Differential patterns of histone methylation and acetylation distinguish active and repressed alleles at X-linked genes.

In female mammals, one of the two X chromosomes is inactivated to compensate for the difference in dosage of X-linked genes between males and females. X inactivation involves sequential alterations to the chromatin that ultimately lead to the transcriptional repression of genes on the X chromosome. Here, histone methylation and acetylation along X-linked genes are investigated by chromatin immunoprecipitation (ChIP) of adult fibroblast cell lines. At PGK1 and HPRT, chromatin on the active X chromosome reveals H3 lysine 4 methylation and acetylation of histones H3 and H4. These modifications are absent on the repressed allele, which is marked by H3 lysine 9 methylation. On the expressed allele of XIST (on the inactive X chromosome), we found that H3 acetylation is confined to the promoter, whereas H3 lysine 4 methylation and H4 acetylation are present along the entire gene. On the repressed XIST allele, in contrast, the promoter and gene exhibit H3 lysine 9 methylation. At only 1.5 kb upstream of the XIST gene, chromatin on the inactive X chromosome has strongly reduced levels of H4 acetylation and is marked by both H3 lysine 9 and H3 lysine 4 methylation. These data demonstrate that patterns of histone methylation and acetylation are distinct along and upstream of XIST and suggest that the inactive X chromatin configuration occurs at a region close to the 5' end of the gene.

Functional analysis of the highly conserved exon IV of XIST RNA.

X inactivation is effected by a large CIS-acting RNA molecule termed the X inactive specific transcript (XIST). Exon IV of XIST RNA is highly conserved at the primary sequence level and is predicted to form a stable stem-loop structure. These features suggest that it is important for XIST RNA function. We have used homologous recombination to delete exon IV of the mouse XIST gene. Surprisingly we found no detectable effects on X inactivation. Heterozygous female animals show normal random X inactivation and transcripts from the mutant allele were seen to localise IN CIS over the length of the inactive X chromosome. There was however a reduced steady state level of mutant relative to wild type XIST RNA. This effect was not attributable to decreased stability, suggesting that the deletion affects transcription or processing of XIST RNA.

Centrosomal association of histone macroH2A1.2 in embryonic stem cells and somatic cells.

The histone 2A variant macroH2A1.2 is expressed in female and male mammals and is implicated in X-chromosome inactivation and autosomal gene silencing. In undifferentiated and early differentiating murine embryonic stem (ES) cells a cytosolic pool of macroH2A1.2 has recently been reported and found to be associated with the centrosome. Here, we show that the centrosomal association of macroH2A1.2 is a widespread phenomenon and is not restricted to undifferentiated and early differentiating ES cells. By indirect immunofluorescence we detect macroH2A1.2 protein in a juxtanuclear structure that duplicates once per cell cycle and colocalizes with centrosomal gamma-tubulin in both XX and XY ES cells prior to and throughout their differentiation. MacroH2A1.2 localization to the centrosome is also observed in female and male somatic cells, both in interphase and in mitosis. Biochemical analysis demonstrates that the association between macroH2A1.2 and the centrosome in somatic cells is stable, as macroH2A1.2 copurifies with centrosomes isolated from human lymphoblasts. Therefore, in addition to a nuclear pool of macroH2A1.2 a fraction of the histone is associated with the centrosome in various cell types and throughout ES cell differentiation.

Loss of Xist imprinting in diploid parthenogenetic preimplantation embryos.

We have analysed Xist expression patterns in parthenogenetic and control fertilised preimplantation embryos by using RNA FISH. In normal XX embryos, maternally derived Xist alleles are repressed throughout preimplantation development. Paternal alleles are expressed as early as the 2-cell stage. In parthenogenetic embryos, we observed Xist RNA expression and accumulation from the morula stage onwards, indicating loss of maternal imprinting. In the majority of cells, expression was from a single allele, indicating that X chromosome counting occurs to establish appropriate monoallelic Xist expression. We discuss these data in the context of models for regulation of imprinted and random X inactivation.

Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence.

