X inactivation analysis and DNA methylation studies of the ubiquitin activating enzyme E1 and PCTAIRE-1 genes in human and mouse

Previously reported data on the X inactivation status of the ubiquitin activating enzyme E1 (UBE1) gene have been contradictory, and the issue has remained unsettled. Here we present three lines of evidence that UBE1 is expressed from the inactive X chromosome and therefore escapes X inactivation. First, by RNA in situ hybridization, UBE1 RNA is detected from both the active and inactive X chromosomes in human female fibroblasts. Second, UBE1 is expressed in a large panel of somatic cell hybrids retaining inactive human X chromosomes, including two independent hybrids that did not require UBE1 expression for survival. And third, sites at the 5' end of UBE1 are unmethylated on both active and inactive X chromosomes, consistent with the gene escaping inactivation. In order to address whether other genes that escape inactivation map to the same region of the X chromosome, we have also examined the expression of genes mapping adjacent to UBE1. The gene for PCTAIRE-1 (PCTK1) maps within 5 kb of UBE1 and similarly escapes X inactivation by the somatic cell hybrid assay, whereas six other genes that are within 1 Mb of UBE1 in Xp11.23 are silenced on the inactive X chromosome. Comparative mapping studies of the homologous loci in mouse establish that Ube1-x and Pctk1 are also within close physical proximity on the murine X chromosome, and expression studies of the Pctk1 gene determine that, similar to Ube1-x, it is subject to X inactivation in mouse. Methylation of CpG residues at restriction sites at the 5' end of both genes on the murine inactive X chromosome is consistent with both genes being subject to X inactivation in mouse, in contrast to their expression status in humans.      

DNA methylation of two X chromosome genes in female somatic and embryonal carcinoma cells

The extent of methylation of DNA sequences upstream and within the two X-linked genes,Pgk-1 andHprt, was analyzed in male and female somatic cells and in female embryonal carcinoma cells carrying either two active X chromosomes (Xa) or one active and one inactive X chromosome (Xi). Sites upstream and within the first intron of bothPgk-1 andHprt were heavily methylated on the Xi in somatic cells and in embryonal carcinoma cells with an Xi. Reactivation of this Xi was accompanied by extensive demethylation of these sites. In female embryonal carcinoma cells with two active X chromosomes, one X inactivates during differentiation in culture; however, methylation did not occur during differentiation, consistent with the idea that DNA methylation does not play a role in the initiation of X inactivation but may be involved in maintaining inactivation of those genes on the Xi.     

An assay for X inactivation based on differential methylation at the fragile X locus,FMR1

We describe an assay analyzing methylation at the fragile X mental retardation gene, FMR1, to examine patterns of random or non-random X chromosome inactivation. Digestion of genomic DNA with the methylation-sensitive enzyme HpaII cleaves two restriction sites near the CGG repeat of the FMR1 gene if they are unmethylated on the active X chromosome, but fails to digest these sites on the inactive chromosome. Subsequent PCR using primers that flank the sites and the variable CGG repeat within the FMR1 gene amplifies alleles only on undigested, methylated inactive X chromosomes. Amplification of the hypervariable CGG repeat distinguishes alleles in heterozygous samples, while the relative ratio of alleles within a HpaII-digested sample reflects the randomness or non-randomness of inactivation. To demonstrate that methylation of the HpaII sites within the amplified FMR1 fragment correlates strictly with the activity state of the X chromosome, we have tested the validity of this assay by comparing DNA from normal males and females, as well as DNA from mouse/human somatic cell hybrids carrying either active or inactive human X chromosomes. The data demonstrate that this assay provides a reliable means of assessing the inactivation status of X chromosomes in individuals with X-linked disorders or X chromosome abnormalities. © 1996 Wiley-Liss, Inc.     

