Stability of the "two active X" phenotype in triploid somatic cells

Silencing XIST on the future active X: Searching human and bovine preimplantation embryos for the repressor

X inactivation is the means of equalizing the dosage of X chromosomal genes in male and female eutherian mammals, so that only one X is active in each cell. The XIST locus (in cis) on each additional X chromosome initiates the transcriptional silence of that chromosome, making it an inactive X. How the active X in both males and females is protected from inactivation by its own XIST locus is not well understood in any mammal. Previous studies of autosomal duplications suggest that gene(s) on the short arm of human chromosome 19 repress XIST on the active X. Here, we examine the time of transcription of some candidate genes in preimplantation embryos using single-cell RNA sequencing data from human embryos and qRT-PCR from bovine embryos. The candidate genes assayed are those transcribed from 19p13.3-13.2, which are widely expressed and can remodel chromatin. Our results confirm that XIST is expressed at low levels from the future active X in embryos of both sexes; they also show that the XIST locus is repressed in both sexes when pluripotency factors are being upregulated, during the 4-8 cell and morula stages in human and bovine embryos - well before the early blastocyst (E5) when XIST on the inactive X in females starts to be upregulated. Our data suggest a role for DNMT1, UHRF1, SAFB and SAFB2 in XIST repression; they also exclude XACT and other 19p candidate genes and provide the transcriptional timing for some genes not previously assayed in human or bovine preimplantation embryos.

Choosing the Active X: The Human Version of X Inactivation

Humans and rodents differ in how they carry out X inactivation (XI), the mammalian method to compensate for the different number of X chromosomes in males and females. Evolutionary changes in staging embryogenesis and in mutations within the XI center alter the process among mammals. The mouse model of XI is predicated on X counting and subsequently choosing the X to 'inactivate'. However, new evidence suggests that humans initiate XI by protecting one X in both sexes from inactivation by XIST, the noncoding RNA that silences the inactive X. This opinion article explores the question of how the active X is protected from silencing by its own Xist locus, and the possibility of different solutions for mouse and human.

Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silenced in utero by XIST, the Inactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing by XIST, we updated the search for a key dosage sensitive XIST repressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivate XIST. Unlike males, the females who duplicate this region of chromosome 19 (partial 19 trisomy) do not survive embryogenesis; this preimplantation loss of females may be one reason that more human males are born than females.

X inactivation in triploidy and trisomy: the search for autosomal transfactors that choose the active X

Only one X chromosome functions in diploid human cells irrespective of the sex of the individual and the number of X chromosomes. Yet, as we show, more than one X is active in the majority of human triploid cells. Therefore, we suggest that (i) the active X is chosen by repression of its XIST locus, (ii) the repressor is encoded by an autosome and is dosage sensitive, and (iii) the extra dose of this key repressor enables the expression of more than one X in triploid cells. Because autosomal trisomies might help locate the putative dosage sensitive trans-acting factor, we looked for two active X chromosomes in such cells. Previously, we reported that females trisomic for 18 different human autosomes had only one active X and a normal inactive X chromosome. Now we report the effect of triplication of the four autosomes not studied previously; data about these rare trisomies - full or partial - were used to identify autosomal regions relevant to the choice of active X. We find that triplication of the entire chromosomes 5 and 11 and parts of chromosomes 1 and 19 is associated with normal patterns of X inactivation, excluding these as candidate regions. However, females with inherited triplications of 1p21.3-q25.3, 1p31 and 19p13.2-q13.33 were not ascertained. Thus, if a single key dose-sensitive gene induces XIST repression, it could reside in one of these locations. Alternatively, more than one dosage-sensitive autosomal locus is required to form the repressor complex.

SILENCING OF THE MAMMALIAN X CHROMOSOME

Mammalian X chromosome inactivation is one of the most striking examples of epigenetic gene regulation. Early in development one of the pair of approximately 160-Mb X chromosomes is chosen to be silenced, and this silencing is then stably inherited through subsequent somatic cell divisions. Recent advances have revealed many of the chromatin changes that underlie this stable silencing of an entire chromosome. The key initiator of these changes is a functional RNA, XIST, which is transcribed from, and associates with, the inactive X chromosome, although the mechanism of association with the inactive X and recruitment of facultative heterochromatin remain to be elucidated. This review describes the unique evolutionary history and resulting genomic structure of the X chromosome as well as the current understanding of the factors and events involved in silencing an X chromosome in mammals.

