Nonhistone nuclear proteins specific to certain mouse embryonal carcinoma clones having an inactive X chromosome

By means of one-dimensional polyacrylamide slab gel electrophoresis nonhistone nuclear proteins were compared in murine embryonal carcinoma cell clones with two X chromosomes; both are active in some clones and one of them is inactive in others and in a population of cells having only one X chromosome. Under our experimental conditions, we succeeded in finding two extra bands at approximately 46,000 Da in cells having an inactive X chromosome. Furthermore, a band at approximately 71,000 Da was significantly heavier in cells having an inactive X chromosome than in those having two active X or those having only one X chromosome.     

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0728-8) contains supplementary material, which is available to authorized users.     

Spontaneous high expression of heat-shock proteins in mouse embryonal carcinoma cells and ectoderm from day 8 mouse embryo

When submitted to a heat-shock, mouse embryonal carcinoma (EC) and fibroblast cells show very different behavior. All the EC cells so far analyzed express very high levels of several heat-shock proteins (HSP) in the absence of stress and independent of their origin and culture conditions. In such cells, the 89-kd, 70-kd and 59-kd HSP are the most prominent proteins after actin. In addition, the 89-kd and 59-kd HSP are not stimulated by an arsenite shock in contrast to what is observed with fibroblasts or cells of the parietal yolk sac type. Arsenite induces the synthesis of a 105-kd polypeptide in fibroblasts but not in EC cells. In vitro differentiation of F9 cells induced by retinoic acid and dibutyryl cAMP is accompanied by a decrease in the spontaneous relative abundance of HSP and restores the arsenite-induced synthesis of the 105-kd polypeptide. EC cells are usually believed to be similar to inner cell mass cells of mouse blastocyst. Furthermore, data in the literature together with our own results suggest that the same three HSP are also spontaneously expressed in high amounts in the early mouse embryo.     

Reactivation of inactive X chromosome in buccal smear of carcinoma of breast

Buccal mucosal smears of 100 female patients of carcinoma of breast were compared with 100 controls matched accordingly. The frequency of Barr bodies was significantly lower in carcinoma of breast patients (menstruating and menopausal women) P < 0.001 when compared with controls indicating reactivation of the inactive X chromosome.     

X chromosome reactivation initiates in nascent primordial germ cells in mice

During primordial germ cell (PGC) development, epigenetic reprogramming events represented by X chromosome reactivation and erasure of genomic imprinting are known to occur. Although precise timing is not given, X reactivation is thought to take place over a short period of time just before initiation of meiosis. Here, we show that the cessation of Xist expression commences in nascent PGCs, and re-expression of some X-linked genes begins in newly formed PGCs. The X reactivation process was not complete in E14.5 PGCs, indicating that X reactivation in developing PGCs occurs over a prolonged period. These results set the reactivation timing much earlier than previously thought and suggest that X reactivation may involve slow passive steps.     

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.     

Single channel currents in mouse embryonal multipotential carcinoma cells

Electrical membrane properties of embryonal non-differentiated carcinoma cells which have been extensively used for the study of early mammalian embryogenesis were investigated by using patch clamp techniques. These multipotential cells were found to contain a restricted repertoire of a small number of ionic channels on the whole cell membrane. The most abundant type was a voltage- and calcium-activated potassium channel with characteristics similar to those described in fully differentiated cells.     

Replication variants of the human inactive X chromosome

Replication variants of the inactive X chromosome were investigated in lymphocytes from six donors by means of terminal BrdU or thymidine incorporation. There were interindividual differences in the incidence of particular variants. In endoreduplicated and tetraploid cells both allocyclic X chromosomes showed the same replication sequence. The Xp22 band of the allocyclic X chromosome seemed to replicate later than the homologous material in some cells. Initiation time of DNA synthesis within the inactive X chromosome was found to be stable; termination time, however, varied greatly relative to the other chromosomes. Early completion of replication within the heterochromatic X chromosome could be demonstrated preferentially for the Xq25–27 terminal sequence, but other variants expressed the phenomenon also. A variable replication rate of the inactive X chromosome is believed to be responsible for its asynchronous, independent replication. The biological significance of the phenomenon is discussed with respect to cell differentiation.     

Replication variants of the human inactive X chromosome

The sequence of DNA replication was studied within the inactive X chromosome in human lymphocytes, by means of the FPG method. Several variants of the replication sequence were found. The number of variants in the cells of a single donor exceeded 2 in each of the 4 normal individuals studied. The phenomenon is discussed with respect to the regulation of DNA synthesis and to the cell differentiation process.     

