Dosage compensation and sex-chromatin in non-mammals

Some inconvenient truths about sex chromosome dosage compensation and the potential role of sexual conflict

Sex chromosome dosage compensation was once thought to be required to balance gene expression levels between sex-linked and autosomal genes in the heterogametic sex. Recent evidence from a range of animals has indicated that although sex chromosome dosage compensation exists in some clades, it is far from a necessary companion to sex chromosome evolution, and is in fact rather rare in animals. This raises questions about why complex dosage compensation mechanisms arise in some clades when they are not strictly needed, and suggests that the role of sex-specific selection in sex chromosome gene regulation should be reassessed. We show there exists a tremendous diversity in the mechanisms that regulate gene dosage and argue that sexual conflict may be an overlooked agent responsible for some of the variation seen in sex chromosome gene dose regulation.

Progress and prospects toward our understanding of the evolution of dosage compensation

In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes.

X chromosome reactivation perturbs intracellular self/not-self discrimination

New reports indicate a chromosomal rather than hormonal basis for the susceptibility of females to autoimmune disease. It is held that if females reactivate an inactivated X chromosome, there will be overexpression of certain X-located genes affecting immune function. Hence, normal mechanisms of self/not-self discrimination might be impaired resulting in immune reaction to self antigens. However, the data are also consistent with the long-held view that the demands of intracellular self/not-self discrimination have driven the evolution of X-chromosome dosage compensation. It was proposed that, whether cells are in male or female bodies, concentrations of proteins are fine-tuned up to their aggregation thresholds. A disruption of this equilibrium, by agents originating either externally (for example, virus) or internally (for example, reactivated X chromosome), generates homoaggregates that trigger responses against the respective not-self or self antigens. Thus, female susceptibility to autoimmune disease may not be because certain immune system genes happen to be X-located, but because self/not-self discrimination was the raison d'être for X-chromosome dosage compensation in the first place.

Effects of gene dosage and hormones on the expression of Dr in the platyfish, Xiphophorus maculatus (Poeciliidae)

Platyfish, Xiphophorus maculatus, are polymorphic for the patterns red-dorsal (Dr) and spotted-dorsal (Sd) fins, both controlled by closely linked loci on the X chromosome of Jamapa strain, Jp 163A. The intensity of red pigment looks the same in males and females, but spectrophotometric analysis of dorsal fin extracts showed that heterozygous intact males have significantly more red pigment (drosopterin) than homozygous or heterozygous females or castrated males. The mechanism of Dr expression in Jamapa is, thus, similar to the one present in the Belize stock, where a sex difference is readily apparent that is known to be under androgenic control. The Sd phenotype is identical in both sexes. Sd and Dr are not restricted to the X chromosome, and no evidence for gene dosage compensation has been obtained. Within the Jamapa stock the expression of Sd and Dr are best described in terms of dominance and recessiveness. Dr is strongly augmented by a testicular hormone. Dr and Sd have been separated by crossing-over. In natural populations both genes can occur by themselves, linked to each other or to other pigment genes. The development of the Sd macromelanophores is not contingent upon the presence of pterinophores (Dr) in the dorsal fin or elsewhere in the body.

Sex determination in birds: progeny of nondisjunction canaries of Durham (1926)

The heterogametic sex in birds (ZW) is female for presence of the W or for lack of a second Z chromosome. These alternatives can be distinguished given ZO or ZZW aneuploids and segregation of a Z-linked marker in their progeny. Having discovered the Z-linked cinnamon locus with two alleles (B, black eyes; b, red eyes), Durham observed 21 black-eyed daughters (BO or BbW) of bb cocks and B hens. Using Durham's data on sex–colour phenotypes of 14 young of two of the 21 matroclinous females show that the sex chromosome constitution of the two exceptional hens were more likely ZO than ZZW. This case plus that of Crew's (1983) trisomic rooster (ZZW) shows that sex determination in birds follows the ‘genic balance’ scheme as in Drosophila, not the ‘dominant Y’ scheme as in mammals.

The silkworm Z chromosome is enriched in testis-specific genes

The role of sex chromosomes in sex determination has been well studied in diverse groups of organisms. However, the role of the genes on the sex chromosomes in conferring sexual dimorphism is still being experimentally evaluated. An unequal complement of sex chromosomes between two sexes makes them amenable to sex-specific evolutionary forces. Sex-linked genes preferentially expressed in one sex over the other offer a potential means of addressing the role of sex chromosomes in sexual dimorphism. We examined the testis transcriptome of the silkworm, Bombyx mori, which has a ZW chromosome constitution in the female and ZZ in the male, and show that the Z chromosome harbors a significantly higher number of genes expressed preferentially in testis compared to the autosomes. We hypothesize that sexual antagonism and absence of dosage compensation have possibly led to the accumulation of many male-specific genes on the Z chromosome. Further, our analysis of testis-specific paralogous genes suggests that the accumulation on the Z chromosome of genes advantageous to males has occurred primarily by translocation or tandem duplication.

