We recently have identified a ubiquitously transcribed mouse Y chromosome gene, Uty, which encodes a tetratricopeptide repeat (TPR) protein. A peptide derived from the UTY protein confers H-Y antigenicity on male cells. Here we report the characterization of a widely transcribed X-linked homologue of Uty, called Utx, which maps to the proximal region of the mouse X chromosome and which detects a human X-linked homologue at Xp11.2. Given that Uty is ubiquitously transcribed, we assayed for Utx expression from the inactive X chromosome (Xi) in mice and found that Utx escapes X chromosome inactivation. Only Smcx and the pseudoautosomal Sts gene on the mouse X chromosome have been reported previously to escape inactivation. The human UTX gene was also found to be expressed from Xi. We discuss the significance of these data for our understanding of dosage compensation of X-Y homologous genes in humans and mice.
The mammalian Y chromosome contains genes essential for male development, most notably the testis determining gene SRY and genes active during spermatogenesis. The observation that most Y-linked genes share an X-linked homologue has led to the widely held view that the mammalian Y chromosome represents a small subset of genes originating from the X chromosome, this subset varying somewhat from species to species. In this view, Y-linked genes are in a dynamic state of degradation, resulting in eventual loss, unless conserved due to their acquisition of male-specific functions (1). One potential driving force behind this evolution of the Y chromosome is X chromosome inactivation. Only a single copy of most X-linked genes is required for normal female development, and males thus have an extra, superfluous copy of any Y-linked gene which may diverge from the X-linked copy. Those few genes that escape X chromosome inactivation are predicted to have a widely expressed, functionally equivalent Y-linked homologue. There are, however, exceptions to this prediction (reviewed in ref. 1). Another complication is presented by the observed phenotypic difference between mice with an XO genotype and 45,X humans.
In humans, 99% of 45,X embryos die in utero, and those females that survive exhibit Turner stigmata (2,3). In mice, only 35% of XO individuals die in utero, and XO adult females, whilst exhibiting some reproductive deficiencies such as shortened reproductive lifespan and reduced litter size, are fertile and near normal phenotypically (4-6). The impact of X monosomy on viability and development has been attributed to the dosage deficiency of a gene or genes on the X chromosome which are normally expressed from both copies of the X chromosome and which are supplemented by functionally equivalent Y-linked homologues in males (7,8). To date, 17 genes localized to both the pseudoautosomal region and the X-specific portion of the X chromosome have been shown to be expressed from the inactive human X chromosome (9). Only two murine X-linked genes which escape X inactivation have been described: Smcx in the unique region (10,11) and Sts in the pseudoautosomal region (12). This discrepancy between mice and humans in the number of genes known to escape X inactivation has been used to explain the difference in viability of XO embryos between the two species (13). The validity of this explanation clearly depends on how many additional mouse X-linked genes are shown to escape X inactivation.
We recently have described a mouse Y-linked gene, Uty, which is widely expressed and encodes a tetratricopeptide repeat (TPR) protein (14). TPR motifs are found in a variety of functionally distinct proteins and are believed to mediate protein-protein interaction (15). The 5.5 kb Uty transcript encodes an 1186 amino acid protein with eight TPR motifs at its N-terminus. Here we describe the isolation of an X-linked homologue of this gene, called Utx (ubiquitously-transcribed TPR gene on the X chromosome), which is expressed from the inactive X chromosome in both mice and humans.
