Genomic organization and expression of the doublesex-related gene cluster in vertebrates and detection of putative regulatory regions for DMRT1

Evolutionary insights and expression patterns of sex-related gene families in the zig-zag eel Mastacembelus armatus

The zig-zag eel exhibits both sexual dimorphism and sex reversal, making it crucial to understand the mechanisms of sex determination and differentiation. Additionally, the wild populations of the zig-zag eel are significantly declining, emphasizing the need for urgent conservation efforts. In this study, we identified 7 Dmrt, 62 HMG-box, and 73 TGF-β family members in the zig-zag eel genome. Evolutionary analysis revealed that the HMG-box and TGF-β families in the zig-zag eel are primarily characterized by purifying selection. Furthermore, we identified 52 differentially expressed genes between males and females, with more male-biased genes than female-biased genes within these three gene families. ZzDmrt2a was highly expressed in the ovary, while ZzDmrt2b was highly expressed in the testis. Interestingly, Zzgdf9, located on the Y chromosome, was significantly expressed in the ovary. Our results highlight the complexity of sex differentiation mechanisms and underscores the importance of further research to elucidate the specific functions and regulatory networks of these sex-biased genes. Such insights could inform breeding strategies in aquaculture, contributing to the conservation and management of the zig-zag eel.

A Novel Investigation for Early Sex Determination in Alive Adult European Seabass (Dicentrarchus labrax) Using cyp19a1a, dmrt1a, and dmrt1b Genes Expression in Tail Fin tissues

This study is the first investigation for using sex-related gene expression in tail fin tissues of seabass as early sex determination without killing the fish. The European seabass (Dicentrarchus labrax) is gonochoristic and lacks distinguishable sex chromosomes, so, sex determination is referred to molecular actions for some sex-related genes on autosomal chromosomes which are well known such as cyp19a1a, dmrt1a, and dmrt1b genes which play crucial role in gonads development and sex differentiation. cyp19a1a is expressed highly in females for ovarian development and dmrt1a and dmrt1b are for testis development in males. In this study, we evaluated the difference in the gene expression levels of studied genes by qPCR in tail fins and gonads. We then performed discriminant analysis (DA) using morphometric traits and studied gene expression parameters as predictor tools for fish sex. The results revealed that cyp19a1a gene expression was significantly higher in future females' gonads and tail fins (p ≥ 0.05). Statistically, cyp19a1a gene expression was the best parameter to discriminate sex even the hit rate of any other variable by itself could not correctly classify 100% of the fish sex except when it was used in combination with cyp19a1a. In contrast, Dmrt1a gene expression was higher in males than females but there were difficulties in analyzing dmrt1a and dmrt1b expressions in the tail because levels were low. So, it could be used in future research to differentiate and determine the sex of adult fish using the cyp19a1a gene expression marker without killing or sacrificing fish.

Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bug Oncopeltus fasciatus

Sexual dimorphism is common in animals. The most complete model of sex determination comes from Drosophila melanogaster, where the relative dosage of autosomes and X chromosomes leads indirectly to sex-specific transcripts of doublesex (dsx). Female Dsx interacts with a mediator complex protein encoded by intersex (ix) to activate female development. In males, the transcription factor encoded by fruitless (fru) promotes male-specific behaviour. The genetics of sex determination have been examined in a small number of other insects, yet several questions remain about the plesiomorphic state. Is dsx required for female and male development? Is fru conserved in male behaviour or morphology? Are other components such as ix functionally conserved? To address these questions, we report expression and functional tests of dsx, ix and fru in the hemipteran Oncopeltus fasciatus, characterizing three sexual dimorphisms. dsx prevents ix phenotypes in all sexes and dimorphic traits in the milkweed bug. ix and fru are expressed across the body, in females and males. fru and ix also affect the genitalia of both sexes, but have effects limited to different dimorphic structures in different sexes. These results reveal roles for ix and fru distinct from other insects, and demonstrate distinct development mechanisms in different sexually dimorphic structures.

Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures

The sex ratio is a key ecological demographic parameter crucial for population viability. However, the epigenetic mechanisms operating during gonadal development regulating gene expression and the sex ratio remain poorly understood. Moreover, there is interest in the development of epigenetic markers associated with a particular phenotype or as sentinels of environmental effects. Here, we profiled DNA methylation and gene expression of 10 key genes related to sex development and stress, including steroidogenic enzymes, and growth and transcription factors. We provide novel information on the sex-related differences and on the influence of elevated temperature on these genes in zebrafish, a species with mixed genetic and environmental influences on sex ratios. We identified both positive (e.g., amh, cyp11c and hsd11b2) and negative (e.g., cyp11a1 and dmrt1) correlations in unexposed males, and negative correlation (amh) in exposed females between DNA methylation and gene expression levels. Further, we combined DNA methylation analysis with machine learning procedures and found a series of informative CpGs capable not only of correctly identifying sex (based on cyp19a1a DNA methylation levels) but also of identifying whether males and females had been exposed to abnormally elevated temperature when young (based on amh and foxl2a DNA methylation levels, respectively). This was achieved in the absence of conspicuous morphological alterations of the gonads. These DNA methylation-based epigenetic biomarkers represent molecular resources that can correctly recapitulate past thermal history and pave the way for similar findings in other species to assess potential ecological effects of environmental disturbances in the context of climate change.