X chromosome inactivation: theme and variations

My contribution to this special issue on Vertebrate Sex Chromosomes deals with the theme of X chromosome inactivation and its variations. I will argue that the single active X--characteristic of mammalian X dosage compensation--is unique to mammals, and that the major underlying mechanism(s) must be the same for most of them. The variable features reflect modifications that do not interfere with the basic theme. These variations were acquired during mammalian evolution--to solve special needs for imprinting and locking in the inactive state. Some of the adaptations reinforce the basic theme, and were needed because of species differences in the timing of interacting developmental events. Elucidating the molecular basis for the single active X requires that we distinguish the mechanisms essential for the basic theme from those responsible for its variations.

Species differences in TSIX/Tsix reveal the roles of these genes in X-chromosome inactivation

Transcriptional silencing of the human inactive X chromosome is induced by the XIST gene within the human X-inactivation center. The XIST allele must be turned off on one X chromosome to maintain its activity in cells of both sexes. In the mouse placenta, where X inactivation is imprinted (the paternal X chromosome is always inactive), the maternal Xist allele is repressed by a cis-acting antisense transcript, encoded by the Tsix gene. However, it remains to be seen whether this antisense transcript protects the future active X chromosome during random inactivation in the embryo proper. We recently identified the human TSIX gene and showed that it lacks key regulatory elements needed for the imprinting function of murine Tsix. Now, using RNA FISH for cellular localization of transcripts in human fetal cells, we show that human TSIX antisense transcripts are unable to repress XIST. In fact, TSIX is transcribed only from the inactive X chromosome and is coexpressed with XIST. Also, TSIX is not maternally imprinted in placental tissues, and its transcription persists in placental and fetal tissues, throughout embryogenesis. Therefore, the repression of Xist by mouse Tsix has no counterpart in humans, and TSIX is not the gene that protects the active X chromosome from random inactivation. Because human TSIX cannot imprint X inactivation in the placenta, it serves as a mutant for mouse Tsix, providing insights into features responsible for antisense activity in imprinted X inactivation.

Identification of TSIX, encoding an RNA antisense to human XIST, reveals differences from its murine counterpart: implications for X inactivation

X inactivation is the mammalian method for X-chromosome dosage compensation, but some features of this developmental process vary among mammals. Such species variations provide insights into the essential components of the pathway. Tsix encodes a transcript antisense to the murine Xist transcript and is expressed in the mouse embryo only during the initial stages of X inactivation; it has been shown to play a role in imprinted X inactivation in the mouse placenta. We have identified its counterpart within the human X inactivation center (XIC). Human TSIX produces a >30-kb transcript that is expressed only in cells of fetal origin; it is expressed from human XIC transgenes in mouse embryonic stem cells and from human embryoid-body-derived cells, but not from human adult somatic cells. Differences in the structure of human and murine genes indicate that human TSIX was truncated during evolution. These differences could explain the fact that X inactivation is not imprinted in human placenta, and they raise questions about the role of TSIX in random X inactivation.

Gonadal pathology in triploidy

There are numerous reports describing the pathology of the fetus and placenta in triploidy. Although gonadal pathology is described in many of these reports, consistent changes have not been noted nor is it clear whether genital ambiguity can be considered part of the triploid phenotype. We present a case of triploidy of probable diandric origin, in which there were dysgenetic gonads with abnormal seminiferous tubules, nodules of undifferentiated stroma, and focal absence of the tunica albuginea. As this finding was distinctly unusual in our experience of triploid gonadal pathology, we reviewed the gonadal histology in 51 fetal and infant triploids examined in our autopsy/embryopathology laboratory. The gonads were compared to age-matched normal controls to determine if there was a specific gonadal pathology associated with triploidy and if there was any correlation of this pathology with parental origin of the triploidy. Our review of the triploid gonads indicated that while minor, nonspecific changes were not uncommon, overtly dysgenetic gonads, as observed in the index case, are rare.

Human X inactivation center induces random X chromosome inactivation in male transgenic mice

X chromosome inactivation is the means to downregulate the transcriptional output of X chromosomes in female mammals. Essential DNA from the murine X inactivation center (Xic) has been identified by introducing it into male embryonic stem (ES) cells. To identify the essential sequences on human X chromosomes, we transfected male mouse ES cells with a YAC transgene containing 480 kb of the putative human X inactivation center (XIC). Despite little DNA sequence conservation, the human transgene is recognized as a second Xic in these XY mouse cells and induces random inactivation in chimeric mice derived from these cells. Inactivation is extensive on the X chromosome, but more localized on chromosome 11 carrying the transgene, demonstrating that initial inactivation and spreading of inactivation signals along the chromosome are independent events. Our results show for the first time that the DNA included in the human XIC transgene is sufficient to initiate random X inactivation, even in cells of another species. Interspecies XIC trangenes should facilitate further investigation of this process in humans and other mammals.