Location, location, location! Monotremes provide unique insights into the evolution of sex chromosome silencing in mammals

Platypus and echidnas are the only living representative of the egg-laying mammals that diverged 166 million years ago from the mammalian lineage. Despite occupying a key spot in mammalian phylogeny, research on monotremes has been limited by access to material and lack of molecular genetic resources. This has changed recently, and the sequencing of the platypus genome has promoted monotremes into a generally accessible tool in comparative genomics. The most extraordinary aspect of the monotreme genome is an amazingly complex sex chromosomes system that shares extensive homology with bird sex chromosomes and no homology with sex chromosomes of other mammals. This raises important questions about dosage compensation of the five pairs of sex chromosomes in females and meiotic silencing in males, and we are only beginning to unravel possible mechanisms and pathways that may be involved. The homology between monotreme and bird sex chromosomes makes comparison between those species worthwhile, also as they provide a well-defined example where the same sex chromosomes changed from female heterogamety (chicken) to male heterogamety (monotremes). We summarize recent research on monotreme and chicken sex chromosomes and discuss possible mechanisms that may contribute to sex chromosome silencing in monotremes.

A bird's-eye view of sex chromosome dosage compensation

Intensive study of a few genetically tractable species with XX/XY sex chromosomes has produced generalizations about the process of sex chromosome dosage compensation that do not fare well when applied to ZZ/ZW sex chromosome systems, such as those in birds. The inherent sexual imbalance in dose of sex chromosome genes has led to the evolution of sex-chromosome-wide mechanisms for balancing gene dosage between the sexes and relative to autosomal genes. Recent advances in our knowledge of avian genomes have led to a reexamination of sex-specific dosage compensation (SSDC) in birds, which is less effective than in known XX/XY systems. Insights about the mechanisms of SSDC in birds also suggest similarities to and differences from those in XX/XY species. Birds are thus offering new opportunities for studying dosage compensation in a ZZ/ZW system, which should shed light on the evolution of SSDC more broadly.

Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes

Background

The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes, and between sex chromosomes and autosomes. In many organisms, dosage compensation has thus evolved to equalize sex-linked gene expression in males and females. In mammals this is achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma.

Results

Here, we use a microarray approach to show that male chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4–1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci. Intriguingly, without global dosage compensation, the female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds.

Conclusion

The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Importantly, this report, together with a recent study of sex-biased expression in somatic tissue of chicken, demonstrates the first example of an organism with a lack of global dosage compensation, providing an unexpected case of a viable system with large-scale imbalance in gene expression between sexes.

Dosage compensation in birds

The Z and W sex chromosomes of birds have evolved independently from the mammalian X and Y chromosomes [1]. Unlike mammals, female birds are heterogametic (ZW), while males are homogametic (ZZ). Therefore male birds, like female mammals, carry a double dose of sex-linked genes relative to the other sex. Other animals with nonhomologous sex chromosomes possess "dosage compensation" systems to equalize the expression of sex-linked genes. Dosage compensation occurs in animals as diverse as mammals, insects, and nematodes, although the mechanisms involved differ profoundly [2]. In birds, however, it is widely accepted that dosage compensation does not occur [3-5], and the differential expression of Z-linked genes has been suggested to underlie the avian sex-determination mechanism [6]. Here we show equivalent expression of at least six of nine Z chromosome genes in male and female chick embryos by using real-time quantitative PCR [7]. Only the Z-linked ScII gene, whose ortholog in Caenorhabditis elegans plays a crucial role in dosage compensation [8], escapes compensation by this assay. Our results imply that the majority of Z-linked genes in the chicken are dosage compensated.

