Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome

The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.

Coordinated histone modifications mediated by a CtBP co-repressor complex

The transcriptional co-repressor CtBP (C-terminal binding protein) is implicated in tumorigenesis because it is targeted by the adenovirus E1A protein during oncogenic transformation. Genetic studies have also identified a crucial function for CtBP in animal development. CtBP is recruited to DNA by transcription factors that contain a PXDLS motif, but the detailed molecular events after the recruitment of CtBP to DNA and the mechanism of CtBP function in tumorigenesis are largely unknown. Here we report the identification of a CtBP complex that contains the essential components for both gene targeting and coordinated histone modifications, allowing for the effective repression of genes targeted by CtBP. Inhibiting the expression of CtBP and its associated histone-modifying activities by RNA-mediated interference resulted in alterations of histone modifications at the promoter of the tumour invasion suppressor gene E-cadherin and increased promoter activity in a reporter assay. These findings identify a molecular mechanism by which CtBP mediates transcriptional repression and provide insight into CtBP participation in oncogenesis.

Genetic control of germline sexual dimorphism in Drosophila

Females produce eggs and males produce sperm. Work in Drosophila is helping to elucidate how this sex-specific germline differentiation is genetically encoded. While important details remain somewhat controversial, it is clear that signals generated by somatic cells, probably in the embryonic gonads, are required as extrinsic factors for germline sex determination. It is equally clear that the sex chromosome karyotype of the germ cell is an intrinsic factor for germline sex determination. There is also extensive somatic signaling required for differentiation of germline cells in the adult gonads. Mismatched germline and somatic line sexual identities place germ cells in an inappropriate signaling milieu, which results in either failed maintenance of germline stems cells when female germ cells are in a male soma or overproliferation of germline cells when male germ cells are in a female soma. The well-studied somatic sex determination genes including transformer, transformer-2, and doublesex are clearly involved in the nonautonomous signaling from somatic cells, while the autonomous functions of genes including ovo, ovarian tumor, and Sex-lethal are involved in the germline. The integration of these two pathways is not yet clear.

Comparative genome analysis of the primary sex-determining locus in salmonid fishes

We compared the Y-chromosome linkage maps for four salmonid species (Arctic charr, Salvelinus alpinus; Atlantic salmon, Salmo salar; brown trout, Salmo trutta; and rainbow trout, Oncorhynchus mykiss) and a putative Y-linked marker from lake trout (Salvelinus namaycush). These species represent the three major genera within the subfamily Salmoninae of the Salmonidae. The data clearly demonstrate that different Y-chromosomes have evolved in each of the species. Arrangements of markers proximal to the sex-determining locus are preserved on homologous, but different, autosomal linkage groups across the four species studied in detail. This indicates that a small region of DNA has been involved in the rearrangement of the sex-determining region. Placement of the sex-determining region appears telomeric in brown trout, Atlantic salmon, and Arctic charr, whereas an intercalary location for SEX may exist in rainbow trout. Three hypotheses are proposed to account for the relocation: translocation of a small chromosome arm; transposition of the sex-determining gene; or differential activation of a primary sex-determining gene region among the species.

Sex chromosomes and sex determination in weird mammals

Weird mammals are of two types. Highly divergent mammals, such as the marsupials and monotremes, have informed us of the evolutionary history of the Y chromosome and sex-determining gene, and the recently specialized rodents can help us predict its future. The Y chromosome has had a short but eventful history, and is already heading briskly for oblivion. It originated as a homologous partner of the X when it acquired a sex-determining gene (not necessarily SRY). Most of the genes on the Y, even those with a male-specific function, evolved from genes now on the X. At the mercy of a high rate of variability and the forces of drift and selection, the Y has lost genes at a rate of 3-6 genes/million years, sparing those that acquired critical male-specific functions. Even these genes have disappeared from one mammalian lineage or another as their functions were usurped by genes elsewhere in the genome. The mammalian testis-determining gene, SRY, is a typical Y-borne gene. It arose by truncation of a gene (SOX3) on the X that is expressed in brain development, and it may work by interacting with (inhibiting?) related genes, including SOX9. Variant sex-determining systems in rodents show that the action of SRY can change, as it evidently has in the mouse, and SRY can be inactivated, as in akodont rodents, or even completely superseded, as in mole voles.

Comparative mapping of CDY and DAZ in higher primates

The human male specific expressed gene families CDY and DAZ are known to be repetitively clustered in the Y-specific region of the human Y chromosome. Comparative FISH-mapping of DNA clones specific for CDY and DAZ resulted in a Y-specific but diverse signal pattern within the non-recombining region of the Y-chromosomes of human and great apes. It can be concluded that the non-recombining part of the Y-chromosomes including CDY and DAZ, was exposed to species-specific amplifications, diversifications and rearrangements. Evolutionary fast fixation of any of these variations was possible as long as they did not interfere with male fertility.

Genetic and functional analysis of DD44, a sex-linked gene from the dioecious plant Silene latifolia, provides clues to early events in sex chromosome evolution

Silene latifolia is a dioecious plant with heteromorphic sex chromosomes. The sex chromosomes of S. latifolia provide an opportunity to study the early events in sex chromosome evolution because of their relatively recent emergence. In this article, we present the genetic and physical mapping, expression analysis, and molecular evolutionary analysis of a sex-linked gene from S. latifolia, DD44 (Differential Display 44). DD44 is homologous to the oligomycin sensitivity-conferring protein, an essential component of the mitochondrial ATP synthase, and is ubiquitously expressed in both sexes. We have been able to genetically map DD44 to a region of the Y chromosome that is genetically linked to the carpel-suppressing locus. Although we have physically mapped DD44 to the distal end of the long arm of the X chromosome using fluorescence in situ hybridization (FISH), DD44 maps to the opposite arm of the Y chromosome as determined by our genetic map. These data suggest that chromosomal rearrangements have occurred on the Y chromosome, which may have contributed to the genetic isolation of the Y chromosome. We discuss the implications of these results with respect to the structural and functional evolution of the S. latifolia Y chromosome.

Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes

We have identified a new class of ribosomal protein (RP) genes that appear to have been retrotransposed from X-linked RP genes. Mammalian ribosomes are composed of four RNA species and 79 different proteins. Unlike RNA constituents, each protein is typically encoded by a single intron- containing gene. Here we describe functional autosomal copies of the X-linked human RP genes, which we designated RPL10L (ribosomal protein L10-like gene), RPL36AL and RPL39L after their progenitors. Because these genes lack introns in their coding regions, they were likely retrotransposed from X-linked genes. The identities between the retrotransposed genes and the original X-linked genes are 89-95% in their nucleotide sequences and 92-99% in their amino acid sequences, respectively. Northern blot and PCR analyses revealed that RPL10L and RPL39L are expressed only in testis, whereas RPL36AL is ubiquitously expressed. Although the role of the autosomal RP genes remains unclear, they may have evolved to compensate for the reduced dosage of X-linked RP genes.

Characterization of integration patterns and flanking cellular sequences of hepatitis B virus in childhood hepatocellular carcinomas

Hepatitis B virus (HBV) DNA integration into host chromosomes is detected in more than 80% of HBV-related hepatocellular carcinomas (HCC), yet its significance in tumor development remains obscure. In this study, we re-examined the integration pattern of HBV in childhood HCC tissues, which has less environmental confounding factors than adult HCC. The HBV junctions and flanking cellular sequences were amplified from five childhood HCC patients by the inverse polymerase chain reaction (IPCR) method using primers located near HBV direct repeats (DR) 1 and 2. The viral junctions in nine of the ten obtained IPCR clones were demonstrated to be located near HBV DR1, and their patterns were classified to type I integrants. Southern blot analyses demonstrate that the cellular junctions derived from two of the five HCC tissues were male specific and contained sequences homologous to human long interspersed DNA elements (LINE-1). HBV integrant of one HCC tissue (1217T) was integrated into a RNA binding motif Y chromosome (RBMY) gene. The expression of RBMY, which is normally found only in male germ cells, was detected in HCC tissue 1217T by RT-PCR but not in the corresponding non-tumor liver tissue. The prevalence of RBMY expression in liver tissues from the tumor and non-tumor parts of ten other HCC children and seven biliary atresia (BA) children was studied by RT-PCR. No RBMY transcripts were detected in the non-tumor parts of HCC patients or the cirrhotic livers of BA children, whereas 30% (three of ten) of HCC tissues specifically expressed RBMY. The results indicate that HBV integration and activation of RBMY gene expression in liver cells may be associated with the development of childhood HCC.

Y chromosome genes and male infertility

Normal spermatogenesis is a complex process that depends on many factors. Genetics plays a major role in many of these factors including providing a normal hormonal milieu, the development of the testis and ductal system, and control of the stepwise maturation of sperm in the testis. The Y chromosome plays a key role in testis determination and control of spermatogenesis. Understanding how these genes work together can elucidate of the exact cause of infertility in some patients once thought to have idiopathic infertility. It is not only important that patients understand the cause of their infertility. Using sperm from these men to attain pregnancies by assisted reproductive techniques will probably result in infertile male offspring. Additional consequences are currently unknown but are the topic of research investigations.

Biological potential of a functional human SNAIL retrogene

Snail genes encode zinc finger transcription factors required for the development of vertebrate and invertebrate embryos. They trigger epithelial to mesenchymal transitions (EMTs), thereby allowing epithelial cells to emigrate from their place of origin and form tissues such as the mesoderm and the neural crest. Snail genes are also involved in the EMTs responsible for the acquisition of invasiveness during tumor progression. This aspect of their activity is associated with their ability to directly repress E-cadherin transcription. Here we describe the existence of an active human Snail retrogene, inserted within an intron of a novel evolutionarily conserved gene and expressed in different human tissues and cell lines. Functional analyses in cell culture show that this retrogene maintains the potential to induce EMTs, conferring migratory and invasive properties to epithelial cells. In light of this data, we have renamed it SNAIL-like, a new player that must be considered in both physiological and pathological studies of SNAIL function in humans.

A comparative study of Y chromosome microdeletions in infertile males from two Chinese populations

PURPOSE

To compare the prevalence and type of Y-microdeletions in Hong Kong and Shanghai men with severe male-factor infertility.

METHODS

Seven Y-linked sequence tagged site (STS) primers and seven gene-specific primers were screened in 293 infertile males (139 from Hong Kong and 154 from Shanghai) and 161 fertile men (61 from Hong Kong and 100 from Shanghai). Serum FSH, LH, and testosterone levels were also measured in these men.

RESULTS

The incidence of Yq microdeletions in nonobstructive azoospermic men from Hong Kong (8.5%) and Shanghai (6%) was similar. Yq microdeletions were observed in severe oligospermic patients (8.5%) from Hong Kong but not from Shanghai. Among the 9 Hong Kong men with Y-microdeletions, 8 had AZFc deletion and one had AZFb deletion. In contrast, 6 of 9 men from Shanghai with Y-microdeletions had AZFb deletion. The incidence of AZFb deletion among Y-microdeleted men was statistically different between the two populations. Two of the men with AZFb deletion also had AZFa and AZFc deletions.