A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human

new gene, designated Smcx, was cloned from the mouse X chromosomeby its homology to the Y located gene Smcy. Using direct insitu hybridisation Smcx was mapped to the distal end of themouse X chromosome (XF2–XF4) and its human homologue,SMCX, was mapped to proximal Xp (Xp11.1–Xp11.2). Furthermeiotic mapping in the mouse placed Smcx in the Plp–Pdha1interval. As Smcx/SMCX have widely expressed homologues on theY chromosome, they appeared good candidates for genes that escapeX-inactivation. In the human we show this to be the case asSMCX is expressed in hamster-human hybrids containing eitheran active or inactive human X chromosome. Two alleles of Smcxwere found to be expressed in T(16; X)16H female mice despitethe intact X chromosome being inactive in all cells. This indicatesthat Smcx is also not subject to X-inactivation and providesthe first example of a gene that is expressed from inactiveand active X chromosomes in the mouse.     

Tissue and lineage-specific variation in inactive X chromosome expression of the murine Smcx gene

To understand how gene expression patterns are established on the inactive X chromosome during development, we have studied the murine gene Smcx, which is expressed from both the active and inactive mouse X chromosomes. In all tissues assayed, Smcx only partially escapes X inactivation, with expression levels from the inactive X allele approximately 30-65% that of the active X allele. Additionally, inactive X expression levels differed between extraembryonic and embryonic tissues and among different tissues from newborn and adult mice. Imprinted extraembryonic tissue had the lowest levels of inactive X Smcx expression, whereas the highest levels were in heart. These data suggest that the chromosomal basis of X inactivation differs among tissues, perhaps reflecting differences in the timing or regulation of inactivation in these cell lineages.      

X-chromosome inactivation in cultured cells from human chorionic villi

X-chromosome inactivation was investigated in human chorionic villi in the first trimester of pregnancy and cultured cells established from them. Expression of glucose-6-phosphate dehydrogenase (G6PD) was evaluated in these extraembryonic cells from four females heterozygous for the electrophoretic variants (AB) of G6PD. In each case the uncultured villi as well as derived cultured cells expressed the AB phenotype for G6PD with about equal intensity for the A and B bands. Single-cell-derived clones established from two of the four cases expressed either G6PD A or B. One clone expressing G6PD B was fused with mouse cells, and a hybrid clone retaining the inactive human X chromosome was isolated; there was no evidence of human G6PD expression in this clone retaining an inactive human X. DNA methylation in the first intron of the human gene for hypoxanthine phosphoribosyltransferase (HPRT) was evaluated in the four pairs of cultured villi and fetal cells. No differences were detected between the cultured villi and fetal cells as they all showed bands characteristic of an inactive X from somatic cells. These results show that there is no preferential inactivation of an X in the majority of cells that constitute human tertiary chorionic villi or in cultured cells derived from them. Long-term cultures established from chorionic villi appear to be no different from somatic cells with respect to X-chromosome inactivation.     

The DXS423E gene in Xp11.21 escapes X chromosome inactivation

The DXS423E gene has been localized to Xp11.21 and is expressedin somatic cell hybrids retaining either the human active orinactive X chromosome, demonstrating that DXS423E escapes Xchromosome inactivation. The XE169 (DXS1272E or SMCX) gene thatescapes X chromosome Inactivation is also located in Xp11.21–11.22and maps within the same YAC as DXS423E. Thus the DXS423E andXE169 genes define a new region in the proximal short arm ofthe X chromosome that is not subject to X chromosome inactivation,supporting a regional basis for escape from inactivation.     

Physical mapping of loci in the distal half of the short arm of the human X chromosome: Implications for the spreading of X-chromosome inactivation

The relative order of 11 loci in the distal half of the short arm of the human X chromosome was examined using a panel of somatic cell hybrids containing structurally rearranged X chromosomes. The results show that the gene for phosphoribosylpyrophosphate synthetase 2 (PRPS2) is located betweenZFX (zinc finger protein, X-linked) andSTS (steroid sulfatase). The results also confirm the localization ofZFX distal toPOLA (-DNA polymerase). Previous studies have shown thatSTS andZFX escape X-inactivation whereasPOLA undergoes inactivation. Evaluation ofPRPS2 expression in somatic cell hybrids containing inactive human X chromosomes showed thatPRPS2 undergoes X-inactivation. These results provide further evidence for interspersion of loci that do and do not undergo X-inactivation on the human X chromosome.     

