Homologous ribosomal protein genes on the human X and Y chromosomes: escape from X inactivation and possible implications for Turner syndrome

Embryonic growth and the evolution of the mammalian Y chromosome. II. Suppression of selfish Y-linked growth factors may explain escape from X-inactivation and rapid evolution of Sry

The mammalian Y chromosome may be an attractor for selfish growth factors. A suppressor of the selfish growth effects would be expected to spread were it to have an appropriate parent-specific expression rule. A suppressor could act by boosting the resource demands of competing female embryos. This possibility may explain incidences of the escape from X-inactivation and provides a rationale for why these genes typically have Y-linked homologues. Alternatively, a suppressor could act to decrease the resource demands of males with the selfish Y. This possibility is supported by the finding that the size of male, but not female, human infants is negatively correlated to the number of X chromosomes. A protracted arms race between a selfish gene and its suppressor may ensue. Both the variation in copy number of Zfy and the unusually fast sequence evolution of Sry may be explained by such an arms race. As required by the model, human Sry is known to have an X-linked suppressor. Preliminary evidence suggests that, as predicted, rapid sequence evolution of Sry may be correlated with female promiscuity. The case for fast sequence evolution as the product of maternal/foetal conflict is strengthened by consideration of the rapid evolution of placental lactogens in both ruminants and rodents.

Ribosomal heterogeneity from chromatin diminution in Ascaris lumbricoides

The genome of Ascaris lumbricoides encodes both germline- and soma-specific proteins homologous to the eukaryotic small ribosomal protein (Rp) S19. The two Ascaris homologs differ by 24 amino acid substitutions and are both components of the small ribosomal subunits. In oocytes, the germline RpS19 homolog (RpS19G) predominates. During chromatin diminution, however, the gene is eliminated from all presomatic cells, and RpS19G is replaced by the product of the somatic gene (RpS19S). Chromatin diminution in A. lumbricoides causes a change in the protein composition of ribosomes during development and represents an alternative means of gene regulation.

Primary structure and expression of a gene encoding the cytosolic ribosomal protein S4 from potato

The primary structure of a cDNA clone encoding the S4 protein from the small subunit of 80S ribosomes from potato was determined. Cytosolic ribosomal protein S4 is hydrophilic and has a prevalence for positively charged residues. In potato it is 264 amino acids long and contains a putative nuclear targeting signal close to the N-terminus. Having 65-69% identical amino acids cytosolic ribosomal protein S4 from mammals, fungi and plants belongs to the highly conserved proteins. The S4 gene is transcribed in all potato tissues analysed and has a relatively high expression level in comparison to nuclear genes encoding mitochondrial proteins.

X;Y translocation in a girl with short stature and some features of Turner's syndrome: cytogenetic and molecular studies

A 13 year old girl referred for chromosome analysis because of disproportionate short stature (short neck, curved legs, pectus excavatum) with an initial clinical diagnosis of Turner's syndrome was found to have the karyotype 46,X, + der(X) in 100% of her blood lymphocytes. By means of conventional differential staining (QFH/AcD, FPG, and RBA banding) supplemented with distamycin A treatment, the karyotype of the proband was interpreted as 46,X,t(X;Y) (p22.3;q11). The rearranged marker X chromosome was found to be active in 91% of lymphocytes studied. PCR analysis with Y chromosome specific oligoprimers showed the presence of some Y chromosome long arm DNA in both lymphocyte and gonadal tissue biopsy cells. At laparoscopy the patient was found to have small gonads with a rudimentary uterus and fallopian tubes. Histological examination of gonadal tissue showed primary follicles with dystrophic changes of the germ cells and numerous follicular cysts (polycystic ovaries). The proband's phenotype and its correlation with the genetic imbalance of the rearranged X chromosomes, as well as with non-random t(X;Y) chromosome inactivation, are briefly discussed.

Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos

A novel approach to study the higher level packaging of specific DNA sequences has been developed by coupling high-resolution fluorescence hybridization with biochemical fractionation to remove histones and distend DNA loops to form morphologically reproducible nuclear "halos." Results demonstrate consistent differences in the organization of specific sequences, and further suggest a relationship to functional activity. Pulse-incorporated bromodeoxyuridine representing nascent replicating DNA localized with the base of the chromatin loops in discrete clustered patterns characteristic of intact cells, whereas at increasing chase times, the replicated DNA was consistently found further out on the extended region of the halo. Fluorescence hybridization to unique loci for four transcriptionally inactive sequences produced long strings of signal extending out onto the DNA halo or "loop," whereas four transcriptionally active sequences remained tightly condensed as single spots within the residual nucleus. In contrast, in non-extracted cells, all sequences studied typically remained condensed as single spots of fluorescence signal. Interestingly, two transcriptionally active, tandemly repeated gene clusters exhibited strikingly different packaging by this assay. Analysis of specific genes in single cells during the cell cycle revealed changes in packaging between S-phase and non S-phase cells, and further suggested a dramatic difference in the structural associations in mitotic and interphase chromatin. These results are consistent with and suggestive of a loop domain organization of chromatin packaging involving both stable and transient structural associations, and provide precedent for an approach whereby different biochemical fractionation methods may be used to unravel various aspects of the complex higher-level organization of the genome.

[Genetics of human sex determination and its disturbances]

The genetics of human sex determination is considered in view of the various disorders of gonad development. The Y chromosome plays an important role in the induction of sex determination by encoding the testis-determining factor (TDF). However, not all deviations in regular development can be explained by mutations of the TDF as unique factor. Therefore, it is necessary to postulate other mutations in still unknown genes of the cascade for male-specific determination as well as the requirement of an ovary-determining factor for regular female development.

Analysis of replication timing properties of human X-chromosomal loci by fluorescence in situ hybridization

We have used fluorescence in situ hybridization on interphase nuclei of normal female cells to compare the replication timing patterns of genes on the human X chromosome that are known to escape X inactivation with those that are inactivated. By this procedure it was possible not only to determine the relative time of replication of the earlier-replicating allele for different loci but also to estimate the degree of asynchrony of replication of the two alleles for each individual locus. Loci such as HPRT and FRAXA, which are normally inactivated, displayed a high degree of replication asynchrony, whereas loci that are not inactivated (ZFX and RPS4X) were found to replicate very synchronously. Interestingly, examination of XIST, which is expressed only from the inactive X chromosome, by this procedure revealed that it also replicated asynchronously, with the expressed copy apparently replicating first. Therefore, by examining different loci from the X chromosome it was determined that there is a strict correlation between the expression and relative time of replication of individual genes.

Search for linkage to schizophrenia on the X and Y chromosomes

Markers for X chromosome loci were used in linkage studies of a large group of small families (n = 126) with at least two schizophrenic members in one sibship. Based on the hypothesis that a gene for schizophrenia could be X-Y linked, with homologous loci on both X and Y, our analyses included all families regardless of the pattern of familial inheritance. Lod scores were computed with both standard X-linked and a novel X-Y model, and sib-pair analyses were performed for all markers examining the sharing of maternal alleles. Small positive lod scores were obtained for loci pericentromeric, from Xp11.4 to Xq12. Lod scores were also computed separately in families selected for evidence of maternal inheritance and absence of male to male transmission of psychosis. The lod score for linkage to the locus DXS7 reached a maximum of 1.83 at 0.08% recombination, assuming dominant inheritance on the X chromosome in these families (n = 34). Further investigation of the X-Y homologous gene hypothesis focussing on this region is warranted.

Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes

The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.