CONCLUSIONS

Regional variations in the type of Y-microdeletion existed between Hong Kong and Shanghai infertile males.

Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis

During spermiogenesis (the maturation of spermatids into spermatozoa) in many vertebrate species, protamines replace histones to become the primary DNA-packaging protein. It has long been thought that this process is facilitated by the hyperacetylation of histone H4. However, the responsible histone acetyltransferase enzymes are yet to be identified. CDY is a human Y-chromosomal gene family expressed exclusively in the testis and implicated in male infertility. Its mouse homolog Cdyl, which is autosomal, is expressed abundantly in the testis. Proteins encoded by CDY and its homologs bear the "chromodomain," a motif implicated in chromatin binding. Here, we show that (i) human CDY and mouse CDYL proteins exhibit histone acetyltransferase activity in vitro, with a strong preference for histone H4; (ii) expression of human CDY and mouse Cdyl genes during spermatogenesis correlates with the occurrence of H4 hyperacetylation; and (iii) CDY and CDYL proteins are localized to the nuclei of maturing spermatids where H4 hyperacetylation takes place. Taken together, these data link human CDY and mouse CDYL to the histone-to-protamine transition in mammalian spermiogenesis. This link offers a plausible mechanism to account for spermatogenic failure in patients bearing deletions of the CDY genes.

Gene-based screening for Y chromosome deletions in Taiwanese men presenting with spermatogenic failure

OBJECTIVE

To develop a simple and rapid protocol for detecting deletions of the Y chromosome and to evaluate the feasibility of gene-based screening in men with spermatogenic failure.

DESIGN

Prospective case study.

SETTING

University-based reproductive clinics and genetics laboratory.

PATIENT(S)

Two hundred two infertile men presenting with severe oligozoospermia and nonobstructive azoospermia.

INTERVENTION(S)

Fifteen gene-specific primers were used to detect deletions of Y chromosome genes in men with spermatogenic failure. A multiplex polymerase chain reaction amplification system was developed to facilitate rapid screening. Another 24 markers for sequence-tagged sites (STS) were used to ensure the adequacy of gene-based screening.

MAIN OUTCOME MEASURE(S)

Detection of deletions of Y chromosome genes.

RESULT(S)

Of 180 patients evaluated, 19 (10.6%) had deletions of one or more genes, including DFFRY, DBY, RBM1, DAZ, CDY1, and BPY2. A second round of STS-based screenings did not show an increase in the deletion rate but more clearly defined the extent of deletion in 14 of the 19 patients. In most patients, deletions detected by gene-based screening were similar to those detected by STS markers.

CONCLUSION(S)

Gene-based screening with multiplex polymerase chain reaction is a rational alternative for detecting deletions of Y chromosome genes in infertile men.

The rise and fall of SRY

Comparisons between species reveal when and how SRY, the testis-determining gene, evolved. SRY is younger than the Y chromosome, and so was probably not the original mammal sex-determining gene that defined the Y. SRY is typical of genes on the Y chromosome. It arose from a gene on the proto-sex chromosome pair with a function (possibly brain-determination) in both sexes. It has been buffeted in evolution, and shows variation in copy number, structure and expression. And it is dispensable, having been lost at least twice independently in different rodent lineages. At the observed rate of attrition, the human Y chromosome will be gone in 5-10 million years. This could lead to the extinction of our species or to a burst of hominid speciation.

Structure and evolution of mtanga, a retrotransposon actively expressed on the Y chromosome of the African malaria vector Anopheles gambiae

Here we report the discovery of a novel family of long terminal repeat (LTR)-retrotransposons designated mtanga-Y, specific to the Y chromosome of the African malaria vector, Anopheles gambiae. mtanga-Y elements represent the first Y-linked sequences and the first members of the Ty1-copia superfamily of retrotransposons described from this mosquito. Analysis of a full-length 4,284-bp element revealed the presence of two intact overlapping open reading frames bounded by LTRs of 119 bp. Evidence suggests that the elements are capable of retrotransposition, as transcripts and potential replication intermediates (one-LTR circles) were detected. However, the approximately 12 copies of mtanga-Y appear to be clustered rather than dispersed on the Y chromosome. Absent from the Y chromosome of four sibling species (A. arabiensis, A. quadriannulatus, A. melas, and A. merus), similar, but often defective, mtanga elements are present elsewhere in these genomes, as well as in A. gambiae. These data are consistent with a relatively recent invasion of the A. gambiae Y chromosome by an intact element. The presence of functional mtanga-Y elements suggests that the Y chromosome may be a source, not just a sink, for retrotransposons.

Gene family evolution and homology: genomics meets phylogenetics

With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Generation of two homologous and intronless zinc-finger protein genes, zfp352 and zfp353, with different expression patterns by retrotransposition

We have previously reported a mouse zinc-finger protein gene, Zfp352 (formerly 2czf48), that is expressed in early mouse embryos. Here, we report the genomic structure of Zfp352 and its lung-specific homolog, Zfp353. The two genes map on different chromosomes at 4C6 and 8B3.1. Both genes are intronless, except for the presence of a single 4.6-kb intron in the 5' untranslated region of Zfp352. The genes use different RNA start sites located 1.2 kb apart within the 5' homologous region. LINE1 sequences are structurally associated with the genes and form an integral part of Zfp353 transcripts, suggesting previous retrotransposition events. We propose a model of evolution of the genes. The main feature of the model is the presence of a fortuitous upstream promoter and an intron in the first retrotransposition site, creating a pre-Zfp352 gene with a 5' untranslated region intron. A second retrotransposition event copying from the pre-Zfp352 retroposon and removing the fortuitous intron resulted in the intronless Zfp353 at a different chromosomal location and with a different mode of expression. The model may be applicable to other genes with a similar structure with a single intron in the 5' untranslated region. The exact role of LINE1 in the retrotransposition events remains to be elucidated.

