Bipartite structure of the inactive mouse X chromosome

BackgroundIn mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems.ResultsWe find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary region. Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele.ConclusionsBy applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.

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DNA hypomethylation causes an increase in DNase-I sensitivity and an advance in the time of replication of the entire inactive X chromosome

Summary We have examined the effect of 5-azacytidine (5-aza-C) induced hypomethylation of DNA on the time of replication and DNase I sensitivity of the X chromosomes of female Gerbillus gerbillus (rodent) lung fibroblast cells. Using in situ nick translation to visualise the potential state of activity of large regions of metaphase chromosomes we show that 5-aza-C causes a dramatic increase in the DNase-I sensitivity of the entire inactive X chromosome of female G. gerbillus cells and this increase in nuclease sensitivity correlates with a large shift in the time of replication of the inactive X chromosome from late S phase to early S phase. These effects of 5-aza-C on the inactive X chromosome are associated with a 15% decrease in DNA methylation. Our results indicate that DNA methylation concomitantly affects both the time of replication and the chromatin conformation of the inactive X chromosome.     

Coreactivation of four inactive X genes in a hamster x human hybrid and persistence of late replication of reactivated X chromosome

Hamster-human hybrids which contained an inactive human X chromosome were treated by 5-azacytidine. Hypoxanthine guanine phosphoribosyltransferase derepressed hybrids were selected and derepression of three other loci, phosphoglycerate kinase, alpha-galactosidase, and glucose-6-phosphate dehydrogenase were studied. Among 32 hybrids selected for hypoxanthine guanine phosphoribosyltransferase, two were found to be reactivated at four X loci. The independence or nonindependence of the reactivation events will be discussed. No correlation was found between the time of replication and the expression or nonexpression of the X chromosome genes: X chromosomes reactivated at four loci remained late replicating; conversely early replication can exist without the expression of some X genes.     

Kinetic heterogeneity of the replication of genetically inactive X chromosome in human cells

Kinetics of DNA replication in genetically non-active X chromosome was studied in peripheral lymphocytes and skin fibroblasts from four phenotypically normal women and one fetus using BrdU 33258 Hoechst-Giemsa techniques. The localization of the earliest replicated chromosomal segment was shown to be unstable, varying from cell to cell in both lymphocytes and fibroblasts of all persons examined. Several variants of replication sequence in the X chromosome were found in both types of cells. The variants revealed were classified, according to Willard. The statistically significant differences in replication sequence were found between blood lymphocytes and skin fibroblasts in two individuals. The problem of tissue specificity in replication kinetics of the genetically non-active X chromosome is discussed.     

Spontaneous reactivation of the inactive X chromosome in mouse embryonal carcinoma cells

The mouse embryonal carcinoma cell line MC12 carries two X chromosomes, one of which replicates late in S phase and shares properties with the normal inactive X chromosome and, therefore, is considered to be inactivated. Since the hypoxanthine phosphoribosyl transferase (HPRT) gene on the active X chromosome is mutated (HPRT(NDASH;)), MC12 cells lack HPRT activity. After subjecting MC12 cells to selection in HAT medium, however, a number of HAT-resistant clones (HAT(R)) appeared. The high frequency of HAT resistance (3.18 x 10(-4)) suggested reactivation of HPRT(PLUS;) on the inactive X chromosome rather than reversion of HPRT(NDASH;). Consistent with this view, cytological analyses showed that the reactivation occurred over the length of the inactive X chromosome in 11 of 20 HAT(R) clones isolated. The remaining nine clones retained a normal heterochromatic inactive X chromosome. The spontaneous reactivation rate of the HPRT(PLUS;) on the inactive X chromosome was relatively high (1.34 x 10(-6)) and comparable to that observed for XIST-deleted somatic cells (Csankovszki et al., 2001), suggesting that the inactivated state is poorly maintained in MC12 cells.     