Sex determining gene on the X chromosome short arm: dosage sensitive sex reversal

The present review article summarizes current knowledge concerning the sex determining gene on Xp21, termed DSS (dosage sensitive sex reversal). The presence of DSS has been based on the finding that, in the presence of SRY, partial active Xp duplications encompassing the middle part of Xp result in sex reversal, whereas those of the distal or proximal part of Xp permit male sex development. Because Klinefelter patients develop as males, it is believed that DSS is normally subject to X-inactivation, and that two active copies of DSS override the function of SRY, resulting in gonadal dysgenesis because of meiotic pairing failure. It may be possible that DSS encodes a target sequence for repressing function of SRY or that DSS is involved in an X chromosome-counting mechanism. Molecular approaches have localized DSS to a 160 kb region and isolated candidate genes such as DAX-1 and MAGE-Xp, but there has been no formal evidence equating the candidate gene with DSS. In addition to its clinical importance, the exploration of DSS must provide a useful clue to phylogenetic studies of sex chromosomes and dosage compensation.

Sex determination and dosage compensation: lessons from flies and worms

In both Drosophila melanogaster and Caenorhabditis elegans somatic sex determination, germline sex determination, and dosage compensation are controlled by means of a chromosomal signal known as the X:A ratio. A variety of mechanisms are used for establishing and implementing the chromosomal signal, and these do not appear to be similar in the two species. Instead, the study of sex determination and dosage compensation is providing more general lessons about different types of signaling pathways used to control alternative developmental states of cells and organisms.

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

X-chromosome inactivation results in the cis-limited dosage compensation of genes on one of the pair of X chromosomes in mammalian females. Although most X-linked genes are believed to be subject to inactivation, several are known to be expressed from both active and inactive X chromosomes. Here we describe an X-linked gene with a novel expression pattern--transcripts are detected only from the inactive X chromosome (Xi) and not from the active X chromosome (Xa). This gene, called XIST (for Xi-specific transcripts), is a candidate for a gene either involved in or uniquely influenced by the process of X inactivation.

Complete reactivation of X chromosomes from human chorionic villi with a switch to early DNA replication

Mammalian sex-dosage compensation is mediated by maintaining activity of only one X chromosome. The asynchronous DNA synthesis characterizing the silent human X chromosome is thought to be reversible only during ontogeny of oocytes. We have previously shown that the glucose-6-phosphate dehydrogenase (G6PD) locus (G6PD) on the allocyclic X chromosome in chorionic villi is partially expressed. We now show that in hybrids derived from a clone of chorionic villi cells (heterozygous for G6PD A) and mouse A9 cells, the loci for G6PD, hypoxanthine phosphoribosyltransferase (HPRT) and phosphoglycerate kinase are expressed on both human X chromosomes; the human X chromosomes carrying either G6PD A or B replicate synchronously with each other and with murine chromosomes. The X chromosome with G6PD A was identified as the original late-replicating X, because methylation in the body of the HPRT gene on this chromosome remained characteristic of the inactive X chromosome. These results indicate that X-chromosome inactivation is completely reversible in cells of trophoblast origin; induction of full transcriptional activity is accompanied by acquisition of isocyclic replication, showing an intimate relationship between these processes. The molecular events responsible for this reversal may be similar to those occurring during maturation of oocytes. Chorionic villi and derivative hybrids provide in vitro models for exploring early events that program the single active X chromosome.

Evidence for a relationship between DNA methylation and DNA replication from studies of the 5-azacytidine-reactivated allocyclic X chromosome

We examined the sequence of DNA synthesis of the human active, inactive and reactivated X chromosomes in mouse-human hybrid cells. The two independent reactivants, induced by 5-azacytidine (5-azaC), expressed human hypoxanthinephosphoribosyl transferase (HPRT), and one also expressed human glucose-6-phosphate dehydrogenase (G6PD) and phosphoglycerate kinase (PGK). Restriction enzyme analysis of DNA methylation at the re-expressed loci revealed hypomethylation of CpG clusters, that characterizes the relevant genes on the active X. The transfer of active and inactive X chromosomes from the native environment of the human fibroblast to the foreign environment of the hybrid cell did not affect the specific replication sequence of either human X chromosome. The silent X chromosome when reactivated, remained allocyclic, and the first bands to replicate were the same as prior to reactivation. In one reactivant, however, further progression of replication was significantly altered with respect to the order in which bands were synthesized. This alteration in the replication of the silent X following 5-azaC-induced reactivation suggests that DNA methylation may modulate the replication kinetics of chromosomal DNA.