The X--a sexy chromosome

There is new and convincing evidence that the mammalian X chromosome, as well as the Y chromosome, contains an atypically high proportion of genes involved in sex and reproduction (SRR genes). Here we consider alternative explanations for this concentration. One possibility is that a particularly well-endowed autosome was "chosen" for a career as a sex chromosome. Alternatively, the high concentration of SRR genes may have resulted from the accumulation of these genes on the X after the degradation of the Y, either by transposition of autosomal SRR genes to a "selfish X", or by acquisition of SRR functions by widely expressed genes on the X. We suggest experiments to distinguish these possibilities, and speculate on the implications of gathering evidence that genes with other functions, too, are not distributed uniformly over the genome.

Regulation of human glutamate dehydrogenases: implications for glutamate, ammonia and energy metabolism in brain

Glutamate dehydrogenase (GDH) catalyzes the oxidative deamination of glutamate to alpha-ketoglutarate using NAD or NADP as cofactors. In mammalian brain, GDH is located predominantly in astrocytes, where it is probably involved in the metabolism of transmitter glutamate. The exact mechanisms that regulate glutamate fluxes through this pathway, however, have not been fully understood. In the human, GDH exists in heat-resistant and heat-labile isoforms, encoded by the GLUD1 (housekeeping) and GLUD2 (nerve tissue-specific) genes, respectively. These forms differ in their catalytic and allosteric properties. Kinetic studies showed that the K(m) value for glutamate for the nerve tissue GDH is within the range of glutamate levels in astrocytes (2.43 mM), whereas for the housekeeping enzyme, this value is significantly higher (7.64 mM; P < 0.01). The allosteric activators ADP (0.1-1.0 mM) and L-leucine (1.0-10.0 mM) induce a concentration-dependent enzyme stimulation that is proportionally greater for the nerve tissue-specific GDH (up to 1,600%) than for the housekeeping enzyme (up to 150%). When used together at lower concentrations, ADP (10-50 mM) and L-leucine (75-200 microM) act synergistically in stimulating GDH activity. GTP exerts a powerful inhibitory effect (IC(50) = 0.20 mM) on the housekeeping GDH; in contrast, the nerve tissue isoenzyme is resistant to GTP inhibition. Thus, although the housekeeping GDH is regulated primarily by GTP, the nerve tissue GDH activity depends largely on available ADP or L-leucine levels. Conditions associated with enhanced hydrolysis of ATP to ADP (e.g., intense glutamatergic transmission) are likely to activate nerve tissue-specific GDH leading to an increased glutamate flux through this pathway.

The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes

SET domains are conserved amino acid motifs present in chromosomal proteins that function in epigenetic control of gene expression. These proteins can be divided into four classes as typified by their Drosophila members E(Z), TRX, ASH1 and SU(VAR)3-9. Homologs of all four classes have been identified in yeast and mammals, but not in plants. A BLASTP screening of the Arabidopsis genome identified 37 genes: three E(z) homologs, five trx homologs, four ash1 homologs and 15 genes similar to Su(var)3-9. Seven genes were assigned as trx-related and three as ash1-related. Only four genes have been described previously. Our classification is based on the characteristics of the SET domains, cysteine-rich regions and additional conserved domains, including a novel YGD domain. RT-PCR analysis, cDNA cloning and matching ESTs show that at least 29 of the genes are active in diverse tissues. The high number of SET domain genes, possibly involved in epigenetic control of gene activity during plant development, can partly be explained by extensive genome duplication in Arabidopsis. Additionally, the lack of introns in the coding region of eight SU(VAR)3-9 class genes indicates evolution of new genes by retrotransposition. The identification of putative nuclear localization signals and AT-hooks in many of the proteins supports an anticipated nuclear localization, which was demonstrated for selected proteins.

The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men

Deletions of the AZFc (azoospermia factor c) region of the Y chromosome are the most common known cause of spermatogenic failure. We determined the complete nucleotide sequence of AZFc by identifying and distinguishing between near-identical amplicons (massive repeat units) using an iterative mapping-sequencing process. A complex of three palindromes, the largest spanning 3 Mb with 99.97% identity between its arms, encompasses the AZFc region. The palindromes are constructed from six distinct families of amplicons, with unit lengths of 115-678 kb, and may have resulted from tandem duplication and inversion during primate evolution. The palindromic complex contains 11 families of transcription units, all expressed in testis. Deletions of AZFc that cause infertility are remarkably uniform, spanning a 3.5-Mb segment and bounded by 229-kb direct repeats that probably served as substrates for homologous recombination.

