Examination of the X chromosome by STS-PCR screening for the presence of submicroscopic deletions

Cytogenetically undetectable deletions are suspected to be an important cause of mental retardation and developmental delay, as suggested by the observation that about 7% of children with undiagnosed mental retardation have rearrangements affecting the chromosome ends. Screening the whole genome for regions of aneuploidy smaller than 5 Mb is not feasible, but the availability of a high resolution map of the X chromosome means that it is possible to look for deletions in males by PCR. We have screened 96 affected males and their 96 unaffected fathers with 110 markers distributed across the X chromosome. No deletions were found in either group. Our results show that the prevalence of deletions greater than 1 Mb in children with mental retardation is less than 3.9% (95% confidence interval). We conclude that X chromosome deletions in the size range 1–5 Mb are a rare cause of mental retardation in males. Received: 22 July 1998 / Accepted: 11 September 1998     

Properties of the sex chromosomes of Lucilia cuprina deduced from radiation studies

From a study of radiation-induced X-chromosome deletions the locus of black body (b) has been localized to the proximal portion of C-band defined euchromatin. Radiation produced mostly X-chromosome deletions rather than point mutations, total X or Y chromosome loss through breakage, or increased frequency of non-disjunction. Aberrant sex ratios obtained indicate that the X chromosome carries vital loci that were deleted with b ⁺ in many cases. The X/O karyotype produces fertile adult females with a characteristic phenotype which is also produced by X deletions. Sex chromosome non-disjunction to give X/O females and X/X/Y males is normally rare but is enhanced by the presence of chromosome rearrangements even when the X and Y are not involved.     

Pigmentary mosaicism in hypomelanosis of Ito

We report on a female with mental and motor retardation, facial dysmorphism, abnormal pigmentation reminiscent to hypomelanosis of Ito (HI), and karyotypic mosaicism involving a small supernumerary marker chromosome. The marker chromosome was defined by fluorescence in situ hybridisation (FISH) as a ring X chromosome with breakpoints in the juxtacentromeric region. FISH analysis showed that the ring does not include the XIST locus at the X-inactivation centre and, therefore, may not be subject to X inactivation. X-inactivation studies with the HUMARA (human androgen receptor) and FMR1 assay showed a skewed X-inactivation pattern (85:15) with preferential inactivation of the paternal X chromosome. These results are discussed with respect to the role of functional disomy of Xp in the pathogenesis of HI. Received: 16 February 1998 / Accepted: 17 July 1998     

Localization of G6PD and HPRT to different arms of the X chromosome of the North American marsupial (Didelphis virginiana) by in situ hybridization and delection mapping: Evolutionary significance

We have mapped HPRT and G6PD loci on the X chromosome in the American opossum, Didelphis virginiana, by in situ hybridization to cells derived from two females by using genomic opossum DNA as probes. The localizations (G6PD to Xp13 and HPRT to Xq21), indicating that the two genes are separated by the centromere, were confirmed by results of hybridization to X chromosomes with deletions that include the HPRT locus and opossum-mouse cell hybrids containing the relevant fragment of the opossum X chromosome.     

The Turner syndrome-associated neurocognitive phenotype maps to distal Xp

Turner syndrome (TS) is associated with a characteristic neurocognitive profile that includes impaired visuospatial/perceptual abilities. We used a molecular approach to identify a critical region of the X chromosome for neurocognitive aspects of TS. Partial deletions of Xp in 34 females were mapped by FISH or by loss of heterozygosity of polymorphic markers. Discriminant function analysis optimally identified the TS-associated neurocognitive phenotype. Only subjects missing approximately 10 Mb of distal Xp manifested the specified neurocognitive profile. The phenotype was seen with either paternally or maternally inherited deletions and with either complete or incomplete skewing of X inactivation. Fine mapping of informative deletions implicated a critical region of <2 Mb within the pseudoautosomal region (PAR1). We conclude that haploinsufficiency of PAR1 gene(s) is the basis for susceptibility to the TS neurocognitive phenotype.     

Brain carnitine deficiency causes nonsyndromic autism with an extreme male bias: A hypothesis

Could 10–20% of autism be prevented? We hypothesize that nonsyndromic or “essential” autism involves extreme male bias in infants who are genetically normal, but they develop deficiency of carnitine and perhaps other nutrients in the brain causing autism that may be amenable to early reversal and prevention. That brain carnitine deficiency might cause autism is suggested by reports of severe carnitine deficiency in autism and by evidence that TMLHE deficiency ? a defect in carnitine biosynthesis ? is a risk factor for autism. A gene on the X chromosome (SLC6A14 ) likely escapes random X‐inactivation (a mixed epigenetic and genetic regulation) and could limit carnitine transport across the blood‐brain barrier in boys compared to girls. A mixed, common gene variant‐environment hypothesis is proposed with diet, minor illnesses, microbiome, and drugs as possible risk modifiers. The hypothesis can be tested using animal models and by a trial of carnitine supplementation in siblings of probands. Perhaps the lack of any Recommended Dietary Allowance for carnitine in infants should be reviewed. Also see the video abstract here: https://youtu.be/BuRH_jSjX5Y

