A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome

Genetic analysis of the mouse X inactivation center defines an 80-kb multifunction domain

Dosage compensation in mammals occurs by X inactivation, a silencing mechanism regulated in cis by the X inactivation center (Xic). In response to developmental cues, the Xic orchestrates events of X inactivation, including chromosome counting and choice, initiation, spread, and establishment of silencing. It remains unclear what elements make up the Xic. We previously showed that the Xic is contained within a 450-kb sequence that includes Xist, an RNA-encoding gene required for X inactivation. To characterize the Xic further, we performed deletional analysis across the 450-kb region by yeast-artificial-chromosome fragmentation and phage P1 cloning. We tested Xic deletions for cis inactivation potential by using a transgene (Tg)-based approach and found that an 80-kb subregion also enacted somatic X inactivation on autosomes. Xist RNA coated the autosome but skipped the Xic Tg, raising the possibility that X chromosome domains escape inactivation by excluding Xist RNA binding. The autosomes became late-replicating and hypoacetylated on histone H4. A deletion of the Xist 5' sequence resulted in the loss of somatic X inactivation without abolishing Xist expression in undifferentiated cells. Thus, Xist expression in undifferentiated cells can be separated genetically from somatic silencing. Analysis of multiple Xic constructs and insertion sites indicated that long-range Xic effects can be generalized to different autosomes, thereby supporting the feasibility of a Tg-based approach for studying X inactivation.

X inactive-specific transcript (Xist) expression and X chromosome inactivation in the preattachment bovine embryo

Expression of the X inactive-specific transcript (Xist) is thought to be essential for the initiation of X chromosome inactivation and dosage compensation during female embryo development. In the present study, we analyzed the patterns of Xist transcription and the onset of X chromosome inactivation in bovine preattachment embryos. Reverse transcription-polymerase chain reaction (RT-PCR) revealed the presence of Xist transcripts in all adult female somatic tissues evaluated. In contrast, among the male tissues examined, Xist expression was detected only in testis. No evidence for Xist transcription was observed after a single round of RT-PCR from pools of in vitro-derived embryos at the 2- to 4-cell stage. Xist transcripts were detected as a faint amplicon at the 8-cell stage initially, and consistently thereafter in all stages examined up to and including the expanded blastocyst stage. Xist transcripts, however, were subsequently detected from the 2-cell stage onward after nested RT-PCR. Preferential [3H]thymidine labeling indicative of late replication of one of the X chromosomes was noted in female embryos of different developmental ages as follows: 2 of 7 (28.5%) early blastocysts, 6 of 13 (46.1%) blastocysts, 8 of 11 (72.1%) expanded blastocysts, and 14 of 17 (77.7%) hatched blastocysts. These results suggest that Xist expression precedes the onset of late replication in the bovine embryo, in a pattern compatible with a possible role of bovine Xist in the initiation of X chromosome inactivation.

The genetic origins of ovarian failure

Premature ovarian failure (POF) is a condition characterized by cessation of ovarian function before the age of 40. The recent meeting at the National Institute of Child Health and Human Development brought together experts from diverse disciplines to share current perspectives on the genetic and physiologic origins of POF, with the idea that insights gained from these studies may provide important clues about the regulation of normal ovarian aging and perhaps aging processes in general. It was suggested that several murine genes, including Zfx, c = kit, and the kit ligand, should be fertile candidates for investigation of the etiology of POF in human families. The specific roles of the human DIA and FMR1 gene products in germ cell development need clarification in murine models, and there are more as yet unidentified genes residing on the long arm of the X chromosome that are also implicated in the regulation of human ovarian function. Genes acting at later stages of oocyte or ovarian follicle function, such as gonadotropin hormones and receptors, are responsible for POF in some women. POF has been found to be a heterogeneous disorder, the dissection of which offers promising insights into mechanisms governing germ cell origination, migration, and proliferation, meiotic mechanisms, and factors governing oocyte maturation and survival.

Developmentally regulated Xist promoter switch mediates initiation of X inactivation

Developmental regulation of the mouse Xist gene at the onset of X chromosome inactivation is mediated by RNA stabilization. Here, we show that alternate promoter usage gives rise to distinct stable and unstable RNA isoforms. Unstable Xist transcript initiates at a novel upstream promoter, whereas stable Xist RNA is transcribed from the previously identified promoter and from a novel downstream promoter. Analysis of cells undergoing X inactivation indicates that a developmentally regulated promoter switch mediates stabilization and accumulation of Xist RNA on the inactive X chromosome.

Comparative methylation analysis of murine transgenes that undergo or escape X-chromosome inactivation

We analyzed an X-linked metallothionein-vasopressin (MTVP) fusion transgene that undergoes X-chromosome inactivation (X inactivation) and an X-linked transferrin (TFN) transgene that escapes X inactivation with respect to methylation in the 5' regulatory regions. The MTVP transgene promoter region is unmethylated when the transgene is on the active X chromosome and methylated when on the inactive X chromosome. Interestingly, the MTVP transgene is not detectably transcribed from the male X chromosome, although it is unmethylated, consistent with its availability for transcription. The TFN transgene promoter region is hypomethylated on both the active and inactive X chromosomes, consistent with its expression from both chromosomes. The TFN and MTVP transgenes have been mapped to chromosomal regions D and C, respectively, by fluorescence in situ hybridization. These observations are discussed in the context of our understanding of the role of DNA methylation in the spread and maintenance of X-chromosome inactivation.

