An association and haplotype analysis of porcine maternal infanticide: a model for human puerperal psychosis?

An association analysis using the Illumina porcine SNP60 beadchip was performed to identify SNPs significantly associated with porcine maternal infanticide. We previously hypothesised that this was a good animal model for human puerperal psychosis, an extreme form of postnatal mood disorder. Animals were selected from carefully phenotyped unrelated infanticide and control groups (representing extremes of the phenotypic spectrum), from four different lines. Permutation and sliding window analyses and an analysis to see which haplotypes were in linkage disequilibrium (LD) were compared to identify concordant regions. Across all analyses, intervals on SSCs 1, 3, 4, 10, and 13 were constant, contained genes associated with psychiatric or neurological disorders and were significant in multiple lines. The strongest (near GWS) consistent candidate region across all analyses and all breeds was the one located on SSC3 with one peak at 23.4 Mb, syntenic to a candidate region for bipolar disorder and another at 31.9 Mb, syntenic to a candidate region for human puerperal psychosis (16p13). From the haplotype/LD analysis, two regions reached genome wide significance (GWS): the first on SSC4 (KHDRBS3 to FAM135B), which was significant (-logP 5.57) in one Duroc based breed and is syntenic to a region in humans associated with cognition and neurotism; the second on SSC15, which was significant (-log10P 5.68) in two breeds and contained PAX3, which is expressed in the brain.

Association of multi-pathogenic infections with BAT2, CXCL12, Mx1 and EHMT2 variations in pigs

Porcine reproductive and respiratory syndrome virus (PRRSV), Haemophilus parasuis and Pseudorabies become a widespread problem causing great economic losses associated with reproductive disturbance, respiratory diseases, neonatal mortality, fibrinous polyserositis, meningitis and arthritis in the pig industry. The important candidate genes are assumed to play crucial roles in host defense against the diseases. The aims of this study were to evaluate the variants in HLA-B associated transcript 2 (BAT2), CXCL12, myxovirus resistance protein 1 (Mx1) and EHMT2 genes and their effects on the risk of infection PRRSV and H. parasuis in a case-control (diseased-healthy pigs) population of Duroc × Landrace × LargeWhite. The results showed that the mutations in BAT2, Mx1 and EHMT2 genes were significantly associated with the antibody and the reisk of infection PRRSV and H. parasuis. Those individuals with AA genotype of BAT2 had significantly higher Pseudorabies virus antibody than that with GG and GA (P < 0.05), and the individuals with TT genotype of EHMT2 generated higher Hog Cholera and Pseudorabies virus antibody than that wtih GG and GA (P < 0.01). These results indicated that the polymorphisms in Mx1, BAT2 and EHMT2 genes changed the diseases susceptibility and could be the potential markers assisting the pig breeding selection and disease resistance.

Effects of FUT1 gene mutation on resistance to infectious disease

Alpha-(1,2)-fucosyltransferase (FUT1) gene has been identified as a candidate gene for regulating the expression of Escherichia coli F18 receptor gene (ECF18R) which promotes adherence of Enterotoxigenic (ETEC) and Verotoxigenic (VTEC) Escherichia coli (E. coli) via F18 fimbriae. In order to illustrate the polymorphisms of FUT1 and their effects on resistance to natural infection by Porcine Respiratory and Reproductive Symdrome Virus (PRRSV) and Haemophilus parasuis, the distributions of different genotypes and the relative risks of disease incidence in pigs were investigated. A total of 1,041 pigs representing three European breeds (Duroc, Landrace and LargeWhite), five Chinese local breeds (Wild pig, Small MeiShan, QinPing, JinHua, and JianLi) and three commercial populations (LargeWhite × JianLi, Duroc × Landrace × LargeWhite and Duroc × wild pig) were selected to analyze the genotype of the FUT1 gene by PCR-RFLP. Only the GG genotype associated with susceptibility to ECF18 bacteria was detected in Chinese local pig breeds and a population of LargeWhite × JianLi, while the AA genotype which confers resistance to ECF18 was detected in two European breeds (Duroc and LargeWhite), two populations of Duroc × wild pig and Duroc × Landrace × LargeWhite. Regarding relative risk of incidence, Duroc × Landrace × LargeWhite with genotypes GG or AG showed greater relative risk (OR = 2.040, P = 0.025; OR = 1.750, P = 0.081, respectively) than those with genotype AA during natural infection by both PRRSV and Haemophilus parasuis. It can be concluded that the mutation of FUT1 gene might play a role in pig infection by multi-pathogens, and that AA may be a favourable genotype for increasing the resistance to disease.

Analysis of X chromosome genomic DNA sequence copy number variation associated with premature ovarian failure (POF)

BACKGROUND

Premature ovarian failure (POF) is a heterogeneous disease defined as amenorrhoea for >6 months before age 40, with an FSH serum level >40 mIU/ml (menopausal levels). While there is a strong genetic association with POF, familial studies have also indicated that idiopathic POF may also be genetically linked. Conventional cytogenetic analyses have identified regions of the X chromosome that are strongly associated with ovarian function, as well as several POF candidate genes. Cryptic chromosome abnormalities that have been missed might be detected by array comparative genomic hybridization.

METHODS

In this study, samples from 42 idiopathic POF patients were subjected to a complete end-to-end X/Y chromosome tiling path array to achieve a detailed copy number variation (CNV) analysis of X chromosome involvement in POF. The arrays also contained a 1 Mb autosomal tiling path as a reference control. Quantitative PCR for selected genes contained within the CNVs was used to confirm the majority of the changes detected. The expression pattern of some of these genes in human tissue RNA was examined by reverse transcription (RT)-PCR.

RESULTS

A number of CNVs were identified on both Xp and Xq, with several being shared among the POF cases. Some CNVs fall within known polymorphic CNV regions, and others span previously identified POF candidate regions and genes.

CONCLUSIONS

The new data reported in this study reveal further discrete X chromosome intervals not previously associated with the disease and therefore implicate new clusters of candidate genes. Further studies will be required to elucidate their involvement in POF.

Transcriptional profiling of luteinizing hormone receptor-deficient mice before and after testosterone treatment provides insight into the hormonal control of postnatal testicular development and Leydig cell differentiation

Luteinizing hormone (LH) is a key regulator of male fertility through its effects on testosterone secretion by Leydig cells. Transcriptional control of this is, however, currently poorly understood. Mice in which the LH receptor is knocked out (LuRKO) show reduced testicular size, reduced testosterone, elevated serum LH, and a spermatogenic arrest that can be rescued by the administration of testosterone. Using genome-wide transcription profiling of LuRKO and control testes during postnatal development and following testosterone treatment, we show that the transcriptional effects of LH insensitivity are biphasic, with an early testosterone-independent phase and a subsequent testosterone-dependent phase. Testosterone rescue re-enables the second, testosterone-dependent phase of the normal prepubertal transcription program and permits the continuation of spermatogenesis. Examination of the earliest responses to testosterone highlights six genes that respond rapidly in a dose-dependent fashion to the androgen and that are therefore candidate regulatory genes associated with the testosterone-driven progression of spermatogenesis. In addition, our transcriptional data suggest a model for the replacement of fetal-type Leydig cells by adult-type cells during testicular development in which a testosterone feedback switch is necessary for adult Leydig cell production. LH signaling affects the timing of the switch but is not a strict requirement for Leydig cell differentiation.