The Epstein-Barr virus (EBV) small RNA EBER1 binds and relocalizes ribosomal protein L22 in EBV-infected human B lymphocytes

Epstein-Barr virus (EBV), an oncogenic herpesvirus, encodes two small RNAs (EBERs) that are expressed at high levels during latent transformation of human B lymphocytes. Here we report that a 15-kDa cellular protein called EAP (for EBER associated protein), previously shown to bind EBER1, is in fact the ribosomal protein L22. Approximately half of the L22 in EBV-positive cells is contained within the EBER1 ribonucleoprotein (RNP) particle, whereas the other half residues in monoribosomes and polysomes. Immunofluorescence with anti-L22 antibodies demonstrates that L22 is localized in the cytoplasm and the nucleoli of uninfected human cells, as expected, whereas EBV-positive lymphocytes also show strong nucleoplasmic staining. In situ hybridization indicates that the EBER RNPs are predominantly nucleoplasmic, suggesting that L22 relocalization correlates with binding to EBER1 in vivo. Since incubation of uninfected cell extracts with excess EBER1 RNA does not remove L22 from preexisting ribosomes, in vivo binding of L22 by EBER1 may precede ribosome assembly. The gene encoding L22 has recently been identified as the target of a chromosomal translocation in certain patients with leukemia, suggesting that L22 levels may be a determinant in cell transformation.

Deletions of Xq and growth deficit: a review

A critical review of the literature disclosed 44 cases with a 46,X,Xq- karyotype without apparent mosaicism. Of these, 17 were of normal height (compared to the respective population), 11 had a height of over 1 SD below the mean, and 16 had a height of over 2 SD below the mean with breakpoints between Xq13 and Xq25. Since patients of normal height occurred with breakpoints as proximal as Xq13 we conclude that there is no major "growth gene" on Xq distal to q13. The most likely explanation for the variable phenotypic effect of Xq- is to assume that growth gene(s) in Xp or proximal Xq are inactivated on such a chromosome with some variability similar to the variable spreading of X inactivation seen in some X-autosome translocations.

Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes

The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.

Molecular characterization of the mouse ribosomal protein S24 multigene family: a uniquely expressed intron-containing gene with cell-specific expression of three alternatively spliced mRNAs

A family of 16 genes encoding the mouse ribosomal protein S24 was identified, and four members from this family were cloned. A single expressed intron-containing S24 gene (termed mrpS24) and one pseudogene (mrpS24p) were completely sequenced and characterized. The mrpS24 gene has seven exons and six introns spanning over 5.1 x 10(3) nucleotides (nt). The cap site of S24 was mapped to a G residue four nt upstream of a polypyrimidine tract and 15 nt downstream of a TATA-like (TATGA) element. The 5' region (-325 to +33) of the mrpS24 gene has a functional promoter that was able to express the fused chloramphenicol acetyltransferase (CAT) reporter gene. Two different forms of mouse S24 cDNA clones were previously isolated. Sequence analysis showed that one of these cDNA clones (termed S24a) lacks the entire exon V sequence (18 nt), and the deduced amino acid sequence is missing a C-terminal lysine residue encoded by the other cDNA (S24b). The pseudogene mrpS24p is flanked by an 11-bp direct repeat, and its sequence is almost identical to the S24 cDNA sequence, but it lacks two mini-exons, V and VI (20 nt), as in the cases of the human and rat S24 cDNAs. RT-PCR experiments demonstrated the existence of a third form (S24c) that similarly lacks both of the mini-exons, and suggested that different species of S24 mRNA might arise from alternative splicing of the mini-exons V and VI. Northern blot analysis showed that S24 expression is down- and up-regulated during adipocyte differentiation and in cellular transformation, respectively. RNase protection assays and RT-PCR experiments suggested that these cell-specific changes of S24 mRNA levels are mainly due to fluctuations in S24c mRNA level. Our results provide the first indication that a ribosomal protein gene is regulated by alternative usage of two mini-exons in a cell-specific manner.