Function of Foxl2 and Dmrt1 proteins during gonadal differentiation in the olive flounder Paralichthys olivaceus

Study on fish sex differentiation is important both from academic and practical aspects. Foxl2 and Dmrt1 are important transcription factors that should be involved in fish gonadal differentiation, but there is still no direct evidence to clarify their protein functions. Olive flounder Paralichthys olivaceus, an important mariculture fish in China, Japan, and Korea, shows sex-dimorphic growth. In this study, the Foxl2 and Dmrt1 proteins were detected in granulosa cells of the ovary and Sertoli cells of the testis, respectively, showing significant sex-dimorphic expression patterns. Then, bioactive high-purity Foxl2 and Dmrt1 recombinant proteins were obtained in vitro. Furthermore, effects of the recombinant Foxl2 and Dmrt1 during gonadal differentiation period were evaluated by intraperitoneal injection in juvenile fish. Compared with the control group, the male rate in the Dmrt1 group increased from 0 % to 82 %, showing for the first time in fish that the recombinant Dmrt1 could alter the sex phenotype. In addition, transcription levels of cyp19a and its transcription factors also changed after the recombinant Foxl2 and Dmrt1 injection. These findings reveal that Foxl2 and Dmrt1 are vital regulators for fish gonadal differentiation by regulating cyp19a expression, and also provide a new approach for sex control in fish aquaculture.

High Polymorphism in the Dmrt2a Gene Is Incompletely Sex-Linked in Spotted Scat, Scatophagus argus

Unlike mammals and birds, many fishes have young sex chromosomes, providing excellent models to study sex chromosome differentiation at early stages. Previous studies showed that spotted scat possesses an XX-XY sex determination system. The X has a complete Dmrt3 copy (termed normal) and a truncated copy of Dmrt1 (called Dmrt1b), while the Y has the opposite (normal Dmrt1, which is male-specific, and a truncated Dmrt3 called Dmrt3△-Y). Dmrt1 is the candidate sex determination gene, while the differentiation of other sex-linked genes remains unknown. The spotted scat has proven to be a good model to study the evolution of sex chromosomes in vertebrates. Herein, we sequenced a neighbor gene of this family, Dmrt2, positioned farther from Dmrt1 and closer to Dmrt3 in the spotted scat, and analyzed its sequence variation and expression profiles. The physical locations of the three genes span across an estimated size of >40 kb. The open reading frames of Dmrt2a and its paralog Dmrt2b are 1578 bp and 1311 bp, encoding peptides of 525 and 436 amino acid residues, respectively. Dmrt2a is positioned close to Dmrt3 but farther from Dmrt1 on the same chromosome, while Dmrt2b is not. Sequence analysis revealed several mutations; insertions, and deletions (indels) on Dmrt2a non-coding regions and single-nucleotide polymorphisms (SNPs) on the Dmrt2a transcript. These indels and SNPs are sex-linked and showed high male heterogeneity but do not affect gene translation. The markers designed to span the mutation sites tested on four different populations showed varied concordance with the genetic sexes. Dmrt2a is transcribed solely in the gonads and gills, while Dmrt2b exists in the gonads, hypothalamus, gills, heart, and spleen. The Dmrt2a and Dmrt2b transcripts are profoundly expressed in the male gonads. Analyses of the transcriptome data from five other fish species (Hainan medaka (Oryzias curvinotus), silver sillago (Sillago sihama), Nile tilapia (Oreochromis niloticus), Hong Kong catfish (Clarias fuscus), and spot-fin porcupine fish (Diodon hystrix)) revealed testes-biased expression of Dmrt1 in all, similar to spotted scat. Additionally, the expression of Dmrt2a is higher in the testes than the ovaries in spotted scat and Hainan medaka. The Dmrt2a transcript was not altered in the coding regions as found in Dmrt1 and Dmrt3 in spotted scat. This could be due to the functional importance of Dmrt2a in development. Another possibility is that because Dmrt2a is positioned farther from Dmrt1 and the chromosome is still young, meaning it is only a matter of time before it differentiates. This study undeniably will aid in understanding the functional divergence of the sex-linked genes in fish.