Drosophila rhino encodes a female-specific chromo-domain protein that affects chromosome structure and egg polarity

Here we describe our analyses of Rhino, a novel member of the Heterochromatin Protein 1(HP1) subfamily of chromo box proteins. rhino (rhi) is expressed only in females and chiefly in the germline, thus providing a new tool to dissect the role of chromo-domain proteins in development. Mutations in rhi disrupt eggshell and embryonic patterning and arrest nurse cell nuclei during a stage-specific reorganization of their polyploid chromosomes, a mitotic-like state called the "five-blob" stage. These visible alterations in chromosome structure do not affect polarity by altering transcription of key patterning genes. Expression levels of gurken (grk), oskar (osk), bicoid (bcd), and decapentaplegic (dpp) transcripts are normal, with a slight delay in the appearance of bcd and dpp mRNAs. Mislocalization of grk and osk transcripts, however, suggests a defect in the microtubule reorganization that occurs during the middle stages of oogenesis and determines axial polarity. This defect likely results from aberrant Grk/Egfr signaling at earlier stages, since rhi mutations delay synthesis of Grk protein in germaria and early egg chambers. In addition, Grk protein accumulates in large, actin-caged vesicles near the endoplasmic reticulum of stages 6-10 egg chambers. We propose two hypotheses to explain these results. First, Rhi may play dual roles in oogenesis, independently regulating chromosome compaction in nurse cells at the end of the unique endoreplication cycle 5 and repressing transcription of genes that inhibit Grk synthesis. Thus, loss-of-function mutations arrest nurse cell chromosome reorganization at the five-blob stage and delay production or processing of Grk protein, leading to axial patterning defects. Second, Rhi may regulate chromosome compaction in both nurse cells and oocyte. Loss-of-function mutations block nurse cell nuclear transitions at the five-blob stage and activate checkpoint controls in the oocyte that arrest Grk synthesis and/or inhibit cytoskeletal functions. These functions may involve direct binding of Rhi to chromosomes or may involve indirect effects on pathways controlling these processes.

Sex from W to Z: evolution of vertebrate sex chromosomes and sex determining genes

Sex determination in major vertebrate groups appears to be very variable, including systems of male heterogamety, female heterogamety and a variety of genetic and environmental sex determining systems. Yet comparative studies of sex chromosomes and sex determining genes now suggest that these differences are more apparent than real. The sex chromosomes of even widely divergent groups now appear to have changed very little over the last 300+ million years, and even independently derived sex chromosomes seem to have followed the same set of evolutionary rules. The sex determining pathway seems to be extremely conserved, although the control of the genes in this pathway is vested in different elements. We present a scenario for the independent evolution of XY male heterogamety in mammals and ZW female heterogamety in birds and some reptiles. We suggest that sex determining genes can be made redundant, and replaced by control at another step of a conserved sex determining pathway, and how choice of a gene as a sex switch has led to the evolution of new sex chromosome systems. J. Exp. Zool. 290:449-462, 2001.

The Y chromosome in the liverwort Marchantia polymorpha has accumulated unique repeat sequences harboring a male-specific gene

The haploid liverwort Marchantia polymorpha has heteromorphic sex chromosomes, an X chromosome in the female and a Y chromosome in the male. We here report on the repetitive structure of the liverwort Y chromosome through the analysis of male-specific P1-derived artificial chromosome (PAC) clones, pMM4G7 and pMM23-130F12. Several chromosome-specific sequence elements of approximately 70 to 400 nt are combined into larger arrangements, which in turn are assembled into extensive Y chromosome-specific stretches. These repeat sequences contribute 2-3 Mb to the Y chromosome based on the observations of three different approaches: fluorescence in situ hybridization, dot blot hybridization, and the frequency of clones containing the repeat sequences in the genomic library. A novel Y chromosome-specific gene family was found embedded among these repeat sequences. This gene family encodes a putative protein with a RING finger motif and is expressed specifically in male sexual organs. To our knowledge, there have been no other reports for an active Y chromosome-specific gene in plants. The chromosome-specific repeat sequences possibly contribute to determining the identity of the Y chromosome in M. polymorpha as well as to maintaining genes required for male functions, as in mammals such as human.

Characterization of the genomic organization, localization and expression of four PRY genes (PRY1, PRY2, PRY3 and PRY4)

PRY (PTP-BL related on the Y chromosome) has been proposed as a candidate spermatogenesis gene. We report the characterization of the genomic structure, the number of copies on the Y chromosome and the expression of the gene. By comparison of the cDNA sequence with the genomic sequence, five exons were identified. Analysis of GenBank-derived clones on the Y chromosome revealed the presence of two full-length copies in azoospermia factor region b (AZFb) (PRY1 and PRY2) and two shorter versions of the PRY gene containing exons 3, 4 and 5 in AZFc (PRY3 and PRY4). A clone containing sequences homologous to exons 3, 4 and 5 is located in area 5L (between AZFa and AZFb), a clone containing a sequence homologous to exon 5 is located in area 5M (in AZFb) and a clone containing a fragment homologous to exon 3 is located in 6F. A repeat structure of exons 1 and 2 is present on the short arm of the Y chromosome as well as on the long arm. PRY1 and PRY2, two gene copies that are located in AZFb, a region often deleted in patients with severe male infertility, were shown to be expressed in the testis. PRY may therefore play an important role in spermatogenesis.

Y chromosome polymorphism is a strong determinant of male fitness in Drosophila melanogaster

In many species, the Y (or W) chromosome carries relatively few functional genes. This observation motivates the null hypothesis that the Y will be a minor contributor to genetic variation for fitness. Previous data and theory supported the null hypothesis, but evidence presented here shows that the Y of Drosophila melanogaster is a major determinant of a male's total fitness, with standing genetic variation estimated to be 68% of that of an entire X/autosome genomic haplotype. Most Y-linked genes are expressed during spermatogenesis, and correspondingly, we found that the Y influences fitness primarily through its effect on a male's reproductive success (sperm competition and/or mating success) rather than his egg-to-adult viability. But the fitness of a Y highly depended on the genetic makeup of its bearer, reverting from high to low in different genetic backgrounds. This pattern leads to large epistatic (inconsistent among backgrounds) but no additive (consistent among backgrounds) Y-linked genetic variance for fitness. On a microevolutionary scale, the observed large epistatic variation on the Y substantially reduces heritable variation for fitness among males, and on a macroevolutionary scale, the Y produces strong selection for genomic rearrangements that move interacting genes onto the nonrecombining region of the Y.

