Y-linked Homologue Research Articles

Sex chromosome-encoded protein homologs: current progress and open questions.

The complexity of biological sex differences is markedly evident in human physiology and pathology. Although many of these differences can be ascribed to the expression of sex hormones, another contributor to sex differences lies in the sex chromosomes beyond their role in sex determination. Although largely nonhomologous, the human sex chromosomes express seventeen pairs of homologous genes, referred to as the 'X-Y pairs.' The X chromosome-encoded homologs of these Y-encoded proteins are crucial players in several cellular processes, and their dysregulation frequently results in disease development. Many diseases related to these X-encoded homologs present with sex-biased incidence or severity. By contrast, comparatively little is known about the differential functions of the Y-linked homologs. Here, we summarize and discuss the current understanding of five of these X-Y paired proteins, with recent evidence of differential functions and of having a potential link to sex biases in disease, highlighting how amino acid-level sequence differences may differentiate their functions and contribute to sex biases in human disease.

Developmental transcriptomic patterns can be altered by transgenic overexpression of Uty

The genetic material encoded on X and Y chromosomes provides the foundation by which biological sex differences are established. Epigenetic regulators expressed on these sex chromosomes, including Kdm6a (Utx), Kdm5c, and Ddx3x have far-reaching impacts on transcriptional control of phenotypic sex differences. Although the functionality of UTY (Kdm6c, the Y-linked homologue of UTX), has been supported by more recent studies, its role in developmental sex differences is not understood. Here we test the hypothesis that UTY is an important transcriptional regulator during development that could contribute to sex-specific phenotypes and disease risks across the lifespan. We generated a random insertion Uty transgenic mouse (Uty-Tg) to overexpress Uty. By comparing transcriptomic profiles in developmental tissues, placenta and hypothalamus, we assessed potential UTY functional activity, comparing Uty-expressing female mice (XX + Uty) with wild-type male (XY) and female (XX) mice. To determine if Uty expression altered physiological or behavioral outcomes, adult mice were phenotypically examined. Uty expression masculinized female gene expression patterns in both the placenta and hypothalamus. Gene ontology (GO) and gene set enrichment analysis (GSEA) consistently identified pathways including immune and synaptic signaling as biological processes associated with UTY. Interestingly, adult females expressing Uty gained less weight and had a greater glucose tolerance compared to wild-type male and female mice when provided a high-fat diet. Utilizing a Uty-overexpressing transgenic mouse, our results provide novel evidence as to a functional transcriptional role for UTY in developing tissues, and a foundation to build on its prospective capacity to influence sex-specific developmental and health outcomes.

Dosage sensitivity of X-linked genes in human embryonic single cells

BackgroundDuring the evolution of mammalian sex chromosomes, the degeneration of Y-linked homologs has led to a dosage imbalance between X-linked and autosomal genes. The evolutionary resolution to such dosage imbalance, as hypothesized by Susumu Ohno fifty years ago, should be doubling the expression of X-linked genes. Recent studies have nevertheless shown that the X to autosome expression ratio equals ~ 1 in haploid human parthenogenetic embryonic stem (pES) cells and ~ 0.5 in diploid pES cells, suggesting no doubled expression for X-linked genes and refuting Ohno’s hypothesis.ResultsHere, by reanalyzing an RNA-seq-based single-cell transcriptome dataset of human embryos, we found that from the 8-cell stage until the time-point just prior to implantation, the expression levels of X-linked genes are not two-fold upregulated in male cells and gradually decrease from two-fold in female cells. Additional analyses of gene expression noise further suggest that the dosage sensitivity of X-linked genes is weaker than that of autosomal genes in differentiated female cells, which contradicts a key assumption in Ohno’s hypothesis, that most X-linked genes are dosage sensitive. Moreover, the dosage-sensitive housekeeping genes are preferentially located on autosomes, implying selection against X-linkage for dosage-sensitive genes.ConclusionsWe observed dosage imbalance between X-linked and autosomal genes, as well as relatively high expression noise from X-linked genes. These results collectively suggest that X-linked genes are less dosage sensitive than autosomal genes, putting one primary assumption of Ohno’s hypothesis in question.