Stabilization and localization of Xist RNA are controlled by separate mechanisms and are not sufficient for X inactivation

These studies address whether XIST RNA is properly localized to the X chromosome in somatic cells where human XIST expression is reactivated, but fails to result in X inactivation (Tinker, A.V., and C.J. Brown. 1998. Nucl. Acids Res. 26:2935-2940). Despite a nuclear RNA accumulation of normal abundance and stability, XIST RNA does not localize in reactivants or in naturally inactive human X chromosomes in mouse/ human hybrid cells. The XIST transcripts are fully stabilized despite their inability to localize, and hence XIST RNA localization can be uncoupled from stabilization, indicating that these are separate steps controlled by distinct mechanisms. Mouse Xist RNA tightly localized to an active X chromosome, demonstrating for the first time that the active X chromosome in somatic cells is competent to associate with Xist RNA. These results imply that species-specific factors, present even in mature, somatic cells that do not normally express Xist, are necessary for localization. When Xist RNA is properly localized to an active mouse X chromosome, X inactivation does not result. Therefore, there is not a strict correlation between Xist localization and chromatin inactivation. Moreover, expression, stabilization, and localization of Xist RNA are not sufficient for X inactivation. We hypothesize that chromosomal association of XIST RNA may initiate subsequent developmental events required to enact transcriptional silencing.

The spreading of X inactivation into autosomal material of an x;autosome translocation: evidence for a difference between autosomal and X-chromosomal DNA

X inactivation involves initiation, propagation, and maintenance of genetic inactivation. Studies of replication timing in X;autosome translocations have suggested that X inactivation may spread into adjacent autosomal DNA. To examine the inactivation of autosomal material at the molecular level, we assessed the transcriptional activity of X-linked and autosomal loci spanning an inactive translocation in a phenotypically normal female with a karyotype of 46,X,der(X)t(X;4)(q22;q24). Since 4q duplications usually manifest dysmorphic features and severe growth and mental retardation, the normal phenotype of this individual suggested the spreading of X inactivation throughout the autosomal material. Consistent with this model, reverse transcription-PCR analysis of 20 transcribed sequences spanning 4q24-qter revealed that three known genes and 11 expressed sequence tags (ESTs) were not expressed in a somatic-cell hybrid that carries the translocation chromosome. However, three ESTs and three known genes were expressed from the t(X;4) chromosome and thus "escaped" X inactivation. This direct assay of expression demonstrated that the spreading of inactivation from the adjoining X chromosome was incomplete and noncontiguous. These findings are broadly consistent with the existence of genes known to escape inactivation on normal inactive X chromosomes. However, the fact that a high proportion (30%) of tested autosomal genes escaped inactivation may indicate that autosomal material lacks X chromosome-specific features that are associated with the spreading and/or maintenance of inactivation.

Induction of XIST expression from the human active X chromosome in mouse/human somatic cell hybrids by DNA demethylation

X chromosome inactivation occurs early in mammalian development to transcriptionally silence one of the pair of X chromosomes in females. The XIST RNA, a large untranslated RNA that is expressed solely from the inactive X chromosome, is implicated in the process of inactivation. As previous studies have shown that the XIST gene is methylated on the active X chromosome, we have treated a mouse/human somatic cell hybrid retaining an active human X chromosome with demethylating agents to determine whether expression of the human XIST gene could be induced. Stable expression of XIST was observed after several rounds of demethylation and stability of XIST expression correlated with the loss of methylation at the three sites analysed. We conclude that methylation is sufficient to inhibit expression of the XIST gene in somatic cell hybrids. No loss of expression was detected for eight other X-linked genes from the active X chromosome that was expressing XIST , suggesting that additional developmental or species-specific factors are required for the inactivation process.

Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals

In female mammals one of the X chromosomes is rendered almost completely transcriptionally inactive to equalize expression of X-linked genes in males and females. The inactive X chromosome is distinguished from its active counterpart by its condensed appearance in interphase nuclei, late replication, altered DNA methylation, hypoacetylation of histone H4, and by transcription of a large cis-acting nuclear RNA called Xist. Although it is believed that the inactivation process involves the association of specific protein(s) with the chromatin of the inactive X, no such proteins have been identified. We discovered a new gene family encoding a core histone which we called macroH2A (mH2A). The amino-terminal third of mH2A proteins is similar to a full-length histone H2A, but the remaining two-thirds is unrelated to any known histones. Here we show that an mH2A1 subtype is preferentially concentrated in the inactive X chromosome of female mammals. Our results link X inactivation with a major alteration of the nucleosome, the primary structural unit of chromatin.

Regulation of X-chromosome inactivation in development in mice and humans

Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females. X-chromosome inactivation (XCI) occurs during development, coupled with cell differentiation. In somatic cells, XCI is random, whereas in extraembryonic tissues, XCI is imprinted in that the paternally inherited X chromosome is preferentially inactivated. Inactivation is initiated from an X-linked locus, the X-inactivation center (Xic), and inactivity spreads along the chromosome toward both ends. XCI is established by complex mechanisms, including DNA methylation, heterochromatinization, and late replication. Once established, inactivity is stably maintained in subsequent cell generations. The function of an X-linked regulatory gene, Xist, is critically involved in XCI. The Xist gene maps to the Xic, it is transcribed only from the inactive X chromosome, and the Xist RNA associates with the inactive X chromosome in the nucleus. Investigations with Xist-containing transgenes and with deletions of the Xist gene have shown that the Xist gene is required in cis for XCI. Regulation of XCI is therefore accomplished through regulation of Xist. Transcription of the Xist gene is itself regulated by DNA methylation. Hence, the differential methylation of the Xist gene observed in sperm and eggs and its recognition by protein binding constitute the most likely mechanism regulating imprinted preferential expression of the paternal allele in preimplantation embryos and imprinted paternal XCI in extraembryonic tissues. This article reviews the mechanisms underlying XCI and recent advances elucidating the functions of the Xist gene in mice and humans.