Bm kettin, homologue of the Drosophila kettin gene, is located on the Z chromosome in Bombyx mori and is not dosage compensated

In Bombyx mori, the female is the heterogametic sex and the sex determining system is referred to as ZZ/ZW. In a previous study, we found that this insect does not show dosage compensation at the transcriptional level. To confirm the validity of our conclusion, we investigated whether or not another sex-linked gene is dosage compensated. To identify new Z-linked genes, total RNA from reciprocal hybrid females between the silkworm strains p50 and C108 was compared using the differential display technique. Nine cDNA fragments corresponding to several differentially expressed mRNAs were cloned and sequenced. The analysis of nucleotide sequence polymorphisms confirmed that one of these cDNAs, ZDD4, originated from the Z chromosome. The amino acid sequence deduced from ZDD4 has homology with kettin, a modular protein in the Z-disc of Drosophila melanogaster muscles. On immunoblots of Bombyx larval muscle proteins a polypeptide of 380 kDa was labelled with antibody to the ZDD4 peptide. We considered that the gene corresponding to ZDD4 encodes a kettin homologue in the silkworm, and denote it as Bm kettin. By a three-point cross, Bm kettin was mapped at 40.0 CM on the Z chromosome. Southern blot analysis revealed that Bm kettin was present at one copy in the genome. Northern blot analysis showed that Bm Kettin mRNA was 9.1kb in length, and that the level of the mRNA in males was two times greater than that of females. Taken together with our previous observations, the present data suggest that lack of dosage compensation is a general rule in B. mori. Moreover, the twofold difference in Bm kettin expression between males and females may help explain the sexual difference in the wing flapping activity observed in some groups of Lepidoptera.

An apparent excess of sex- and reproduction-related genes on the human X chromosome

We describe here the results of a search of Mendelian inheritance in man, GENDIAG and other sources which suggest that, in comparison with autosomes 1, 2, 3, 4 and 11, the X chromosome may contain a significantly higher number of sex- and reproduction-related (SRR) genes. A similar comparison between X-linked entries and a subset of randomly chosen entries from the remaining autosomes also indicates an excess of genes on the X chromosome with one or more mutations affecting sex determination (e.g. DAX1), sexual differentiation (e.g. androgen receptor) or reproduction (e.g. POF1). A possible reason for disproportionate occurrence of such genes on the X chromosome could be that, during evolution, the 'choice' of a particular pair of homomorphic chromosomes for specialization as sex chromosomes may be related to the number of such genes initially present in it or, since sex determination and sexual dimorphism are often gene dose-dependent processes, the number of such genes necessary to be regulated in a dose-dependent manner. Further analysis of these data shows that XAR, the region which has been added on to the short arm of the X chromosome subsequent to eutherian-marsupial divergence, has nearly as high a proportion of SRR genes as XCR, the conserved region of the X chromosome. These observations are consistent with current hypotheses on the evolution of sexually antagonistic traits on sex chromosomes and suggest that both XCR and XAR may have accumulated SRR traits relatively rapidly because of X linkage.

Absence of dosage compensation at the transcription level of a sex-linked gene in a female heterogametic insect, Bombyx mori

To confirm whether sex-linked genes of the silkworm are dosage compensated or not, we investigated three RAPDs and one RFLP marker which have been mapped to the Z chromosome as candidate genes to test for dosage compensation. Northern blot analysis demonstrated that one of the RAPDs, T15.180a, is transcribed into several mRNAs in the embryo, midgut, Malpighian tubule, testis and ovary. Southern blot analysis revealed that T15.180a is present at one copy in the genome. Sequence data showed that T15.180a contained two open-reading frames (ORFs) separated by an intron of 605 bp. These ORFs encoded a possible polypeptide of 445 amino acids containing the proline cluster. These results suggested that T15.180a is part of a functional gene on the Z chromosome of the silkworm. We have called this gene T15, and compared its transcriptional level between males and females. Northern blot analysis showed that the level of T15 mRNA in males was twice that of females. For a more precise analysis, the levels of transcription from both alleles of T15 (T15P, T15C) were measured by the single-nucleotide primer extension (SNuPE) assay. The results indicated that the amount of transcription from each T15 allele in both sexes (male, T15P/T15C; female, T15P/W) was equivalent. All the results suggest that sex-linked genes in the silkworm are not dosage compensated.

A case of abnormal sex-dimorphism for bristle number in Drosophila melanogaster

A line of Drosophila melanogaster with average male sternopleural bristle number higher than that of females was obtained after many generations of disruptive selection, where males with high bristle score were mated to females with low scores. This abnormal sex-dimorphism did not influence other bristle traits. Dose compensation mechanisms were not involved, and by means of chromosome substitutions it could be shown that both X-linked and autosomal loci contributed to the sex-dimorphism.