     

Molecular analysis of chromosome region 11p13 in patients with Drash syndrome

Summary The association of nephropathy, Wilms' tumour and genital abnormalities is known as Drash syndrome. Two of these features are also seen in the WAGR (Wilms' tumour, aniridia, genito-urinary abnormalities, mental retardation) complex, known to be associated with deletions of chromosome region 11p1S. We have carried out karyotypic and molecular studies in 10 Drash patients, 5 males and 5 females. All the males had a 46XY karyotype as did 3/5 of the phenotypic females, the other two having a 46XX karyotype. One of the 46XX females also had a deletion of region 11p13–p12, the only detectable autosomal chromosome abnormality in any of the patients studied. Lymphoblastoid cell lines were prepared from 6 of the Drash patients and were used in dosage studies using a variety of DNA probes from the 11p13 region. There was no evidence of microdeletions in any patient with a normal karyotype. Because of the 46XY karyotype in phenotypic females, selected X and Y chromosome loci were analysed and all found to be normal. Although Drash syndrome is likely to be of genetic origin, there are no readily detected deletions within the 11p13 region.     

X chromosome inactivation and micronuclei in normal and Turner individuals

Studies on aneuploidy have shown that the X is the most frequently lost chromosome in females, and that the number of X chromosome-positive micronuclei increases with age in women. Recently, we showed that the inactive X chromosome is incorporated preferentially in micronuclei. The objectives of the current study were, firstly, to determine the incidence of X chromosome incorporation into micronuclei in males and, secondly, to determine the incidence of X chromosome incorporation into micronuclei of females with Turner syndrome. Blood samples were obtained from 18 male newborns and 35 normal adult males ranging in age from 22 to 79 years and from seven women with non-mosaic Turner syndrome aged 11–39 years. Isolated lymphocytes were cultured in the presence of cytochalasin B and 2000 binucleated cells per subject were scored for micronuclei. Cells were then hybridized with the biotinylated X centromere-specific probe, pBamX7, and visualized with fluorescein-conjugated avidin. All micronucleated cells were relocated and evaluated for the presence or absence of the X chromosome. Of the 335 micronuclei observed, 6.6% (22/335) contained an X chromosome. Analysis of variance shows a statistically significant increase, for both males and Turner females, in the number of X chromosome-positive micronuclei with age (P < 0.001). These data also show that the X chromosome is included in micronuclei from males more often than would be expected by chance (P < 0.005; χ² analysis, 15 df). Here we show that there is a tenfold difference in the frequency of X chromosome-positive micronuclei in 46,XX females compared to 46,XY males and 45,X females, providing further support to our previous finding that the X chromosome in micronuclei is the inactive chromosome. Received: 29 April 1997 / Accepted: 9 May 1997     

An X chromosome locus in Drosophila melanogaster that enhances survival of the triplo-lethal genotype,Dp-(Tpl)

Only a single locus (Tpl) is known in the Drosophila melanogaster genome that leads to early lethality when present as a heterozygous duplication (three doses) or deficiency (one dose). We report the recovery of third instar larvae (and of occasional adults) carrying a duplication for the triplo-lethal locus, Dp(Tpl). Karyotype analysis of the larvae showed that the individuals surviving were almost entirely 3X;2A metafemales. We examined the question of whether the entire X or a single X locus was a major factor permitting survival. X-Y translocations were used to produce females hyperploid for different portions of the X and carrying Dp(Tpl). Analysis of metaphase chromosomes by quinacrine fluorescence pattern indicates that the X chromosome region between 6D and 7DE must be present in an extra copy to enhance the survival of Tpl duplication-bearing females. Another type of experiment suggests that it is the region between 7C and 7DE which is essential.     

CpG islands detected by self-primed in situ labeling (SPRINS)

We have studied the distribution and methylation of CpG islands on human chromosomes, using the novel technique of self-primed in situ labeling (SPRINS). The SPRINS technique is a hybrid of the two techniques primed in situ labeling (PRINS) and nick translation in situ. SPRINS detects chromosomal DNA breaks, as in nick translation in situ, and not annealed primers, as is the case in PRINS. We analyzed in situ-generated DNA breaks induced by the restriction enzymes HpaII and MspI. These restriction enzymes enable the detection of chromosomal CpG islands. Both HpaII- and MspI-SPRINS produce a banding pattern resembling R-banding, indicating a higher level of CpG islands in R-positive bands than in R-negative bands. Our SPRINS banding observations also indicate differences in sequence copy number in the satellites of homologous acrocentric chromosomes. Furthermore, a comparison of homologous HpaII-SPRINS-banded X chromosomes of females from lymphocyte cultures grown without methotrexate or bromodeoxyuridine revealed methylation difference between them. The same comparison of homologous X chromosomes from the cell line GM01202D, which has four X chromosomes, one active and three inactive, revealed the active X chromosome to be hypermethylated. Received: 5 February 1998; in revised form: 8 May 1998 / Accepted: 11 May 1998     