Divalent antibodies to mouse embryonal carcinoma cells inhibit compaction in the mouse embryo

Divalent antibodies from two antisera to embryonal carcinoma (EC) cells, F9 line, inhibited compaction in the preimplantation mouse embryo. One of these antisera, AF9-2, completely inhibited compaction at the 8-cell stage when the embryos were continuously incubated in a $\text{1}\text{100}$ dilution of the antiserum in culture medium from the 4-cell stage. Cell divisions continued and no cellular degeneration occurred. When cultured control embryos (preimmune and nonimmune sera) were normal blastocysts, many of the AF9-2-treated embryos were characterized by vacuolated cells and rounded rather than squamous, trophoectodermal cells. Anti-mouse spleen serum ($\text{1}\text{10}$, $\text{1}\text{100}$) had no effect on development. Purified divalent IgGs from AF9-2 (ammonium sulfate precipitation and DEAE chromatography) also were inhibitory at 30 μg/ml. Inhibition of compaction by AF9-2 was reversible. When uncompacted midmorula-stage embryos in AF9-2 ($\text{1}\text{10}$) were transferred to medium without serum, there was a threefold increase in the percentage (70%) of normal blastocysts at the end of culture. Fluorescence microscopy demonstrated that AF9-2 antibodies, unlike preimmune and nonimmune sera, were bound to the surface of 8-cell and early morula-stage embryos. Inhibition by AF9-2 does not occur merely by nonspecifically coating cell surfaces so that they no longer recognize each other, since antispleen antibodies show similar binding by immunofluorescence but no inhibition. This study provides strong evidence that AF9-2 has specific divalent antibodies which block morphogenesis. Since newly compacted embryos lost their compacted appearance in AF9-2, these divalent antibodies cause a loss of cell adhesion, do not extensively cross-link adjacent cell surfaces, and cannot cause the compacted phenotype by agglutination.     

The lesser known story of X-chromosome reactivation: A closer look into the reprogramming of the inactive X chromosome

X-chromosome inactivation (XCI) is an important mechanism employed by mammalian XX female cells to level X-linked gene expression with that of male XY cells. XCI occurs early in development as the pluripotent cells of the inner cell mass (ICM) in blastocysts successively differentiate into cells of all three germ layers. X-chromosome reactivation (XCR), the reversal of XCI, is critical for germ cell formation as a mechanism to diversify the X-chromosome gene pool. Here we review the characterization of XCR, and further explore its natural occurrence during development and the in vitro models of cellular reprogramming. We also review the key regulators involved in XCI for their role in suppressing the active histone marks and the genes in the active chromosome for their inhibition of X inactivation signals.Key words: X-chromosome reactivation, RNF12, reprogramming, primordial germ cells, iPS cellsX-chromosome inactivation (XCI) is an essential process occurring in female XX cells as a dosage compensation measure during development.¹ It ensures balanced X-chromosome-encoded proteins in male and female cells, and occurs randomly during early development, thus accounting for the mosaicism observed in female somatic cells. Once the cell has inactivated one of the X chromosomes, the pattern is maintained throughout the subsequent series of cell divisions. In mice, the paternal inactive X chromosome (Xi) is maintained throughout the early cleavage until the blastocyst stage, where cells of the inner cell mass (ICM) reactivate the inactive X chromosome.² At subsequent phases of early development, humans and mice share the pattern of XCI. Epiblast cells randomly inactivate one X chromosome, while the primordial germ cells (PGCs) reactivate the Xi during their migration to the genital ridges.^3–6 Interestingly, murine extra-embryonic trophoblast cells show non-random inactivation of the paternal X chromosome maintained in trophectoderm.^6,7 This pattern is, however, not conserved, as human trophectoderm cells randomly inactivate the paternal or maternal X chromosome. In addition to the PGCs and early developing embryo, cells cultured under defined conditions or undergoing reprogramming show X-chromosome reactivation (XCR).⁸ XCI has been extensively studied, while XCR is not well-understood, mainly due to the lack of easily accessible models. Here, we will review the developmental process of XCR and molecular mechanism involved in XCI and XCR.     

Accelerated telomere shortening in the human inactive X chromosome

Telomeres are nucleoprotein complexes at the end of eukaryotic chromosomes, with important roles in the maintenance of genomic stability and in chromosome segregation. Normal somatic cells lose telomeric repeats with each cell division both in vivo and in vitro. To address a potential role of nuclear architecture and epigenetic factors in telomere-length dynamics, the length of the telomeres of the X chromosomes and the autosomes was measured in metaphases from blood lymphocytes of human females of various ages, by quantitative FISH with a peptide nucleic-acid telomeric probe in combination with an X-chromosome centromere-specific probe. The activation status of the X chromosomes was simultaneously visualized with antibodies against acetylated histone H4. We observed an accelerated shortening of telomeric repeats in the inactive X chromosome, which suggests that epigenetic factors modulate not only the length but also the rate of age-associated telomere shortening in human cells in vivo. This is the first evidence to show a differential rate of telomere shortening between and within homologous chromosomes in any species. Our results are also consistent with a causative role of telomere shortening in the well-documented X-chromosome aneuploidy in aging humans.     

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.