Cloning a pseudogene and cDNA encoding a 17-kDa ribosomal protein from mouse: structure and regulation of expression

An rp lambda 5 cDNA encoding a ribosomal protein (r-protein) and a pseudogenic form of the corresponding gene (rp lambda 7) have been cloned from mouse. This cDNA codes for a highly basic protein of 160 amino acids (aa) with a deduced M(r) of 17,601, and most likely represents the species homolog of a recently cloned rat cDNA, which has been proposed to encode a homolog of the yeast r-protein, YL43. The entire rp lambda 5 gene encompasses less than 1.5 kb of genomic DNA and apparently is composed of only two exons, as deduced from sequence comparison with its very similar pseudogenic variant, rp lambda 7. Southern analysis, using the rp lambda 5 cDNA as a probe, indicates the existence of a great number of highly related sequences in the mouse genome. The mRNA for rp lambda 5 is approximately 800 nucleotides (nt) long and is found to be ubiquitously expressed at high levels in embryonic and adult mouse tissues, as shown by Northern and in situ analyses. Retinoic acid (RA) seems to have a moderate down-regulatory effect on this mRNA in differentiating P19 embryonal carcinoma cells. Several degenerate/nondegenerate RA-response element (RARE) motifs are found within 560 bp upstream from the degenerate start codon in rp lambda 7. However, it is unknown whether this RA effect is exerted at the transcriptional and/or posttranscriptional levels.

Chromosomal localisation of a gene(s) for Turner stigmata on Yp

Although recent cytogenetic and molecular studies in patients with Turner stigmata are consistent with a gene(s) for Turner stigmata being present on both Xp and Yp, the precise location has not been determined. In this report, we describe a phenotypically female infant with Turner stigmata and a partial Yp deletion and review genotype-phenotype correlations of the putative Turner gene(s) in non-mosaic patients with Y chromosome rearrangements resulting from chromosomal breakage at Yp or Yc (pericentromeric region). The results indicate that the putative Turner gene(s) on Yp is located in the Y specific region from interval 1A1A to interval 2B. In addition, assessment of ZFX/ZFY and RPS4X/RPS4Y in the context of the Turner gene(s) suggests that ZFX/ZFY rather than RPS4X/RPS4Y could be a candidate gene for the Turner stigmata.

Sequence and expression of a gene encoding a ribosomal protein S4 homolog from Drosophila melanogaster

We describe a Drosophila melanogaster cDNA clone encoding an amino acid (aa) sequence 75% identical to human ribosomal protein S4 (RPS4). The D. melanogaster RPS4 has 260 aa, if the NH2-terminal methionine is removed after translation of the mRNA. The mRNA for the protein is about 1 kb in length and is detected throughout the developmental stages tested (i.e., embryo, larva, pupa and adult). The cDNA clone hybridizes to two sites on the X chromosome, 1B1-2 and 3A3-6.

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.

The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression

We have immunolabeled human and mouse metaphase chromosomes with antibodies specific for the acetylated isoforms of histone H4. All chromosomes were labeled in regions corresponding to conventional R bands (regions enriched in coding DNA), except for a single chromosome in female cells, which was largely unlabeled and which we have identified as the inactive X (Xi). Three sharply defined immunofluorescent bands, enhanced by butyrate pretreatment, were observed in homologous positions on the human and mouse Xi, showing limited, regional persistence of H4 acetylation. Two of these bands are in cytogenetic regions known to contain genes expressed on Xi. We propose that H4 hyperacetylation defines regions of the genome containing potentially transcriptionally active chromatin, while virtual absence of H4 acetylation defines both constitutive and facultative heterochromatin.

Functional equivalence of human X- and Y-encoded isoforms of ribosomal protein S4 consistent with a role in Turner syndrome

Several genes are found on both the human X and Y chromosomes in regions that do not recombine during male meiosis. In each case, nucleotide sequence analysis suggests that these X-Y gene pairs encode similar but nonidentical proteins. Here we show that the human Y- and X-encoded ribosomal proteins, RPS4Y and RPS4X, are interchangeable and provide an essential function: either protein rescued a mutant hamster cell line that was otherwise incapable of growth at modestly elevated temperatures. These findings are consistent with the hypothesis that RPS4 deficiency has a role in Turner syndrome, a complex human phenotype associated with monosomy X.