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus

Background

Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult.

Results

In this report, we have analyzed native host (piglets) gene expression changes in response to acute pseudorabies virus infection of the brain and lung using a printed human oligonucleotide gene set from Illumina. A total of 210 and 1130 out of 23,000 transcript probes displayed differential expression respectively in the brain and lung in piglets after PRV infection (p-value < 0.01), with most genes displaying up-regulation. Biological process and pathways analysis showed that most of the up-regulated genes are involved in cell differentiation, neurodegenerative disorders, the nervous system and immune responses in the infected brain whereas apoptosis, cell cycle control, and the mTOR signaling pathway genes were prevalent in the infected lung. Additionally, a number of differentially expressed genes were found to map in or close to quantitative trait loci for resistance/susceptibility to pseudorabies virus in piglets.

Conclusion

This is the first comprehensive analysis of the global transcriptional response of the native host to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to be of interest for the further study and understanding of host viral gene interactions.

Sex ratio bias in early-dead embryos of chickens collected during the first week of incubation

According to Mendelian heredity laws, the sex ratio of a given chicken population during hatching is expected to be 1:1. In this study, we collected 432 chicken embryos that died during the first week of incubation from 5 different breeds. The sexes of the early-dead embryos were determined by using the previously described molecular sexing technique of double PCR. The female-to-male sex ratio was analyzed for departure from the expected 1:1 sex ratio by chi(2) testing. These results showed that the number of female dead embryos was significantly greater than that of males in the Hubei local breeding stock, Zhusi, and Hy-line Variety Brown (P < 0.05, P < 0.01, P < 0.01 respectively), with observed female-to-male sex ratios of 1.40:1, 2.03:1, and 2.22:1, respectively. Two other Chinese local breeds (the Yellow chicken and the Aijiaohuang chicken) also showed altered sex ratios, although the differences were not significant. Altogether, these results indicated that female chickens were more likely than male chickens to die at the early stages of incubation.

Identification of mutations of zona pellucida glycoprotein (ZP3) and its association with pig reproductive traits

Reproduction is a complex trait, controlled by genetic and environmental factors. Genetic improvement of this trait is important for animal breeders to improve the animal's production efficiency. Apart from genetic factors, animal production can be affected by environmental factors, i.e. the nursing ability of the sow, which is in turn affected directly by effective teat number (teats producing milk normally, TN) and number of piglets born alive (NBA). The objective of this study was to find new mutations, such as single nucleotide polymorphisms (SNPs) from the Zona Pellucida glycoprotein gene (ZP3) using Single Strand Chain Polymorphism (SSCP) and nucleotide sequencing and to investigate association between genetic variations and sow reproductive traits. We identified 13 new SNPs from exon 1, two new SNPs from intron 2, one SNP from intron 6 and a 18 bp (GCACGTGGTCCTCCTGG)-deletion/insertion from intron 2 of the ZP3 gene. Five out of these mutations were selected to genotype in five different breeds (Small Meishan, Qingping, Duroc, Landrace and Large White) and association with reproductive traits in European breeds (Duroc, Landrace and Large White). The sows with genotype AA had more 1.11 piglets NBA than of the sows with genotype AB (p < 0.05) in the 18 bp deletion/insertion of intron 2, while non-significant associations between the other mutations and reproductive traits (NBA and TN) were found.

Analysis of sex chromosome abnormalities using X and Y chromosome DNA tiling path arrays

BACKGROUND

Array comparative genomic hybridisation is a powerful tool for the detection of copy number changes in the genome.

METHODS

A human X and Y chromosome tiling path array was developed for the analysis of sex chromosome aberrations.

RESULTS

Normal X and Y chromosome profiles were established by analysis with DNA from normal fertile males and females. Detection of infertile males with known Y deletions confirmed the competence of the array to detect AZFa, AZFb and AZFc deletions and to distinguish between different AZFc lesions. Examples of terminal and interstitial deletions of Xp (previously characterised through cytogenetic and microsatellite analysis) have been assessed using the arrays, thus both confirming and refining the established deletion breakpoints. Breakpoints in iso-Yq, iso-Yp and X-Y translocation chromosomes and X-Y interchanges in XX males are also amenable to analysis.

DISCUSSION

The resolution of the tiling path clone set used allows breakpoints to be placed within 100-200 kb, permitting more precise genotype/phenotype correlations. These data indicate that the combined X and Y tiling path arrays provide an effective tool for the investigation and diagnosis of sex chromosome copy number aberrations and rearrangements.

Transcript profiles of some developmentally important genes detected in bovine oocytes and in vitro-produced blastocysts using RNA amplification and cDNA microarrays

To study the mRNA transcript profiles of some potential candidate developmental genes during bovine oocyte and blastocyst stages, RNA amplification procedures, cDNA microarray of 82 target genes spotted onto glass slide and real-time polymerase chain reaction (PCR) were used. Messenger RNAs were isolated from in vitro-produced bovine matured oocytes and blastocysts. Using equal amounts of input mRNAs but different cycles of amplifications, cDNAs were produced and served as template for RNA amplification by the in vitro transcriptions. After amplification, the RNA yields transcribed from cDNAs of different cycles were evaluated both by hybridization on the cDNA microarrays and by using real-time PCR techniques. The analyses indicated best results from lower amplification cycle templates with consistent signals at hybridization. Generally, the RNA yield was directly proportional to the amplification cycle but inversely related with signal consistency at repeated hybridizations. Using the protocols established, equal amounts of amplified RNA from matured oocytes and blastocysts were hybridized to the array. Analyses of replicated hybridizations indicated that 35 transcripts were differentially expressed. Most of these were not described in previous bovine embryo studies. Independent analyses of 23 transcripts with real-time PCR and unamplified RNA confirmed the results of 22 genes. Moreover, the functional analyses showed various roles related to development. Hence, it is possible to conclude that the genes identified here are potential candidates for characterizing developmental competence, and that the methods established can be used for large-scale gene expression analysis with more comprehensive arrays.