The role of Xist in X-inactivation

The past year has seen important progress in our understanding of the role of the X inactive specific transcript gene (Xist) in the initiation and propagation of X-inactivation. A 35 kb Xist transgene had been shown to recapitulate the functions of the X-inactivation centre, progress has been made towards indentifying factors controlling the randomness of X-inactivation, and RNA stabilisation has been shown to play a role in Xist regulation at the onset of X-inactivation.

Xist and X chromosome inactivation

X inactivation acts in female mammals to equalise X-linked gene dosage between XX females and XY males. X inactivation is controlled by a single X-linked cis-acting locus called the X inactivation centre (Xic). In 1991 the Xist gene was identified as a candidate for the Xic. Xist is expressed in all adult female tissues, but only from the allele on the inactive X. The Xist transcript does not encode a protein but remains sequestered within the nucleus and co-localises with the inactive X chromosome. Transgenic and knockout studies have shown that a genomic region covering only a few kilobases either side of Xist carries all of the functions attributed to the Xic. The major questions currently occupying researchers studying X inactivation are: how do cells count their number of X chromosomes to determine whether X inactivation is necessary, and how does the Xist transcript inactivate all genes on the X chromosome?

Radiosensitivity and repair of the inactive X-chromosome. Insights from FISH and immunocytogenetics

The inactive X-chromosome provides a unique opportunity to study the role of transcriptional activity and chromatin condensation in the repair of chromosome damage. We induced chromosome breakage in human lymphocytes with X-rays (1 or 2 Gy) in either G0 and G1 phase of the cell cycle, and in the presence or absence of an inhibitor of double strand break repair, adenine 9-beta-D-arabinofuranoside (Ara-A). Chromosomal aberrations involving the X-chromosome were detected by means of fluorescence in situ hybridization with an X-chromosome specific red painting probe. The activation status of the X-chromosomes involved in the chromosomal aberrations was determined by simultaneous immunocytogenetics with FITC-conjugated antibodies against BrdUrd incorporated at late S-phase to distinguish the late replicating inactive X-chromosome in green-yellow. This multicolor approach allowed us to study and compare breakage and the extent of repair in the active and inactive X-chromosome. Our data indicate that both chromosomes responded with a similar radiosensitivity. This observation was consistent at both X-ray doses and at the two stages of the cell cycle analyzed. However, the number of chromosomal aberrations involving the inactive X-chromosome was increased after repair inhibition with Ara-A. The differential sensitivity to repair inhibition was observed in G0 after 1 Gy and in G1 after 2 Gy. Thus, the activation status of the X-chromosome might be a source of heterogeneity in breakage and repair. These observations suggest that there is heterogeneous repair when the active and the inactive X-chromosomes are compared and that the observed fragility is the result of a compromise between the actual number of breaks induced in each chromosome and their differential processing.

Expression of an Xist promoter-luciferase construct during spermatogenesis and in preimplantation embryos: regulation by DNA methylation

Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females, a process involving a regulatory gene, Xist (X-inactive specific transcript). Xist maps to the X-inactivation centre and is expressed from the inactive X chromosome in female somatic cells and at the time of X inactivation during spermatogenesis in the male. In female preimplantation embryos, Xist demonstrates imprinting in that the paternal allele inherited from the sperm is preferentially expressed. This preferential paternal Xist expression is correlated with paternal X inactivation in the extraembryonic lineages at the blastocyst stage. We have analysed a 233-bp Xist promoter fragment (nt -220 to +13) for its ability to direct appropriate expression and its regulation by DNA methylation. This minimal promoter sequence directs expression of the luciferase reporter gene following injection of the construct into one-cell embryos. In vitro methylation of the construct before injection represses transcription. In six different transgenic lines, expression of the Xist promoter-luciferase transgene occurs only in the testis of the males (as for the endogenous Xist gene). The testis-specific expression is correlated with hypomethylation of the transgene, although to different extents in different lines. Following paternal transmission, expression of the Xist promoter-luciferase construct in preimplantation embryos is correlated with degree of hypomethylation in the testis and the degree of hypomethylation of the transgene in embryos at the morula stage. It is concluded that the patterns of methylation of the transgene in sperm (and in microinjected transgenes) can regulate the activity of the Xist promoter in the preimplantation embryo and thus support the hypothesis that gametic methylation patterns govern imprinted expression of the endogenous Xist gene in development.

Role of the Xist gene in X chromosome choosing

In female mammals a "random choice" mechanism decides which of the two X chromosomes will be inactivated. It has been postulated that Xist is crucial for heterochromatinization and thus functions downstream of the choice mechanism. Here we report that females heterozygous for an internal deletion in the Xist gene, which includes part of exon 1 and extends to exon 5, undergo primary nonrandom inactivation of the wild-type X chromosome. The Xist gene, therefore, not only has a role in chromatin remodeling, but also includes an element required for X chromosome choosing. In conflict with the prevailing view of how choosing occurs, the element identified by the deletion plays a positive role in the choice mechanism and forces a reassessment of how X chromosome choosing is thought to occur.