The human pseudoautosomal GM-CSF receptor alpha subunit gene is autosomal in mouse

The gene encoding the granulocyte macrophage colony stimulating factor receptor alpha subunit (CSF2RA) has previously been mapped to the pseudoautosomal region of the human sex chromosomes. In contrast, we report that the murine locus, Csf2ra, maps to an autosome in the laboratory mouse. By in situ hybridization and genetic mapping, Csf2ra maps at telomeric band D2 of mouse chromosome 19. This first instance of a pseudoautosomal locus in human being autosomal in mouse, indicates incomplete conservation between the human and mouse X chromosomes and suggests that the genetic content of the pseudoautosomal region may differ between species of eutherian mammals due to chromosomal rearrangements.

Inactivation of an X-linked transgene in murine extraembryonic and adult tissues

Transgenes located on the X chromosome have been used to study the mechanisms involved in X-chromosome inactivation. Analysis of the transgenic mouse strain M-TKneo1 carrying a neomycin resistance gene inserted in the X chromosome showed that, in adult somatic tissues, this transgene is subject to X-inactivation and to de novo methylation as other endogenous X-linked genes. During mouse embryogenesis, X-linked genes show a preferential paternal inactivation in extraembryonic tissues, whereas these genes are subject to random inactivation in embryonic tissues. It has been suggested that, in the mouse, the extraembryonic tissues carry a parental imprint at the time of inactivation. The study of the neo transgene expression in extraembryonic endoderm has shown not only that neo is inactivated but also that, at the RNA level, paternal inactivation of the transgene seems essentially complete. The differences between our results and previously obtained results with a mouse alpha-fetoprotein transgene, which was only inactivated in neonatal tissues but not in extraembryonic tissues, are discussed.

Turner syndrome: the case of the missing sex chromosome

Turner syndrome is the phenotype associated with the absence of a second sex chromosome in humans. Recent observations support the hypothesis that the phenotype results from haploid dosage of genes that are common to the X and Y chromosomes and that escape X inactivation. A goal of current studies is the identification of these "Turner' genes.

An evaluation of the inactive mouse X chromosome in somatic cell hybrids

The expression of mouse Zfx, Rps4, Ube1x, and Xist was evaluated in hamster-mouse somatic cell hybrids containing either an active or an inactive mouse X chromosome using polymerase chain reaction of reverse transcribed RNA (RT-PCR). The results showed that Zfx, Rps4, and Ube1x are expressed exclusively from the active mouse X, while Xist is expressed exclusively from the inactive X. These findings confirm the pattern of X inactivation for these mouse genes reported previously based on expression in somatic tissues of F1 females from interspecific crosses. These results demonstrate the existence of differences between human and mouse X inactivation, as the corresponding human genes, ZFX, RPS4X, and UBE1 escape X inactivation.

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).

Maintenance of X inactivation of the Rps4, Zfx, and Ube1 genes in a mouse in vitro system

Several genes, including RPS4X (ribosomal protein subunit 4), ZFX (zinc finger on the X chromosome), and UBE1 (ubiquitin-activating enzyme), have been shown to be expressed from the inactive X chromosome of cultured human cells. By contrast, these genes are subject to X-chromosome inactivation in tissues from adult mice. We have now examined the inactivation status of these genes in cultured mouse cells to determine whether the differences in X-chromosome inactivation between species is due to an intrinsic difference between human and mouse X-chromosome genes or whether it is a function of gene reactivation in cell culture per se. The expression of three mouse X-chromosome genes, Rps4, Zfx, and Ube1 was examined by reverse transcriptase polymerase chain reaction (RT-PCR) in heterozygous cultured cells from a cross of a laboratory mouse by Mus spretus, which were selected to uniformly express the X chromosome from the laboratory mouse parent. No expression of the M. spretus alleles of these genes was observed in the cell line (Hobmski), which is consistent with the patterns of expression previously observed in mouse in vivo and indicates that these genes remain stably inactivated in an immortalized mouse cell line. By cytogenetic and RT-PCR analyses the Hobmski cell line was shown to retain a late-replicating X chromosome from M. spretus, which expressed the M. spretus allele of the X (inactive) specific transcript (Xist). The Hobmski cell line will be a useful resource for studying the features that maintain X-chromosome genes inactive.