Sex-reversal and Histopathological Assessment of Potential Endocrine-Disrupting Effects of Graphene Oxide on Japanese medaka (Oryzias latipes) Larvae

Sex-ratio is considered as an end point during endocrine disrupting chemicals (EDCs) evaluation. Many fish species including Japanese medaka have XX/XY sex determination mechanism, however, sex reversal (SR) can be induced by external and genetic factors. SR imposed an imbalance in natural sex ratio of a population living in any ecosystem. Considering SR as an end point, we aimed to investigate the potential EDC effects of graphene oxide (GO), a nanocarbon, using Japanese medaka as a model. One-day post-hatch (dph) medaka fries were exposed to GO (2.5, 5.0, 10.0 and 20 mg/L) for 96 h without food, followed by 6 weeks depuration in a GO-free environment with feeding. Phenotypic sex was determined by gonad histology; genotypic sex by genotyping Y-chromosome-specific male sex determining gene, dmy. Our data indicated testes in both XY and XX genotypes, while ovaries were only in XX females. Histopathology of XY and XX testis showed isogenic spermatocysts with active spermatogenesis. Distribution of spermatocytes (SPTs), not the spermatogonium (SPGs), showed enhancement in XY than XX testis. Female phenotypes had single ovary, either in stage 0 or 1. Ovo-testis/testis-ova were absent in XX or XY gonads. GO (2.5-20 mg/L) had inconsistent concentration-dependent effect in both SPGs and SPTs; however, no effect on ovarian follicles. Despite genotypic differences (XY/XX), in the histopathology/histochemistry of liver and kidneys GO effects was found to be minimum. Taken together, present study showed spontaneous induction of SR in some XX genotypes; however, exposure of fasting fries to GO had no apparent EDC effects.

The Role of Transcription Factors in Gonad Development and Sex Differentiation of a Teleost Model Fish-Guppy (Poecilia reticulata)

The guppy (Poecilia reticulata) is one of the world's most popular ornamental fish. Due to lecithotrophic viviparous, it is commonly used in toxicological studies and environmental monitoring. This study aimed to investigate the molecular mechanisms of gonad development and differentiation during guppy ontogenesis. The study mainly focused on the role and localization of potential specific sex markers and transcription factors: Sox9, Dmrt1, Erβ. For histological analysis, guppies of both sexes were collected at 1, 60, and 360 dph (day post-hatching). The gonads morphology and immunohistochemistry detection of mentioned markers localization were performed. The expression of Sox9 protein was compared between sexes. Histological analysis revelated all types of male germinal cells in 60 dph guppy's testes. Maturated oocytes were visible in the ovaries of 360 dph fish. The Sox9 expression varied in spermatocytes and spermatids, from cellular to nuclear localization, and was higher in ovaries. Dmrt1 was detected in all testes groups and 360 dph ovaries. The Erβ was observed in both sexes at 60 and 360 dph. For the first time, the localization of transcription factors in guppy during ontogenesis was traced. The Sox9 designation as a factor regulating the development of germinal cells in adult guppies may facilitate the analysis of xenobiotics' influence on fish's reproductive system.

Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration

Vertebrate locomotion is orchestrated by spinal interneurons making up a central pattern generator. Proper coordination of activity, both within and between segments, is required to generate the desired locomotor output. This coordination is altered during acceleration to ensure the correct recruitment of muscles for the chosen speed. The transcription factor Dmrt3 has been proposed to shape the patterned output at different gaits in horses and mice.

Vertebrate locomotion is orchestrated by spinal interneurons making up a central pattern generator. Proper coordination of activity, both within and between segments, is required to generate the desired locomotor output. This coordination is altered during acceleration to ensure the correct recruitment of muscles for the chosen speed. The transcription factor Dmrt3 has been proposed to shape the patterned output at different gaits in horses and mice. Here, we characterized dmrt3a mutant zebrafish, which showed a strong, transient, locomotor phenotype in developing larvae. During beat-and-glide swimming, mutant larvae showed fewer and shorter movements with decreased velocity and acceleration. Developmental compensation likely occurs as the analyzed behaviors did not differ from wild-type at older larval stages. However, analysis of maximum swim speed in juveniles suggests that some defects persist within the mature locomotor network of dmrt3a mutants. Our results reveal the pivotal role Dmrt3 neurons play in shaping the patterned output during acceleration in vertebrates.