We previously have described the detection of presumptive X-linked restriction fragments by Southern analysis of male (XY) and female (XX) genomic DNA with a Uty probe (14). Two mouse embryo cDNA libraries were screened with Uty probes in order to isolate the X-linked transcript, and four overlapping cDNAs were obtained (Fig. 1a). The single, 4001 bp open reading frame (ORF) of the largest Utx cDNA (1E) remains open at the 5' end. We have been unable to isolate more of the transcript by conventional methods such as library screening and RACE-PCR. However, comparison with the ORFs of murine Uty and the recently reported human UTX gene (16) suggests that only some 200 bp of ORF at the 5' end remains to be cloned. The Utx ORF is predicted to encode a member of the TPR protein family (Fig. 1b), exhibiting strong similarity to Uty at the both the nucleotide and amino acid level (Fig. 1c).a
In order to confirm the chromosomal origin of the Utx transcript, a Utx cDNA clone (1.1N) was hybridized to TaqI-digested genomic DNA samples from progeny of an interspecific backcross, previously typed for a range of X-linked markers (17). A single hybridizing fragment was detected, differing in size between the two species [Mus musculus (C57BL/6) = 8.5 kb and Mus spretus = 7.5 kb] (data not shown). Haplotype analysis of 50 backcross progeny mice positions the gene between the X-linked markers DXMit50 (3/50 recombinants, 6 ± 3.3 cM) and DXMit72 (2/50 recombinants, 4 ± 2.8 cM) in the proximal region of the mouse X chromosome (Fig. 2a). In order to obtain a localization with respect to known genes in the proximal region of the mouse X chromosome, segregation of 1.1N was also analysed in 24 interspecific backcross progeny mice already typed for the genes Otc, Ube1x and Hprt and known to harbour recombination breakpoints between them (18). Haplotype analysis of these recombinant mice showed Utx to map between Otc and Ube1x (data not shown). Extrapolating from the two sets of mapping data, Utx can be positioned in a small interval on the mouse X chromosome proximal to Ube1x and distal to marker DXMit72 (Fig. 2b). This interval contains the markers Maoa and Maob,and places Utx in band A2-A3 (19).a
Reverse-transcriptase polymerase chain reaction (RT-PCR) with Utx-specific primers yielded a product in all male and female tissues tested in 13.5 days post-coitum(dpc) mouse embryos (Fig. 3a). Northern analysis of female mouse poly(A)+ RNA samples using cDNA clone 1.1N detected a transcript of 5.0-5.5 kb in several adult tissues (Fig. 3b).
Figure
The predicted Utx gene product shows strong similarity to the predicted product of the mouse Uty gene (14). Figure 1c shows an alignment of the ORFs of Utx and Uty, indicating a central region of divergence between the two genes where similarity drops to ~66%, at both the nucleotide and amino acid level. Utx and Uty share strong homology outside of the variant region (Fig. 1c). In addition, a region of ~500 bp of the 4kb Utx ORF appears to have no equivalent in the Uty composite cDNA described (14). RT-PCR employing primers in this region was used to confirm that it is exonic and not a contaminating intron (data not shown). This region is conserved in the human UTX cDNA (16).
Database searches with the Utx sequence identify other members of the TPR protein family, the best match to a gene product of known function being the yeast glucose repressor protein, Ssn6p (20), which acts as a transcriptional repressor. This best match is identical to that previously described for Uty (14).
In order to identify an X-linked human homologue of Utx, primers were designed (hUTX-1 and hUTX-2) from the sequence of a human expressed sequence tag (EST; R64076) which shows 95% identity at the nucleotide level to murine Utx. An RT-PCR product, derived from human female fibroblast cDNA using these primers, was used in Southern analysis of a panel of rodent-human somatic cell hybrids carrying derivative X chromosomes (data not shown).This hybridization analysis indicated a location at Xp11.23-Xp11.3 between the t75-2ma-1b and SIN76 breakpoints (21). To confirm this localization of human UTX, high density cosmid filter arrays from a flow-sorted X chromosome library (22,23) were then screened with mouse cDNA clone 4.2 (Fig. 1a). A single positive cosmid was isolated and mapped by fluorescent in situ hybridization (FISH) on normal human metaphase spreads to Xp11.2 (data not shown).