The Xist locus plays a central role in the regulation of X chromosome inactivation in mammals, although its exact mode of action remains to be elucidated. Evolutionary studies are important in identifying conserved genomic regions and defining their possible function. Here we report cloning, sequence analysis, and detailed characterization of the Xist gene from four closely related species of common vole (field mouse), Microtus arvalis. Our analysis reveals that there is overall conservation of Xist gene structure both between different vole species and relative to mouse and human Xist/XIST. Within transcribed sequence, there is significant conservation over five short regions of unique sequence and also over Xist-specific tandem repeats. The majority of unique sequences, however, are evolving at an unexpectedly high rate. This is also evident from analysis of flanking sequences, which reveals a very high rate of rearrangement and invasion of dispersed repeats. We discuss these results in the context of Xist gene function and evolution.

Primary non-random X inactivation associated with disruption of Xist promoter regulation.

In this report we demonstrate primary non-random X chromosome inactivation following targeted mutagenesis of a region immediately upstream of XIST promoter P(1). In heterozygous animals there is a preferential inactivation of the targeted X chromosome in 80--90% of cells. The phenotype correlates with inappropriate activation of XIST in a proportion of the mutant XY embryonic stem cells. Strand-specific analysis revealed increased sense transcription initiating upstream of XIST promoter P(1). There was, however, no discernible effect on transcription from the antisense Tsix gene. We demonstrate that the in vitro and in vivo phenotypes are specifically attributable to the presence of a PGKneo cassette at the targeted locus. These findings are discussed in the context of understanding mechanisms of XIST gene regulation in X inactivation.

A feature-sampling account of the time course of old-new recognition judgments.

This article describes the feature-sampling theory of recognition (FESTHER), a new model of the time course of recognition judgments based on a model of the time course of perceptual processing in categorization (K. Lamberts, 1995, 1998). FESTHER is applied to previous results and to data from 4 old-new recognition experiments. Experiments 1 and 2 provided a preliminary test of the model's ability to explain recognition judgments of simple objects under response deadlines. Experiments 3 and 4 involved a response-signal procedure to elicit recognition judgments at different time lags after presentation of a stimulus. Simple objects and words were used as stimuli in Experiments 3 and 4, respectively. The new model accounts well for the data from the 4 experiments and offers a parsimonious account of the time course of recognition judgments based on the time-dependent availability of stimulus information.

Histone macroH2A1.2 relocates to the inactive X chromosome after initiation and propagation of X-inactivation.

The histone macroH2A1.2 has been implicated in X chromosome inactivation on the basis of its accumulation on the inactive X chromosome (Xi) of adult female mammals. We have established the timing of macroH2A1.2 association with the Xi relative to the onset of X-inactivation in differentiating murine embryonic stem (ES) cells using immuno-RNA fluorescence in situ hybridization (FISH). Before X-inactivation we observe a single macroH2A1.2-dense region in both undifferentiated XX and XY ES cells that does not colocalize with X inactive specific transcript (Xist) RNA, and thus appears not to associate with the X chromosome(s). This pattern persists through early stages of differentiation, up to day 7. Then the frequency of XY cells containing a macroH2A1.2-rich domain declines. In contrast, in XX cells there is a striking relocalization of macroH2A1.2 to the Xi. Relocalization occurs in a highly synchronized wave over a 2-d period, indicating a precisely regulated association. The timing of macroH2A1.2 accumulation on the Xi suggests it is not necessary for the initiation or propagation of random X-inactivation.

Chromatin structure analysis of the mouse Xist locus.

The Xist gene is expressed exclusively from the inactive X chromosome and plays a central role in regulating X chromosome inactivation. Here we describe experiments aimed at defining the extent of the active chromatin domain of the expressed Xist allele. By using an allele-specific general DNaseI sensitivity assay we show that there is preferential digestion of the expressed allele at sites within the transcribed locus but not in flanking sites located up to 70 kb 5'. A putative proximal boundary for the Xist domain is located within 10 kb upstream of promoter P1. Chromatin in the expressed domain was found to be acetylated at H4 in XX somatic cells but also in XY cells, where Xist is never expressed. A single clear exception to this was the Xist promoter, which is acetylated only in XX cells. These observations concur with the view that H4 acetylation may not be a general marker of active chromatin domains and further support data implicating local promoter acetylation as being of primary functional significance in vivo.

A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation.