Molecular characterization, computational analysis and expression profiling of Dmrt1 gene in Indian major carp, Labeo rohita (Hamilton 1822)

Sexual dimorphism of fish morphology, physiology and behavior is diverse and complex in nature. Doublesex and mab-3 related transcription factor (Dmrt) is a large protein family whose function is sexual development and differentiation in vertebrates. Here, we report a full-length cDNA sequence of Labeo rohita (rohu) Dmrt1 of 907 bp length having 798 bp of open reading frame encoding 265 amino acids. The molecular weight of rohu DMRT1 protein was found to be 28.74 KDa and isoelectric point was 7.53. DMRT1 protein contains 23 positively and 24 negatively charged amino acids with a GRAVY score of -0.618. A characteristic DM domain was found in DMRT1 protein, which is a novel DNA-binding domain. Phylogenetic analysis showed maximum similarity with Cyprinus carpio when compared with DMRT1 of other vertebrates. Molecular docking study identified active sites to be targeted for drug designing. Rohu DMRT1 was observed to interact with other proteins such as FOXL2, CYP19a1a, AMH and SOX9a. Differential expression study revealed higher expression in testis tissue implying its role in male sex differentiation and testicular development. The information generated in the present work could facilitate further research to resolve the issues related to gonadal maturation and reproduction of commercially important aquaculture species.

Molecular Characterization of XX Maleness

Androgens and anti-Müllerian hormone (AMH), secreted by the foetal testis, are responsible for the development of male reproductive organs and the regression of female anlagen. Virilization of the reproductive tract in association with the absence of Müllerian derivatives in the XX foetus implies the existence of testicular tissue, which can occur in the presence or absence of SRY. Recent advancement in the knowledge of the opposing gene cascades driving to the differentiation of the gonadal ridge into testes or ovaries during early foetal development has provided insight into the molecular explanation of XX maleness.

Centromere localization in medaka fish based on half-tetrad analysis

Gene-centromere (G-C) mapping provides insight into vertebrate genome composition, structure and evolution. Although medaka fish are important experimental animals, no genome-wide G-C map of medaka has been constructed. In this study, we used 112 interspecific triploid hybrids and 152 DNA markers to make G-C maps of all 24 linkage groups (LGs). Under the assumption of 50% interference, 24 centromeres were localized onto all corresponding medaka LGs. Comparison with 21 centromere positions deduced from putative centromeric repeats revealed that 19 were localized inside the centromeric regions of the G-C maps, whereas two were not. Based on the centromere positions indicated in the G-C maps and those of centromeric repeats on each LG, we classified chromosomes as either biarmed or monoarmed; n = 24 = 10 metacentrics/submetacentrics + 14 subtelocentrics/acrocentrics, which is consistent with the results of previous karyological reports. This study helps to elucidate genome evolution mechanisms, and integrates physical and genetic maps with karyological information of medaka.

Expression analysis and characterization of dmrt2 in Chinese tongue sole (Cynoglossus semilaevis)

Dmrt2 is a member of the dmrt gene family with a conserved zinc finger-like DNA-binding motif (DM domain). In the present study, CS-dmrt2 was cloned from the gonads of Chinese tongue sole (Cynoglossus semilaevis). The full-length cDNA of CS-dmrt2 is 2834 bp in length, with a 251 bp 5'-untranslated region (UTR), a 1086 bp 3'-UTR and a 1503 bp open reading frame (ORF) that encodes a 501-amino-acid peptide. qPCR revealed that CS-dmrt2 was mainly expressed in C. semilaevis testes. In situ hybridization (ISH) showed CS-dmrt2 expression throughout early gonadal development (36 days after hatching (dah) and 86 dah), but the expression was higher in male gonads than in female gonads. CS-dmrt2 mRNA was highly expressed in male germ cells. Comparison of methylation levels between females and males demonstrated hypo-methylated levels of the CS-dmrt2 promoter in the male gonads, which is consistent with the high mRNA expression. These results suggest that the CS-dmrt2 gene may play a functional role in gonadal differentiation/development and germ cell maturation in the testis.

Expression of dmrt1 and vtg genes during gonad formation, differentiation and early maturation in cultured Russian sturgeon Acipenser gueldenstaedtii

Expression of the dmrt1 and vtg genes was described using the real-time PCR (rt-PCR) method from 25 to 1600 days post-hatch (dph) in cultured Russian sturgeon Acipenser gueldenstaedtii. The level of dmrt1 transcription in gonads in subsequent studied periods increased exponentially while vtg expression increased in gonads and livers of A. gueldenstaedtii examined, but in later stages of development. Both dmrt1 and vtg genes showed elevated expression in intersex individuals probably caused by dietary exposure to phyto-oestrogens.

