -qter) and lies outside from the pairing region. DNAs from several XX male subjects were probed with DXS31 and in all cases a double dose of the X linked fragment was found, and the Y specific fragment was absent. DXS31 detects in chimpanzee a male-female differential pattern identical to that found in man. However results obtained in a more distantly related species, the brown lemur, suggest that the sequences detected by DXS31 in this species might be autosomally coded. The features observed with these X-Y related sequences do not fit with that expected from current hypotheses of homology between the pairing regions of the two sex chromosomes, nor with the pattern observed with other X-Y homologous sequences recently characterized. Our results suggest also that the rule of conservation of X linkage in mammals might not apply to sequences present on the tip of the X chromosome short arm, in bearing with the controversial issue of steroid sulfatase localisation in mouse.     

Identification of 28 DNA fragments that detect RFLPs in 13 distinct physical regions of the short arm of chromosome 5.

A series of 175 lambda phage carrying human inserts isolated from a library that is specific for the short arm of human chromosome 5 (5p) have been regionally mapped on 5p using a deletion mapping panel of 16 human-hamster cell hybrids, each of which contains a chromosome 5 with a different deletion in the short arm. Seventy-five single copy DNA fragments were screened with 12 restriction enzymes for their ability to detect restriction fragment length polymorphisms (RFLPs). Twenty-eight of these DNA fragments, which are located in 13 distinct physical regions of 5p, were found to detect RFLPs. These DNA markers make it possible to construct a linkage map that will span the entire length of 5p and will allow the relationship between genetic and physical distance for this region of the genome to be examined at a high level of resolution.     

The origin of the genetical diversity of Microtus mandarinus chromosomes

Here we describe our comparative studies on two types of X chromosomes, namely X(M) and X(SM,) of the mandarin vole (Microtus mandarinus). By chromosome G- and C-banding analysis, we have found that two different types of X chromosomes exist in mandarin voles. The two types of X chromosomes present two different G- and C-banding patterns: the X(M) chromosome is a longer metacentric X chromosome which is C-band negative; and the X(SM) is a shorter submetacentric X chromosome which has one C-band at the centromere and another one at the middle part of the short arm. The X(SM) has 6 G-bands including one on the kinetochore, one in the middle of the short arm, and four on the long arm. The X(M) has 7 G-bands including one on the kinetochore, two on the short arm, and four on the long arm. We have further found that female voles can be grouped into three types based on the composition of the X chromosome but the male voles have only one type. The three female groups are: (1) female voles (X(M)X(SM)), in which the two X chromosomes are different, the longer one is metacentric and the shorter is submetacentric; (2) female vole (X(SM)X(SM)), in which the two X chromosomes are both submetacentric; (3) female vole (X(M)O), in which there is only one X chromosome that is metacentric. Surprisingly, we have never found female voles with X(M)X(M), females with X(SM)O or males with X(M)Y. We hypothesize that the X(SM) chromosome is derived from the X(M) through its breakage and re-joining. The paper also discusses the formation of X(M)O females.