Modulation of the mouse testis transcriptome during postnatal development and in selected models of male infertility

The aim of this study is to develop an overview of genetic events during spermatogenesis using a novel, specifically targeted gonadal gene set. Two subtracted cDNA libraries enriched for testis specific and germ cell specific genes were constructed, characterized and sequenced. The combined libraries contain >1905 different genes, the vast majority previously uncharacterized in testis. cDNA microarray analysis of the first wave of murine spermatogenesis and of selected germ cell-deficient models was used to correlate the expression of groups of genes with the appearance of defined germ cell types, suggesting their cellular expression patterns within the testis. Real-time RT-PCR and comparison to previously known expression patterns confirmed the array-derived transcription profiles of 65 different genes, thus establishing high confidence in the profiles of the uncharacterized genes investigated in this study. A total of 1748 out of 1905 genes showed significant change during the first spermatogenic wave, demonstrating the successful targeting of the libraries to this process. These findings highlight unknown genes likely to be important in germ cell production, and demonstrate the utility of these libraries in further studies. Transcriptional analysis of well-characterized mouse models of infertility will allow us to address the causes and progression of the pathology in related human infertility phenotypes.

Breakpoint analysis of Turner patients with partial Xp deletions: implications for the lymphoedema gene location

BACKGROUND

Turner syndrome is characterised by a 45,X karyotype and a variety of skeletal, lymphoedemic, and gonadal anomalies. Genes involved in the Turner phenotype are thought to be X/Y homologous with the X genes escaping X inactivation. Haploinsufficiency of the SHOX gene has been reported to cause the short stature seen in Turner syndrome patients. More recently, mutations of this gene have been shown to be associated with other skeletal abnormalities, suggesting that haploinsufficiency of SHOX causes all the Turner skeletal anomalies. No such gene has yet been identified for the lymphoedemic features.

METHODS

Fluorescence in situ hybridisation (FISH) analysis with PAC clones on nine patients with partially deleted X chromosomes was performed.

RESULTS/DISCUSSION

The Turner syndrome stigmata for each patient are described and correlation between the breakpoint and the phenotype discussed. A lymphoedema critical region in Xp11.4 is proposed and its gene content discussed with respect to that in the previously reported Yp11.2 lymphoedema critical region.

A novel poly(A)-binding protein gene (PABPC5) maps to an X-specific subinterval in the Xq21.3/Yp11.2 homology block of the human sex chromosomes

The gene-poor human-specific Xq21.3/Yp11.2 block of homology exhibits 99% nucleotide identity, with the exception of an internal X-specific region containing the marker DXS214. This paper describes the characterization of a novel gene (PABPC5) from this X-specific subinterval that belongs to the poly(A)-binding protein gene family. The genomic structure of PABPC5 covers 4061 bp of an uninterrupted open reading frame (ORF) and a 5'UTR spanning across two exons and associated with a CpG island; the potential 382-amino-acid protein contains four RNA recognition motif domains. PABPC5 has 73% nucleotide identity with PABPC4 over 1801 bp of the ORF. At the protein level, 60% identity and 75% similarity are obtained in the comparison with human PABPC4, as well as human, mouse, and Xenopus PABPC1. RT-PCR indicates that PABPC5 is expressed in fetal brain and in a range of adult tissues. Conservation of the PABPC5 ORF and genomic structure is shown in primates and rodents. The close proximity of this gene to translocation breakpoints associated with premature ovarian failure makes it a potential candidate for this condition.

Characterization of the human Xq21.3/Yp11 homology block and conservation of organization in primates

The Xq21.3/Yp11 homology block on the human sex chromosomes represents a recent addition to the Y chromosome through a transposition event. It is believed that this transfer of material occurred after the divergence of the hominid lineage from other great apes. In this paper we investigate the structure and evolution of the block through fluorescence in situ hybridisation, contig assembly, the polymerase chain reaction, exon trapping, sequence comparison, and annotation of sequence data. The overall structure is well conserved between the human X chromosome and the Y chromosome as well as between the X chromosomes from different primates. Although the sequence data reveal a high level of nucleotide sequence identity for the human X and Y, there are regions of significant divergence, such as that around the marker DXS214. These are presumably the consequence of multiple rearrangements during evolution and are of particular importance with respect to the potential gene content in this segment of the interval.

Insights into the molecular basis of male infertility

The study of the genetic basis of human male infertility is complicated by genetic heterogeneity and because linkage analysis studies are difficult. The study has been limited so far to the analysis of genes located on the Y chromosome. Several genes and gene families have been discovered and mutation analysis of these candidate genes in infertile patients is ongoing. In recent years, several mouse models with impaired spermatogenesis or fertility have also been analysed, expanding our knowledge about the molecular basis of spermatogenesis and male fertility.

The role of the Y chromosome in male infertility

It was suggested by Ronald Fisher in 1931 that genes that benefit the male (including those required for spermatogenesis) would accumulate on the Y chromosome. Following the discovery that microdeletions of the Y chromosome were associated with diverse spermatogenic phenotypes, at least three intervals that contain one or more genes controlling male germ-cell differentiation have been identified in humans. These intervals, named AZFa, AZFb and AZFc, have been mapped, cloned and examined in detail for the presence of functional genes. In this review, I have discussed the genes that map to the AZF intervals and the evidence indicating which ones are the most likely candidates underlying Y-linked male infertility. In addition, I have considered the analysis of key intervals on the mouse Y chromosome, where it provides comparative data supporting the role of a candidate gene in an infertility phenotype.

The role of human and mouse Y chromosome genes in male infertility

It was suggested by Ronald Fisher in 1931 that genes involved in benefit to the male (including spermatogenesis genes) would accumulate on the Y chromosome. The analysis of mouse Y chromosome deletions and the discovery of microdeletions of the human Y chromosome associated with diverse defective spermatogenic phenotypes has revealed the presence of intervals containing one or more genes controlling male germ cell differentiation. These intervals have been mapped, cloned and examined in detail for functional genes. This review discusses the genes mapping to critical spermatogenesis intervals and the evidence indicating which are the most likely candidates underlying Y-linked male infertility.

Conservation of PCDHX in mammals; expression of human X/Y genes predominantly in brain

Protocadherins are members of the cadherin superfamily involved in cell-cell interactions critical in the development of the central nervous system. This paper describes the isolation, sequence, and expression analysis of two novel protocadherin genes from the hominid specific Yp11.2/Xq21.3 block of homology between the sex chromosomes. The X-(PCDHX) and Y-linked (PCDHY) genes share 98.1% nucleotide and 98.3% amino acid identity and have an identical gene structure of six exons. The open reading frames of PCDHX and PCDHY encode proteins of 1025 and 1037 amino acids respectively and specify seven extracellular cadherin domains. Small differences in amino acid sequence affect regions that potentially have a large impact on function: thus, the X and Y genes may be differentiated in this respect. Sequence analysis of cDNA clones shows that both the X and Y loci are transcribed. RT-PCR expression analysis of mRNA from a variety of tissues and cell lines has demonstrated that both transcripts are expressed predominantly in the brain, with differential regional expression. From studies in the NTERA pluripotential cell line (which differentiates along neuronal and spermatogenic pathways in response to retinoic acid), it emerges that the X and Y-linked genes are regulated differently. This indicates that PCDHX and PCDHY possess different promoter regions. These findings suggest a role for PCDHX and PCDHY in the brain, consistent with the involvement of protocadherins in segmental brain morphogenesis and function. The implications of Y-linked genes expressed predominantly in tissues and organs other than the testis are considered within the context of the concept of sexual selection.