Evolutionarily conserved, DMRT1, encodes alternatively spliced transcripts and shows dimorphic expression during gonadal differentiation in the lizard, Calotes versicolor

An orthologue of Dmrt1 has been cloned and characterized in the lizard, Calotes versicolor (CvDmrt1). CvDmrt1 encodes alternatively spliced transcripts in genital ridge during gonadal differentiation and in adult testis. Its expression in genital ridge initiates from day 3 and is restricted to mesenchymal cells, which differentiate into the Sertoli cells. Lack of expression in the coelomic epithelium of GR shows that CvDmrt1 expression occurs only in the testicular pathway, and that the Sertoli and granulosa cells in GR may originate from different primordia. From day 25 onwards, the expression shifts majorly towards the germ cells both in testis and ovary. Thus its role in sexual differentiation of C. versicolor, which lacks CSD and TSD, is well documented.

Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis

The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.

Disorders of Sex Development with Testicular Differentiation in SRY-Negative 46,XX Individuals: Clinical and Genetic Aspects

Virilisation of the XX foetus is the result of androgen excess, resulting most frequently from congenital adrenal hyperplasia in individuals with typical ovarian differentiation. In rare cases, 46,XX gonads may differentiate into testes, a condition known as 46,XX testicular disorders of sex development (DSD), or give rise to the coexistence of ovarian and testicular tissue, a condition known as 46,XX ovotesticular DSD. Testicular tissue differentiation may be due to the translocation of SRY to the X chromosome or an autosome. In the absence of SRY, overexpression of other pro-testis genes, e.g. SOX family genes, or failure of pro-ovarian/anti-testis genes, such as WNT4 and RSPO1, may underlie the development of testicular tissue. Recent experimental and clinical evidence giving insight into SRY-negative 46,XX testicular or ovotesticular DSD is discussed.

Genetics of sexual development: an evolutionary playground for fish

Teleost fishes are the most species-rich clade of vertebrates and feature an overwhelming diversity of sex-determining mechanisms, classically grouped into environmental and genetic systems. Here, we review the recent findings in the field of sex determination in fish. In the past few years, several new master regulators of sex determination and other factors involved in sexual development have been discovered in teleosts. These data point toward a greater genetic plasticity in generating the male and female sex than previously appreciated and implicate novel gene pathways in the initial regulation of the sexual fate. Overall, it seems that sex determination in fish does not resort to a single genetic cascade but is rather regulated along a continuum of environmental and heritable factors.

Characterization of the Dmrt1 gene in the black rockfish Sebastes schlegeli revealed a remarkable sex-dimorphic expression

The Dmrt genes encode a large family of transcription factors with a conserved zinc finger-like DNA-binding DM domain. The function of Dmrt1, one of the family members, in sexual development has been well studied in invertebrates and vertebrates. In the present study, the full-length cDNA of Dmrt1 was isolated from the testis of Sebastes schlegeli. The full-length cDNA of S. schlegeli Dmrt1 (SsDmrt1) was 1,587 bp and contained a 189-bp 5' UTR, a 489-bp 3' UTR and a 909-bp open reading frame, which encoded 302 amino acids with a conserved DM domain and an male-specific motif domain. Phylogenetic analysis showed the evolutionary relationships of SsDmrt1 with other known Dmrt genes in fish and tetrapods. Several transcriptional factor-binding sites in the 5' promoter were identified that might regulate SsDmrt1 expression. Quantitative real-time PCR analysis indicated that SsDmrt1 was expressed in all of the inspected larval developmental stages from 1 to 35 days after birth and that the level of expression gradually decreased. The expression of SsDmrt1 in adult gonads was sexually dimorphic with extremely high expression in the testis, but very low expression in the ovary. No expression was detected in other tissues. Using in situ hybridization, we demonstrated that SsDmrt1 was specifically expressed in the germ cells of both the testis and the ovary. Thus, our results suggest that SsDmrt1 may have an important role in the differentiation of both the testis and the ovary of S. schlegeli.

Molecular players involved in temperature-dependent sex determination and sex differentiation in Teleost fish

The molecular mechanisms that underlie sex determination and differentiation are conserved and diversified. In fish species, temperature-dependent sex determination and differentiation seem to be ubiquitous and molecular players involved in these mechanisms may be conserved. Although how the ambient temperature transduces signals to the undifferentiated gonads remains to be elucidated, the genes downstream in the sex differentiation pathway are shared between sex-determining mechanisms. In this paper, we review recent advances on the molecular players that participate in the sex determination and differentiation in fish species, by putting emphasis on temperature-dependent sex determination and differentiation, which include temperature-dependent sex determination and genetic sex determination plus temperature effects. Application of temperature-dependent sex differentiation in farmed fish and the consequences of temperature-induced sex reversal are discussed.