Multiple and independent cessation of recombination between avian sex chromosomes

Birds are characterized by female heterogamety; females carry the Z and W sex chromosomes, while males have two copies of the Z chromosome. We suggest here that full differentiation of the Z and W sex chromosomes of birds did not take place until after the split of major contemporary lineages, in the late Cretaceous. The ATP synthase alpha-subunit gene is now present in one copy each on the nonrecombining part of the W chromosome (ATP5A1W) and on the Z chromosome (ATP5A1Z). This gene seems to have evolved on several independent occasions, in different lineages, from a state of free recombination into two sex-specific and nonrecombining variants. ATP5A1W and ATP5A1Z are thus more similar within orders, relative to what W (or Z) are between orders. Moreover, this cessation of recombination apparently took place at different times in different lineages (estimated at 13, 40, and 65 million years ago in Ciconiiformes, Galliformes, and Anseriformes, respectively). We argue that these observations are the result of recent and traceable steps in the process where sex chromosomes gradually cease to recombine and become differentiated. Our data demonstrate that this process, once initiated, may occur independently in parallel in sister lineages.

The human Y chromosome, in the light of evolution

Most eukaryotic chromosomes, akin to messy toolboxes, store jumbles of genes with diverse biological uses. The linkage of a gene to a particular chromosome therefore rarely hints strongly at that gene's function. One striking exception to this pattern of gene distribution is the human Y chromosome. Far from being random and diverse, known human Y-chromosome genes show just a few distinct expression profiles. Their relative functional conformity reflects evolutionary factors inherent to sex-specific chromosomes.

CDY1 analysis in infertile patients with DAZ deletions

The DAZ (deleted in azoospermia) gene family is considered the major AZFc ("azoospermia factor" c) candidate responsible for male infertility. However, other genes have been recently mapped to this region and they could contribute to the AZFc phenotype. In particular, the testis-specific CDY1 (chromadomain protein 1) gene has one copy within the DAZ cluster and another one at its distal end. Therefore, this gene could be associated with the spermatogenic damage observed in DAZ-deleted patients since at least one CDY1 copy is invariably absent in these patients. In this study, we investigated whether selected infertile patients affected by different testiculopathies caused by DAZ deletions retained CDY1 and if a genotype-phenotype relation could be demonstrated. We found 3 out of 17 patients with absence of both CDY1 copies, while 14 patients have only one CDY1 copy absent. Two out of the 3 patients with deletion of both copies of CDY1 were affected by severe hypospermatogenesis while one patient presented Sertoli cell-only syndrome. Therefore, there was no clear relation between genotype and phenotype, and the loss of the distal copy of CDY1 does not seem to worsen the phenotype of infertile patients with deletion of the DAZ gene cluster. However, a possible contribution of CDY1 in determining the spermatogenic alteration could not be excluded.

Towards a complete sequence of the human Y chromosome

A few dozen genes are known on the human Y chromosome. The completion of the human genome sequence will allow identification of the remaining loci, which should shed further light on the function and evolution of this peculiar chromosome.

Expression of CDY1 may identify complete spermatogenesis

OBJECTIVE

To investigate the expression of deleted in azoospermia (DAZ), RNA-binding motif (RBM), and chromodomain y1 (CDY1) genes in the testes of men with azoospermia with variable histopathologies.

DESIGN

Prospective study.

SETTING

Andrology laboratory of a university-affiliated maternity hospital.

PATIENT(S)

Sixty-six men with azoospermia.

INTERVENTION(S)

Testicular sperm extraction.

MAIN OUTCOME MEASURE(S)

The results of gene expression in testicular tissue tested by RT-PCR were correlated with those of histopathologically and microscopically examined minced testicular tissue. Y chromosome microdeletion testing and karyotyping were performed, as was direct sequencing of CDY1-PCR products.

RESULT(S)

CDY1-minor expression was detected in all biopsies in which mature spermatids/spermatozoa were observed by histological analysis and/or in the minced tissue. CDY1-minor expression was also detected in two biopsies with arrest at the spermatocyte stage during which no mature spermatids/spermatozoa were observed. A previously unreported CDY1-minor alternative splicing transcript was identified. DAZ and RBM gene expressions were detected in all biopsies in which at least a few germinal cells in early stages were found and in one biopsy histologically determined as Sertoli cell only.

CONCLUSION(S)

Our preliminary results suggest that CDY1-minor expression might increase the prospect for complete spermatogenesis, while RBM and DAZ expression can only be indicative of the presence of germinal cells.

The human cytochrome P450 3A locus. Gene evolution by capture of downstream exons

Using a bacterial artificial chromosome (BAC) clone, we have mapped the human cytochrome P450 3A (CYP3A) locus containing the genes encoding for CYP3A4, CYP3A5 and CYP3A7. The genes lie in a head-to-tail orientation in the order of 3A4, 3A7 and 3A5. In both intergenic regions (3A4-3A7 and 3A7-3A5), we have detected several additional cytochrome P450 3A exons, forming two CYP3A pseudogenes. These pseudogenes have the same orientation as the CYP3A genes. To our surprise, a 3A7 mRNA species has been detected in which the exons 2 and 13 of one of the pseudogenes (the one that is downstream of 3A7) are spliced after the 3A7 terminal exon. This results in an mRNA molecule that consists of the 13 3A7 exons and two additional exons at the 3' end. The additional two exons originating from the pseudogene are in an altered reading frame and consequently have the capability to code a completely different amino acid sequence than the canonical CYP3A exons 2 and 13. These findings may represent a generalized evolutionary process with genes having the potential to capture neighboring sequences and use them as functional exons.

Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides

The molecular identity and function of the Drosophila melanogaster Y-linked fertility factors have long eluded researchers. Although the D. melanogaster genome sequence was recently completed, the fertility factors still were not identified, in part because of low cloning efficiency of heterochromatic Y sequences. Here we report a method for iterative blast searching to assemble heterochromatic genes from shotgun assemblies, and we successfully identify kl-2 and kl-3 as 1beta- and gamma-dynein heavy chains, respectively. Our conclusions are supported by formal genetics with X-Y translocation lines. Reverse transcription-PCR was successful in linking together unmapped sequence fragments from the whole-genome shotgun assembly, although some sequences were missing altogether from the shotgun effort and had to be generated de novo. We also found a previously undescribed Y gene, polycystine-related (PRY). The closest paralogs of kl-2, kl-3, and PRY (and also of kl-5) are autosomal and not X-linked, suggesting that the evolution of the Drosophila Y chromosome has been driven by an accumulation of male-related genes arising de novo from the autosomes.

Male infertility caused by a de novo partial deletion of the DAZ cluster on the Y chromosome

Deletions in distal Yq interval 6 represent the cause of 10-15% of idiopathic severe male infertility and map to a region defined AZFc (azoospermia factor c). The testis-specific gene DAZ is considered a major AZFc candidate, and its deletion has been associated with a severe disruption in spermatogenesis. However, DAZ is actually a multicopy gene family consisting of seven clustered copies spanning about 1 megabase. Only deletions removing the entire DAZ gene cluster together with other genes have been reported in infertile males. Because no case of spermatogenic failure has been traced to intragenic deletions, point mutations, or even deletions not involving all the DAZ copies, the definitive proof for a requirement of DAZ for spermatogenesis is still debatable. Here we report the first case of a partial deletion of the DAZ cluster removing all but one of the copies. This deletion is present in a patient affected with severe oligozoospermia who had a testicular phenotype characterized by a great quantitative reduction of germ cells (severe hypospermatogenesis). The absence of this deletion in the fertile brother of the patient suggests that this de novo mutation indeed caused the spermatogenic failure.

Human Y chromosome, sex determination, and spermatogenesis- a feminist view

In this review I want to argue that, far from being a macho entity with an all-powerful role in male development, the human Y chromosome is a "wimp." It is merely a relic of the X chromosome, and most or all of the genes it bears-including the genes that determine sex and control spermatogenesis-are relics of genes on the X chromosome that have other functions altogether.

New uses for new haplotypes the human Y chromosome, disease and selection

Recent discoveries of many new genes have made it clear that there is more to the human Y chromosome than a heap of evolutionary debris, hooked up to a sequence that happens to endow its bearer with testes. Coupled with the recent development of new polymorphic markers on the Y, making it the best-characterized haplotypic system in the genome, this gives us new opportunities to assess its role in disease and selection, through association studies with phenotypes such as infertility and cancers. However, the peculiar genetics of this bizarre chromosome means that we should interpret such studies particularly cautiously.

New concepts in operative andrology: a review

Several recently published, or about to be published, controversial issues in operative andrology are clarified and reviewed in this paper. The microsurgical technique for sperm retrieval for nonobstructive azoospermia, the round spermatid controversy and the varicocoele dilemma (why does everybody keep doing varicocoelectomy for male factor infertility?) are presented with salient points that have recently been presented elsewhere and referenced. Finally, at the end, we review briefly what is known about the likelihood of genetic transmission of infertility from male factor patients to their offspring as a result of the new ICSI technology.

Transposons and genome evolution in plants

Although it is known today that transposons comprise a significant fraction of the genomes of many organisms, they eluded discovery through the first half century of genetic analysis and even once discovered, their ubiquity and abundance were not recognized for some time. This genetic invisibility of transposons focuses attention on the mechanisms that control not only transposition, but illegitimate recombination. The thesis is developed that the mechanisms that control transposition are a reflection of the more general capacity of eukaryotic organisms to detect, mark, and retain duplicated DNA through repressive chromatin structures.

Analysis and significance of messenger RNA in human ejaculated spermatozoa

Human ejaculate spermatozoa contain multiple mRNA species carried over from earlier stages in spermatogenesis. To date, gene-specific RT-PCR or in situ hybridization has detected transcripts for beta-actin, heat shock proteins (HSP) 70 and 90, protamines (PRM) 1 and 2, transition protein (TNp) 2, HLA II, beta-integrins, and, most recently, phosphodiesterase subtypes. We have further evidence for a complex population of transcripts based on screening a human testis cDNA library with a heterologous spermatozoal probe. High levels of transcribed repetitive sequences are present in human spermatozoa, including medium reiteration repeats (MERs) and short and long nuclear interspersed repeats (SINES and LINES). Both SINES and LINES belong to the retroposon class of repeat elements, which are thought to proliferate via an intermediate RNA that is converted to DNA by an RNA-dependent DNA polymerase (reverse transcriptase). We have circumstantial evidence for the presence of an RT in ejaculate sperm based on the detection of transcripts for ORF2 of LINE 1 encoding such an enzyme. Our data suggests the following: 1. Ejaculate spermatozoa may be a very useful tool in the identification of genes linked to an infertile phenotype. 2. Spermatozoa (or spermatids) may express a reverse transcriptase, the role of which is unknown. 3. RNA isolated from spermatozoa or washed semen samples may facilitate the detection of mutations and deletions in testis-expressed AZF-linked genes.