Incomplete X chromosome dosage compensation in chorionic villi of human placenta

Studies of glucose-6-phosphate dehydrogenase (G6PD) in heterozygous cells from chorionic villi of five fetal and one newborn placenta show that the locus on the allocyclic X is expressed in many cells of this trophectoderm derivative. Heterodimers were present in clonal populations of cells with normal diploid karyotype and a late replicating X chromosome. The expression of the two X chromosomes was unequal, based on ratios of homodimers and heterodimers in clones. Studies of DNA, digested with Hpa II and probed with cloned genomic G6PD sequences, indicate that expression of the locus in chorionic villi is associated with hypomethylation of 3' CpG clusters. These findings suggest that dosage compensation, at least at the G6PD locus, has not been well established or maintained (or both) in placental tissue. Furthermore, the active X chromosome in these human cells of trophoblastic origin can be either the paternal or maternal one; therefore, paternal X inactivation in extraembryonic lineages is not an essential feature of mammalian X dosage compensation.

Complete concordance between glucose-6-phosphate dehydrogenase activity and hypomethylation of 3' CpG clusters: implications for X chromosome dosage compensation

To explore the molecular basis of X chromosome inactivation, we have examined the human locus for glucose-6-phosphate dehydro-genase (G6PD) in various human tissues. Studies of DNA from males and females and from somatic cell hybrids with active or inactive X chromosomes, show that two remarkably dense clusters of CpG dinucleotides in the 3' coding sequences are hypomethylated in active G6PD genes but extensively methylated in inactive ones. Reacquisition of G6PD activity, either spontaneous or induced by 5-azacytidine, is accompanied by demethylation of both clusters; however, the clusters remain methylated in reactivants that express HPRT but not G6PD. Our observations implicate these 3' CpG clusters in the transcription of G6PD and in maintenance of dosage compensation for X linked housekeeping genes.

Activity of X-linked genes in stem and differentiated Mus musculus X Mus caroli hybrid cells

Hypoxanthine phosphoribosyltransferase-deficient (HPRT-) F9-derived teratocarcinoma stem cells carrying an SV40 genome (12-16TG cells) were fused with Mus caroli (M. car.) spleen cells, and a stem cell hybrid containing reduced numbers of M. car. chromosomes was isolated (BC6 stem cell). The BC6 cells containing an active X chromosome from each parental cell were induced to differentiate in retinoic acid, and differentiated clones were isolated. Most differentiated clones retained both parental X chromosomes in active form. One differentiated clone, BC6-13, grew equally well in hypoxanthine/aminopterin/thymidine (HAT) selective medium (which requires an active M. car. HPRT (E.C.2.4.2.8) locus) or in 6-thioguanine (6TG, which would require either loss or inactivation of the M. car. HPRT locus). Using cDNA probes for HPRT and phosphoglycerate kinase (PGK) (E.C.2.7.2.3) loci and biochemical assays for HPRT and PGK enzymes, it was shown that BC6-13 cells, whether grown in nonselective medium, HAT medium, or 6TG-containing medium, retain the HPRT and PGK genes of both parental cells, but the M. car. forms of HPRT and PGK were inactivated in cells treated with 6TG. 6-Thioguanine seems to act as an inducer, one effect of which is X chromosome inactivation, which seems to be complete and irreversible as early as 24 h after addition of 6TG to BC6-13 cells.

Characterization of reiterated human DNA with respect to mammalian X chromosome homology

Recombinants containing human repetitive DNA sequences were identified by dot hybridization and classified with respect to presence on the X chromosome and homology to mouse DNA. Using genomic probes that differ in number of X chromosomes, we observed extensive homology between human autosomal and X sequences. Hybridization to genomic probes that differ in species of origin indicate that these reiterated sequences have diverged between mouse and man. Eleven recombinants, each containing a different reiterated sequence(s), were hybridized in situ to metaphase chromosomes of mouse and man. These studies indicate that reiterated DNA which is homologous to the human X chromosome is more similar to DNA of human autosomes than to any murine chromosome. Therefore, it seems that reiterated DNA sequences on the human X chromosome have diverged as much during mammalian evolution as sequences on human autosomes. Moreover, the extensive modification of the original mammalian X has not interferred with the X inactivation process.