Five cases of isolated glycerol kinase deficiency, including two families: failure to find genotype:phenotype correlation

Little is understood of the genotype/phenotype correlations in X linked glycerol kinase deficiency (GKD) where most cases are caused by extensive deletions of Xp21, which often include genes flanking the GK locus. Few cases of isolated GKD have been investigated where the phenotype is not influenced by neighbouring genes. In this paper, we present the mutation data from four confirmed and one suspected case of non-deletion, isolated, X linked GKD and therefore extend the base of patients that can allow an assessment of genotype/phenotype correlations for this disease. The mutations found were two terminations leading to premature truncation of the GK polypeptide chain, one insertion, and an amino acid substitution. Phenotypic variation was observed in two families, where there was more than one affected subject carrying the same mutation, confirming previous studies that suggest there is no correlation between disease severity and genotype. Furthermore, the nature of the mutation in different families does not appear to influence the spectrum of phenotypic variation. In addition, one coding polymorphism in exon 3 has been found. The characterisation of the gene structure has been completed and shows that instead of 19 there are 21 exons.

Comparative sequence analysis of the VHL tumor suppressor gene

Comparative genome analysis may provide novel insights into gene evolution and function. To investigate the von Hippel-Lindau (VHL) disease tumor suppressor gene, we sequenced the VHL gene in seven primate species. Comparative analysis was performed for human, primate, and rodent VHL genes and for a putative Caenorhabditis elegans VHL homologue identified by database analysis. The VHL gene has two translation initiation sites (at codons 1 and 54); however, the relative importance of the full-length translation product (pVHL30) and that translated from the second internal translation initiation site (pVHL19) is unclear. The N-terminal sequence of pVHL30 contains eight copies of a GXEEX acidic repeat motif in human and higher primates, but only three copies were present in the marmoset, and only one copy was present in rodent VHL genes. Evolutionary analysis suggested that the N-terminal repetitive sequence in pVHL30 was of less functional importance than those regions present in both pVHL30 and pVHL19. The VHL gene product is reported to form complexes with various proteins including elongin B, elongin C, VBP-1, fibronectin, Spl, CUL2, and HIF-1. Although most of the regions in pVHL that had been implicated in binding specific proteins demonstrated evolutionary conservation, the carboxy-terminal putative VBP-1 binding site was less well conserved, suggesting that VBP-1 binding may have less functional significance. Although an amino acid substitution (K171T) close to the pVHL elongin binding region was found in baboon, analysis of the structure of human pVHL suggested that this substitution would not interfere with pVHL/elongin C interaction. In general, there was a good correlation between the pVHL domains that demonstrated most evolutionary conservation and those that were most frequently mutated in tumors. Analysis of human/C. elegans conservation and human germline and somatic mutation patterns identified a highly conserved mutation cluster region between codons 74 and 90. However, this region is likely to be important for the structural integrity of pVHL rather than representing an additional protein binding domain.

Familial clear cell renal cell carcinoma (FCRC): clinical features and mutation analysis of the VHL, MET, and CUL2 candidate genes

Familial renal cell carcinoma (RCC) is genetically heterogeneous. Genetic predisposition to clear cell RCC (CCRCC) is a major feature of von Hippel-Lindau (VHL) disease (MIM 193300) and has rarely been associated with chromosome 3 translocations. In addition, familial papillary (non-clear cell) RCC may result from germline mutations in the MET proto-oncogene (MIM 164860). However, rare kindreds with familial CCRCC (FCRC) not linked to the VHL tumour suppressor gene have been described suggesting that further familial RCC susceptibility genes exist. To investigate the genetic epidemiology of FCRC, we undertook a clinical and molecular study of FCRC in nine kindreds with two or more cases of CCRCC in first degree relatives. FCRC was characterised by an earlier age at onset (mean 47.1 years, 52% of cases <50 years of age) than sporadic cases. These findings differ from the only previous report of two FCRC kindreds and have important implications for renal surveillance in FCRC. The molecular basis of CCRCC susceptibility was investigated in nine FCRC kindreds and seven isolated cases with features of possible genetic susceptibility to CCRCC (four bilateral CCRCC aged <50 years and three with unilateral CCRCC aged <30 years). No germline mutations were detected in the VHL or MET genes, suggesting that FCRC is not allelic with VHL disease or HPRC. As binding of the VHL gene product to the CUL2 protein is important for pVHL function, we then searched for germline CUL2 mutations. Although CUL2 polymorphisms were identified, no pathogenic mutations were detected. These findings further define the clinical features of FCRC and exclude a major role for mutations in VHL, MET, or CUL2 in this disorder.

The critical region of overlap defining the AZFa male infertility interval of proximal Yq contains three transcribed sequences

The position of deletion breakpoints in a series of four AZFa male infertility patients has been refined using new markers derived from BAC clone DNA sequence covering the AZFa male infertility interval. The proximal half of the AZFa interval is occupied by pseudogene sequences with homology to Xp22. The distal half contains an anonymous expressed sequence tag (named AZFaT1) found transcribed in brain, testis, and skeletal muscle and the DFFRY and DBY genes. All the patients have AZFaT1 and DFFRY deleted in their entirety and three patients additionally have DBY deleted. The three patients with AZFaT1, DFFRY, and DBY deleted show a severe Sertoli cell only syndrome type I phenotype, whereas the patient that has retained DBY shows a milder oligozoospermic phenotype. The expression of DBY in a cell line from this latter patient is unaltered; this shows that it is the loss of genes lying within the deletion that is responsible for the observed oligozoospermia. RT-PCR analysis of mouse testis RNA from normal and XXSxr(a) mice (devoid of germ cells) has shown that Dby is expressed primarily in somatic cells and that the level of expression is unaltered during germ cell differentiation. This contrasts with Dffry where no transcripts are detectable in XXSxr(a) mouse testis and expression occurs specifically in testis mRNA in a germ cell dependent fashion.

An exon map of the AZFc male infertility region of the human Y chromosome

STS markers spanning the AZFc region of human Y Chromosome (Chr) were used to isolate a series of 14 P1 artificial chromosome (PAC) clones covering at least 560 kb of DNA. End clone analysis of these PAC clones was used to derive 10 new STS markers. Together with other markers mapped to the region, an STS content analysis was used to assemble these PAC clones into three distinct contigs. A minimum tiling path of ten PAC clones was subjected to exon trapping to identify potentially new genes mapping to the AZFs region. In all, 39 potential exons were isolated, including 2 exons from the DAZ gene, 3 exons from the BPY2 gene, 2 exons from the PRY gene, and 1 exon from a member of the RBM II gene family; all these genes have been shown previously to map to the AZFc region. One further exon was found that shows homology to the DFFRY gene, which maps to Yq11. 2, indicating that there may be a further copy of this gene or a pseudogene in the distal Yq euchromatin. The majority of the remaining potential exons appear to be novel, suggesting that additional genes lie in the AZFc region. Mapping of these exons by PCR analysis of somatic cell hybrids has shown that six of these exons are homologous to autosomal sequences, and five to sequences on the X Chr. RT-PCR analysis of primary cDNA from adult testis, brain, liver, and skeletal muscle mRNA has shown that 11 of the novel exons are expressed in one or a combination of these tissues, indicating that they form parts of genuine transcripts.