Imprinting and splicing join together

A gene thought to be involved in RNA splicing, and which is imprinted in mice, may play an important part in Prader-Willi syndrome.

Telomere-associated chromosome fragmentation: applications in genome manipulation and analysis

Telomere-associated chromosome fragmentation (TACF) is a new approach for chromosome mapping based on the non-targeted introduction of cloned telomeres into mammalian cells. TACF has been used to generate a panel of somatic cell hybrids with nested terminal deletions of the long arm of the human X chromosome, extending from Xq26 to the centromere. This panel has been characterized using a series of X chromosome loci. Recovery of the end clones by plasmid rescue produces a telomeric marker for each cell line and partial sequencing will allow the generation of sequence tagged sites (STSs). TACF provides a powerful and widely applicable method for genome analysis, a general way of manipulating mammalian chromosomes and a first step towards constructing artificial mammalian chromosomes.

Structure of the X-linked Kallmann syndrome gene and its homologous pseudogene on the Y chromosome

The gene for the X-linked Kallmann syndrome (KAL), a developmental disorder characterized by hypogonadotropic hypogonadism and anosmia, maps to Xp22.3 and has a homologous locus, KALP, on Yq11. We show here that KAL consists of 14 exons spanning 120-200 kilobases that correlate with the distribution of domains in the predicted protein including four fibronectin type III repeats. The KALP locus reveals several large deletions and a number of small insertions, deletions and base substitutions which indicate it is a non-processed pseudogene. The sequence divergence between KAL and KALP in humans, and the chromosomal location of KAL homologous sequences in other primates, suggest that KALP and the steroid sulphatase pseudogene on Yq11 were involved in the same rearrangement event on the Y chromosome during primate evolution.

Evolution of DNA sequence homologies between the sex chromosomes in primate species

Cloned DNA sequences from 18 X-Y homologous loci have been used to examine the evolution of regions of homology between the human X and Y chromosomes. The pattern of X-Y linkage in different primate species has enabled the charting of the chronology of their appearance and removal from the sex chromosomes during evolution. Examination of the pattern of differences in restriction enzyme sites at different loci has been used to estimate the degree of divergence in three different regions of homology. These studies have indicated that (1) blocks of homology have arisen at different points in evolution, (2) different regions of homology are heterogeneous in composition in that they contain X-Y homologous sequences of different age, and (3) the combination of X and Y locations together with the point of evolutionary origin has defined five new patterns of homology.

XY sex reversal associated with a deletion 5' to the SRY "HMG box" in the testis-determining region

The human testis-determining factor resides within a 35-kilobase (kb) region of the Y chromosome immediately adjacent to the pseudoautosomal boundary. A candidate gene for human sex determination (SRY) was isolated in this region. Here, we describe a study of 25 cases of XY females with pure gonadal dysgenesis for mutations on the Y chromosome short arm, including SRY. Southern blotting revealed a sex-reversed female harboring a deletion extending from approximately 8 kb from the pseudoautosomal boundary of the Y chromosome to at least 33 kb and no more than 60 kb upstream, toward the centromere. The deletion begins no more than 1.8 kb upstream from the first ATG of the SRY open reading frame present in the clone pY53.3. To our knowledge, no mutation has been described previously outside the SRY "HMG box" on the short arm of the Y chromosome, which is associated with sex reversal. Since the 5' extent of the SRY transcriptional unit has not been defined, the deletion may remove upstream exons of SRY and/or transcriptional regulatory motifs, either situation resulting in lack of testicular development. It cannot be formally excluded that the mutation removes a second locus, independent of SRY, that is critical for sex determination. Denaturant gradient gel electrophoresis analysis of the SRY open reading frame in the remaining 24 cases revealed de novo single base-pair transitions in the SRY conserved domain in 4 cases.