Cytogenetic and biochemical investigations on fibroblast cultures and clones with one and two active X chromosomes of a 69,XXY triploidy

Bromodeoxyuridine replication patterns showed that fibroblasts from a 69,XXY triploidy carried either one or two early replicating X chromosomes. The activity of alpha-galactosidase A measured in single cells fell into two classes with a ratio of 1:2. Dilute plating produced clones of both types with the activity of alpha-galactosidase A corresponding to the number of active X chromosomes. To our knowledge, this is the first report on clones of a triploidy with different numbers of active X chromosomes, and on a gene-dosage effect of an X-linked gene using triploid cells with one active X as control.

Unbalanced X chromosome mosaicism in B cells of mice with X-linked immunodeficiency

The immunodeficiency in CBA/N mice is reflected by abnormal development of a subset of B lymphocytes. However, it is not clear how xid, the mutant gene in CBA/N mice, affects the development of this subset. Specifically, it is not known if the xid gene influences the development of the B cell subset directly or indirectly by providing the improper developmental milieu through effects on other cells. We investigated this question using female mice heterozygous for two x chromosomal genes, xid and Pgk-1 (phosphoglycerate kinase-1). Since females are mosaic because of x chromosome inactivation, their lymphocytes can be studied for the choice of the x chromosome, using the two PGK-1 isoenzymes as the cytological marker. We find that B lymphocytes in the spleen prefer the x chromosome without xid while the remaining splenocytes and cells from other tissues do not. This suggests that xid affects B lymphocytes directly and not through their developmental milieu. Furthermore, our data suggest that the precursors for IgG1- and IgG3-producing cells may be both few and different.

Derepression with decreased expression of the G6PD locus on the inactive X chromosome in normal human cells

Studies of a unique clone of skin fibroblasts from a normal 46 XX female reveal that the G6PD locus on the inactive X chromosome has been derepressed. The reactivation event occurs spontaneously, and is associated with normal karyotype, including the presence of a late-replicating X chromosome. Analysis of mouse-human hybrids with the relevant chromosome provides evidence that the derepressed locus is on the inactive X, and that reactivation is not extensive (the PGK locus is not derepressed). Nor is any general change in DNA methylation of this chromosome detectable with Hpa II and an X-specific DNA probe. Studies of the glucose-6-phosphate dehydrogenase phenotype in these heterozygous cells indicate that the reactivated X produces only half the enzyme subunits as are produced by the active X. Although this dosage difference may be related to the mutational event responsible for derepression of the locus, these observations along with other evidence suggest that loci on the inactive X, when expressed, have less activity than corresponding loci on the active X.

Studies of X chromosome DNA methylation in normal human cells

Studies of methylation along 28 kilobases of X-chromosome DNA, assayed by Southern blot analysis using cloned X-chromosome-specific probes, indicates that X DNA methylation in normal human cells changes with replication, is not correlated with number of X chromosomes or transcriptional activity, and is less stable and more prevalent than when the human X is in the foreign environment of mouse-human hybrid cells. In contrast with observations of others in heteroploid cells, we observed no derepression of the inactive X in clonal populations of normal human fibroblasts treated with 5-azacytidine. This may reflect the differences in stability of the methylation of the human X in a foreign environment. Our observations preclude ubiquitous methylation differences as the molecular basis for X-chromosome inactivation.

Undercondensation and localized euchromatinization of the x chromosome in the grasshopper Melanoplus femur-rubrum

In most animals, including grasshoppers, the X chromosome is heterochromatic (heteropycnotic) during prophase I and metaphase I of spermatogenesis. This report describes one grasshopper male in which at these states some of the X chromosomes contained an euchromatic (E) segment. In grasshoppers, the heteropycnotic state of the X is apparently established prior to the formation of the cysts. The spermatocytes containing the E segments, however, did not comprise whole cysts. It was concluded, therefore, that the E segments resulted from a localized euchromatinization rather than a failure to become heteropycnotic. The cytology of this male was unusual in two other respects. In most of the spermatocytes the chromosomes were longer and thinner than those of other males. In addition, in some of the cells undergoing meiosis, the cytoplasm failed to divide during both meiotic divisions and the resulting spermatids failed to differentiate into sperm. Because in this species both the presence of Xs with E segments and undercondensation are very rare and both involve condensation, it is likely that they are in some way related. Evidence for and against the possibility that the E segments were genetically active and that this activity led to the arrest of some of the spermatids is discussed.