The human/mouse imprinted genesIGF2, H19, SNRPN andZNF127 map to two conserved autosomal clusters in a marsupial

The four genesIGF2, H19, SNRPN andZNF127 are imprinted in mouse and human.IGF2 andH19 form one conserved cluster on the distal part of mouse chromosome 7 and human chromosome 11p15.5, whereasSNRPN andZNF127 form another on the middle of mouse chromosome 7 and on human chromosome 15q11-13. We have explored the evolution of these imprinted regions by cloning and mappingIGF2, H19, SNRPN andZNF127 homeologues in marsupials. Specifically, we wished to determine whether the arrangements were shared in eutherian and marsupial mammals, and to determine whether they lay on autosomes, or on the X, as might be predicted by the hypothesis that imprinting evolved from X inactivation. Using fluorescencein situ hybridization, we localized the marsupial homeologues ofIGF2 andH19 to the distal part of tammar wallaby chromosome 2p and the marsupial homeologues ofSNRPN andZNF127 to the middle of chromosome 1q. Thus, these genes were originally organized in two separate autosomal clusters in the therian ancestor 180 million years ago, the conservation of which may suggest a functional relationship. The autosomal location of these clusters does not suggest a recent evolutionary relationship between imprinting and X chromosome inactivation.accepted for publication by M. Schmid     

Autonomous gene expression on the human inactive X chromosome

Local derepression of the hpt locus on the human inactive X chromosome obtained in human female fibroblast x mouse L cell somatic cell hybrids was not correlated with the presence or absence of any specific human chromosome in the hybrids. Loss of the human active X, in particular, did not result in observable derepression of genes on the inactive X. Introduction of an active X, via a second hybridization of human cells having an active X with hybrid cells containing a locally derepressed X chromosome, did not restore repression of the derepressed hpt allele. The rate of hpt locus derepression in hybrid cells was estimated to be 10^–6 per inactive X chromosome per cell generation.     

Chromosome localizations of genes for five cAMP-specific phosphodiesterases in man and mouse

Cyclic nucleotides are important second messengers that mediate a number of cellular responses to external signals. Cyclic nucleotide phosphodiesterases play a role in signal transduction by regulating the cellular concentrations of these messengers. Here, we have applied Southern analyses of somatic cell hybrid lines and of recombinant inbred (RI) mouse strains as well as fluorescence chromosomal in situ hybridization (FISH) to chromosomally localize five cAMP-specific nucleotide phosphodiesterase genes in human and mouse. GenesDPDE1, DPDE2, DPDE3, andDPDE4 that share sequence homology with theDrosophila dunce gene were assigned to human chromosomes 19 (DPDE1 andDPDE2), 5q12 (DPDE3), and 1p31 (DPDE4) and to mouse chromosomes 8, 9, 13, and 4, respectively. The high-affinity cAMP-specific phosphodiesterase gene (HCP1) was mapped to human chromosome 8q13-q22. Since these genes are potential candidates for involvement in psychiatric or behavioral disorders, knowledge of their chromosomal localizations will facilitate the discovery of their association with disease genes as they are being mapped by linkage studies.     

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.      

TheIL-4 andIL-5 genes are closely linked and are part of a cytokine gene cluster on mouse chromosome 11

The murine IL-4and IL-5genes encode hemopoietic growth factors involved in the stimulation, proliferation, and differentiation of cells of the T lymphocyte, B lymphocyte, and granulocyte lineages. We have mapped the Il-4 and Il-5 loci representing the structural genes for IL-4and IL-5,respectively, to mouse chromosome 11 using Chinese hamster ×mouse and rat × mouse somatic cell hybrids. Physical linkage studies of the IL-4and IL-5genes by pulsed field gel electrophoresis have shown that they are closely linked, being 110–180 kb apart. Since the Il-5 locus maps to the interface of bands A5 and B1 in the same location as the genes for IL-3and GM-CSF, this places these three cytokine genes, as well as the IL-4 gene, within a region of about 5000–10,000 kb. The present physical linkage studies indicate that the IL-4and IL-5genes are a minimum of 600 kb apart from the closely linked IL-3and GM-CSFgenes. The gene clustering, together with similarities in gene structure, regulation, and biological function, raises the possibility that the four genes may be part of a distantly related cytokine gene family.