An X-linked human collagen transgene escapes X inactivation in a subset of cells

Transgenic mice carrying one complete copy of the human alpha 1(I) collagen gene on the X chromosome (HucII mice) were used to study the effect of X inactivation on transgene expression. By chromosomal in situ hybridization, the transgene was mapped to the D/E region close to the Xce locus, which is the controlling element. Quantitative RNA analyses indicated that transgene expression in homozygous and heterozygous females was about 125% and 62%, respectively, of the level found in hemizygous males. Also, females with Searle's translocation carrying the transgene on the inactive X chromosome (Xi) expressed about 18% transgene RNA when compared to hemizygous males. These results were consistent with the transgene being subject to but partially escaping from X inactivation. Two lines of evidence indicated that the transgene escaped X inactivation or was reactivated in a small subset of cells rather than being expressed at a lower level from the Xi in all cells, (i) None of nine single cell clones carrying the transgene on the Xi transcribed transgene RNA. In these clones the transgene was highly methylated in contrast to clones carrying the transgene on the Xa. (ii) In situ hybridization to RNA of cultured cells revealed that about 3% of uncloned cells with the transgene on the Xi expressed transgene RNA at a level comparable to that on the Xa. Our results indicate that the autosomal human collagen gene integrated on the mouse X chromosome is susceptible to X inactivation. Inactivation is, however, not complete as a subset of cells carrying the transgene on Xi expresses the transgene at a level comparable to that when carried on Xa.

Autosomal localization of the amelogenin gene in monotremes and marsupials: implications for mammalian sex chromosome evolution

We have determined by Southern blot analysis that DNA sequences homologous to the AMG gene probe are present in the genomes of both marsupial and monotreme mammals, although adult monotremes lack teeth. In situ hybridization and Southern analysis of cell hybrids demonstrate that AMG homologues are located on autosomes. In the Tammar Wallaby, AMG homologues are located on chromosomes 5q and 1q and in the Platypus, on chromosomes 1 and 2. The autosomal location of the AMG homologues provides additional support for the hypothesis that an autosomal region equivalent to the human Xp was translocated to the X chromosome in the Eutheria after the divergence of the marsupials 150 million years ago. The region containing the AMG gene is therefore likely to have been added 80-150 million years ago to a pseudoautosomal region shared by the ancestral eutherian X and Y chromosome; the X and Y alleles must have begun diverging after this date.

Absence of Turner stigmata in a 46,XYp-female

A 46,XY female patient with streak gonads and a large deletion of Yp is described. The deletion included the Y chromosomal genes SRY, ZFY, and RPS4Y. The patient did not display any Turner stigmata, such as webbing of the neck, cardiac or other abnormalities. The findings argue against an important role of RPS4Y in the prevention of Turner stigmata in males and are consistent with a role of SRY in testis differentiation in humans.

The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus

The Xist gene maps to the X inactivation center region in both mouse and human, and previous analysis of the 3' end of the gene has demonstrated inactive X-specific expression, suggesting a possible role in X inactivation. We have now analyzed the entire mouse Xist gene. The mature inactive X-specific transcript is 15 kb in length and contains no conserved ORF. The Xist sequence contains a number of regions comprised of tandem repeats. Comparison with the human XIST gene demonstrates significant conservation of sequence and gene structure. Xist RNA is not associated with the translational machinery of the cell and is located almost exclusively in the nucleus. Together with conservation of inactive X-specific expression, these findings support a role for Xist in X inactivation, possibly as a functional RNA or as a chromatin organizer region.

