Primate DAX1, SRY, and SOX9: evolutionary stratification of sex-determination pathway

Ligand-independent actions of the orphan receptors/corepressors DAX-1 and SHP in metabolism, reproduction and disease

DAX-1 and SHP are two closely related atypical orphan members of the nuclear receptor (NR) family that make up the NR0B subfamily. They combine properties of typical NRs and of NR-associated coregulators: both carry the characteristic NR ligand-binding domain but instead of a NR DNA-binding domain they have unique N-terminal regions that contain LxxLL-related NR-binding motifs often found in coregulators. Recent structural data indicate that DAX-1 lacks a ligand-binding pocket and thus should rely on ligand-independent mechanisms of regulation. This might be true, but remains to be proven, for SHP as well. DAX-1 and SHP have in common that they act as transcriptional corepressors of cholesterol metabolism pathways that are related on a molecular level. However, the expression patterns of the two NRs are largely different, with some notable exceptions, and so are the physiological processes they regulate. DAX-1 is mainly involved in steroidogenesis and reproductive development, while SHP plays major roles in maintaining cholesterol and glucose homeostasis. This review highlights the key similarities and differences between DAX-1 and SHP with regard to structure, function and biology and considers what can be learnt from recent research advances in the field. This article is part of a Special Issue entitled 'Orphan Receptors'.

Molecular delineation of the Y-borne Sry gene in the Formosan pangolin (Manis pentadactyla pentadactyla) and its phylogenetic implications for Pholidota in extant mammals

The systematic status of Pholidota has been a matter of debate, particularly regarding the apparent inconsistency between morphological and molecular studies. The Sry gene, a master regulator of male sex determination in eutherian mammals, has not yet been used for phylogenetic analyses of extant mammals. The objective of the present study was to clone and characterize the complete gene (1300 base pairs; bp) and amino acid sequences (229 residues) of Sry from the Formosan pangolin (Manis pentadactyla pentadactyla), a member of Pholidota. The Sry amino acid identity between pangolin and other reported species ranged from 42.5% (mouse, Mus musculus) to 84.1% (European hare, Lepus europaeus). Sequence conservation was primarily in the high motility group (HMG) box (234 bp), whereas homology outside the HMG box was low. The cloned Sry was mapped to the pangolin Y chromosome by fluorescence in situ hybridization (FISH); this was confirmed to be the first Y-borne molecular marker identified in Pholidota. Based on Bayesian phylogenetic analysis for Sry HMG sequences from 36 representative taxa, including the Formosan pangolin, Pholidota was more closely related to Carnivora than to Xenarthra, consistent with the emerging molecular tree inferred from markers not located on the Y chromosome. In conclusion, this study characterized the gene structure of Sry of the Formosan pangolin and provided insights into the phylogenetic position of Pholidota.

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

Heritable diseases are caused by germ-line mutations that, despite tissuewide presence, often lead to tissue-specific pathology. Here, we make a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were systematically mapped to tissues they affect from disease-relevant literature in PubMed to create a disease-tissue covariation matrix of high-confidence associations of >1,000 diseases to 73 tissues. By retrieving >2,000 known disease genes, and generating 1,500 disease-associated protein complexes, we analyzed the differential expression of a gene or complex involved in a particular disease in the tissues affected by the disease, compared with nonaffected tissues. When this analysis is scaled to all diseases in our dataset, there is a significant tendency for disease genes and complexes to be overexpressed in the normal tissues where defects cause pathology. In contrast, cancer genes and complexes were not overexpressed in the tissues from which the tumors emanate. We specifically identified a complex involved in XY sex reversal that is testis-specific and down-regulated in ovaries. We also identified complexes in Parkinson disease, cardiomyopathies, and muscular dystrophy syndromes that are similarly tissue specific. Our method represents a conceptual scaffold for organism-spanning analyses and reveals an extensive list of tissue-specific draft molecular pathways, both known and unexpected, that might be disrupted in disease.

Genetic and environmental influences on 2D:4D finger length ratios: a study of monozygotic and dizygotic male and female twins

Recent studies have shown significant sex differences in the pattern of 2D:4D finger length ratios in humans and several other mammalian species. In humans, these ratios are suggested to be negatively correlated with prenatal exposure to testosterone, positively correlated with prenatal estrogen, and exhibit sex specific patterns of association with sexually dimorphic clinical phenotypes. However, the relative contributions of genetic and environmental influences on digit ratios in men and women are currently unknown. Therefore, the purpose of the current study was to examine genetic and environmental influences on 2D:4D ratios in twins. Participants included 146 monozygotic (MZ) and 154 dizygotic (DZ) adult male and female twins participating in the Michigan State University Twin Study of Behavioral Adjustment and Development. Overall, biometric model-fitting analyses indicated significant additive genetic and nonshared environmental influences on digit ratios. Findings suggest greater similarity between 2D:4D ratios in MZ relative to DZ twins that can be accounted for by genetic and nonshared environmental factors.