A selective difference between human Y-chromosomal DNA haplotypes

DNA analysis is making a valuable contribution to the understanding of human evolution [1]. Much attention has focused on mitochondrial DNA (mtDNA) [2] and the Y chromosome [3] [4], both of which escape recombination and so provide information on maternal and paternal lineages, respectively. It is often assumed that the polymorphisms observed at loci on mtDNA and the Y chromosome are selectively neutral and, therefore, that existing patterns of molecular variation can be used to deduce the histories of populations in terms of drift, population movements, and cultural practices. The coalescence of the molecular phylogenies of mtDNA and the Y chromosome to recent common ancestors in Africa [5] [6], for example, has been taken to reflect a recent origin of modern human populations in Africa. An alternative explanation, though, could be the recent selective spread of mtDNA and Y chromosome haplotypes from Africa in a population with a more complex history [7]. It is therefore important to establish whether there are selective differences between classes (haplotypes) of mtDNA and Y chromosomes and, if so, whether these differences could have been sufficient to influence the distributions of haplotypes in existing populations. A precedent for this hypothesis has been established for mtDNA in that one mtDNA background increases susceptibility to Leber hereditary optic neuropathy [8]. Although studies of nucleotide diversity in global samples of Y chromosomes have suggested an absence of recent selective sweeps or bottlenecks [9], selection may, in principle, be very important for the Y chromosome because it carries several loci affecting male fertility [10] [11] and as many as 5% of males are infertile [11] [12]. Here, we show that one class of infertile males, PRKX/PRKY translocation XX males, arises predominantly on a particular Y haplotypic background. Selection is, therefore, acting on Y haplotype distributions in the population.

Regional assignment and expression analysis of 29 expressed sequence tags mapped to chromosome 3

Of 311 expressed sequenced tags (ESTs) mapped to single human chromosomes by analysis of a monochromosome somatic cell hybrid panel, 29 were localized to chromosome 3. Analysis of somatic cell hybrid lines containing different regions of chromosome 3 has enabled the regional assignment of these 29 ESTs to 13 of 23 intervals covering chromosome 3. Northern analysis of 25 of the EST clones has provided information on the pattern of expression of potential genes represented by these transcripts in 16 human tissue types. Nine of the clones hybridized solely to a transcript(s) in the testis, 12 hybridized to transcripts in testis and other tissues, and 4 hybridized with transcripts in testis and other tissues but in addition have testis-specific transcript sizes. These ESTs will provide useful markers throughout chromosome 3 for the development of physical and transcription maps. In addition, they provide candidate genes for disease loci mapping to the intervals defined by the chromosome 3 deletion panel.

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.

The mouse Y chromosome interval necessary for spermatogonial proliferation is gene dense with syntenic homology to the human AZFa region

The Delta Sxrb deletion interval of the mouse Y chromosome contains Spy, a spermatogenesis factor gene(s) whose expression is essential for the postnatal development of the mitotic germ cells, spermatogonia. The boundaries of Delta Sxrb are defined by the duplicated genes Zfy1 and Zfy2 and four further genes have previously been mapped within the interval: Ube1y and Smcy, linked with Zfy1 on a contig of 250 kb, and Dffry and Uty, which were unanchored. The interval was estimated to be >450 kb. In order to identify any further gene(s) that may underlie Spy, systematic exon trapping was performed on an extended contig, anchored on Zfy1, which covers 750 kb of the Delta Sxrb interval. Exons from two novel genes were isolated and placed together with Dffry and Uty on the contig in the order Dffry-Dby-Uty-Tspy-Eif2gammay-Smcy- Ube1y-Zfy1. All the genes, with the double exception of Tspy, are X-Y homologous and produce putatively functional, spliced transcripts. The tight linkage and order of Dffry, Dby and Uty was shown to be conserved in deletion intervals 5C/5D of the human Y chromosome by the construction of a contig of human PAC and YAC clones; this represents the first example of syntenic homology between Y chromosomes from two distinct mammalian orders. Interval 5C/5D contains the distal boundary of the AZFa interval, which, like Delta Sxrb, is believed to be necessary for spermatogonial development in the prepubertal testis. Our results therefore show that AZFa and Spy may be encoded by homologous genes.

Inactivation of the von Hippel-Lindau (VHL) tumour suppressor gene and allelic losses at chromosome arm 3p in primary renal cell carcinoma: evidence for a VHL-independent pathway in clear cell renal tumourigenesis

Inactivation of tumour suppressor gene(s) (TSGs) on 3p appears to be a critical event in the pathogenesis of clear cell renal cell carcinoma (CC-RCC). Analysis of loss of heterozygosity (LOH) in sporadic RCC samples has implicated roles for TSGs in three specific regions of 3p in RCC development: (1) 3p12-p14, which includes the breakpoint of the familial t(3;8) constitutional translocation involved in hereditary RCC development and a recently cloned putative TSG, the FHIT gene: (2) 3p21.2-p21.3, a common region of deletion in many cancers including lung; and (3) 3p25-p26, which contains the von Hippel-Lindau (VHL) disease TSG. We and others have shown that most primary sporadic CC-RCCs contain somatic VHL gene mutations, clearly implicating inactivation of the VHL gene in the pathogenesis of CC-RCC. It is not known if CC-RCC without VHL gene mutations have alternative mechanisms of VHL gene inactivation or result from an alternative non-VHL pathway to RCC, e.g., inactivation of TSGs in 3p12-p21. We and others have reported hypermethylation and silencing of the VHL TSG in RCC from patients with VHL disease and in CC-RCC cell lines. However, the incidence and specificity of VHL methylation in primary sporadic RCC has not been defined. Therefore, we analysed methylation of the VHL, CDKN2, MYC, and H19 genes in primary RCC samples. Hypermethylation of the VHL promoter region was detected in 11% (11/99) of the primary RCCs analysed. In 10 of these tumours, there was no evidence of concomitant VHL gene mutation. VHL methylation was specific to CC-RCC (15%, 7/45) but was not detected in any non-CC tumours (n = 16). None of the 11 RCCs methylated at VHL had evidence of methylation at either CDKN2 or MYC (methylation at CDKN2 was, however, detected in 3%, or 1/33, of RCCs without VHL methylation). A normal methylation pattern at H19 was demonstrated in the three RCCs with methylated VHL analysed. Previous studies have suggested that, in addition to VHL, other 3p TSGs at 3p12-p14 and 3p21 may be involved in CC-RCC tumourigenesis. However, the interpretation of these studies has been difficult because information on VHL gene status has not been available for these data sets. Therefore, we investigated a subset of 55 sporadic RCCs (of known VHL gene methylation and mutation status) for LOH at polymorphic markers close to candidate TSG loci in the 3p14.2 and 3p21.2-p21.3 regions. Among tumours with LOH at one or more 3p markers, the incidence of 3p25 allele loss was higher in tumours with VHL alterations (mutation or methylation) than in those without. For tumours without detectable VHL alterations, the frequency of 3p14-p21 LOH was significantly higher than the frequency of 3p25-p26 LOH (93%, 13/14 vs. 43%, 6/14; P = 0.013), whereas, in RCC samples with VHL methylation or mutation, the frequency of 3p14-p21 LOH did not differ from that of sp25-p26 (72%, 18/25 vs. 59%, 13/22; P = 0.376). None of the 11 RCCs with 3p25 allele loss that were informative at 3p21 and 3p14 showed LOH at 3p25 only. These findings suggest that (1) VHL methylation is a specific and important event in the pathogenesis of CC-RCC; (2) in CC-RCC with 3p LOH but without VHL inactivation, mutations in TSGs at 3p14-p21 appear to have a primary role in tumourigenesis; and (3) inactivation of other 3p TSGs in addition to VHL may also be required for malignant transformation in tumours with VHL gene inactivation.

