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A gene named SRY, isolated last year from the sex-determining region of the human Y chromosome, satisfies many of the criteria expected of the testis-determining factor gene. Mutations in SRY have been found in XY females, strongly implicating SRY as the testis-determining gene.
The recent cloning of the Y-linked sex-determining gene SRY has ended one of the most notorious gene hunts in mammalian molecular genetics. Attention has now been turned to characterizing this gene further and studying how it acts as a switch in the choice of male or female developmental pathways.
The genetic mechanisms of sex determination in mammals have not yet been clarified. Y-linked and X-linked zinc finger genes from humans and mice were recently cloned and characterized. The Y-linked zinc finger gene was originally thought to be the testis-determining factor. However, at the present time, it seems clear that this gene is not the master gene triggering the cascade of events leading to sex determination. The human testis-determining factor gene is known to be located in the nonhomologous region of the short arm of the Y chromosome, close to an Alu repeat that marks the boundary of the pseudoautosomal region. Lately, this region has been found to contain a new gene that is a strong candidate for the male-determining factor. Data on humans and on laboratory and vole mice showing abnormalities of the sex determination mechanisms indicate that testis development depends on the presence of a testis-determining factor gene functioning in cooperation with X-linked and autosomal genes. Ovary development would depend on the absence of the testis-determining factor and perhaps on an alternative splicing of the transcripts from autosomal and X-linked genes involved in sex determination.
Sex reversal occurs naturally in the wood lemming (Myopus schisticolor) due to the presence in populations of this species of a variant (mutated) X chromosome, designated X*. Thus, X*Y animals develop into females, whereas XY animals develop into normal males. Chromosome mapping by in situ hybridization of DNA sequences homologous to the human ZFY gene localized the wood lemming Zfx sequences to region p12----p11 on both the wild-type X and the mutated X* chromosomes, at or proximal to a presumed breakpoint (Xp12) involved in the generation of the X* chromosome from the normal X, and Zfy sequences along the entire short arm of the Y chromosome. Differences between Zfx and Zfx* were readily detected by Southern blot analysis. However, both the Zfx and Zfx* genes expressed similarly sized transcripts in all adult somatic tissues investigated. Although the precise molecular difference between the Zfx and Zfx* genes is still unknown, their chromosomal location suggests that either Zfx or some other closely linked gene(s) on the X chromosome may be a major X-linked sex-determining gene, Tdx, which in the X* chromosome fails to interact properly with the Y-linked testis-determining gene, Tdy, thus causing X*Y embryos to develop into females. At least 15 copies of wood lemming Zfy sequences are distributed along the short arm of the Y chromosome. Northern hybridization analyses of adult tissues and somatic cell lines indicated that these Zfy repeats were transcriptionally inactive. Normally, 3-kb Zfy (ZFY) transcripts are readily detected in mouse and human testes, especially in the germ cells. It has therefore been postulated that expression of the Zfy (ZFY) gene may be important for spermatogenesis. Whether the lack of sufficient Zfy transcripts in the testis of the adult wood lemming has any impact on spermatogenesis in this species is still to be elucidated by further studies.
We have cloned and sequenced transcripts from the X- and Y-linked zinc-finger genes ZFX and ZFY respectively and discuss a possible mechanism of post-transcriptional control by which these genes can be widely expressed but translated in only specific tissues. We report the identification of a novel 3'UTR (untranslated region) present in ZFY which is highly conserved among primates and contains a series of motifs implicated as mRNA instability determinants. These sequences can be substantially removed by polyadenylation directed from consensus (AATAAA) and non-consensus (AATATAAA) sequences in adult testis. The DNA-binding domains of the ZFY and ZFX proteins are compared using present models for zinc-finger/DNA interactions. Additionally, the genomic organisation of the ZFY coding sequence is presented as compared to that of ZFX.