A mouse gene encoding a novel member of the WD family of proteins is highly conserved and predominantly expressed in the testis (Wdr13)

Wdr13, a novel member of the WD family of proteins and the mouse homolog of WDR13 is localized to the locus XA1.1 and is predominantly expressed in the testis. The expression begins at the early stages of gonadal development and is maintained throughout the adult life with a predominant expression in the germ cells of adult testis. RNA in situ hybridization on the testis and brain sections indicated a cytoplasmic expression of the transcript. The alternatively spliced transcripts of the gene are generated by different methods and showed a differential pattern of expression, suggesting functional diversity. The expression of the gene in the unfertilized egg and in the neural stem cells indicated the functional significance of the gene from the early stages of development. The nuclear localization of the mouse WDR13 protein suggested a regulatory function. Evolutionary analysis of the gene indicated an extensive functional conservation across diverse species. Comparison of the genomic organization of the different homologs revealed a varied organization in the invertebrate homolog and the retention of the functionally significant introns in the same.

The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians

Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes with marsupials: the Marsupionta hypothesis. Various nuclear genes tend to support Theria, but a comprehensive study of long concatenated sequences and broad taxon sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences from the databases to create two large and independent nuclear data sets. One (data set I) emphasized taxon sampling and comprised five genes, with a concatenated length of 2,793 bp, from 21 species (two monotremes, six marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids, from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, minimum evolution, maximum likelihood, and Bayesian methods using various models and data partitions. Data set I gave bootstrap support values for Theria between 55% and 100%, while support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased the support for Theria. Data set II exclusively supported Theria, with the highest possible values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained from two single amino acid deletions and one insertion, while no supporting insertions and deletions were found for Marsupionta. On the basis of our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutheria at 193-186 MYA. The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.

The endless quest for sex determination genes

Disorders in human sex determination cause defects in gonadal function and can result in a spectrum of abnormalities in the internal and external genitalia, ranging from relatively mild sexual ambiguities to complete sex reversal. Several genes involved in sex determination have been validated in humans, and activities of their gene products are being elucidated, particularly in mouse models. However, how these genes interact in an overall process remains far from clear, and it is probable that many additional genes are involved. Management of patients with pathologies in sex determination and subsequent differentiation is currently under debate, but will require not only an understanding of the multiple definitions of an individual's sex but also an increased knowledge of the molecular mechanisms involved in sex determination.

Molecular mechanisms of DAX1 action

DAX1 (dosage sensitive sex reversal (DSS), adrenal hypoplasia congenita (AHC) critical region on the X chromosome, gene 1) encoded by the gene NR0B1, is an unusual orphan nuclear receptor that when mutated causes AHC with associated hypogonadotropic hypogonadism (HH), and when duplicated causes DSS. DAX1 expression has been shown in all regions of the hypothalamic-pituitary-adrenal-gonadal (HPAG) axis during development and in adult tissues, suggesting a critical role for DAX1 in the normal development and function of this axis. Steroidogenic factor 1 (SF1, NR5A1) knockout mice show similar developmental defects as AHC and HH patients, but paradoxically, DAX1 is a negative coregulator of SF1 transactivation. The function of DAX1 as an antagonist of SF1 in gonadal development is consistent with the fact that in humans, duplication of the region of the X chromosome containing DAX1 causes a similar phenotype as mutations in SF1. However, how disruption of DAX1 leads to adrenal, hypothalamic, and pituitary developmental defects similar to SF1 disruption remains to be clarified. The exact mechanism of DAX1 action in each of these tissues during adulthood and critical stages of development are not fully understood. Recent evidence suggests a broader functional role for DAX1 as a negative coregulator of estrogen receptor (ER, NR3A1-2), liver receptor homologue-1 (LRH-1, NR5A2), androgen receptor (AR, NR3C4), and progesterone receptor (PR, NR3C3), each by distinct repression mechanisms. DAX1 may have pleiotropic roles in addition to its function as a negative regulator of steroidogenesis during the development and adult function of the HPAG axis.

Similar gene structure of two Sox9a genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus)

The Sox9 gene encodes a transcription factor that is critical for testis determination and chondrogenesis in vertebrates. Mutations in human SOX9 cause campomelic dysplasia, a dominant skeletal dysmorphology syndrome often associated with male to female sex reversal. Here we show that the Sox9a gene was duplicated during evolution of the rice field eel, Monopterus albus, a freshwater fish which undergoes natural sex reversal from female to male during its life, and has a haploid genome size (0.6-0.8 pg) that is among the smallest of the vertebrates. The duplicated copies of the gene (named Sox9al and Sox9a2) fit within the Sox9 clade of vertebrates, especially in the Sox9a subfamily, not in the Sox9b subfamily. They have similar structures as revealed by both genomic and cDNA analysis. Furthermore, both Sox9al and Sox9a2 are expressed in testis, ovary, and ovotestis; and specifically in the outer layer (mainly gonocytes) of gonadal epithelium with bipotential capacity to form testis or ovary, suggesting that they have similar roles in gonadal differentiation during sex reversal in this species. The closely related gene structure and expression patterns of the two sox9a genes in the rice field eel also suggest that they arose in recent gene duplication events during evolution of this fish lineage.