Gene-by-Gene or Localized Dosage Compensation on the Neo-X Chromosome in Drosophila miranda.

Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be necessary because the degeneration of Y-linked genes occurs independently at different times. We therefore tested whether the up-regulation of X-linked genes depends on the status of their Y-linked homologs, using the young sex chromosomes, neo-X and neo-Y, in Drosophila miranda. In support of the presence of gene-by-gene DC, the extent of up-regulation in males was indeed higher for neo-X-linked genes with pseudogenized neo-Y-linked homologs than for neo-X-linked genes with functional neo-Y-linked homologs. Further molecular evolutionary analysis also supports the idea that many individual neo-X-linked genes first acquired the potential for up-regulation, which then enabled the pseudogenization of neo-Y-linked homologs, without serious deleterious effects on male fitness.

The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome.

The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S.dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7) years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C.

BackgroundA number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment.ResultsUsing a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age/sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP.ConclusionsWe have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.

Slcyt, a Newly Identified Sex-Linked Gene, Has Recently Moved onto the X Chromosome in Silene latifolia (Caryophyllaceae)

The sex chromosomes of the plant species Silene latifolia (white campion) are very young (only 5-10 My old), and all 11 X-linked genes so far described have Y-linked homologues. Theory predicts that X chromosomes should accumulate a nonrandom set of genes. However, little is known about the importance of gene movements between the X and the autosomes in plants, or in any very young sex chromosome system. Here, we isolate from cDNA a new gene, Slcyt, on the S. latifolia X, which encodes a cytochrome B protein. We genetically mapped SlCyt and found that it is located approximately 1 cM from the pseudoautosomal region. Genes in this region of the X chromosome have low divergence values from their homologous Y-linked genes, indicating that the X only recently stopped recombining with the Y. Genetic mapping in Silene vulgaris suggests that Slcyt originally belonged to a different linkage group from that of the other S. latifolia X-linked genes. Silene latifolia has no Y-linked homologue of Slcyt, and also no autosomal paralogues seem to exist. Slcyt moved from an autosome to the X very recently, as the Cyt gene is also X linked in Silene dioica, the sister species to S. latifolia, but is probably autosomal in Silene diclinis, implying that a translocation to the X probably occurred after the split between S. diclinis and S. latifolia/S. dioica. Diversity at Slcyt is extremely low (pi(syn) = 0.16%), and we find an excess of high frequency-derived variants and a negative Tajima's D, suggesting that the translocation was driven by selection.

A selective sweep in or near theSilene latifoliaX-linked geneSlssX

The most prominent feature of Y chromosomes is that they do not recombine and are usually genetically degenerate, containing only a few genes. White campion Silene latifolia has evolved sex chromosomes relatively recently, probably within the last 10-15 million years. Perhaps due to its recent origin, the Y chromosome in this species has not completely degenerated and most isolated X-linked genes have intact Y-linked homologues. A gene encoding a protein with strong homology to spermidine synthases, Slss, is the exception to this rule, as the Y-linked copy of this gene has apparently lost its function. Here I report evidence for a recent selective sweep in the X-linked copy of this gene (SlssX) that could reflect compensatory evolution in an X-linked gene that has lost a functional Y-linked homologue. The spread and fixation of an advantageous mutation in SlssX has resulted in a dramatic loss of genetic diversity and an excess of high-frequency derived polymorphisms in this gene. As the sweep has not affected the closely linked DD44X gene, the selective advantage of the mutation that has driven the sweep in the SlssX gene might have been less than 1%.

ESS gene expression of X-linked imprinted genes subject to sexual selection

We define ESS (Evolutionary Stable Strategy) conditions for the evolution of genomic imprinting at an X-linked locus. The system analysed is designed for mammalian imprinting in which X-linked genes typically undergo random X-inactivation and lack Y-linked homologues. We consider two models that map cellular gene expression to fitness in females subject to random X-inactivation. In the first model, female fitness is simply a function of the average gene expression across all cells. In the second model, each cell contributes independently to fitness, and female fitness is assessed as the average of these contributions across all cells. In both models, imprinting readily evolves when sexual selection favours different levels of gene expression in the two sexes. Imprinting is beneficial as it improves adaptation in both sexes. There are limits to the improvement in adaptation when sexual selection is strong and favours greater gene expression in males (the heterogametic sex). We also consider the consequences of an active Y-linked homologue on the evolution of imprinting. Our analysis suggests that restrictive conditions apply for the evolution of polymorphic ESSs at an X-linked imprinted loci.