Differences were detected between male-specific antigen(s) from BALB/c and C57BL/10 mice. Reciprocal crosses between these strains were analysed by means of a popliteal lymph node assay enumerating cells secreting IgM and IgG in a T-dependent bystander B-cell response. The responses, while being indirect, weak and variable, suggested that there are differences in 'immunogenicity' coded by Y-linked (male-specific) genes. This conclusion was strengthened by the results of experiments carried out in Y-backcross mice, where spleen cells from male C57BL mice with a BALB/c-Y (B10.C-YC) stimulated low popliteal lymph node responses in female littermates in comparison with C57BL mice with their own Y-chromosome. In contradistinction, male spleen cells from a BALB/c with a C57B1/10-Y chromosome (C.B10-YB), injected into a hind footpad of a female littermate, induced a relatively higher popliteal lymph node response.
Campomelic dysplasia (Cd) occurs combined with sex reversal resulting in XY females. The recent identification of candidate genes for sex determination/differentiation and of a sex determining region on the human Y chromosome prompted the authors to study these genes for mutations in patients with Cd and sex reversal. In a total of five cases, no evidence for a mutation in the genes SRY, ZFY, ZFX, MEA and some anonymous Y-linked sequences was found. In addition to Southern analysis, gene expression of ZFY, ZFX and MEA was found to be normal as well. It is concluded that sex reversal in this condition is due to mutation in a so far unidentified gene which may act secondary to the testis-determining factor (TDF).
The Drosophila melanogaster Y chromosome is currently known to contain 13 single-copy protein-coding genes, six of which are essential for male fertility, as well as several non-coding genes and abundant repetitive DNA. Localization of Y-linked sequences has traditionally relied on labor-intensive crosses using Kennison's translocation strains, which map Y-linked loci by generating flies deficient for each of the six Y-chromosome fertility regions (ks-1, ks-2, kl-1, kl-2, kl-3, and kl-5). Here we present Digital Kennison, a computational pipeline that recasts this classical mapping strategy as a sequence-based analysis. The pipeline queries eight genomic databases derived from Kennison's strains using BLAST and read coverage, assigning sequences to fertility regions or the centromeric region with a calibrated confidence score. We benchmarked the method on 60 Y-linked sequences spanning all seven regions, including single-copy protein-coding genes, Mst77Y family members, non-coding RNAs, and the centromere. Digital Kennison achieved 97% precision while resolving challenging cases, including boundary-spanning genes (PRY and Ppr-Y), fragmented Mst77Y copies, and FDY, which has a closely related autosomal paralog. Beyond validating known localizations, the pipeline localized the unmapped gene CG41561 to the kl-1region and reassigned the transcript CR40629-RC from the kl-2 region to kl-5. It also localized 7 of 16 recently transferred Y-linked sequences, including 4 with high confidence. Applied to 904 R6 scaffolds, Digital Kennison assigned 75% to fertility regions, including five currently annotated as autosomal-pericentromeric. Digital Kennison reduces sequence localization from weeks of genetic crosses to minutes of computation while preserving the power of classical translocation mapping.
Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails and platyfish of the genus Xiphophorus, diverse melanic pigmentation patterns are thought to be controlled by a region on the sex chromosomes classically referred to as the "macromelanophore determining locus". Despite nearly a century of study, the identity of the causal gene remains controversial, partially due to previous inability to fully sequence the sex chromosomes. Here, we characterize and investigate two melanin-based pigmentation phenotypes in the species X. nezahualcoyotl: "spotted side" and "marmoratus". We generate a gapless near-telomere-to-telomere X. nezahualcoyotl assembly and perform GWAS to identify regions associated with pigmentation pattern variation and sex-determination. We find both patterns map near the sex-determining region and to a narrow interval near the oncogene xmrk. By generating additional long-read assemblies of sex chromosomes derived from individuals with distinct phenotypes, we find haplotypes containing xmrk can be both X- and Y-linked, and vary dramatically in gene content, structure, and accumulation of repetitive elements including a newly described composite satellite. This variability may impact the region's stability and affect recombination between haplotypes associated with each pattern. Our results shed light on a longstanding debate surrounding the genetic architecture of sex-linked phenotypes. More generally, we showcase how long-read sequencing can reveal phenotypic variation linked to complex and dynamic genomic regions, which may contribute to the evolution of diverse sex-linked traits.
