Nature Reviews Genetics 2, 59-67 (2001); Doi:10

Nature Reviews Genetics 2, 59-67 (2001); doi:10.1038/35047580


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X-CHROMOSOME INACTIVATION: COUNTING, CHOICE AND INITIATION

PhilipAvner1 & EdithHeard2about the authors

1Unité de Génétique Moléculaire Murine Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
e-mail:
2Present address: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
e-mail:

In many sexually dimorphic species, a mechanism is required to ensure equivalent levels of gene expression from the sex chromosomes. In mammals, such dosage compensation is achieved by X-chromosome inactivation, a process that presents a unique medley of biological puzzles: how to silence one but not the other X chromosome in the same nucleus; how to count the number of X's and keep only one active; how to choose which X chromosome is inactivated; and how to establish this silent state rapidly and efficiently during early development. The key to most of these puzzles lies in a unique locus, the X-inactivation centre and a remarkable RNA — Xist — that it encodes.

In mammals, dosage compensation of X-linked genes is achieved by the transcriptional silencing of one of the two X chromosomes in the female during early development — a process known as X inactivation. The early events in X inactivation are under the control of a key regulator, the X-chromosome-inactivation centre or Xic. Initiation of X inactivation involves a recognition step in which the number of X chromosomes in the cell is counted relative to cell ploidy so that only a single X chromosome is functional per diploid adult cell. One hypothesis postulates the existence of a blocking factor that is synthesized in limiting quantities sufficient for the binding of a single Xic per diploid cell. Initiation is also thought to include a process of choosing, whereby one of the two X chromosomes in the female cell might be preferentially selected for inactivation. Examples include the imprinted inactivation of the paternal X chromosome in extra-embryonic tissues and the biased inactivation that results from allelic differences at the X-chromosome-controlling element ( Xce) locus in embryonic tissues.

As defined cytologically, the Xic is a roughly 1 Mb region that contains several elements thought to have a role in X inactivation ( Box 1) and at least four genes1 (Fig. 1 ). One of these, the X (inactive)-specific transcript ( Xist) gene, encodes a large non-coding RNA that is relatively poorly conserved. Xist has been shown to contribute to Xic function and is required for X inactivation. Other elements that lie within the Xic are candidates for involvement in the control of Xist expression, or for the mechanisms of counting and choice. One is the DXPas34 locus, which was originally identified as a result of its unique methylation profile on the active X chromosome2. Another is the Tsix transcript, a non-coding transcript that is synthesized from the strand opposite to Xist and has been hypothesized to regulate the activity of Xist at the onset of X inactivation3.

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Figure 1| The X-inactivation centre.
A summary of the known elements and regions in the X-inactivation centre (Xic) thought to affect choice, counting and cis-inactivation during the initiation of X inactivation. (See Box 1 for more information on Xist, DXPas34, Tsix and Xce.) Genes are shown in bold, with the direction of transcription indicated by the arrow. Brx (brain X-linked)67, Tsx (testis X-linked)68 and Cdx4 (Caudal-4)69 are genes that lie within the Xic that do not have, at least for the moment, any defined X-inactivation function. The 2.1(2)P region shows differential histone H4 hyperacetylation in undifferentiated female and male embryonic stem (ES) cells and has been suggested as a possible regulatory element in X inactivation. P1 and P2 are the somatic Xist promoters, and P0 is a postulated Xist promoter in undifferentiated ES cells and early embryos. S12 and S19 are ribosomal protein pseudogenes found 5' to Xist in the mouse Xic11, 12, 70. The deletions used to dissect the function of different elements in the Xic are shown as black lines and are described in Ref. 16 (1) Ref. 17 (2), Ref. 34, (3) Refs 35,52 (4) and Ref. 33 (5). Blue bars indicate the regions that have been implicated in specific functions. Effects on choice and counting have not so far been distinguished in the regions indicated by light bars. The terminal two Xist exons, lying within the 65-kb deletion, have no effect on counting or choice (C. Morey, P. A. and P. Clerc unpublished observations).