Identification of Dmrt genes and their up-regulation during gonad transformation in the swamp eel (Monopterus albus)

The swamp eel is a teleost fish with a characteristic of natural sex reversal and an ideal model for vertebrate sexual development. However, underlying molecular mechanisms are poorly understood. We report the identification of five DM (doublesex and mab-3) domain genes in the swamp eel that include Dmrt2, Dmrt2b, Dmrt3, Dmrt4 and Dmrt5, which encode putative proteins of 527, 373, 471, 420 and 448 amino acids, respectively. Phylogenetic tree showed that these genes are clustered into corresponding branches of the DM genes in vertebrates. Southern blot analysis indicated that the Dmrt1-Dmrt3-Dmrt2 genes are tightly linked in a conserved gene cluster. Notably, these Dmrt genes are up-regulated during gonad transformation. Furthermore, mRNA in situ hybridisation showed that Dmrt2, Dmrt3, Dmrt4 and Dmrt5 are expressed in developing germ cells. These results are evidence that the DM genes are involved in sexual differentiation in the swamp eel.

Characterization of sex determination and sex differentiation genes in Latimeria

Genes involved in sex determination and differentiation have been identified in mice, humans, chickens, reptiles, amphibians and teleost fishes. However, little is known of their functional conservation, and it is unclear whether there is a common set of genes shared by all vertebrates. Coelacanths, basal Sarcopterygians and unique "living fossils", could help establish an inventory of the ancestral genes involved in these important developmental processes and provide insights into their components. In this study 33 genes from the genome of Latimeria chalumnae and from the liver and testis transcriptomes of Latimeria menadoensis, implicated in sex determination and differentiation, were identified and characterized and their expression levels measured. Interesting findings were obtained for GSDF, previously identified only in teleosts and now characterized for the first time in the sarcopterygian lineage; FGF9, which is not found in teleosts; and DMRT1, whose expression in adult gonads has recently been related to maintenance of sexual identity. The gene repertoire and testis-specific gene expression documented in coelacanths demonstrate a greater similarity to modern fishes and point to unexpected changes in the gene regulatory network governing sexual development.

Molecular cloning and expression profile of sex-specific genes, Figla and Dmrt1, in the protogynous hermaphroditic fish, Halichoeres poecilopterus

The genes folliculogenesis specific basic helix-loop-helix (facor in the germline alpha, Figla) and doublesex and mab-3 related transcription factor 1 (Dmrt1) are female- and male-specific genes that play key roles in sex differentiation. To obtain a better understanding of the molecular mechanisms underlying female-to-male sex change, we cloned the cDNAs of these genes from an ovary and a testis of the protogynus wrasse, Halichoeres poecilopterus. This fish has two isoforms of Dmrt1, Dmrt1a and Dmrt1b, caused by an alternative splicing. The Dmrt1b has an insertion of three nucleotides (CAG) in the open reading frame. Figla and Dmrt1 displayed gonadal-specific expression and abundant in the ovaries and in the testes, respectively. In particular, levels of Figla expression in the ovaries were higher in the spawning season than in the non-spawning season. Once sex change began, Figla mRNA decreased and Dmrt1 mRNA increased with progression of oocyte degeneration and spermatogenesis. These expression levels were maintained until the completion of the sex change. Low Figla and high Dmrt1 were also observed in testes of primary males, which functioned as a gonochoristic male throughout its life span in this wrasse. The results of this study suggest that these genes may regulate the gonadal transition from ovary to testis by the same mechanism as that of formation and maintenance of the primary testis in H. poecilopterus.

Chromosomal evolution in Gekkonidae. I. Chromosome painting between Gekko and Hemidactylus species reveals phylogenetic relationships within the group

Geckos are a large group of lizards characterized by a rich variety of species, different modes of sex determination and diverse karyotypes. In spite of many unresolved questions on lizards' phylogeny and taxonomy, the karyotypes of most geckos have been studied by conventional cytogenetic methods only. We used flow-sorted chromosome-specific painting probes of Japanese gecko (Gekko japonicus), Mediterranean house gecko (Hemidactylus turcicus) and flat-tailed house gecko (Hemidactylus platyurus) to reveal homologous regions and to study karyotype evolution in seven gecko species (Gekko gecko, G. japonicus, G. ulikovskii, G. vittatus, Hemidactylus frenatus, H. platyurus and H. turcicus). Generally, the karyotypes of geckos were found to be conserved, but we revealed some characteristic rearrangements including both fissions and fusions in Hemidactylus. The karyotype of H. platyurus contained a heteromorphic pair in all female individuals, where one of the homologues had a terminal DAPI-negative and C-positive heterochromatic block that might indicate a putative sex chromosome. Among two male individuals studied, only one carried such a polymorphism, and the second one had none, suggesting a possible ZZ/ZW sex determination in some populations of this species. We found that all Gekko species have retained the putative ancestral karyotype, whilst the fission of the largest ancestral chromosome occurred in the ancestor of modern Hemidactylus species. Three common fissions occurred in the ancestor of Mediterranean house and flat-tailed house geckos, suggesting their sister group relationships. PCR-assisted mapping on flow-sorted chromosome libraries with conserved DMRT1 gene primers in G. japonicus indicates the localization of DMRT1 gene on chromosome 6.