Sexually dimorphic expression of the X-linked gene Eif2s3x mRNA but not protein in mouse brain

Higher expression of X-linked genes in females might contribute to brain sexual differentiation. Although X-inactivation is thought to balance gene dosage between the two sexes, some X-linked genes escape X inactivation and therefore are expressed from both X chromosomes in females. Eif2s3x encodes subunit three of eukaryotic translation initiation factor 2, which regulates the rate of protein translation, and escapes X-inactivation in both humans and mice. By Northern blot analysis, we found Eif2s3x to be expressed higher in females than in males in developing and adult brains as well as adult liver. Gonadally intact XX mice had a higher level of Eif2s3x mRNA expression than XY mice regardless of whether they had testes or ovaries, suggesting that sexually dimorphic gene expression arises as a consequence of sex chromosome complement. In situ hybridization indicated that Eif2s3x mRNA was expressed preferentially in specific brain regions including the habenula, anterodorsal thalamic nucleus, hippocampus, hypothalamus, and cerebellum. Females had significantly higher levels of Eif2s3x mRNA expression than males in cortex, hippocampus and paraventricular nucleus but not in the habenula. The effect of a sex difference in Eif2s3x transcription, however, could potentially be offset by the additional expression in male brains of its Y-linked homologue Eif2s3y which was found in similar brain regions. The sex difference in Eif2s3x transcript appears not to be preserved at the protein level, since no difference in the levels of Eif2s3 protein was found between (1) males and females (2) XX and XY mice, or (3) XO and XX females.

X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis

Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.

Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution

Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of human X- and Y-borne genes in distantly related mammals and non-mammalian vertebrates has proved valuable to help deduce the evolution of this unique part of the genome. The platypus, a monotreme mammal distantly related to eutherians and marsupials, has an extraordinary sex chromosome system comprising five X and five Y chromosomes that form a translocation chain at male meiosis. The largest X chromosome (X1), which lies at one end of the chain, has considerable homology to the human X. Using comparative mapping and the emerging chicken database, we demonstrate that part of the therian X chromosome, previously thought to be conserved across all mammals, was lost from the platypus X1 to an autosome. This region included genes flanking the XIST locus, and also genes with Y-linked homologues that are important to male reproduction in therians. Since these genes lie on the X in marsupials and eutherians, and also on the homologous region of chicken chromosome 4, this represents a loss from the monotreme X rather than an additional evolutionary stratum of the human X.

Molecular analysis of TBL1Y, a Y-linked homologue of TBL1X related with X-linked late-onset sensorineural deafness

Recent progress in sequencing the human Y chromosome has unveiled a series of X-Y homologous genes. In the present study, we focused on Transducin beta-like 1Y (TBL1Y), which is a Y-linked homologue of TBL1X that is related with X-linked late-onset sensorineural deafness. Recently, it has been shown that TBLR1, another homologue whose gene resides on chromosome 3, and TBL1X act as a corepressor/coactivator exchanger for several nuclear receptors and transcription factors. However, the expression pattern and function of TBL1Y remain unknown. The RT-PCR analysis of the TBL1 family revealed that TBL1Y was expressed in all 13 tissues examined but not in leukocytes. Among the cell lines tested, however, it was only expressed in NT2/D1 cells and in lymphoblasts transformed with Epstein Barr (EB) virus. To compare the functions of the TBL1 family, we generated a series of expression plasmids for GAL4DBD-fused proteins of the TBL1 family. We carried out dual luciferase assays using these plasmids in combination with a plasmid having a luciferase reporter gene harboring 5xGAL4 binding sites. Unlike the other constructs, GAL4DBD-fused TBL1Y did not repress the promoter activity. Moreover, we found three novel polymorphisms in the TBL1Y gene, IVS7+9G>A, G268C, and IVS7+1G>C, which is presumed to cause splicing error. These polymorphisms are found in males within Y-haplogroup O3 (XO3e), which is defined as the Y-haplogroup O3 excluding O3e, a branch of O3. The results show that TBL1Y differs from other members of the TBL1 family in expression and function, suggesting other roles in maleness.