A group of schwannomas with interstitial deletions on 22q located outside the NF2 locus shows no detectable mutations in the NF2 gene

Schwannomas are tumors arising mainly at cranial and spinal nerves. Bilateral vestibular schwannoma is the hallmark of neurofibromatosis type 2 (NF2). The NF2 gene has been cloned and comprehensive analysis of its mutations in schwannomas shows that up to 60% of tumors carry inactivating mutations. Thus, the genetic mechanism behind the development of more than 40% of schwannomas without NF2 mutations is unknown. We have therefore studied tumor tissue from 50 human schwannomas by allelotyping and have found chromosome 22 deletions in over 80% of the cases. We detected 14 cases (27%) that revealed partial deletions of one copy of chromosome 22, i.e., terminal and/or interstitial deletions. We sequenced the NF2 gene in seven of these tumors and detected only one case with mutations. The deletion mapping of chromosome 22 in tumors with partial deletions indicates that several regions, in addition to the NF2 locus, harbor genes involved in schwannoma tumorigenesis. Our findings suggest that heterogeneity in the mechanisms leading to the development of schwannomas probably exists. These findings are in agreement with the recent analysis of schwannomas from familial and sporadic cases of schwannomatosis and point to a possible role of an additional gene, which, in cooperation with the NF2 tumor suppressor, causes schwannomas. Received: 12 November 1998 / Accepted: 1 March 1999     

Genetic rescue of lethal genotypes in the mouse

Deletions of gene sequences in chromosome 7 of the mouse are known to interfere with biochemical and cellular development differentiation with lethal effects in homozygotes. The presence of the corresponding wild-type alleles in Cattanach's translocation (chromosomes 7 to X) is able to “rescue” potentially lethal females if they are made heterozygous for the translocation-carrying X chromosome. This holds true for those chromosome 7 deletions with perinatally lethal effects, whereas “rescue” is not readily accomplished with the deletions that cause early embryonic lethality. Females homozygous for the relevant deletion sequences and heterozygous for the translocation-carrying X chromosome are mosaics of two cell types: those in which the wild-type alleles included in the translocated piece complement the depleted sequences, resulting in a normal cellular phenotype, and those with the ordinary X chromosome expressing the lethal phenotype. The developmental interactions between the two cell types and their role in the mechanisms responsible for survival of females homozygous for lethal deletions are discussed. The failure of “rescue” of embryonic lethals reflects as yet unknown temporal and functional aspects of X-inactivation early embryogenesis.     

A study of females with deletions of the short arm of the X chromosome

We have undertaken a clinical and molecular study of 25 females with deletions of the short arm of the X chromosome. We have determined the deletion breakpoints, the parental origin and the activation status of the deleted X chromosomes. Genotype–phenotype correlations suggest that the presence of a single copy of the DFFRX gene, previously postulated as a gene involved in the ovarian failure seen in Turner syndrome, may be compatible with normal ovarian function, and that there may be a gene for Turner-like features located in distal Xp22.3. Received: 26 November 1997 / Accepted: 18 December 1997     

Structural differences between XX and ZW sex lampbrush chromosomes inRana rugosa females (Anura: Ranidae)

In this study we investigated the morphology and pairing behavior of sex lampbrush chromosomes of XX and ZW females of Rana rugosa from five localities in Japan. Whereas lampbrush chromosomes of XX females from Hiroshima and Isehara had subterminally located centromeres and showed remarkable similarity, those of XX females from Hamakita had the centromeres in the middle. Analysis of landmark configurations revealed that chromosome Xq of Hamakita females closely resembled a part of Xq of Hiroshima and Isehara females, whereas Xp of Hamakita females was inverted compared with the other part of Xq of Hiroshima and Isehara females. Z chromosomes from Kanazawa and Niigata closely resembled the Hiroshima X, whereas the W closely resembled the Hamakita X. XX pairings from Hiroshima, Isehara, and Hamakita were found to be joined by one to four chiasmata at various points all along the axis in both the short and long arms, whereas chromosomal pairs from Kanazawa and Niigata showed only one chiasma between Zp and the distal region of Wq. From these findings we conclude that (1) both the W and the Hamakita X must have evolved from the more primitive Hiroshima and Isehara X chromosomes by a series of pericentric inversions; and (2) females distributed in Hamakita possess two X chromosomes similar to the W, suggesting that either sex-determining or sex-modifying genes on the Hamakita X are clearly different from those on the Kanazawa and Niigata W chromosome. Received: 27 February 1996; in revised form: 22 May 1996 / Accepted: 25 May 1996     