Genetic analysis of meiotic recombination in humans by use of sperm typing: reduced recombination within a heterozygous paracentric inversion of chromosome 9q32-q34.3

To investigate patterns of genetic recombination within a heterozygous paracentric inversion of chromosome 9 (46XY inv[9] [q32q34.3]), we performed sperm typing using a series of polymorphic microsatellite markers spanning the inversion region. For comparison, two donors with cytogenetically normal chromosomes 9, one of whom was heterozygous for a pericentric chromosome 2 inversion (46XY inv[2] [p11q13]), were also tested. Linkage analysis was performed by use of the multilocus linkage-analysis program SPERM, and also CRI-MAP, which was adapted for sperm-typing data. Analysis of the controls generated a marker order in agreement with previously published data and revealed no significant interchromosomal effects of the inv(2) on recombination on chromosome 9. FISH employing cosmids containing appropriate chromosome 9 markers was used to localize the inversion breakpoint of inv(9). Analysis of inv(9) sperm was performed by use of a set of microsatellite markers that mapped centromeric to, telomeric to, and within the inversion breakpoints. Three distinct patterns of recombination across the region were observed. Proximal to the centromeric breakpoint, recombination was similar to normal levels. Distal to the telomeric breakpoint, there was an increase in recombination found in the inversion patient. Finally, within the inversion, recombination was dramatically reduced, but several apparent double recombinants were found. A putative model explaining these data is proposed.

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.

An autosomal or X linked mutation results in true hermaphrodites and 46,XX males in the same family

It is now well established that the differentiation of the primitive gonad into the testis during early human embryonic development depends on the presence of the SRY gene. However, the existence of total or partial sex reversal in 46,XX males with genetic mutations not linked to the Y chromosome suggests that several autosomal genes acting in association with SRY may contribute to normal development of the male phenotype. We report a family in which four related 46,XX subjects with no evidence of Y chromosome DNA sequences underwent variable degrees of male sexual differentiation. One 46,XX male had apparently normal male external genitalia whereas his brother and two cousins had various degrees of sexual ambiguity and were found to be 46,XX true hermaphrodites. The presence of male sexual development in genetic females with transmission through normal male and female parents indicates that the critical genetic defect is most likely to be an autosomal dominant mutation, the different phenotypic effects arising from variable penetrance. Other autosomal loci have been implicated in male sexual development but the genetic mechanisms involved are unknown. In this family there may be an "activating" mutation which mimics the initiating role of the SRY gene in 46,XX subjects.

Genetic predisposition to phaeochromocytoma: analysis of candidate genes GDNF, RET and VHL

Inherited predisposition to phaeochromocytoma (MIM No 171300) occurs in multiple endocrine neoplasia type 2 (MEN 2) (MIM No 171400), von Hippel-Lindau (VHL) disease (MIM No 199300), and neurofibromatosis type 1 (NF1) (MIM No 162200). In addition, familial phaeochromocytoma alone has also been reported and we and others have identified germline VHL mutations in five of six kindreds analysed previously. Germline mutations in the RET proto-oncogene, which encodes a receptor tyrosine kinase, and in the VHL tumour suppressor gene cause MEN 2 and VHL disease, respectively. To further investigate the genetics of phaeochromocytoma predisposition, we analysed three groups of patients with no evidence of VHL disease, MEN 2 or NF1: Group A, eight kindreds with familial phaeochromocytoma; Group B, two patients with isolated bilateral phaeochromocytoma; and Group C, six cases of multiple extra-adrenal phaeochromocytoma or adrenal phaeochromocytoma with a family history of neuroectodermal tumours. Germline missense VHL mutations were identified in three of eight kindreds with familial phaeochromocytoma. A germline VHL mutation was also characterised in one of the two patients with bilateral phaeochromocytoma. No VHL or RET mutations were detected in the final group of patients with multiple extra-adrenal phaeochromocytoma or adrenal phaeochromocytoma with a family history of neuroectodermal tumours. The absence of germline VHL and RET gene mutations in many of these families suggested that other phaeochromoeytoma susceptibility loci may exist. Glial cell line-derived neurotrophic factor (GDNF) has been recently identified as a natural ligand for RET. Thus, it seems plausible that GDNF is a good candidate gene to play a role in phaeochromocytoma susceptibility. We searched for germline mutations in GDNF in 16 cases of familial phaeochromocytoma (groups A, B and C) and looked for evidence of somatic change in GDNF in 28 sporadic phaeochromocytomas, 12 MEN 2 phaeochromocytomas and five VHL phaeochromocytomas. No GDNF mutations were identified in patients with familial phaeochromocytoma disease, but a c277C-->T (R93W) sequence variant was identified in one of 28 sporadic tumours. This candidate mutation was identified in the germline and tumour tissue but was not present in 104 control GDNF alleles. GDNF sequence variants including R93W have been suggested previously to represent low penetrance susceptibility mutations for Hirschsprung disease and the R93W was not identified in 376 control alleles studied by others. These findings suggest that although GDNF mutations do not appear to have a major role in the pathogenesis of familial or sporadic phaeochromocytomas, allelic variation at the GDNF locus may modify phaeochromocytoma susceptibility.