Difference in chromatin packaging between active and inactive X chromosomes by fractionation and allele-specific detection

Using a novel method consisting of chromatin fractionation and allele-specific detection, chromatin packaging is compared between active X (Xa) and inactive X (Xi) chromosomes for five tumor cell clones that were derived from inter-subspecific F1 female mice. Separation of heterochromatic (H) and euchromatic (E) fractions is monitored by hybridization with subtelomeric satellite DNA and ribosomal RNA gene and by PCR amplification of p53 gene/pseudogene with one primer set. The H fraction was enriched with satellite and p53 pseudogene probably existing in heterochromatic regions while the E fraction showed inverse, suggesting fair separation. Analysis with seven marker and three gene loci revealed concentration of alleles on Xi in the H fraction and those on Xa in the E fraction, though the concentration levels varied. This implies that the packaging level of Xi is higher than that of active or inactive euchromatin on Xa. Intriguingly, one cell line showed biallelic expression and chromatin relaxation of the Pgk-1 locus, suggesting that the relaxation occur regionally on X chromosome.

Genomic imprinting in mammals

A handful of autosomal genes in the mammalian genome are inherited in a silent state from one of the two parents, and in a fully active form from the other, thereby rendering the organism functionally hemizygous for imprinted genes. To date 19 imprinted genes have been identified; 5 are expressed from the maternal chromosome while the rest are expressed from the paternal chromosome. Allele-specific methylation of CpG residues, established in one of the germlines and maintained throughout embryogenesis, has been clearly implicated in the maintenance of imprinting in somatic cells. Although the function of imprinting remains a subject of some debate, the process is thought to have an important role in regulating the rate of fetal growth.

X-chromosome inactivation in mammals

The inactive X chromosome differs from the active X in a number of ways; some of these, such as allocyclic replication and altered histone acetylation, are associated with all types of epigenetic silencing, whereas others, such as DNA methylation, are of more restricted use. These features are acquired progressively by the inactive X after onset of initiation. Initiation of X-inactivation is controlled by the X-inactivation center (Xic) and influenced by the X chromosome controlling element (Xce), which causes primary nonrandom X-inactivation. Other examples of nonrandom X-inactivation are also presented in this review. The definition of a major role for Xist, a noncoding RNA, in X-inactivation has enabled investigation of the mechanism leading to establishment of the heterochromatinized X-chromosome and also of the interactions between X-inactivation and imprinting as well as between X-inactivation and developmental processes in the early embryo.

Genomic imprinting in testicular germ cell tumours

Genomic imprinting refers to the parental origin-specific functional difference between the paternally and maternally-derived mammalian haploid genome. Normal embryogenesis depends on the presence of both a paternal and a maternal copy of particular chromosomal regions, containing the so-called imprinted genes. Genomic imprinting is established somewhere in the maturation from a primordial germ cell to a mature gamete, either spermatid or oocyte. We discuss the value of testicular cancers, especially those derived from the germ cell lineage, as a model to study erasement of the biparental pattern of genomic imprinting as present in the zygote and establishment of the paternal pattern during spermatogenesis. In addition, we will present data on the presence of X-inactivation in these cancers.

Regulatory elements in the minimal promoter region of the mouse Xist gene

The Xist gene plays a central role in regulating X chromosome inactivation and Xist transcription has recently been shown to be necessary for X inactivation in mouse. We are currently analysing regulation of the Xist gene in order to determine the mechanisms underlying initiation of Xist expression and X inactivation. Sequence comparisons indicate that a region of approximately 0.4 kb upstream of the the major transcriptional start site comprises the Xist minimal promoter. Analysis of reporter constructs demonstrates that the minimal promoter region is active both in embryonic stem (ES) cells and in differentiated derivatives, indicating that sequences either further upstream or downstream are required for appropriate developmental control of Xist transcription. We have examined the minimal promoter region in detail, and in addition to common promoter elements have identified two previously uncharacterised transcription-factor binding sites. Mutation of these sites in reporter constructs indicates that they are functionally important.

A promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation

X-chromosome inactivation is the process by which a cell recognizes the presence of two copies of an X chromosome early in the development of XX embryos and chooses one to be active and one to be inactive. Although it is commonly believed that the initiation of X inactivation is random, with an equal probability (50:50) that either X chromosome will be the inactive X in a given cell, significant variation in the proportion of cells with either X inactive is observed both in mice heterozygous for alleles at the Xce locus and among normal human females in the population. Families in which multiple females demonstrate extremely skewed inactivation patterns that are otherwise quite rare in the general population are thought to reflect possible genetic influences on the X-inactivation process. Here we report a rare cytosine to guanine mutation in the XIST minimal promoter that underlies both epigenetic and functional differences between the two X chromosomes in nine females from two unrelated families. All females demonstrate preferential inactivation of the X chromosome carrying the mutation, suggesting that there is an association between alterations in the regulation of XIST expression and X-chromosome inactivation.