The nucleotide sequence of the human cDNA encoding ubiquitin-activating enzyme E1 is more than 99% identical with the human A1S9T cDNA, a gene that has been shown to complement the temperature-sensitive mutant mouse cell line, tsA1S9. The amino acid sequences of the proteins encoded by these two cDNA sequences are identical, and both cDNAs were previously shown to be located in the same region of the human X chromosome; thus, ubiquitin-activating enzyme E1 and A1S9T appear to be the same gene, designated UBE1. By in situ hybridization to metaphase chromosomes from male mice and by Southern blot analysis of male and female mouse DNA, we show that, in the mouse, a human UBE1 cDNA probe identified both X- and Y-linked loci. Ube1 is located at band A2 of the mouse X Chromosome (Chr) and Ube2 on the short arm of the Y Chr. This is in contrast to the situation in the human, where there is no evidence for Y-linked sequences related to UBE1. Mapping of the Ube1 gene in interspecific backcrosses between Mus spretus and C57BL/6 shows that the Ube1 locus maps close to Timp, in a conserved region of the mouse and human X Chrs that include Otc, Cybb, Syn1, Timp, and Araf. Expression of Ube1 on the inactive X Chr was examined to determine whether this gene is subject to X-Chr inactivation in the mouse, as there is previous evidence that the human UBE1 gene escapes, at least partially, X inactivation. Sequencing of reverse transcriptase polymerase chain reaction (RT-PCR) products from M. spretus, C57BL/6J, and T(X;16)16H x M. spretus F1 female mice indicates that the mouse Ube1 gene is subject to X-Chr inactivation in vivo. This represents a new example of differences between the sex chromosomes of mouse and human.
Frequencies of sex chromosome aneuploid sperm were measured for standard and "sex-ratio" Drosophila pseudoobscura males with identical genetic backgrounds. The "sex-ratio" males produced a 15.6-fold higher frequency of nullo-XY sperm than the standard males produced, but diplo-XY sperm were produced at the same rate in the two types of males. "Sex-ratio" males with the same SR chromosome but with different chromosome backgrounds were found to produce different frequencies of sterile sons. These results indicate that strains of D. pseudoobscura differ at autosomal or Y-linked modifiers of sr. Such modifiers are similar to the msr genes found in the L116 strain of this species.
In order to evaluate the role of SRY in the determination of the testis, we sequenced the conserved domain of the SRY gene in 8 patients with 46,XY gonadal dysgenesis and 3 patients with related disorders, and compared our data with those obtained in 6 other similar studies. In our study, a 609-bp fragment of SRY was amplified by the polymerase chain reaction and the internal conserved motif was sequenced. SRY sequences did not differ from those in normal males in any of our patients. Overall, 5 de novo mutations have been identified among 56 patients with sporadic XY gonadal dysgenesis (8.9%), and 2 de novo mutations have been identified among 18 patients with related conditions (11%). The unexpectedly low frequency of mutations within the SRY conserved domain in these patients could be caused by undetected Y-linked mutations outside the conserved domain in regions that control transcription during development (e.g., promoter/enhancer regions) or to downstream mutations in other sex-determining genes that need not map to the Y.