The use of compound heterozygotes and Hprt selection to analyze X-linked mottled alleles associated with prenatal lethality

X-linked mutant alleles associated with prenatal male lethality are difficult to analyze because only heterozygous females are readily available for study. Genomic analysis of the mutant allele is facilitated by the construction of somatic cell hybrids because this enables the segregation of the X Chromosomes (Chrs) that carry the mutant and wild-type alleles. We describe here a method that ensures that the X Chr carrying the mutant allele is retained in somatic cell hybrids in an active selectable state. This is achieved by mating heterozygous females to males that carry a mutation at the hypoxanthine phosphoribosyl transferase (Hprt) locus. The resultant F₁ females are compound heterozygotes, and when cells from these females are fused to HPRT− Chinese hamster cells and subjected to selection in HAT medium, the only survivors are those hybrid cells that retain an active X Chr carrying the mutant allele together with the wild-type Hprt allele. We use hybrids constructed by this method to demonstrate that there are no gross deletions or genomic rearrangements present in three mottled alleles associated with prenatal male lethality. Received: 8 January 1996 / Accepted: 29 February 1996     

RevSex duplication-induced and sex-related differences in the SOX9 regulatory region chromatin landscape in human fibroblasts

It was recently shown that duplications of the RevSex element, located 0.5 Mb upstream of SOX9, cause XX-disorder of sex development (DSD), and that deletions cause XY-DSD. To explore how a 148 kb RevSex duplication could have turned on gonadal SOX9 expression in the absence of SRY in an XX-male, we examined the chromatin landscape in primary skin fibroblast cultures from the index, his RevSex duplication-carrier father and six controls. The ENCODE project supports the notion that chromatin state maps show overlap between different cell types, i.e., that our study of fibroblasts could be of biological relevance. We examined the SOX9 regulatory region by high-resolution ChIP-on-chip experiments (a kind of “chromatin-CGH”) and DNA methylation investigations. The RevSex duplication was associated with chromatin changes predicting better accessibility of the SRY-responsive TESCO enhancer region 14–15 kb upstream of SOX9. Four kb downstream of the TESCO evolutionary conserved region, a peak of the enhancer/promoter-associated H3K4me3 mark was found together with a major dip of the repressive H3K9me3 chromatin mark. Similar differences were also found when three control males were compared with three control females. A marked male/female difference was a more open chromatin signature in males starting ~400 kb upstream of SOX9 and increasing toward the SOX9 promoter. In the RevSex duplication-carrier father, two positions of DNA hypomethylation were also found, one corresponding to the H3K4me3 peak mentioned above. Our results suggest that the RevSex duplication could operate by inducing long-range epigenetic changes. Furthermore, the differences in chromatin state maps between males and females suggest that the Y chromosome or X chromosome dosage may affect chromatin conformation, i.e., that sex-dependent gene regulation may take place by chromatin modification.     

Genetic analysis of the X-chromosomal region 1E-2A of Drosophila melanogaster

Reversion mutagenesis of three single P elements located in the cytogenetic interval 1E-2A at the tip of the X chromosome of Drosophila melanogaster was used to recover new deletions in this chromosomal region. The deletions obtained include small aberrations within region 2A and larger lesions extending from 2A into 1E and 1B. All three screens also yielded terminal deficiencies. The new deficiencies, together with previously characterized rearrangements, were analyzed for their complementation behaviour with the maternal effect locus fs(1)Nasrat and lethal loci in the region. These analyses provide an overall genetic map of the interval 1E-2A. In addition, the smaller deletions were physically mapped within cloned genomic DNA of the 2A region.     

A high-resolution map of the brown (b,Tyrp1) deletion complex of mouse Chromosome 4

For over 40 years germ-cell mutagenesis experiments have generated many new mutations at the brown (b or Tyrp1) locus on mouse Chromosome (Chr) 4. These mutations, many of which are deletions, were recovered by the specific-locus mutagenesis technique. Previous analysis of a panel of brown deletions, generated at Oak Ridge, has enabled both a preliminary molecular and a functional map around the locus to be generated. We have used a panel of hybrid DNA from 25 Oak Ridge deletions, where the deleted chromosome was heterozygous with a Mus spretus chromosome, to map polymorphic markers including microclones, microsatellites, and cloned DNA markers. We have generated a fine structure map, based on 25 new markers, of an 8.5-cM region surrounding the brown locus. This map will prove useful in future mapping studies of this region and in the isolation of the genes that lie within it.