Evidence for uniparental, paternal expression of the human GABAA receptor subunit genes, using microcell-mediated chromosome transfer

We have constructed mouse A9 hybrids containing a single normal human chromosome 15, via microcell-mediated chromosome transfer. Cytogenetic and DNA-polymorphic analyses identified mouse A9 hybrids that contained either a paternal or maternal human chromosome 15. Paternal specific expression of the known imprinted genes SNRPN (small nuclear ribonucleoprotein-associated polypeptide N gene) and IPW (imprinted gene in the Prader-Willi syndrome region) was maintained in the A9 hybrids. Using this system, we first demonstrated that human GABAAreceptor subunit genes, GABRB3 , GABRA5 and GABRG3 , were expressed exclusively from the paternal allele and that E6-AP (E6-associated protein or UBE3A ) was biallelically expressed. Moreover, the 5' portion of the GABRB3 gene was found to be hypermethylated on the paternal allele. Our data imply that GABAAreceptor subunit genes are imprinted and are possible candidates for Prader-Willi syndrome, and that this human monochromosomal hybrid system enables the efficient analysis of imprinted loci.

Coordinate control and variation in X-linked gene expression among female mice

In normal female mammals, one of the two X Chromosome (Chr) homologs per cell is silenced coordinately during early embryogenesis. The genes located on the inactivated X homolog are predicted to be influenced by the same underlying repression mechanism. To test the uniformity of cis-acting gene repression, 32 genetically identical F1 female mice were analyzed for differential expression of homologous alleles at three X-linked genes-Otc, Atp7a (= Mottled), and Hprt. Gene expression was assayed by the single-nucleotide primer extension (SNuPE) method, thereby allowing the three genes to be quantitated from the same RNA sample. Although variable between individual animals, the relative expression of the two alleles (allelic expression ratio) of the genes is significantly correlated within each steady-state RNA pool. When examined by animal age (3 months to 12 months), no statistically significant differences were observed in the mean or variance of allelic expression ratio. Together, the results confirm that X inactivation is coordinately controlled and is stable across the early- to mid-adult life span.

Stabilization of Xist RNA mediates initiation of X chromosome inactivation

The onset of X inactivation is preceded by a marked increase in the level of Xist RNA. Here we demonstrate that increased stability of Xist RNA is the primary determinant of developmental up-regulation. Unstable transcript is produced by both alleles in XX ES cells and in XX embryos prior to the onset of random X inactivation. Following differentiation, transcription of unstable RNA from the active X chromosome allele continues for a period following stabilization and accumulation of transcript on the inactive X allele. We discuss the implications of these findings in terms of models for the initiation of random and imprinted X inactivation.

X chromosome inactivation is mediated by Xist RNA stabilization

Low level Xist expression can be detected from both active X chromosomes (Xa) in female embryonic stem cells prior to X inactivation. After differentiation, Xist is expressed at high levels only from the inactive X chromosome (Xi). Differentiating female cells increase Xist expression from the Xi prior to silencing low level Xist expression from the Xa. The transition from low level to high level expression is regulated by the stabilization of Xist transcripts at the Xi. We suggest that these developmentally modulated changes in Xist expression are regulated by several different mechanisms: factors that stabilize Xist transcripts at the Xi, an activity that blocks this stabilization at the Xa, and a mechanism that silences low level Xist expression from the Xa.

Histone underacetylation is an ancient component of mammalian X chromosome inactivation

Underacetylation of histone H4 is thought to be involved in the molecular mechanism of mammalian X chromosome inactivation, which is an important model system for large-scale genetic control in eukaryotes. However, it has not been established whether histone underacetylation plays a critical role in the multistep inactivation pathway. Here we demonstrate differential histone H4 acetylation between the X chromosomes of a female marsupial, Macropus eugenii. Histone underacetylation is the only molecular aspect of X inactivation known to be shared by marsupial and eutherian mammals. Its strong evolutionary conservation implies that, unlike DNA methylation, histone underacetylation was a feature of dosage compensation in a common mammalian ancestor, and is therefore likely to play a central role in X chromosome inactivation in all mammals.

Epilepsy and mental retardation limited to females: an X-linked dominant disorder with male sparing

Several X-linked disorders affect females disproportionately or exclusively. These including focal dermal hypoplasia, oral-facial-digital syndrome type I (ref. 3) and epilepsy with bilateral periventricular heterotopias. X-linked dominant inheritance with male lethality is probably responsible for sex-limited expression of these disorders, as affected women have frequent spontaneous abortions and the sex ratio of their live offspring is often skewed. The same inheritance pattern has been proposed for Rett syndrome, Aicardi syndrome and microphthalmia with linear skin defects, but in these sporadic conditions, evidence of male lethality is lacking. We investigated an unusual family with epilepsy and mental retardation limited to females (EFMR, #121250 in ref. 9); this disorder is transmitted both by females and by completely unaffected carrier males. Assignment of the EFMR disease locus (EFMR) to the X chromosome indicates that selective involvement of females in X-linked disease may in some instances result from male sparing rather than male lethality.

Escape from X inactivation of two new genes associated with DXS6974E and DXS7020E

Most genes on the X chromosome undergo "inactivation," being transcribed from only one copy in female somatic cells, but several human genes have been shown to be expressed from both the active and the otherwise inactivated homologue. To assess further the fraction and location of genes that escape inactivation, we have analyzed the inactivation status of a set of 73 expressed sequence tags that were derived from the sequencing of cDNA collections and mapped to the X chromosome. Of 33 that were expressed in cultured cells, as assessed by reverse transcription and PCR, 4 (about 12%) were transcribed from both the active and the inactive X chromosome. Two, RPS4 and PCTAIRE1, are already known to escape inactivation; the other 2, of unknown function, include a short cDNA with a full open reading frame and a transcript with no detectable open reading frame. They map, respectively, to Xp11.3-p11.4 and Xp22.2; both regions were previously reported to encode sequences transcribed from the inactive X. Neither transcript has a corresponding sequence on the Y. Thus, they exhibit double dosage in females compared to males, and inactivation status may be inconsequential for these transcribed sequences.