Akodon sex reversed females: the never ending story

The existence of fertile A. azarae females with a chromosome sex pair indistinguishable from that of males was reported more than 35 years ago. These heterogametic females were initially thought to occur due to an extreme process of dosage compensation in which X inactivation was restricted to Xp and complemented by a deletion of Xq (Xx females). Later on, a C-banding analysis of A. mollis variant females showed that these specimens were in fact XY* sex reversed and not Xx females. The finding of positive testing for Zfy and Sry multiple-copy genes in Akodon males and heterogametic females confirmed the XY* assumption. At the present time, XY* sex reversed females have been found to exist in nine Akodon species. Akodon heterogametic females produce X and Y* oocytes, which upon sperm fertilization give rise to viable XX (female), XY* (female), and XY (male) embryos, and to non-viable Y*Y zygotes. Heterozygous females exhibit a better reproductive performance than XX females in order to compensate the Y*Y zygote wastage. XY* sex reversed females are assumed to occur due to a deficient Sry expression resulting in the development of ovaries instead of testes. Moreover, the appearance of Y* elements is a highly recurrent event. It is proposed that homozygosity for an autosomal or pseudoautosomal recessive mutation (s-) inhibits Sry expression giving rise to XY* embryos with ovary development. Location of the Y* chromosome in the female germ cell lineage produces an ovary-specific imprinting of the Sry* gene maintaining its defective expression through generations independently from the presence or absence of s- homozygosity. By escaping the ovary-specific methylation some Y* chromosomes turn back to normal Ys producing Y oocytes capable of generating normal male embryos when fertilized by an X sperm. Fluctuations in the rate of variant females in field populations and in laboratory colonies of Akodon depend on the balance between the appearance of new variant females (s-/s-, XY* specimens) and the extinction of sex reversed specimens due to imprinting escape.

Genetic network identification by high density, multiplexed reversed transcriptional (HD-MRT) analysis in steroidogenic axis model cell lines

Transcriptional network analysis in steroidogenic axis cell lines requires an understanding of cellular network composition and complexity. Previous studies have shown that absence of transcriptional network components in a cell line compromises that cell line's functional capacity for transcriptional regulation. Our goal was to analyze qualitatively steroidogenic axis-derived cell lines' expression of a putative transcriptional network involved in human and mouse development. To pursue this analysis we used Northern blots and a high density-multiplexed reverse transcription-polymerase chain reaction (HD-MRT-PCR) approach. Our results revealed that, while some members of this putative network were universally expressed, only a minority of the non-constitutive targeted transcripts were present in any single line. Based on our data and previously published results for contextual expression of these transcription factors, a model was constructed possessing the topology suggestive of a scale-free network: certain network members were highly connected nodes and would represent critical sites of vulnerability. The importance of these highly connected nodes for network function is supported by the severe phenotypes exhibited by human patients and animal models when these genes are mutated. We conclude that knowledge of network composition in specific cell lines is essential for their use as models to investigate functional interactions within selected subnetworks.

SOX9 has both conserved and novel roles in marsupial sexual differentiation

In addition to an essential role in chondrogenesis, SOX9 is a highly conserved and integral part of the testis determining pathway in human and mouse. To determine whether SOX9 is involved in sex determination in noneutherian mammals we cloned a marsupial orthologue and studied its expression. The tammar wallaby SOX9 gene proved to be highly conserved, and maps to a region of the tammar genome syntenic to human chromosome 17. Marsupial SOX9 transcripts were detected by RT-PCR in the developing limb buds and both the developing ovary and testis from the first sign of gonadal development through to adulthood. Northern blot, in situ hybridisation, and immunohistochemical analyses showed that SOX9 reaches high levels of expression in the developing testis, where it is confined to the Sertoli cell nuclei, and the brain. This is similar to the expression pattern seen in human and mouse embryos and is consistent with a conserved role for SOX9 in vertebrate brain, skeletal, and gonadal development. In addition, SOX9 was expressed in the developing scrotum and mammary gland primordium regions of the tammar up to the time of birth. SOX9 protein was also detected in the developing Wolffian duct epithelium in the male mesonephros. These previously undescribed locations of SOX9 expression suggest that SOX9 may play additional roles in the differentiation of the marsupial reproductive system.

A map of the common chimpanzee genome

The completion of the chimpanzee genome will greatly help us determine which genetic changes are unique to humanity. Chimpanzees are our closest living relative, and a recent study has made considerable progress towards decoding the genome of our sister taxon.1 Over 75,000 common chimpanzee (Pan troglodytes) bacterial artificial chromosome end sequences were aligned and mapped to the human genome. This study shows the remarkable genetic similarity (98.77%) between humans and chimpanzees, while highlighting intriguing areas of potential difference. If we wish to understand the genetic basis of humankind, the completion of the chimpanzee genome deserves high priority.