Estimates of genetic parameters in turkeys. 3. Sexual dimorphism and its implications in selection procedures

Live, carcass, and skeletal data taken at 16 wk of age on 504 female and 584 male turkeys from 34 sires and 168 dams were utilized to evaluate sex differences in genetic parameter estimates. Data were transformed to common mean and variance to evaluate possible scaling effects. Genetic parameters were estimated from transformed and untransformed data. Further analyses were conducted with a model that included sire by sex and dams within sire by sex interactions, and the variance estimates were used to calculate genetic correlations between the sexes and genetic regression parameters. Heritability estimates from transformed and untransformed data were similar, indicating that sex differences were present in the genetic parameters, but scaling effects were not an important factor. Genetic correlation estimates from paternal (PHS) and maternal (MHS) half-sib estimates were close to unity for BW (1.14, PHS; 1.09, MHS), shank width (.99, PHS; .93, MHS), breast muscle weight (1.23, PHS; 1.04, MHS), and shank length (1.09, PHS; .97, MHS). However, abdominal fat (.79, PHS; .59 MHS), total drumstick muscle weight (.75, PHS; 1.14, MHS), rough cleaned shank weight (.78, PHS; not estimatable, MHS), and shank bone density (1.00, PHS; .53, MHS) estimates were somewhat lower. The estimates suggest that the measurement of these latter "traits" at the same age in the two sexes may, in fact, be measuring different genetic effects and that selection procedures in turkeys need to take these correlations into account in order to make optimum progress. The genetic regression parameters indicated that more intense selection in the sex that has the smaller genetic variation could be practiced to make greater gains in the opposite sex.

The evolution of heteromorphic sex chromosomes

The facts and ideas which have been discussed lead to the following synthesis and model. 1. Heteromorphic sex chromosomes evolved from a pair of homomorphic chromosomes which had an allelic difference at the sex-determining locus. 2. The first step in the evolution of sex-chromosome heteromorphism involved either a conformational or a structural difference between the homologues. A structural difference could have arisen through a rearrangement such as an inversion or a translocation. A conformational difference could have occurred if the sex-determining locus was located in a chromosomal domain which behaved as a single control unit and involved a substantial segment of the chromosome. It is assumed that any conformational difference present in somatic cells would have been maintained in meiotic prophase. 3. Lack of conformational or structural homology between the sex chromosomes led to meiotic pairing failure. Since pairing failure reduced fertility, mechanisms preventing it had a selective advantage. Meiotic inactivation (heterochromatinization) of the differential region of the X chromosome in species with heterogametic males and euchromatinization of the W in species with heterogametic females are such mechanisms, and through them the pairing problems are avoided. 4. Structural and conformational differences between the sex chromosomes in the heterogametic sex reduced recombination. In heterogametic males recombination was reduced still further by the heterochromatinization of the X chromosome, which evolved in response to selection against meiotic pairing failure. 5. Suppression of recombination resulted in an increase in the mutation rate and an increased rate of fixation of deleterious mutations in the recombination-free chromosome regions. Functional degeneration of the genetically isolated regions of the Y and W was the result. In XY males this often led to further meiotic inactivation of the differential region of the X chromosome, and in this way an evolutionary positive-feedback loop may have been established. 6. Structural degeneration (loss of material) followed functional degeneration of Y or W chromosomes either because the functionally degenerate genes had deleterious effects which made their loss a selective advantage, or because shorter chromosomes were selectively neutral and became fixed by chance. 7. The evolutionary routes to sex-chromosome heteromorphism in groups with female heterogamety are more limited than in those with male heterogamety. Oocytes are usually large and long-lived, and are likely to need the products of X- or Z-linked genes. Meiotic inactivation of these chromosomes is therefore unlikely. In the oocytes of ZW females, meiotic pairing failure is avoided through euchromatinization of the W rather than heterochromatinization of the Z chromosome.(ABSTRACT TRUNCATED AT 400 WORDS)

Insect sex chromosomes. VI. A presumptive hyperactivation of the male X chromosome in Acheta domesticus (L.)

The functional status of the X chromosome in Acheta domesticus has been analysed at the whole chromosome level on the basis of (1) 3H-thymidine autoradiography, (2) 5-BrdU/AO fluorescence microscopy (3) in vivo 5-BrdU incorporation and (4) 3H-UdR induced aberrations. The rationale of these techniques in relation to the functional aspect of the X chromosome is that the inactive X chromosome would (1) show asynchrony in DNA synthesis, (2) show differential fluorescence, (3) respond differentially to in vivo 5-BrdU treatment and (4) the active X chromosome would show aberrations when treated with 3H-Uridine. From the results, it appears that the X chromosomes in both male (XO) and female (XX) somatic cells of Acheta are euchromatic (active). Further, the single X in the male is transcriptionally as active as the two X chromosomes in the female. In other words, the single X in the male is hyperactive when compared with the single X in the female. From this it is inferred that the male X chromosome is differentially regulated in order to bring about an equalization of it's gene product(s) to that produced by both Xs in the female. Drosophila melanogaster has a comparable system of dosage compensation. Thus, Acheta is yet another insect showing evidence for an X chromosome regulatory mechanism of dosage compensation. Additionally, it is surmised that sex determination in Acheta is based on an autosomes/X chromosome balance mechanism.