We have investigated the role of histone acetylation in X chromosome inactivation, focusing on its possible involvement in the regulation of Xist, an essential gene expressed only from the inactive X (Xi). We have identified a region of H4 hyperacetylation extending up to 120 kb upstream from the Xist somatic promoter P1. This domain includes the promoter P0, which gives rise to the unstable Xist transcript in undifferentiated cells. The hyperacetylated domain was not seen in male cells or in female XT67E1 cells, a mutant cell line heterozygous for a partially deleted Xist allele and in which an increased number of cells fail to undergo X inactivation. The hyperacetylation upstream of Xist was lost by day 7 of differentiation, when X inactivation was essentially complete. Wild-type cells differentiated in the presence of the histone deacetylase inhibitor Trichostatin A were prevented from forming a normally inactivated X, as judged by the frequency of underacetylated X chromosomes detected by immunofluorescence microscopy. Mutant XT67E1 cells, lacking hyperacetylation upstream of Xist, were less affected. We propose that (i) hyperacetylation of chromatin upstream of Xist facilitates the promoter switch that leads to stabilization of the Xist transcript and (ii) that the subsequent deacetylation of this region is essential for the further progression of X inactivation.

Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis.

The propagation of X chromosome inactivation is thought to be mediated by the cis- limited spreading of the non-protein coding Xist transcript. In this report we have investigated the localization of Xist RNA on rodent metaphase chromosomes. We show that Xist RNA exhibits a banded pattern on the inactive X and is excluded from regions of constitutive heterochromatin. The banding pattern suggests a preferential association with gene-rich, G-light regions. Analysis of X:autosome rearrangements revealed that restricted propagation of X inactivation into cis -linked autosomal material is reflected by a corresponding limited spread of Xist RNA. We discuss these results in the context of models for the function of Xist RNA in the propagation of X inactivation.

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.

Characterization of genes encoding translation initiation factor eIF-2gamma in mouse and human: sex chromosome localization, escape from X-inactivation and evolution.

The Delta Sxrb interval of the mouse Y chromosome is critical for spermatogenesis and expression of the male-specific minor transplantation antigen H-Y. Several genes have been mapped to this interval and each has a homologue on the X chromosome. Four, Zfy1 , Zfy2 , Ube1y and Dffry , are expressed specifically in the testis and their X homologues are not transcribed from the inactive X chromosome. A further two, Smcy and Uty , are ubiquitously expressed and their X homologues escape X-inactivation. Here we report the identification of another gene from this region of the mouse Y chromosome. It encodes the highly conserved eukaryotic translation initiation factor eIF-2gamma. In the mouse this gene is ubiquitously expressed, has an X chromosome homologue which maps close to Dmd and escapes X-inactivation. The coding regions of the X and Y genes show 86% nucleotide identity and encode putative products with 98% amino acid identity. In humans, the eIF-2gamma structural gene is located on the X chromosome at Xp21 and this also escapes X-inactivation. However, there is no evidence of a Y copy of this gene in humans. We have identified autosomal retroposons of eIF-2gamma in both humans and mice and an additional retroposon on the X chromosome in some mouse strains. Ark blot analysis of eutherian and metatherian genomic DNA indicates that X-Y homologues are present in all species tested except simian primates and kangaroo and that retroposons are common to a wide range of mammals. These results shed light on the evolution of X-Y homologous genes.

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.

X chromosome inactivation and the Xist gene.

Recent years have seen rapid progress towards understanding the molecular mechanisms involved in X chromosome inactivation (X inactivation). This progress has largely revolved around the discovery of the X inactive specific transcript (Xist) gene, which is known now to represent the master switch locus regulating X inactivation. In adult cells Xist is transcribed exclusively from the inactive X chromosome. The transcript has no apparent protein-coding potential and is retained in the nucleus in close association with the domain occupied by the inactive X chromosome. It is thus thought to represent a functional RNA molecule which acts as the primary signal responsible for the propagation of X inactivation. Developmental regulation of Xist correlates with the developmental timing of X inactivation. Recent results have demonstrated that Xist is both necessary and sufficient for X inactivation. Goals for the future are to understand the mechanism of Xist regulation which underlies the establishment of appropriate X inactivation patterns and to determine how Xist RNA participates in the process of propagating inactivation in cis.

Comparative mapping of X chromosomes in vole species of the genus Microtus.