Sex differences in sex chromosome gene expression in mouse brain.

A major question is whether genes encoded on the sex chromosomes act directly in non-gonadal tissues to cause sex differences in development or function, or whether all sex differences in somatic tissues are induced by gonadal secretions. As part of this question we asked whether mouse X-Y homologous gene pairs are expressed in brain in a sex-specific fashion. Using RT-PCR and northern blot analysis, we assessed mRNA expression in brain of eight Y-linked genes as well as their X-linked homologues, at three ages: 13.5 days post coitum, the day of birth (P1) and adult. Transcripts of six Y genes were expressed at one or more ages: Usp9y, Ube1y, Smcy, Eif2s3y, Uty and Dby. Their expression also occurred in XY female brain, and therefore does not require testicular secretions. Six X-linked homologues (Usp9x, Ube1x, Smcx, Eif2s3x, Utx and Dbx) were also expressed in brain, and in adulthood all of these transcripts were expressed at significantly higher levels in brains of females than in brains of males, irrespective of their X-inactivation status. For five of these gene pairs, the expression of the Y-linked homologue in males was not sufficient to compensate for the female bias in X gene expression. Three X-Y gene pairs, Usp9x/y, Ube1x/y and Eif2s3x/y, appeared to be differentially regulated (expressed in brain in a different age- or tissue-dependent pattern), and hence may not be functionally equivalent. These sex differences in X-Y gene expression suggest several mechanisms by which these genes may participate in sex differences in brain development and function.

An X-linked gene with a degenerate Y-linked homologue in a dioecious plant : Guttman DS, Charlesworth D: Natu 1998, 393:263–266

An X-linked gene with a degenerate Y-linked homologue in a dioecious plant : Guttman DS, Charlesworth D: Natu 1998, 393:263–266

An X-linked gene with a degenerate Y-linked homologue in a dioecious plant.

Most flowering plants are hermaphroditic, having flowers with both male and female parts. Less than 4% of plant species are dioecious (with individuals of separate sexes), and many of these species have chromosome-mediated sex determination. The taxonomic distribution of separate sexes and chromosomal sex-determination systems in the flowering plants indicates that plant sex chromosomes have evolved recently through replicated, independent events, contrasting with the ancient origins of mammalian and insect sex chromosomes. Plant sex chromosomes, therefore, offer opportunities to study the most interesting early stages of the evolution of sex chromosomes. Here we show that a gene encoding a male-specific protein is linked to the X chromosome in the dioecious plant Silene latifolia, and that it has a degenerate homologue in the non-pairing region of the Y chromosome. The Y-linked locus has degenerated as a result of nucleotide deletion and the accumulation of repetitive sequences. We have identified both the first X-linked gene and the first pair of homologous sex-linked loci to be found in plants. The homology between the active X-linked locus and the degenerate Y-linked locus supports a common ancestry for these two loci.

Characterisation of the coding sequence and fine mapping of the human DFFRY gene and comparative expression analysis and mapping to the Sxrb interval of the mouse Y chromosome of the Dffry gene.

DFFRY (the Y-linked homologue of the DFFRX Drosophila fat-facets related X gene) maps to proximal Yq11.2 within the interval defining the AZFa spermatogenic phenotype. The complete coding region of DFFRY has been sequenced and shows 89% identity to the X-linked gene at the nucleotide level. In common with DFFRX , the potential amino acid sequence contains the conserved Cys and His domains characteristic of ubiquitin C-terminal hydrolases. The human DFFRY mRNA is expressed in a wide range of adult and embryonic tissues, including testis, whereas the homologous mouse Dffry gene is expressed specifically in the testis. Analysis of three azoospermic male patients has shown that DFFRY is deleted from the Y chromosome in these individuals. Two patients have a testicular phenotype which resembles Sertoli cell-only syndrome, and the third diminished spermatogenesis. In all three patients, the deletions extend from close to the 3' end into the gene, removing the entire coding sequence of DFFRY. The mouse Dffry gene maps to the Sxrb deletion interval on the short arm of the mouse Y chromosome and its expression in mouse testis can first be detected between 7.5 and 10.5 days after birth when type A and B spermatogonia and pre-leptotene and leptotene spermatocytes are present.