The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus

X chromosome inactivation in mammalian females results in the cis-limited transcriptional inactivity of most of the genes on one X chromosome. The XIST gene is unique among X-linked genes in being expressed exclusively from the inactive X chromosome. Human XIST cDNAs containing at least eight exons and totaling 17 kb have been isolated and sequenced within the region on the X chromosome known to contain the X inactivation center. The XIST gene includes several tandem repeats, the most 5' of which are evolutionarily conserved. The gene does not contain any significant conserved ORFs and thus does not appear to encode a protein, suggesting that XIST may function as a structural RNA within the nucleus. Consistent with this, fluorescence in situ hybridization experiments demonstrate localization of XIST RNA within the nucleus to a position indistinguishable from the X inactivation-associated Barr body.

Marsupial Y chromosome encodes a homologue of the mouse Y-linked candidate spermatogenesis gene Ube1y

The mammalian subclass Theria consists of infraclasses Metatheria (marsupials) and Eutheria ('placentals') which diverged from each other 120-150 million years before present (Myr BP). Both infraclasses have Y chromosome-dependent testis determination but direct molecular evidence linking the Metatherian and Eutherian Y chromosomes is lacking. Comparative analyses indicate that three mammalian genes have remained Y-linked for at least 80 Myr, since the divergence of the Eutherian orders from a common ancestor. These are Zfy, a gene encoding a transcription factor of the zinc-finger type; Sry, the putative primary testis-determining gene; and Ube1y (formerly Sby or A1s9Y-1), a candidate for the mouse spermatogenesis gene Spy, encoding a ubiquitin-activating enzyme E1 homologue. Although in marspials Zfy homologues are autosomal, a Y homologue of Sry has recently been isolated. We report here the identification of a functional marsupial Y-linked homologue of the murine Ube1y gene establishing that Metatherian and Eutherian Y chromosomes diverged from a common ancestor. This extreme conservation indicates that Ube1y plays a critical role in male development.

The human Y chromosome: overlapping DNA clones spanning the euchromatic region

The human Y chromosome was physically mapped by assembling 196 recombinant DNA clones, each containing a segment of the chromosome, into a single overlapping array. This array included more than 98 percent of the euchromatic portion of the Y chromosome. First, a library of yeast artificial chromosome (YAC) clones was prepared from the genomic DNA of a human XYYYY male. The library was screened to identify clones containing 160 sequence-tagged sites and the map was then constructed from this information. In all, 207 Y-chromosomal DNA loci were assigned to 127 ordered intervals on the basis of their presence or absence in the YAC's, yielding ordered landmarks at an average spacing of 220 kilobases across the euchromatic region. The map reveals that Y-chromosomal genes are scattered among a patchwork of X-homologous, Y-specific repetitive, and single-copy DNA sequences. This map of overlapping clones and ordered, densely spaced markers should accelerate studies of the chromosome.

The human Y chromosome: a 43-interval map based on naturally occurring deletions

A deletion map of the human Y chromosome was constructed by testing 96 individuals with partial Y chromosomes for the presence or absence of many DNA loci. The individuals studied included XX males, XY females, and persons in whom chromosome banding had revealed translocated, deleted, isodicentric, or ring Y chromosomes. Most of the 132 Y chromosomal loci mapped were sequence-tagged sites, detected by means of the polymerase chain reaction. These studies resolved the euchromatic region (short arm, centromere, and proximal long arm) of the Y chromosome into 43 ordered intervals, all defined by naturally occurring chromosomal breakpoints and averaging less than 800 kilobases in length. This deletion map should be useful in identifying Y chromosomal genes, in exploring the origin of chromosomal disorders, and in tracing the evolution of the Y chromosome.

Human ribosomal protein S3a: cloning of the cDNA and primary structure of the protein

The amino acid (aa) sequence of human ribosomal protein S3a (hRPS3a) was deduced partially from the nucleotide sequence of the corresponding cDNA and confirmed by direct aa sequencing from the N terminus of the purified hRPS3a protein. The cDNA clone was isolated from a cDNA expression library in the pEX vector using antibodies. The hRPS3a protein has 263 aa and its calculated M(r) is 29 813.