A reverse transcriptase-polymerase chain reaction assay (RT-PCR) was used quantitatively to measure accumulated levels of RNA transcripts in total mouse RNAs derived from male germ cells at various spermatogenic stages. RNA levels for two X-linked enzymes, phosphoglycerate kinase (PGK-1) and hypoxanthine phosphoribosyl transferase (HPRT), both decrease during spermatogenesis, although the transcript levels decrease much more rapidly for PGK-1. RNA for the Y-linked ZFY (zinc finger protein) is elevated in all spermatogenic cell fractions tested, being particularly high in leptotene/zygotene spermatocytes and round spermatids. RNA for adenine phosphoribosyltransferase (APRT) increases 5-fold to a peak during late pachynema. RNA for PGK-2, undetectable in spermatogonial cells, increases at least 50-fold by the round spermatid stage. DNA (cytosine-5-)-methyltransferase (MTase) transcript levels are over an order of magnitude higher throughout spermatogenesis than in non-dividing liver cells.
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Field-female killing (FK) systems based on deleterious mutations and Y-autosome translocations are being evaluated for genetic control of the Australian sheep blowfly, Lucilia cuprina. Experience during field trials has shown that mass-reared colonies of FK strains are subject to genetic deterioration, caused mainly by genetic recombination in males. A previous study found higher male recombination frequencies in two Y-linked translocation strains than in chromosomally normal males. However, the results of the present study indicate that breakage of the Y chromosome is neither sufficient nor necessary for increased levels of male recombination. The frequency of male recombination appears to be unrelated to the presence of specific chromosome rearrangements.
To determine whether the gene that controls the expression of H-Y ("male") antigen on human cells is Y-linked, we have compared the H-Y antigen level in normal males with that in three males with two Y chromosomes. Leukocytes from one XXYY and two XYY males express more H-Y antigen than leukocytes from normal XY males. We conclude that a structural gene or positive regulatory gene for H-Y antigen is on the human Y chromosome. Testing for the H-Y antigen may be of benefit in patients who have signs of masculinization but who lack an identifiable Y chromosome. Positive results for the H-Y antigen would be tentative evidence that the corresponding region of the Y chromosome was present, perhaps as part of a translocation, despite the absence of a typical Y chromosome.
41 Y-linked DNA probes that detect sequences on the Y chromosome long arm have been used to analyse genomic DNA from a series of 23 patients with deletions of Yq. Southern blot analysis has differentiated 15 distinct breakpoints, which divide Yq into 14 mapping intervals. From the pattern of DNA sequences present in each patient, it has been possible to produce a congruent deletion map, with the exception of two cases which are not compatible with the consensus order. These patients can be explained by the presence of inversion polymorphisms on Yq in the general population or by complex rearrangements induced during the formation of the deleted chromosomes. The distribution of sequences on the Y long arm has defined distinct regions of homology with autosomes, the Y short arm and the long and short arms of the X. A number of the patients have been typed for the presence or absence of H-Y antigen (as determined by the cytotoxic T-cell assay) and it has been possible, from analysis of informative cases, to assign the locus to the proximal region of the Yq euchromatin.
Dependable methods were developed for preimplantation sexing of human IVF embryos, for use in clinical settings where prospective parents are at high risk for transmission of X-linked diseases. Using single cultured cells and blastomeres from human embryos as model systems, a multiplex protocol was developed for rapid analysis via nested polymerase chain reaction (PCR). Reliability was enhanced by co-amplification of conserved amelogenin gene segments from both X and Y chromosomes, as well as Y-linked DYZ1 repetitive elements. Each cell was manually isolated and individually washed to avoid potential contaminants. Multiplex amplification allowed recognition of spurious amplification failures specific to particular amelogenin single-copy targets. The X-linked internal control and multiple Y-linked markers allowed recognition and exclusion of most aberrant samples, thus averting potential misdiagnosis. The optimized single-cell protocol reduced experimental sexing errors to < 2% (1/60), but also revealed potential pitfalls of single-cell analysis. With human triploid embryos, separate sampling of individual blastomeres provided concordant female or male signals. Slight modification adapted the procedure for diagnosis of biopsy material from blastocyst stage embryos, allowing separate analysis of multiple tubes containing multiple cells for improved reliability.