Southern analysis of male and female human genomic DNA with a murine Uty probe revealed male-specific fragments and fragments shared between males and females (data not shown). Hybridization of this probe to a series of contiguous yeast artificial chromosome (YAC) clones from the human Y chromosome (24) showed strong hybridization to yOX YAC clone 237, indicating a localization of human UTY to band 5D/5E of Yq (data not shown). Recently, UTY was shown to map to band 5C on the basis of deletion mapping (16). Band 5 of Yq is known to contain a gene(s) functioning in spermatogenesis (25) and a Y-specific growth gene (26).
In order to assay for expression from the inactive mouse X chromosome, females carrying the T(X;16)16H (T16H) translocation were used. As previously described (13,27-29), T16H females undergo non-random inactivation of the normal, paternally derived X chromosome. We exploited two variants between the normal X chromosome, derived from M.castaneus, and the T16H translocation X chromosome in order to assay for expression of Utx from Xi. Utx RT-PCR products derived from parental mice and F1 females carrying the T16H translocation were either analysed by gel electrophoresis (Fig. 4a) or sequenced directly (Fig. 4b). In the case of both variants analysed, the T16H and M.castaneus Utx alleles were detected in F1 T16H females, indicating that Utx escapes X chromosome inactivation in the mouse.
To determine whether the human UTX gene was expressed from the inactive X chromosome, RT-PCR using the hUTX primers described above was employed. A series of mouse-human somatic cell hybrids that retain independent active or inactive X chromosomes (30) were analysed for UTX expression. As shown in Figure 4c, the control gene PGK1 is subject to inactivation, and although PGK1 is expressed in the two hybrids carrying active human X chromosomes, no expression was seen in any of the five independent hybrids retaining inactive X chromosomes. In contrast, UTX expression was observed in both active and inactive X hybrids, demonstrating that the human gene escapes X inactivation. These data confirm the recent report of UTX expression from human Xi (16).
We have identified and characterized an X-linked gene which escapes X chromosome inactivation in both mice and humans. In mice, Utx is only the second gene from the X-specific portion of the X chromosome known to be expressed from the inactive X (Xi), the other being Smcx (10,11,29,31). In contrast, its human counterpart UTX is an addition to an already long list of genes which are expressed from human Xi (9,32).
The existence of human genes that escape X chromosome inactivation is widely believed to explain the 45,X Turner syndrome phenotype. Such X-linked `Turner' genes are predicted to have a functionally equivalent Y-linked homologue (7,8). Thus in 46,XX and 46,XY individuals, a normal phenotype would result from an effective double dose of each of these genes, whilst in 45,X individuals, haploinsufficiency would result in death in utero or characteristic Turner stigmata in survivors. While several candidates have been proposed, including the recently identified SHOX gene (33), the gene(s) responsible for Turner syndrome have not been identified. UTX maps to a region of the human X chromosome (Xp11-22) associated with Turner syndrome in females bearing interstitial deletions (3) and escapes X chromosome inactivation. Whilst it is not yet known whether its Y-linked homologue UTY is functionally equivalent, the potential role of UTX in Turner syndrome should be investigated further.
The functional equivalence of UTX and UTY can be addressed directly in the mouse by targeted mutagenesis. Mouse Utx and Uty show strong overall homology, but the central region of divergence between the two could reflect either a lower requirement for structural conservation in this region or functional non-equivalence between the two proteins and a male-specific role for Uty.Comparison of the phenotype of males with females bearing one allele of Utx inactivated by homologous recombination should determine whether Uty or some other loci can function in the place of Utx. These experiments will also determine whether haploinsufficiency of Utx contributes to any of the phenotypic characteristics of the XO mouse, such as its reduced ability to support the survival and prenatal growth of embryos (6,34).
Differences in phenotype between 45,X humans and XO mice have been attributed to an absence of X-specific mouse genes escaping X inactivation (13). However, it is now clear that at least two such genes exist. Localized areas of persistent histone H4 acetylation have been detected on both mouse and human Xi, identifying three homologous chromosomal areas with potential transcriptional competence (35). UTX maps to one of these homologous regions: Xp11.2 in humans and band A2 in the mouse (Fig. 2). It will be interesting to determine whether these regions contain other genes escaping X chromosome inactivation, particularly on the mouse X chromosome.