Somatic inactivation of the VHL gene in Von Hippel-Lindau disease tumors

Von Hippel-Lindau (VHL) disease is a dominantly inherited disorder predisposing to retinal and CNS hemangioblastomas, renal cell carcinoma (RCC), pheochromocytoma, and pancreatic tumors. Interfamilial differences in predisposition to pheochromocytoma reflect allelic heterogeneity such that there is a strong association between missense mutations and risk of pheochromocytoma. We investigated the mechanism of tumorigenesis in VHL disease tumors to determine whether there were differences between tumor types or classes of germ-line mutations. Fifty-three tumors (30 RCCs, 15 hemangioblastomas, 5 pheochromocytomas, and 3 pancreatic tumors) from 33 patients (27 kindreds) with VHL disease were analyzed. Overall, 51% of 45 informative tumors showed loss of heterozygosity (LOH) at the VHL locus. In 11 cases it was possible to distinguish between loss of the wild-type and mutant alleles, and in each case the wild-type allele was lost. LOH was detected in all tumor types and occurred in the presence of both germ-line missense mutations and other types of germline mutation associated with a low risk of pheochromocytoma. Intragenic somatic mutations were detected in three tumors (all hemangioblastomas) and in two of these could be shown to occur in the wild-type allele. This provides the first example of homozygous inactivation of the VHL by small intragenic mutations in this type of tumor. Hypermethylation of the VHL gene was detected in 33% (6/18) of tumors without LOH, including 2 RCCs and 4 hemangioblastomas. Although hypermethylation of the VHL gene has been reported previously in nonfamilial RCC and although methylation of tumor-suppressor genes has been implicated in the pathogenesis of other sporadic cancers, this is the first report of somatic methylation in a familial cancer syndrome.

Chromosomal assignment of 311 sequences transcribed in human adult testis

A total of 311 expressed sequence tags (ESTs) derived from human adult testis have been assigned to human chromosomes by Southern analysis of a monochromosome somatic cell hybrid panel. Over 70% of the ESTs show conservation to hamster and mouse DNA, and the overall distribution of transcripts correlates well with physical chromosome size and to a greater extent with male meiotic chromosome length. The notable exception is the X chromosome, for which the number of testis-derived ESTs is greatly underrepresented. This finding may reflect inactivation of the X chromosome during the meiotic phase of spermatogenesis and a consequent selection against large numbers of X-linked germ cell transcripts. Further analysis of the distribution of testis ESTs showed that the EST density remains significantly correlated with the recombination density of each autosome. Analysis of a comparable number (320) of brain EST autosome assignments showed no similar correlation. These data suggest a specific association between transcription in testis tissue and male meiotic recombination.

The Drosophila developmental gene fat facets has a human homologue in Xp11.4 which escapes X-inactivation and has related sequences on Yq11.2

EST 221 derived from human adult testis detects homology to the Drosophila fat facets gene (fat) and has related sequences on both the X and Y chromosomes mapping to Xp11.4 and Yq11.2 respectively. These two loci have been termed DFFRX and DFFRY for Drosophila fat facets related X and Y. The major transcript detected by EST 221 is-8 kb in size and is expressed widely in a range of 16 human adult tissues. RT-PCR analysis of 13 different human embryonic tissues with primers specific for the X and Y sequences demonstrates that both loci are expressed in developing tissues and quantitative RT-PCR of lymphoblastoid cell lines carrying different numbers of X chromosomes reveals that the X-linked gene escapes X-inactivation. The amino acid sequence (2547 residues) of the complete open reading frame of the X gene has 44% identity and 88% similarity to the Drosophila sequence and contains the conserved Cys and His domains characteristic of deubiquitinating enzymes, suggesting its biochemical function may be the hydrolysis of ubiquitin from protein-ubiquitin conjugates. The requirement of faf for normal oocyte development in Drosophila combined with the map location and escape from X-inactivation of DFFRX raises the possibility that the human homologue plays a role in the defects of oocyte proliferation and subsequent gonadal degeneration found in Turner syndrome.

Characterization of a novel human dynein-related gene that is specifically expressed in testis

A novel dynein-related transcript (designated DNEL1) from human adult testis has been identified that can encode a protein with a size of 91087 Da. The complete nucleotide sequence of the open reading frame is the first to be described for a human dynein-related gene. Northern blot analysis of mRNA from 16 different tissues has shown that DNEL1 is expressed specifically in testis. Analysis of somatic cell hybrids has mapped DNEL1 to Chromosome (Chr) 17. Analysis of a panel of 129 whole genome radiaton hybrid clones including 17q22-q25.3 has placed DNEL1 in 17q distal to the ERBA2L locus. DNEL1 shares a high degree of sequence identity and amino acid similarity with the C-terminal region of the outer arm axonemal dynein beta-heavy chains derived from sea urchin and other species, but not to any gene encoding dynein intermediate or light chains described to date. The close similarity of DNEL1 to the C-terminal part of the axonemal beta-heavy chain may suggest an origin from a common progenitor gene and the testis-specific pattern of expression a possible role in sperm development or motility.

Characterization of a kinesin-related gene ATSV, within the tuberous sclerosis locus (TSC1) candidate region on chromosome 9Q34

In the search for candidate genes for the tuberous sclerosis (TSC1) disease locus on chromosome 9q34, we have isolated an overlapping series of 22 plasmid and phage cDNA clones covering nearly 7 kb and with an open reading frame of 5070 bp encoding a protein of 1690 amino acids. The putative protein product is a member of the kinesin superfamily and is homologous to the mouse KIF1A and the Caenorhabditas elegans unc-104 genes. Both KIF1A and unc-104 function in the anterograde axonal transport of synaptic vesicles. The human homolog is therefore termed H-ATSV (axonal transporter of synaptic vesicles, HGMW-approved nomenclature ATSV) Screening of DNA from 107 tuberous sclerosis patients and 80 unaffected individuals with H-ATSV cDNA probes by pulsed-field gel electrophoresis/Southern blotting following digestion by rare-cutting methylation-sensitive restriction enzymes showed variant banding patterns in three patients with tuberous sclerosis. However, further analysis indicated that these variant fragments represent a rare polymorphism probably associated with methylation of clustered restriction sites. There is no evidence to support H-ATSV as a candidate gene for TSC1.

The sequence organization of Yp/proximal Xq homologous regions of the human sex chromosomes is highly conserved

Detailed deletion analysis of patients with breakpoints in Yp has allowed the definition of two distinct intervals on the Y chromosome short arm outside the pseudoautosomal region that are homologous to Xq2l.3. Detailed YAC contigs have been developed over these regions on both the X and Y chromosomes, and the relative order of markers has been compared to assess whether rearrangements on either sex chromosome have occurred since the transposition events creating these patterns of homology. On the X chromosome, the region forms almost one contiguous block of homology, whereas on the Y chromosome, there has been one major rearrangement leading to the two separate Yp-Xq2l blocks of homology. The rearrangement breakpoint has been mapped. Within these separate X-Y homologous blocks on Yp, the order of loci homologous to X has been conserved to a high degree between the sex chromosomes. With the exception of the amelogenin gene (proximal Yp block), all the XY homologous sequences in the two Yp blocks have homolognes in Xq2l.3, with the former having its X counterpart in Xp22.2. This suggests an independent evolutionary event leading to the formation of the amelogenin X-Y homology.