XIST expression in human oocytes and preimplantation embryos

During mouse preimplantation development, the exclusive expression of the Xist gene from the paternally inherited allele is thought to play a role in the inactivation of the paternally inherited X chromosome in the extra-embryonic cell lineages of the developing female embryo. Recently, inactivation of the paternally inherited X chromosome has also been shown to occur in the extraembryonic cell lineages of the human female conceptus. In this paper, we determine whether the pattern of XIST expression in human preimplantation embryos is similarly correlated with paternal X inactivation. We developed procedures sensitive to the single cell, for the simultaneous analysis of XIST and HPRT expression and of sexing, initially using human fibroblast cells. Application of these procedures to human cleavage-stage embryos derived by in vitro fertilization revealed a pattern of XIST expression different from that in the mouse. Transcripts of the XIST gene were detected as early as the 1-cell zygote and, with increasing efficiency, through to the 8-cell stage of preimplantation development. In addition, transcripts of XIST were detected in both male (hence from the maternally inherited allele) and female preimplantation embryos. This pattern of expression is not consistent with a role for the early expression of the XIST gene in the choice of paternal X inactivation in the extraembryonic cell lineages of the developing human embryo.

Identification and characterization of the human XIST gene promoter: implications for models of X chromosome inactivation

The XIST gene in both humans and mice is expressed exclusively from the inactive X chromosome and is required for X chromosome inactivation to occur early in development. In order to understand transcriptional regulation of the XIST gene, we have identified and characterized the human XIST promoter and two repeated DNA elements that modulate promoter activity. As determined by reporter gene constructs, the XIST minimal promoter is constitutively active at high levels in human male and female cell lines and in transgenic mice. We demonstrate that this promoter activity is dependent in vitro upon binding of the common transcription factors SP1, YY1 and TBP. We further identify two cis -acting repeated DNA sequences that influence reporter gene activity. First, DNA fragments containing a set of highly conserved repeats located within the 5'-end of XIST stimulate reporter activity 3-fold in transiently transfected cell lines. Second, a 450 bp alternating purine-pyrimidine repeat located 25 kb upstream of the XIST promoter partially suppresses promoter activity by approximately 70% in transient transfection assays. These results indicate that the XIST promoter is constitutively active and that critical steps in the X inactivation process must involve silencing of XIST on the active X chromosome by factors that interact with and/or recognize sequences located outside the minimal promoter.

A methylation-dependent DNA-binding activity recognising the methylated promoter region of the mouse Xist gene

Differential methylation of CpG sites in the promoter region of the mouse Xist gene is correlated with Xist expression and X-chromosome inactivation in the female. Using oligonucleotides encompassing the differentially methylated sites as probes in band-shift assays, we have identified a nuclear protein which binds to a specific region of the promoter (between base pairs -45 and -30 upstream from the transcription start site) only when CpG sites within the CG rich region (GCGCCGCGG, -44 to -36) are methylated. Competition experiments with methylated or unmethylated heterologous oligonucleotides demonstrate that the activity is sequence-specific as well as methylation-dependent. Analysis by Southwestern blot identifies a protein of approximately 100 kDa molecular weight and confirms strong binding to the methylated Xist promoter oligonucleotide. Using a 233bp Xist-promoter luciferase construct in which the cytosines in the three CpG sites in the -44 to -36 region are mutated to thymine, we have established that this region is required for transcription from the mouse Xist promoter. Therefore, we suggest that the binding of the 100kDa protein to the methylated sequence leads to repression of transcription from the methylated Xist allele, thus suggesting a role in the regulation of both imprinted and random Xist transcription and X-chromosome inactivation.

Karyotype-phenotype correlation in females with X chromosome abnormalities

In mammals, females have a pair of X chromosomes, whereas males have one X chromosome and one Y chromosome, which is much smaller and contains fewer genes than a X chromosome. One of the pair of X chromosomes is inactivated in females. The inactivated X chromosome is late-replicating, heterochromatic, and genetically unexpressed. An X inactivation center (XIC) located at a proximal region on Xq is thought to control inactivation of an X chromosome. There has been increasing scientific interest in the relationship between chromosomal and clinical findings in different chromosomal aberrations, whether affecting the sex chromosomes or the autosomes. The genetic and molecular implications of the karyotype/phenotype controversy have recently been considered with the aim of better understanding the interplay of specific genes carried on different chromosomes in organ development and differentiation. Karyotype/phenotype correlation showed the gradation of severity of clinical phenotype to be related to the number of X chromosomes.

Prune-belly syndrome and other anomalies in a stillborn fetus with a ring X chromosome lacking XIST

Ring X chromosomes that lack the X inactivation center and fail to be inactivated have been implicated as a cause of mental retardation and multiple congenital anomalies. We report on a stillborn fetus with karyotype mos45,X/46,X,r(X) and early urethral obstruction or prune-belly sequence, single umbilical artery, limb deficiency, horseshoe kidney, cardiac hypertrophy, persistent left superior vena cava, and axial skeleton abnormalities. Fluorescent in situ hydridization (FISH) studies confirmed that the ring chromosome is X-derived and demonstrated that it lacks the XIST locus. The findings in this fetus are discussed with regard to the spectrum of phenotypes associated with monosomy X and small ring X chromosomes.