During random X inactivation, counting and choice must either precede, or be concomitant with, the onset of initiation and its earliest manifestation, the coating of the presumptive inactive X by Xist. Silencing of X-linked genes and replication asynchrony follow rapidly. Both seem to precede global histone hypoacetylation, the accumulation of a novel histone variant (macroH2A) and methylation of the inactive X, which seem to function as maintenance mechanisms for X inactivation4-6. However, imprinted X inactivation, which occurs in certain mammals and by which the paternal X is preferentially inactivated, might differ in some respects from random inactivation.

In this article, we review recent results concerning the events that surround the initiation of X inactivation. We place an emphasis on the role of Xist and the events that occur upstream and downstream of Xist expression. For a comprehensive review of the older literature, readers are referred to Refs 1, 7.

Xist — regulation and function

Before random X inactivation initiates in the developing embryo, Xist appears to be expressed at low levels from every Xic in the cell. Using fluorescence in situ hybridization (FISH), Xist RNA can be detected in embryonic stem (ES) cells as two small, punctate signals in female (XX) ES cells and a single punctate signal in male (XY) ES cells (Fig. 2). Female ES cells undergo X inactivation when stimulated to differentiate, and represent a useful model system for the study of X inactivation. Xist RNA first accumulates on and coats the future inactive X chromosome, while the Xist gene on the presumptive active X chromosome in male and female cells becomes silenced. The onset of X inactivation therefore seems to be intimately linked with the accumulation of Xist RNA in the cell.

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Figure 2| Xist transcription in embryonic stem cells.
Patterns of Xist RNA expression in female ES cells undergoing differentiation using RNA fluorescence in situ hybridization. The left panel shows that undifferentiated ES cells have two punctate Xist RNA signals, representing the presence of unstable Xist transcripts at the site of transcription on both (active) X chromosomes. The middle panel shows that, upon differentiation, Xist RNA from one of the two alleles becomes stabilized and coats the X chromosome that is to be inactivated in cis . The X chromosome that remains active continues to express Xist in its unstable form. The right panel shows that, in fully differentiated cells, Xist RNA coats the inactive X chromosome and the Xist gene on the active X has been silenced.

Xist RNA stability. Monoallelic Xist upregulation has been associated with an increase in the half-life of the Xist transcript8, 9. Johnston et al.10 proposed that this change in Xist transcript stability is brought about by a developmentally regulated switch in Xist promoter use. Two promoters (P1 and P2) were shown to be used for transcription of the stable Xist transcript that accumulates on the inactive X chromosome in somatic cells. A putative third promoter (P0) located 6.6 kb further upstream, was hypothesized to generate the unstable Xist transcripts in cells that have not yet undergone X inactivation. Recent findings have raised several questions concerning the existence and role of the P0 promoter. An ES cell line carrying an Xist transgene that was deleted for the P0 promoter region still gave the punctate RNA FISH signal that is normally associated with unstable Xist transcripts in undifferentiated ES cells. This indicated that P0 might not be required for the production of unstable Xist transcripts in ES cells11. The highly repetitive and poorly conserved nature of the P0 region in both voles and humans provides a further argument against this region having an important regulatory role (Tatyana Nesterova et al ., personal communication).

The original observations regarding the P0 promoter were probably complicated by the presence, at that time unsuspected, of antisense transcripts running from the 3' end of Xist through to, and beyond, the P1 promoter3, and by the presence of several ribosomal protein pseudogenes lying upstream of P1, in the proposed P0 region11, 12 ( Fig. 1). Nevertheless, it cannot be ruled out that a series of alternative promoters exists in the region upstream of P1/P2 and even P0, because the more recent experiments of Warshawsky and colleagues11 were based on transgenes truncated just upstream of Xist that might have been influenced by position effects. The issue will only be definitively resolved by either targeted deletion of the region or its functional inhibition.

Another interesting candidate region to be considered in the context of possible regulatory elements upstream of Xist is the 2.1(2)P region, which shows histone H4 hyperacetylation in undifferentiated female ES cells but not in male ES cells13. This H4 hyperacetylation disappears upon differentiation, suggesting that it might well be involved in Xist regulation before, or during, the initiation of X inactivation. Hyperacetylation of this region is substantially reduced in female ES cells carrying a mutated Xic (a partially deleted Xist gene)16, which might reflect involvement of 2.1(2)P in counting and/or choice, both of which involve sensing the presence of two or more Xics in the nucleus1.