Strong conservation of the bird Z chromosome in reptilian genomes is revealed by comparative painting despite 275 million years divergence

The divergence of lineages leading to extant squamate reptiles (lizards, snakes, and amphisbaenians) and birds occurred about 275 million years ago. Birds, unlike squamates, have karyotypes that are typified by the presence of a number of very small chromosomes. Hence, a number of chromosome rearrangements might be expected between bird and squamate genomes. We used chromosome-specific DNA from flow-sorted chicken (Gallus gallus) Z sex chromosomes as a probe in cross-species hybridization to metaphase spreads of 28 species from 17 families representing most main squamate lineages and single species of crocodiles and turtles. In all but one case, the Z chromosome was conserved intact despite very ancient divergence of sauropsid lineages. Furthermore, the probe painted an autosomal region in seven species from our sample with characterized sex chromosomes, and this provides evidence against an ancestral avian-like system of sex determination in Squamata. The avian Z chromosome synteny is, therefore, conserved albeit it is not a sex chromosome in these squamate species.

Establishment and characterization of a testicular cell line from the half-smooth tongue sole, Cynoglossus semilaevis

Spermatogenesis within the adult testis is an excellent system for studying stem cell renewal and differentiation, which is under the control of testicular somatic cells. In order to understanding spermatogenesis in the half-smooth tongue sole (Cynoglossus semilaevis) as a marine fish model of aquaculture importance, we established a cell line called CSGC from a juvenile gonad of this organism. CSGC is composed of fibroblast-like cells, retains a diploid karyotype of 42 chromosomes, lacks the heterogametic W chromosome, lacks a female specific marker and expresses the dmrt, a marker for testicular somatic cells. Therefore, CSGC appears to consist of testicular somatic cell cells. We show that this cell line is effective for infection by the turbot reddish body iridovirus and flounder lymphocystis disease virus as evidenced by the appearance of cytopathic effect and virus propagation in the virus-infected cells, and most convincingly, the observation of viral particles by electon microscopy, demonstrateing that CSGC is suitable to study interactions between virus and host cells. As a first fish testicular somatic cell line of the ZZ-ZW genetic sex determination system, CSGC will be a useful tool to study sex-related events and interactions between somatic cells and germ cells during spermatogenesis.

Nuclear factor-Y (NF-Y) regulates transcription of mouse Dmrt7 gene by binding to tandem CCAAT boxes in its proximal promoter

Dmrt7, a member of the Dmrt family of genes, is required for spermatogenesis. However, promoter functions of the gene Dmrt7 remain unknown. We have cloned and characterized the proximal promoter region of the mouse Dmrt7 gene. Functional analysis of the 5' flanking region by sequential deletion mutations revealed crucial positive elements between -60 and +1, in which two highly conserved and tandem CCAAT boxes: the CCAAT box1 (-48/-44) and the CCAAT box2 (-7/-3) are located. Site-directed mutagenesis studies demonstrated that both CCAAT boxes are indispensable to the promoter activity. Electrophoretic mobility shift assays (EMSAs) and gel-supershift assays indicated that transcription factor NF-Y binds to the promoter. Chromatin immunoprecipitation (ChIP) analysis demonstrated that NF-Y interacts in vivo with the promoter of the Dmrt7 gene in testis. Co-transfection and reporter analysis showed that over-expression of NF-Ys increased transcription of the Dmrt7-luc gene whereas expression of a dominant-negative NF-Ya decreased the transcription. This suggests that NF-Y can activate the Dmrt7 promoter. These results provide evidence of a transcription regulatory mechanism that controls Dmrt7 gene expression in mouse testis.

Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements

Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE) might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes) a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes.