Xist has properties of the X-chromosome inactivation centre

X-chromosome inactivation is the process by which female mammals (with two X chromosomes) achieve expression of X-chromosomal genes equivalent to that of males (one X and one Y chromosome). This results in the transcriptional silencing of virtually all genes on one of the X chromosomes in female somatic cells. X-chromosome inactivation has been shown to act in cis and to initiate and spread from a single site on the X chromosome known as the X-inactivation centre (Xic). The Xic has been localized to a 450-kilobase region of the mouse X chromosome. The Xist gene also maps to this region and is expressed exclusively from the inactive X chromosome. Xist is unusual in that it appears not to code for a protein but produces a nuclear RNA which colocalizes with the inactive X chromosome. The creation of a null allele of Xist in embryonic stem cells has demonstrated that this gene is required for X inactivation to occur in cis. Here we show that Xist, introduced onto an autosome, is sufficient by itself for inactivation in cis and that Xist RNA becomes localized close to the autosome into which the gene is integrated. In addition, the presence of autosomal Xist copies leads to activation of the endogeneous Xist gene in some cells, suggesting that elements required for some aspects of chromosome counting are contained within the construct. Thus the Xist gene exhibits properties of the X-inactivation centre.

Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs

HeT-A elements are non-long terminal repeat (non-LTR) retrotransposons found in head-to-tail arrays on Drosophila chromosome ends, where they form telomeres. We report that HeT-A promoter activity is located in the 3' end of the element, unlike the 5' location seen for other non-LTR retrotransposons. In HeT-A arrays the 3' sequence of one element directs transcription of its downstream neighbor. Because the upstream promoter has the same sequence as the 3' end of the transcribed element, the HeT-A promoter is effectively equivalent to a 5' LTR in both structure and function. Retroviruses and LTR retrotransposons have their promoters and transcription initiation sites in their 5' LTRs. Thus HeT-A appears to have the structure of an evolutionary intermediate between non-LTR and LTR retrotransposons.

Replication timing properties of the human HPRT locus on active, inactive and reactivated X chromosomes

X chromosome inactivation is associated with a highly asynchronous pattern of DNA replication at most X-linked loci in females. We studied the human HPRT locus, which is subject to X inactivation and expressed from only the active homolog, with the goal of comparing replication properties between the active and inactive homologs in this region using a fluorescence in situ hybridization approach. We found that in normal female lymphoblasts this locus is replicated in a highly asynchronous manner across a broad, discrete 500-600 kb zone with earliest replication appearing at the gene coding sequence. This general timing profile is maintained in normal male lymphoblasts, as well as in hamster x human hybrid cells containing the active human X chromosome. However, the inactive human X chromosome in the hamster cell background does not appear to function in a fully equivalent manner to the normal inactive X chromosome in female cells. Furthermore, reactivation of the inactive human X chromosome in a hamster x human hybrid system by 5-azacytidine treatment and HAT selection restores early replication at the HPRT gene itself, but does not change the overall domain behavior.

Agenesis of the corpus callosum in Turner syndrome with ring X

An 8-year-old girl with Turner syndrome and 45,X/46,X,r(X) mosaicism was found to have agenesis of the corpus callosum and various other characteristics including 'kabuki makeup' facial features and mild learning disability. Only two other cases of Turner syndrome associated with agenesis of the corpus callosum have been reported, both in patients with a 45,X karyotype. In both of those patients the constellation of signs differed from those of the present patient in a number of ways. It remains to be confirmed whether there is a higher incidence of CNS malformation in girls who have Turner syndrome with a ring X than has been reported for girls with Turner syndrome in general.

Xist-deficient mice are defective in dosage compensation but not spermatogenesis

The X-linked Xist gene encodes a large untranslated RNA that has been implicated in mammalian dosage compensation and in spermatogenesis. To investigate the function of the Xist gene product, we have generated male and female mice that carry a deletion in the structural gene but maintain a functional Xist promoter. Mutant males were healthy and fertile. Females that inherited the mutation from their mothers were also normal and had the wild-type paternal X chromosome inactive in every cell. In contrast to maternal transmission, females that carry the mutation on the paternal X chromosome were severely growth-retarded and died early in embryogenesis. The wild-type maternal X chromosome was inactive in every cell of the growth-retarded embryo proper, whereas both X chromosomes were expressed in the mutant female trophoblast where X inactivation is imprinted. However, an XO mouse with a paternally inherited Xist mutation was healthy and appeared normal. The imprinted lethal phenotype of the mutant females is therefore due to the inability of extraembryonic tissue with two active X chromosomes to sustain the embryo. Our results indicate that the Xist RNA is required for female dosage compensation but plays no role in spermatogenesis.

Assessment of Clonality and Its Relevance in Acute Myeloid Leukaemia and Bone Marrow Transplantation

The study of clonality in females is a useful tool in assessing states of neoplastic cell expansion in myeloid malignancies and remission status after chemotherapy and bone marrow transplant. Various experimental techniques have been developed based on the Lyon Hypothesis of X chromosome inactivation in females. Specific enzymes are utilised to distinguish active from inactive X chromosomes, distinctive patterns of which are then visualised by Southern blotting or more recently PCR. A valuable contribution to the nature of myeloid malignancies has been gained by these means.

Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure

This study provides a three-dimensional (3D) analysis of differences between the 3D morphology of active and inactive human X interphase chromosomes (Xa and Xi territories). Chromosome territories were painted in formaldehyde-fixed, three-dimensionally intact human diploid female amniotic fluid cell nuclei (46, XX) with X-specific whole chromosome compositive probes. The colocalization of a 4,6-diamidino-2-phenylindole dihydrochloride-stained Barr body with one of the two painted X territories allowed the unequivocal discrimination of the inactive X from its active counterpart. Light optical serial sections were obtained with a confocal laser scanning microscope. 3D-reconstructed Xa territories revealed a flatter shape and exhibited a larger and more irregular surface when compared to the apparently smoother surface and rounder shape of Xi territories. The relationship between territory surface and volume was quantified by the determination of a dimensionless roundness factor (RF). RF and surface area measurements showed a highly significant difference between Xa and Xi territories (P < 0.001) in contrast to volume differences (P > 0.1). For comparison with an autosome of similar DNA content, chromosome 7 territories were additionally painted. The 3D morphology of the chromosome 7 territories was similar to the Xa territory but differed strongly from the Xi territory with respect to RF and surface area (P < 0.001).

Mammals that break the rules: genetics of marsupials and monotremes

Marsupials and monotremes, the mammals most distantly related to placental mammals, share essentially the same genome but show major variations in chromosome organization and function. Rules established for the mammalian genome by studies of human and mouse do not always apply to these distantly related mammals, and we must make new and more general laws. Some examples are contradictions to our assumption of frequent genome reshuffling in vertebrate evolution, Ohno's Law of X chromosome conservation, the Lyon Hypothesis of X chromosome inactivation, sex chromosome pairing, several explanations of Haldane's Rule, and the theory that mammalian Y chromosome contains a male-specific gene with a direct dominant action on sex determination. Significantly, it is not always the marsupials and monotremes (usually considered the weird mammals) that are exceptional. In many features, it appears that humans and, particularly, mice are the weird mammals that break more general mammalian, or even vertebrate rules.

Epigenetic alterations brought about by lithium treatment disrupt mouse embryo development

The commonly accepted mechanism by which LiCl dorsalizes amphibian embryos is a respecification of ventral blastomeres, presumably through realignment of dorsal positional information in the embryo. An alternative mechanism, however, is an epigenetic change in the competence of cells to respond to cues they may be normally exposed to without effect. In order to test this hypothesis, we treated mouse preimplantation embryos, which do not possess any axial positional information, with LiCl, and observed axial abnormalities which must have been elaborated several days after treatment. We interpret this as support for the hypothesis that cellular competence rather than positional information is altered by LiCl, and suggest that this competence may be altered through the action of lithium sensitive enzymes that interact with chromatin.

The development and use of a DNA polymerase arrest assay for the evaluation of parameters affecting intrastrand tetraplex formation

We show here that a K+-dependent block to DNA synthesis is a sensitive and specific indicator of intrastrand tetraplex formation that can be used, both to identify sequences with tetraplex-forming potential and to examine parameters that affect tetraplex formation. We show that tetraplex formation is determined by a complex combination of factors including the size and base composition of its constituent loops and stems. In the process of carrying out this study we have found that the number of sequences with the ability to form tetraplexes is larger than previously thought, and that such sequences are ubiquitous in eukaryote genomes.

DNA hypomethylation can activate Xist expression and silence X-linked genes

Xist and other X-linked gene expression was examined by fluorescence in situ hybridization in cells of wild type and DNA methyltranferase (Dnmt) mutant embryos and embryonic stem (ES) cells to determine whether demethylation-induced Xist expression leads to inappropriate X chromosome inactivation. In undifferentiated ES cells low-level Xist expression was detected from the single active X chromosome (Xa) in male cells and on both Xa's in female cells. Upon differentiation Xist expression was detected only in female cells, in which Xist RNA colocalized with the entire inactive X chromosome (Xi). Differentiated Dnmt mutant ES cells or cells of mutant postgastrulation embryos showed aberrant patterns of Xist expression: Xist transcripts colocalized with the single X chromosome in male cells and with both X chromosomes in female cells. X-linked gene expression was not detected from chromosomes coated with Xist RNA. These results suggest that ectopic Xist expression, induced by DNA hypomethylation, may lead to the inactivation of X-linked genes. We conclude that Xist-mediated X chromosome inactivation can occur in the absence of DNA methylation, arguing that DNA methylation may be required to repress Xist expression for the maintenance of a transcriptionally active Xa. In differentiated Dnmt mutant ES cells the activation of Xist expression correlated with a dramatic increase in apoptotic bodies, suggesting that Xist-mediated X chromosome inactivation may result in cell death and contribute to the embryonic lethality of the Dnmt mutation.

A linkage map of the ovine X chromosome

A genetic linkage map of the ovine X chromosome containing type I and type II markers has been constructed. The map contains 7 known gene markers and 14 microsatellite markers with a recombination length of 141.9 cM. Segregation of polymorphic markers was observed in a three-generation pedigree containing 480 animals. The maximum number of informative meioses was 912. Additional information was obtained for some markers by following segregation in the AgResearch International Mapping Flock, consisting of nine three-generation full-sib pedigrees. A pseudoautosomal region containing two markers has been identified at one end of the linkage map. Comparisons with mouse and human X chromosomes confirms the observation of Ohno (1973) that the gene content of the mammalian X chromosome is retained. In particular, the conserved grouping of the genes PHKA1, ATP7A, and XIST observed in both the human and the mouse X chromosome appears to be conserved in the sheep X chromosome, and XIST has been mapped to near the center of the chromosome. This study provides the first reported genetic linkage map combining both type I and type II markers for any ruminant X chromosome.