A new family of genes and pseudogenes potentially expressing testis- and brain-specific leucine zipper proteins in man and mouse

We have characterized a new mouse gene highly transcribed in the testis, and a derived intronless gene expressed in the embryo. The latter gene is present in Mus musculus domesticus and in Mus musculus castaneus but is absent in Mus spretus. The sequencing of different clones from a testis cDNA library reveals a complex transcriptional regulation for the intron-containing gene. The use of several promoters, alternative splicing and trans-splicing, and of two different polyadenylation sites account for the diversity. The different cDNAs encode proteins with features of basic helix-loop-helix leucine zipper (bHLH-ZIP) DNA-binding factors with homology to a new brain-specific factor. The presence of multiple CK2 and PKC phosphorylation sites suggests that their activity may be regulated by phosphorylation. In man, a pseudogene, apparently derived from the same transcript as in mouse and showing 90% homology in the coding region, is present within an intron of another gene. Interestingly, although the human pseudogene is highly mutated in human, in the mouse it has only four nucleotide changes compared with the cDNA of origin, and is still capable of encoding a protein.

Evolution of the avian sex chromosomes and their role in sex determination

Is it the female-specific W chromosome of birds that causes the avian embryo to develop a female phenotype, analogous to the dominance mode of genic sex differentiation seen in mammals? Or is it the number of Z chromosomes that triggers male development, similar to the balance mode of differentiation seen in Drosophila and Caenorhabditis elegans? Although definite answers to these questions cannot be given yet, some recent data have provided support for the latter hypothesis. Moreover, despite the potentially common features of sex determination in mammals and birds, comparative mapping shows that the avian sex chromosomes have a different autosomal origin than the mammalian X and Y chromosomes.

Human LINE retrotransposons generate processed pseudogenes

Long interspersed elements (LINEs) are endogenous mobile genetic elements that have dispersed and accumulated in the genomes of higher eukaryotes via germline transposition, with up to 100,000 copies in mammalian genomes. In humans, LINEs are the major source of insertional mutagenesis, being involved in both germinal and somatic mutant phenotypes. Here we show that the human LINE retrotransposons, which transpose through the reverse transcription of their own transcript, can also mobilize transcribed DNA not associated with a LINE sequence by a process involving the diversion of the LINE enzymatic machinery by the corresponding mRNA transcripts. This results in the 'retroposition' of the transcribed gene and the formation of new copies that disclose features characteristic of the widespread and naturally occurring processed pseudogenes: loss of intron and promoter, acquisition of a poly(A) 3' end and presence of target-site duplications of varying length. We further show-by introducing deletions within either coding sequence of the human LINE-that both ORFs are necessary for the formation of the processed pseudogenes, and that retroviral-like elements are not able to produce similar structures in the same assay. Our results strengthen the unique versatility of LINEs as genome modellers.

Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of an ancient functional retroposon differentially expressed in testis

Although most retroposons that arose by reverse transcription of cellular mRNAs and by reintegration into the genome are nonfunctional, several examples exist in which the retroposon acquired a novel function and became fixed in the genome as a functional gene. We identified another such case: the ubiquitously expressed X-linked XAP-5 gene with unknown function gave rise to its retroposed counterpart, XAP-5-like (X5L), which has an intronless open reading frame and is autosomal in human. Phylogenetic analysis of the human and mouse XAP-5 and X5L genes shows that the retroposition most likely took place before the radiation of eutherian mammals. The XAP-5 and X5L genes are expressed in a wide range of tissues but are differentially expressed in testis. The ancient origin and broad expression of the X5L retroposon indicate that the XAP-5 and X5L genes may have assumed different functions in somatic cells. In addition to this, because of its autosomal location and its high level and particular pattern of expression in spermatogenic cells, the X5L expression in testis may compensate for the X-linked XAP-5 gene, which may be silenced during spermatogenesis.

The promoter of the Poly(A) binding protein 2 (Pabp2) retroposon is derived from the 5'-untranslated region of the Pabp1 progenitor gene

The mouse Pabp2 retroposon encodes an isoform of poly(A) binding protein that is expressed in meiotic and early haploid spermatogenic cells. In the present study, we have determined the transcription start site of the Pabp2 gene to clarify the source of its promoter, a prerequisite for expression of retroposons and preservation of their function by natural selection. The 5' end of the mouse Pabp2 retroposon exhibits extensive similarity to the entire 5' UTR of the human PABP1 mRNA, but there is no similarity upstream of the transcription start site of the human PABP1 mRNA, indicating that the Pabp2 gene lacks 5' flanking sequences of the parental PABP1 gene. Oligonucleotide-directed RNase H cleavage and 5' rapid amplification of cDNA ends both indicate that the transcription start site of the mouse Pabp2 gene is located approximately 330 bases downstream of the capsite of the PABP1 mRNA, indicating that the Pabp2 promoter is derived from the PABP1 5' UTR.

RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements

While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions. In this article, I argue that differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression. Rapid genomic change by accumulating retrosequences may even facilitate speciation [McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123-126.] In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.

Transmission of a Y chromosomal deletion involving the deleted in azoospermia (DAZ) and chromodomain (CDY1) genes from father to son through intracytoplasmic sperm injection: case report

The transmission of a deleted in azoospermia (DAZ) deletion from a severely oligozoospermic patient to his son following intracytoplasmic sperm injection (ICSI) treatment is reported. The case report highlights the fertilizing capacity of spermatozoa carrying Y chromosome deletions in patients treated with ICSI and stresses the importance of genetic counselling in severe male infertility.