Comparative mapping of X-linked genes has progressed rapidly since Ohno's prediction that genes on the X chromosome should be conserved as a syntenic group in all mammals. Although several conserved blocks of homology between human and mouse have been discovered, rearrangements within the X chromosome have also been characterized. More recently, some exceptions to Ohno's law have been reported. We have used fluorescence in situ hybridization (FISH) to map five genes, Gla, G6pd, Hprt, Pgk1 and Xist, to two of the largest conserved segments of X material in five members of the genus Microtus (grey vole) and show that vole X chromosomes demonstrate greater homology to human than to mouse. Cytogenetic analysis indicates a relatively high frequency of rearrangement during vole evolution, although certain blocks of homology appear to be highly conserved in all species studied to date. On this basis we were able to predict the probable location of the rat X inactivation centre (Xic) based solely on high-resolution G-banding. Our prediction was then confirmed by mapping the rat Xist gene by FISH. The possible significance of conserving long-range chromosome structure in the vicinity of the Xic is discussed with respect to the mechanism of X inactivation.

Repetitive DNA sequences in the common vole: cloning, characterization and chromosome localization of two novel complex repeats MS3 and MS4 from the genome of the East European vole Microtus rossiaemeridionalis.

We have characterized two novel, complex, heterochromatic repeat sequences, MS3 and MS4, isolated from Microtus rossiaemeridionalis genomic DNA. Sequence analysis indicates that both repeats consist of unique sequences interrupted by repeat elements of different origin and can be classified as long complex repeat units (LCRUs). A unique feature of both repeat units is the presence of short interspersed repeat elements (SINEs), which are usually characteristic of the euchromatic part of the genome. Comparative analysis revealed no significant stretches of homology in the nucleotide sequences between the two repeats, suggesting that the repeats originated independently during the course of vole genome evolution. Fluorescence in situ hybridization analysis demonstrates that MS3 and MS4 occupy distinct domains in the heterochromatic regions of the sex chromosomes in M. transcaspicus and M. arvalis but collocalize in M. rossiaemeridionalis and M. kirgisorum heterochromatic blocks. The localization pattern of the repeats on the vole chromosomes confirms the independent origin of the two repeats and suggests that expansion of the heterochromatic blocks has occurred subsequent to speciation.

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.

Cloning of Tabby, the murine homolog of the human EDA gene: evidence for a membrane-associated protein with a short collagenous domain.

X-Linked hypohidrotic ectodermal dysplasia (XLHED) is a human congenital disorder resulting in abnormal tooth, hair and sweat gland development. A candidate gene for the disorder has been cloned, but the function and full size of its putative protein product is unclear. We have identified a candidate cDNA for the mouse Tabby gene (Ta), which, based on phenotype and syntenic mapping, is postulated to represent the analogous murine disorder. Mutations have been identified in three different Ta alleles and Northern analysis indicates that the gene is expressed at increasing levels during embryogenesis (11-17 days p.c.), the period when affected structures develop. The putative protein product encoded by exon 1 is highly homologous (87% identical) to the predicted EDA protein product (135 amino acids), including the presence of a single transmembrane domain. However, the murine cDNA also encodes an additional 246 amino acids, which contains a short collagenous domain (Gly-X-Y)19. This predicted structure is similar to a number of membrane-associated proteins with either single or multiple collagenous domains in their extracellular C-terminal regions. Since mutations can only be identified in 10-15% of families with XLHED, it is likely that additional homologous exons exist for the human EDA gene. Hybridization of YACs from the EDA region with the Ta cDNA support this hypothesis. The predicted extracellular collagenous domain of this membrane protein may play a key role in epithelial-mesenchymal interactions, defects of which are thought to underlie the Ta/XLHED phenotype.

First categorization of stimuli with multivalued dimensions.

The extended generalized context model's (EGCM's) ability to account for the time course of categorization of stimuli with multivalued dimensions was tested in two experiments. In each experiment, the participants were first trained to classify stimuli (semicircles of variable size with a radial line of variable orientation) into two categories. In the subsequent transfer stage, they categorized a set of transfer stimuli. The time available on each transfer trial was manipulated. Response had to be given within 400 msec, within 700 msec, or without time pressure. Different category structures were used in Experiments 1 and 2. The results of both experiments showed reliable effects of response deadline. The EGCM accounted for the data and performed consistently better than an alternative model.