Important information concerning the regulation of Xist has also come from experiments involving a full-length Xist cDNA transgene that contains the P1 and P2 promoters, but under the control of a strong inducible promoter14. High levels of Xist RNA derived from the cDNA transgene were stable in undifferentiated ES cells, with a similar half-life to the Xist transcript in female somatic cells. This indicates that the short RNA half-life associated with low-level endogenous Xist expression cannot be due to an absence of Xist RNA stabilizing factors in undifferentiated ES cells, a result supported by studies involving human XIST transgenes15. One possibility raised by the study of Wutz and Jaenisch14 is that stabilization of Xist RNA might depend on the levels of Xist RNA present, with low expression being associated with instability. Alternatively, the stability of the transgenic Xist transcript could be due to the absence of the 3' or 5' sequences and intronic genomic sequences that might be involved in destabilization of the endogenous Xist transcript in ES cells.

Xist function. The importance of Xist in the X-inactivation process has been shown by both loss- and gain-of-function experiments. Two targeted deletions of the Xist gene showed that Xist is essential for inactivation in cis16, 17. In gain-of-function experiments, extra copies of Xist, often with considerable amounts of flanking sequence, have been introduced as transgenes either into ES cells or, by pronuclear injection, into the mouse oocyte18-21. Studies involving the inducible Xist cDNA transgene14 have been particularly insightful. In undifferentiated or early differentiating ES cells, inducing the expression of the Xist cDNA transgene leads rapidly (within 24 hours or about one cell cycle) to long-range transcriptional repression in cis. This inactivation is dependent on continued Xist expression and can be reversed. It is not accompanied by any of the later characteristics of the inactive X, such as histone hypoacetylation and late replication timing. In cells that have been induced to differentiate, Xist must be expressed during the first 48 hours of differentiation to initiate ectopic silencing. Once 72 hours of differentiation have elapsed, continued silencing is no longer dependent on Xist expression and the full range of secondary X inactivation characteristics is acquired. Irrespective of whether the initial reversible repression of transcription by Xist in undifferentiated ES cells is a normal step in the initiation of X inactivation in female cells (as suggested by Wutz and Jaenisch14 and possibly by recent results with androgenetic embryos), or is an artefact of the high levels of Xist produced by the inducible promoter in the transgene, the results are consistent with the idea that Xist RNA is the key factor that triggers X inactivation in cis.

Clues from Drosophila. Insights into the function of the Xist transcript have come from recent studies in Drosophila melanogaster . Dosage compensation in Drosophila is ensured through the hypertranscription of the single X chromosome present in the male, and this is associated with the hyperacetylated state of histone H4. Despite this fundamental difference with mammals in terms of strategy, certain unifying epigenetic regulatory principles might be common to both systems of dosage compensation. In each case, for instance, it seems that one, or several, molecules bind specifically to an X chromosome and are critical in remodelling the structure of the dosage-compensated chromosome. Once remodelled, the chromatin then maintains the specific transcriptional state associated with the dosage compensated X chromosome.

Dosage compensation in Drosophila depends on the presence of two small non-coding RNAs, roX2 (1.1 kb) and roX1 (3.5 kb), and the five male-specific lethal proteins (MSLs): maleless ( MLE), MSL-1, MSL-2, MSL-3 and MOF (Males absent on the first)22. The MOF protein, which is known to have histone acetyltransferase activity, is present in both sexes but is associated with the X chromosome only in males, in a complex composed of the MSL proteins. The MSL proteins localize together, presumably as a complex, at several hundred X-chromosome sites along the entire length of the male X. In mutants lacking MOF, MLE or MSL function, binding is restricted to about 30 well-distributed sites. These 'core sites' have been proposed to represent assembly sites from which the MSL complexes spread to the other sites on the X chromosome. The association of MOF with the male X chromosome has now been shown to be RNase sensitive and to depend on interaction with the roX2 RNA transcript23. In vivo binding of MOF to roX2 is through its CHROMODOMAIN. Whereas the various MSL proteins in the dosage compensation complex seem to be held together through protein–protein interactions, two other MSL proteins, MLE and MSL-3, (the latter is also a chromodomain protein) might also be RNA-binding factors23, indicating that RNA interaction might be a property of many chromatin regulatory molecules.