Testicular sperm reserves in cockerels bearing Z-autosome translocations

A technique of testicular homogenization and hemocytometric enumeration of elongated spermatids was applied to cockerels bearing Z-autosome translocations to estimate the effects of the translocations on sperm production. Testis weights, numbers of spermatids per gram of testis, and total number of spermatids were not significantly different between translocation-bearing cockerels and those of normal karyotype. In contrast to the adverse effects of X-autosome translocations on mammalian spermatogenesis, these data indicate that Z-autosome translocations do not quantitatively affect sperm production in cockerels.

Gonosome-autosome translocations in fowl: the development of chromosomally unbalanced embryos sired by singly and doubly heterozygous cockerels

Cockerels singly or doubly heterozygous (t1/ +, t2/ + and tl/t2, respectively; collectively heterokaryotypic, HTK) for two different Z-autosome translocations (t1, t2) produce an array of chromosomally balanced and unbalanced spermatozoa owing to adjacent segregation and nondisjunction at the first meiotic division. This study addresses the developmental capacity of embryos derived from matings of control ( + / + ) and HTK (tl/ +, t2/ +, tl/t2) cockerels with hens bearing normal chromosome complements (+ /W).

Estimates of the hatchability of fertile eggs sired by + / +, tl/ +, t2/ + and tl/t2 cockerels were 82·8%, 43·0%, 41·3% and 10·9%, respectively. Approximately 75% of the mortality observed in embryos sired by HTK cockerels occurred by four days of incubation. Developmental arrest generally occurred earlier in embryos sired by t2/+ and tl/t2 cockerels than in those by tl/ + cockerels. These differences reflect variation in the degree of embryonic chromosome unbalance expected among embryos of the different sire groups. The pattern of mortality after three days was similar in embryos sired by HTK cockerels. In control embryos, mortality was highest on days 20–21 of incubation.

Chromosome analysis of 16/18 h embryos, day 1/5 embryos and hatched chicks sired by HTK cockerels revealed that most, if not all, chromosomally unbalanced embryos died during development; the majority before three days of incubation. Partial monosomy for chromosome one was found to be more deleterious to embryonic development than partial trisomy.

Mechanisms and evolutionary origins of variable X-chromosome activity in mammals

The X-chromosome of mammals is remarkable for its variable genetic activity. In somatic cells only a single X-chromosome is active, no matter how many are present, thus providing a dosage compensation mechanism by which males and females effectively have the same gene dosage of X-linked genes. In germ cells, however, it appears that all X-chromosomes present are active. Female germ cells require the presence of two X-chromosomes for normal survival, whereas male germ cells die if they have more than one X-chromosome. This system is found in all eutherian mammals and in marsupials, but is not known in any other animal group. In marsupials the X-chromosome derived from the father seems to be preferentially inactivated, whereas in eutherian mammals that from either parent may be so in different cells of the same animal. The differentiation of a particular X-chromosome as active or inactive is initiated in early embryogeny, and thereafter maintained through all further cell divisions in that individual. The mechanisms by which this is achieved are of great interest in relation to genetic control mechanisms in general. Various recent hypotheses concerning these mechanisms are discussed.

Chromosomal basis of dosage compensation in Drosophila. II. The DNA replication patterns of the male X-chromosome in an autosome--X insertion in D. melanogaster

The functional morphology and the replication pattern of the male X-chromosome in an autosome-X insertion stock (T(1;3) 05) of Drosophila melanogaster have been examined. In larval salivary glands carrying this insertion neither the enlargement and pale staining of the single male X, nor the characteristic early completion of replication cycle, as revealed by 3H-TdR autoradiography is in any way changed. The normal properties of the inserted autosomal segment are also unaltered. The results appear to support a ‘piecemeal’ type of dosage compensation mechanism in Drosophila operating through the male.

X-linked 6-phosphogluconate dehydrogenase in drosophila: subunit associations

6-Phosphogluconate dehydrogenase (PGD) subunits have been dissociated and reassociated in vitro. The intermediate PGD of the heterozygous phenotype is reproduced by reassociation in vitro of subunits derived from the two types of PGD from homozygous flies. This result has a bearingon gene action in the diploid organism and on the mechanism of dosage compensation in Drosophila melanogaster.