A deletion at the mouse Xist gene exposes trans-effects that alter the heterochromatin of the inactive X chromosome and the replication time and DNA stability of both X chromosomes

The inactive X chromosome of female mammals displays several properties of heterochromatin including late replication, histone H4 hypoacetylation, histone H3 hypomethylation at lysine-4, and methylated CpG islands. We show that cre-Lox-mediated excision of 21 kb from both Xist alleles in female mouse fibroblasts led to the appearance of two histone modifications throughout the inactive X chromosome usually associated with euchromatin: histone H4 acetylation and histone H3 lysine-4 methylation. Despite these euchromatic properties, the inactive X chromosome was replicated even later in S phase than in wild-type female cells. Homozygosity for the deletion also caused regions of the active X chromosome that are associated with very high concentrations of LINE-1 elements to be replicated very late in S phase. Extreme late replication is a property of fragile sites and the 21-kb deletions destabilized the DNA of both X chromosomes, leading to deletions and translocations. This was accompanied by the phosphorylation of p53 at serine-15, an event that occurs in response to DNA damage, and the accumulation of gamma-H2AX, a histone involved in DNA repair, on the X chromosome. The Xist locus therefore maintains the DNA stability of both X chromosomes.     

Cell cycle-dependent localization of macroH2A in chromatin of the inactive X chromosome

One of several features acquired by chromatin of the inactive X chromosome (Xi) is enrichment for the core histone H2A variant macroH2A within a distinct nuclear structure referred to as a macrochromatin body (MCB). In addition to localizing to the MCB, macroH2A accumulates at a perinuclear structure centered at the centrosome. To better understand the association of macroH2A1 with the centrosome and the formation of an MCB, we investigated the distribution of macroH2A1 throughout the somatic cell cycle. Unlike Xi-specific RNA, which associates with the Xi throughout interphase, the appearance of an MCB is predominantly a feature of S phase. Although the MCB dissipates during late S phase and G2 before reforming in late G1, macroH2A1 remains associated during mitosis with specific regions of the Xi, including at the X inactivation center. This association yields a distinct macroH2A banding pattern that overlaps with the site of histone H3 lysine-4 methylation centered at the DXZ4 locus in Xq24. The centrosomal pool of macroH2A1 accumulates in the presence of an inhibitor of the 20S proteasome. Therefore, targeting of macroH2A1 to the centrosome is likely part of a degradation pathway, a mechanism common to a variety of other chromatin proteins.     

Deletion of the XIST promoter from the human inactive X chromosome compromises polycomb heterochromatin maintenance

Chromosoma - Silencing most gene expression from all but one X chromosome in female mammals provides a means to overcome X-linked gene expression imbalances with males. Central to establishing gene...     

A practical metaphase marker of the inactive X chromosome.

It is paradoxical that the inactivated X is the only chromosome that can be identified in the interphase nucleus, yet in metaphase, it is indistinguishable from its genetically active homolog unless special culture and staining procedures are employed. A specific inactivation-associated fold in proximal Xq resolves that paradox. We describe here how the fold in the proximal long arm can be used as a simple and reliable marker to identify the inactivated X in G-, Q-, or R-banded preparations. Several examples are given, including localization of the inactivation center to band Xq13 or q21.1, identification of nonrandom inactivation in X-chromosome rearrangements, identification of multiple active X chromosomes in tumor cell lines, analysis of X-inactivation patterns in female carriers of the fragile site at Xq27, and comparison of X-inactivation patterns among primate species.     

SETting the stage. Eed-Enx1 leaves an epigenetic signature on the inactive X chromosome

Despite evidence implicating the Polycomb group protein, Eed (embryonic ectoderm development protein) in imprinted X inactivation, a similar role in random X inactivation in the embryo has remained an open question. Brockdorff and colleagues now report that Eed, along with its binding partner Enx1, transiently associates with the inactive X chromosome (Xi) and likely contributes to the epigenetic signature and long-term stability of the Xi heterochromatin.     

5-azacytidine-induced re-expression of alleles on the inactive X chromosome in a hybrid mouse cell line

In order to test the hypothesis that DNA methylation is involved in mammalian X chromosome inactivation, cells of an HPRT-deficient Mus musculus × M. caroli line, having an inactive M. caroli X, were grown in 5-azacytidine, and HPRT⁺ reactivants selected in HAT medium. Recovery of colonies depended on azacytidine concentration, and on time between treatment and selection; the highest recovery frequency was 0.3%. All colonies re-expressed the M. caroli form of HPRT, showing that the Hpt⁺ allele on the inactive M. caroli X was reactivated by azacytidine treatment. About 6% of HPRT⁺ reactivants also re-expressed M. caroli G6PD, whereas none of the 56 azacytidine-treated unselected colonies did so; thus re-expression of the Hpt and Gpd loci appears to be co-ordinated to some extent. However, no HPRT⁺ reactivants, nor unselected colonies re-expressed M. caroli PGK-A.     