Whilst the PCR experiments employed to assay expression of Utx from the inactive mouse X chromosome were not designed to be quantitative, expression from the active X chromosome appears to exceed that from Xi (Fig. 4a and b). This observation is similar to that originally described for the expression of Smcx from the mouse Xi (10), which was confirmed by quantitative procedures (29,31).It will now be possible to determine whether the stage and tissue specificity which characterize the degree of escape from X inactivation by the murine Smcx gene (29,31) are common to Smcx and Utx, or whether genes active on Xi exhibit unique dynamics of expression. This will allow further insight into the mechanism of spread of inactivation along the X chromosome and the functional significance of the escape of murine X-linked genes from this process.
cDNA clones 1E and 1C were isolated from an oligo(dT)-primed 7.5 dpc mouse embryo cDNA library. Clones 1.1N and 4.2 were isolated from a random-primed 11.5 dpc mouse embryo cDNA library (14). Clones and RT-PCR products were sequenced by dideoxy chain termination, and products were analysed on a 373A DNA Sequencer (Applied Biosystems).
Total RNA was isolated using Trizol reagent (Gibco, BRL) and mRNA was selected with an Oligotex mRNA mini kit (Qiagen). RNA and DNA samples were electrophoresed, transferred to nylon filters and hybridized according to standard procedures (36).
RNA was isolated using Trizol reagent (Gibco BRL) according to the manufacturer's recommendations. cDNA was prepared and PCR reactions were performed as previously described (28,29,37).
The PCR primers used are listed in Table 1.
Mouse Utx RT-PCR products were sequenced with the primer Utx-15: 5'-CCAAGGACTTCTGGAGATAC-3'.
Table 1.
Primers hUTX-1 and hUTX-2 preferentially amplify the human UTX gene, though a faint product from mouse of the same size was also observed. Sequence analysis of this mouse transcript identified several nucleotide differences when compared with the human gene. Therefore, to analyse expression specifically from the human X chromosome in somatic cell hybrids, RT-PCR products were digested with HinfI to cleave the mouse product, and a 299 bp human-specific product remains. To confirm further that the product was human in origin, the products amplified from two somatic cell hybrids containing independent inactive X chromosomes were sequenced and shown to be identical to the human X-linked EST R64076.
We acknowledge J.M.Dunn for technical assistance. We wish to thank Graham Kay, Yvonne Boyd and Steve Brown for useful discussions, Neil Brockdorff for providing interspecific backcross mouse genomic DNA for mapping, and K.E.Davis for fluorescent in situ hybridization. We also thank Mandy Spurdle for supplying a copy of the human Y chromosome yOX YAC contig collection. This work was supported by a grant from the Australian Research Council to P.K. C.P. and A.P.M. were funded by the Wellcome Trust.
Human Molecular Genetics
Pages
Introduction
Results
Isolation and mapping of Utx cDNAs
Expression
Predicted protein product of Utx
Conservation of UTX on the human X chromosome
A human Y-linked homologue
Escape from X inactivation
Discussion
Materials And Methods
cDNA library screening and sequencing
Northern and Southern analyses
RT-PCR
PCR primers
Sequencing primers
PCR amplification of human UTX
Acknowledgements
References
Figure
Figure
Figure
Primer
Sequence
hUTX-1
5'AGACATTGAGGGAAGCTCTC-3'
hUTX-2
5'-TCAAGATGAGGCGGATGGT-3'
Utx-4
5'-ATGAAAATACCAGGAGCTAAAC-3'
Utx-5
5'-AGTGTTTGCTCTGCTACCTG-3'
Utx-6a
5'-GATCTGTTTTGAGTGAAATGGTTAC-3'
Utx-7
5'-AAAATTGTGTACTGGCAGATGT-3'
Utx-12
5'-CAGCATGACCGTGGTCCAAT-3'
Utx-13
5'-CCCTGCACTTTGTCCAATGCT-3'
REFERENCES
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