Germline mutations in the Von Hippel-Lindau disease (VHL) gene in families from North America, Europe, and Japan

Germline mutation analysis was performed in 469 VHL families from North America, Europe, and Japan. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected. Most of the germline VHL mutations (124/137) occurred in 1-2 families; a few occured in four or more families. The common germline VHL mutations were: delPhe76, Asn78Ser, Arg161Stop, Arg167Gln, Arg167Trp, and Leu178Pro. In this large series, it was possible to compare the effects of identical germline mutations in different populations. Germline VHL mutations produced similar cancer phenotypes in Caucasian and Japanese VHL families. Germline VHL mutations were identified that produced three distinct cancer phenotypes: (1) renal carcinoma without pheochromocytoma, (2) renal carcinoma with pheochromocytoma, and (3) pheochromocytoma alone. The catalog of VHL germline mutations with phenotype information should be useful for diagnostic and prognostic studies of VHL and for studies of genotype-phenotype correlations in VHL.

Molecular genetic analysis of the von Hippel-Lindau disease (VHL) tumour suppressor gene in gonadal tumours

Chromosome 3p allele loss is frequent in ovarian and testicular tumours. The von Hippel-Lindau (VHL) disease tumour suppressor gene maps to chromosome 3p25. Gonadal tumours may occur in patients with VHL disease, so somatic VHL gene mutations might be involved in the pathogenesis of sporadic gonadal tumours. To investigate this hypothesis, we screened 60 gonadal tumours (36 ovarian and 24 testicular) for VHL gene mutations and chromosome 3p allele loss. Although 38% (10/26) of informative ovarian and 54% (7/13) of testicular tumours demonstrated 3p allele loss, no somatic VHL gene mutations were detected in the 60 gonadal tumours analysed. This suggested that chromosome 3p tumour suppressor gene(s) other than VHL are involved in gonadal tumorigenesis.

Molecular analysis of de novo germline mutations in the von Hippel-Lindau disease gene

VHL disease is a dominantly inherited familial cancer syndrome with variable expression and age-dependent penetrance. The diagnosis of isolated cases is often delayed compared with familial cases, and estimates of the new mutation rate have varied more than 20-fold. To investigate the frequency and origin of de novo VHL gene mutations we have analysed: (i) families with identical mutations to determine if there is a common haplotype, and (ii) apparent new mutation cases to determine whether the clinical diagnosis of such cases is reliable and to define the parental origin of de novo VHL gene mutations. Haplotyping of 12 VHL mutations occurring in two or more families (total 42 kindreds) revealed that for most mutations there was no evidence of a founder effect. A marked bias for a paternal origin of new mutations has been reported in other familial cancer syndromes such as neurofibromatosis type 1 (NF1), multiple endocrine neoplasia (MEN) 2B and bilateral retinoblastoma, but it is unclear whether this bias results from a greater susceptibility for mutagenesis during male gametogenesis because of the larger number of cell divisions compared with that in oogenesis, or from genomic imprinting effects. Analysis of 13 de novo VHL mutations in which the parent of origin could be established, showed no evidence for a bias for a paternal origin (seven paternal, six maternal), and differed significantly from that reported in NF1, MEN2B and bilateral retinoblastoma. This result demonstrates that an increased susceptibility to paternal allele mutation is not a universal finding in autosomal genetic diseases and that the origin of new mutations may be influenced by both genomic imprinting effects and the increased number of cell divisions in spermatogenesis compared with oogenesis.

Expression analysis, genomic structure, and mapping to 7q31 of the human sperm adhesion molecule gene SPAM1

During the course of systematic sequence tag analysis of clones isolated from an adult testis cDNA library, clones 296 and 576 were found to detect 71-74% sequence identity to the guinea pig sperm surface protein PH-20. This surface protein is involved in sperm-egg adhesion in the guinea pig. Nucleotide sequence for 1919 bp of human DNA from a series of overlapping cDNA clones isolated from a testis cDNA library confirmed the sequence identity within a 1527-bp open reading frame to be 71-74% to the guinea pig gene and the similarity to be 60% for the predicted protein of 509 amino acids. Southern blot analysis of human genomic DNA and DNA from somatic cell hybrids indicates that the gene (SPAM1) is unique and does not form part of a larger family and that it maps to chromosome 7. Fluorescence in situ hybridization with yeast artificial chromosome (YAC) clones isolated from the CEPH megaYAC library has refined this localization to 7q31. PCR analysis of genomic DNA and YAC clone DNA has shown that the 1919 bp of the gene that has been cloned covers approximately 11 kb of genomic DNA and is encoded by at least 4 exons. Northern analysis of poly(A)+ mRNA from a range of 16 human tissues has demonstrated that expression of the gene as a single 2.4-kb transcript is strictly limited to the testis.

Characterization of a novel zinc finger gene (ZNF165) mapping to 6p21 that is expressed specifically in testis

Clone ZF388 was identified during the course of expressed sequence tag analysis of human adult testis cDNAs as being a member of the C2H2 zinc finger gene family. Northern blot analysis of a range of 16 different human tissues has shown that clone ZF388 detects a single 2.2-kb transcript and that the expression of this mRNA species is strictly specific to the testis. Sequence analysis of ZF388 and other clones isolated by rescreening a testis cDNA library has defined a transcript with an extensive N-terminal acidic domain containing 17% aspartic and glutamic acid residues and a C-terminal domain composed of five zinc finger motifs linked through the highly conserved sequence TGE-KPYE. This gene has been designated ZNF165. Analysis of somatic cell hybrids containing single human chromosomes shows that ZNF165 maps to chromosome 6. Fluorescence in situ hybridization of cDNA insert probes to male metaphase spreads shows that the ZNF165 transcript maps to 6p21 close to the human MHC region. Human 6p21 is homologous with the distal inversion of the mouse t-complex, which has been shown to contain a cluster of genes expressed specifically in the testis.

Prevalence and molecular analysis of two hot spots for ectopic recombination leading to XX maleness

Two hot spots of ectopic Xp-Yp recombination have previously been shown to be at the origin of XX maleness (Weil et al., 1994, Nature Genet. 7:414-419). To get more insight into the molecular basis of the abnormal interchange, 25 Y(+) class 3 XX male patients were studied. The two hot spots were found to account for the aberrant exchange in more than 50% of the cases. In addition, there is a correlation between the prevalence of each hot spot and the degree of X-Y homology between the corresponding fragments. Sequencing of the X-Y junctions in six patients, who carried a breakpoint mapping in either of these two hot spot fragments, showed that their precise locations were different from one individual to the other. In particular, the results obtained here in four new patients exclude the possibility that the repeated elements, present in these X-Y homologous fragments, are responsible for the high incidence of X-Y interchanges observed. Moreover, the breakpoints of all 25 class 3 XX males were found to be arranged in the same order on the X and Y chromosomes. This suggests that most ectopic recombinations leading to class 3 XX maleness involve X-Y homologous sequences persisting from an ancestral larger block of homology on the short arms of both sex chromosomes.