Gene Sequence, Localization, and Evolutionary Conservation ofDAZLA,a Candidate Male Sterility Gene

We have isolated the human homologue of the mouse germ cell-specific transcriptTpx2,which we had previously mapped to mouse chromosome 17. Sequence analysis shows that the human gene is part of theDAZ(Deleted in Azoospermia) family, represents the human homologue of the mouseDazlaandDrosophila boulegenes, and is termedDAZLA.LikeDazlaandboule, DAZLAis single copy and maps to 3p25. This defines a new region of synteny between mouse chromosome 17 and human chromosome 3. UnlikeDAZ,which has multiple DAZ repeats,DAZLAencodes a putative RNA-binding protein with a single RNA-binding motif and a single DAZ repeat. DAZLA is more closely related to Dazla in the mouse than to the Y-linked homologue DAZ (88% identity overall with mouse Dazla compared to 76% identity with the human DAZ protein sequence). Southern blot analysis showed thatDAZLAis autosomal in all mammals tested and thatDAZhas been recently translocated to the Y chromosome, sometime after the divergence of Old World and New World primates. To investigate the evolutionary relatedness ofDAZLAandDAZfurther, their partial genomic structures were obtained and compared. This revealed that the genomic organization of both genes in the 5′ region is highly conserved.DAZLAis a new member of theDAZfamily of genes, which is associated with spermatogenesis and male sterility. Familial cases of male infertility in humans show an autosomal recessive mode of inheritance. It is possible that some of these families may carry mutations in theDAZLAgene.

Characterization of a cluster of sulfatase genes on Xp22.3 suggests gene duplications in an ancestral pseudoautosomal region.

An obligatory crossing-over event between the X and Y chromosomes in mammals occurs at each male meiosis within the 2.6 Mb of DNA defining the pseudoautosomal region (PAR). Genes located within or near the human PAR have homologous copies on the X and Y chromosomes, escape X inactivation and appear to be highly divergent throughout evolution. We have characterized the genomic structure of two genes from a recently identified cluster of sulfatase genes (ARSD and ARSE) located in the Xp22.3 region, and of their homologs on the Y chromosome. Our results indicate that the ARSD and ARSE genes from within this cluster have a conserved genomic organization, shared also by another Xp22.3 gene, STS, but completely different from that of all the other sulfatase genes. Sequence analysis of the Y-linked homologs indicate that they represent truncated pseudogenes. Sequence identity values between the X and Y copies of each gene is on average 91%, significantly higher than the values obtained by comparing different members of the family. FISH mapping experiments performed in several primate species revealed an identical localization of the X-linked copies to that in man, but different localizations of the Y homologs. Together, our data indicate that the cluster of sulfatase genes on human Xp22.3 was created through duplication events which probably occurred in an ancestral PAR, and support the view that the PAR has undergone multiple changes during recent mammalian evolution.

Relationship between the Monosomy X Phenotype and Y-Linked Ribosomal Protein S4 (Rps4) in Several Species of Mammals: A Molecular Evolutionary Analysis ofRps4Homologs

Two isoforms of the human ribosomal protein S4 gene,RPS4XandRPS4Y,are located on the X and Y chromosomes. It has been postulated that haploinsufficiency of these genes may contribute to Turner syndrome. We show here that several animal species that show the Turner-like phenotype on monosomy X have no Y-linkedRps4homolog. There may be another gene(s) that contributes to abnormal phenotypes of monosomy X. Molecular evolutionary analysis shows that the Y-linked andRPS4X-related homologs diverged prior to the radiation of placental mammals and evolved independently. Furthermore, the functional constraints against theRPS4X-related homologs are much stronger than those against the Y-linked homologs.