Aging and aneuploidy: evidence for the preferential involvement of the inactive X chromosome

It has been known for some time that there is an association between chronological aging and X-chromosome aneuploidy in peripheral blood lymphocyte cultures from females. In an attempt to elucidate the mechanism of X-chromosome aneuploidy in aging females, we used a BrdU late-labeling technique to determine the X-inactivation pattern in 45,X and 47,XXX lymphocytes of older women. In 50 of 58 X-aneuploid cells the inactive X chromosome was missing or extra. This implies that either the inactive X has a special propensity for mitotic errors or mitotic errors occur at random but subsequent selection is less stringent against cells with a missing or additional inactive X chromosome than against aneuploid cells involving the active X chromosome. Evidence is presented in favor of the former hypothesis.     

Genetic evidence for the inactivation of a human autosomal locus attached to an inactive X chromosome

Mouse-human cell hybrid clones retaining an inactive translocated chromosome involving the human X and 13 were isolated. Esterase D, a marker on the segment of chromosome 13 translocated to the X, was not expressed in these clones. These results provide genetic evidence for the spreading of inactivation into the autosomal segment in an inactive human X-autosome translocation.     

Molecular cytological differentiation of active from inactive X domains in interphase: implications for X chromosome inactivation

A fluorescence in situ hybridization method using a biotinylated DNA probe specific for the centromeric region of the human X chromosome was used to differentiate the genetically active from the inactive X in interphase cells. With this technique, we were able to interpret both the relative position and the degree of condensation of the X chromosomes within the nucleus. We first established the specificity of fluorescence labelling of the hybridized probe by comparing its location and appearance (either dense or diffuse) when associated with a sex chromatin body (SCB) in early passage normal human female fibroblasts. In these cells, where the presence of inactive X chromatin was verified by identification of a 4',6-diamidino-2-phenyl indole (DAPI)-positive SCB in 85% of the cells examined, the X chromatin fluorescence was always associated with the SCB. The signal was dense in structure in 98% and peripheral in location in 80% of the nuclei. A second type of signal, diffuse in form, was observed in 85% of the nuclei and presumably represents the location of the active X chromosome. It was located peripherally or centrally with equal frequency and was not associated with any identifiable nuclear component. This diffuse signal was the major type associated with human male fibroblasts. In rodent x human hybrid cells containing a human inactive X, the fluorescent signal was associated with an SCB-like structure in only 13% of the nuclei; it was dense in 66% of the nuclei and equally peripheral or central in location. This indicates an alteration in the interphase structure of the human inactive X chromosome in hybrid cells which may explain its known instability with respect to genetic activity in such systems.     

X chromosome expression during oogenesis in the mouse.

The activities of glucose-6-phosphate dehydrogenase (G6PD) and lactate dehydrogenase (LDH) have been assayed in mouse oocytes at several stages of follicle development isolated from XX and XO female mice. Throughout the entire growth period the activity of G6PD was proportional to the number of X chromosomes present in the oocyte, whereas no difference in LDH activity was detected between XX and XO oocytes. It is concluded, therefore, that both X chromosomes are functional throughout oogenesis.     

Immunocytochemical evidence for methylation of the inactive X chromosome in human fetal oogonia

The state of DNA methylation of the X chromosomes of human interphase oogonia from a 46,XX and a 46,XX/47,XXX fetus at 17 weeks of gestation was tested immunocytochemically with an antibody to 5-methylcytosine (5MeC). Of 1637 oogonial nuclei from the 46,XX fetal ovary, 313 (19.1%) contained Barr bodies, of which 93.6% were positive for 5MeC. Of 1780 oogonia from the 46,XX/47,XXX fetus 327 (18.4%) contained Barr bodies; 175 oogonia had one Barr body and 152 had two. Of the single Barr bodies 145 (82.8%) had positive 5MeC reaction product. Of the 152 oogonia from the XXX line, 97 (63.8%) had positive 5MeC on both Barr bodies, 35 (23%) had one positive and one negative, and 20 (13.1%) had no product on either Barr body. This immunocytochemical evidence supports the hypothesis that the DNA of the inactive X-chromosome of the human 17-week gestation oogonium is methylated.