Evolutionary innovations and adaptations often require rapid changes in gene regulation. Transposable elements constitute the most dynamic part of eukaryotic genomes. Insertions of transposable elements can influence the expression of surrounding genes by donating new regulatory elements. A longstanding hypothesis postulates that the dispersal of transposable elements may rewire regulatory links between genes, thereby changing regulatory networks and shuffling regulatory cascades. A regulatory hierarchy of remarkable plasticity is the sex determination cascade. In the course of animal evolution, new master regulators frequently replace the sex determination gene on top of the hierarchy. In the medaka fish, a duplicate of the dmrt1 transcription factor gene, dmrt1bY, has become the sex master regulator. Its ancestor dmrt1a, in contrast, has a downstream position in the sex determination cascade. We show that after the duplication of the dmrt1 gene, the new hierarchy has been established by the insertion of a transposable element into the regulatory region of the dmrt1bY gene on the sex chromosome. This transposable element, harboring a Dmrt1 binding site, enables the self- and cross-regulation of dmrt1bY expression by Dmrt1 proteins. Our study therefore provides strong evidence for the important role of transposable elements in the rewiring of gene regulatory networks.

The male-determining gene SRY is a hybrid of DGCR8 and SOX3, and is regulated by the transcription factor CP2

In mammals, sex is determined by the presence or absence of the Y chromosome that bears a male-dominant sex-determining gene SRY, which switches the differentiation of gonads into male testes. The molecular signaling mechanism turning on the switch, however, has remained unclear for 18 years since the identification of the gene. Here, we describe how this gene emerged and started to work. From amino acid homology, we realized that SRY is a hybrid gene between a portion of the first exon of DiGeorge syndrome critical region gene 8 (DGCR8) and the high-mobility group (HMG) box of SRY box-3 (SOX3) gene. We identified the regulatory sequence in the SRY promotor region by searching for a common motif shared with DGCR8 mRNA. From the motif search between DGCR8 mRNA and the SRY upstream sequence, we found that the transcription factor CP2 (TFCP2) binding motif is present in both. TFCP2 overexpression did not show a significant increase of SRY mRNA expression, and TFCP2 suppression by RNA interference (RNAi) significantly reduced SRY mRNA expression. Furthermore, electrophoretic mobility shift assay (EMSA) demonstrated that TFCP2 acts as a regulator by directly binding to the SRY promoter. We conclude that SRY is a hybrid gene composed of two genes, DGCR8 and SOX3; and TFCP2 is an essential transcription factor for SRY expression regulation.

Expression pattern of dmrt4 from olive flounder (Paralichthys olivaceus) in adult gonads and during embryogenesis

The dmrt (doublesex and mab-3 related transcription factor) gene family comprises several transcription factors that share a conserved DM domain. Dmrt1 is considered to be involved in sexual development, but the precise function of other family members is unclear. In this study, we isolated genomic DNA and cDNA sequences of dmrt4, a member of the dmrt gene family, from olive flounder, Paralichthys olivaceus, through genome walking and real-time reverse transcriptase (RT)-PCR. Sequence analysis indicated that its genomic DNA contains two exons and one intron. A transcriptional factor binding sites prediction program identified a sexual development-related protein, Sox9 (Sry-like HMG box containing 9) in its 5' promoter. Protein alignment and phylogenetic analysis suggested that flounder Dmrt4 is closely related to tilapia Dmo (DM domain gene in ovary). The expression of dmrt4 in adult flounder was sexually dimorphic, as shown by real-time RT-PCR analysis, with strong expression in the testis but very weak expression in the ovary. Its expression was also strong in the brain and gill, but there was only weak or no expression at all in some of the other tissues tested of both sexes. During embryogenesis, its expression was detected in most developmental stages, although the level of expression was distinctive of the various stages. Whole mount in situ hybridization revealed that the dmrt4 was expressed in the otic placodes, forebrain, telencephalon and olfactory placodes of embryos at different developmental stages. These results will improve our understanding of the possible role of flounder dmrt4 in the development of the gonads, nervous system and sense organs.

Generation of antibodies against DMRT1 and DMRT4 of Oreochromis aurea and analysis of their expression profile in Oreochromis aurea tissues

Sex determination is composed of somatic and germ-line sex differentiation hierarchies whose interaction is poorly understood. A single gene known to control somatic sex determination, the DM-domain containing (Doublesex/Mab-3 DNA-binding motif) gene, is highly conserved across species. Vertebrate DMRT1 (DM-related transcription factor 1) expression occurs predominantly in the testis. Here, however, isolated two distinct DM-domain cDNA from Oreochromis aurea ovary and testis have been named DMRT4 (DM-related transcription factor 4) and DMRT1 by BLAST, respectively. Despite high homology in the DM-domain, there is little similarity outside the DM-domain. To better understand the structure, function, and possible roles of DMRT4 and DMRT1 as potential candidates for sex differentiation and sex determination, the intact regions encoding DMRT4 and DMRT1 obtained by PCR were sub-cloned into the vector pMAL-c2x and introduced into the Escherichia coli TB1 cell for efficient fusion expression. After purification and cleavage, DMRT4 and DMRT1 proteins were used to immunize adult rabbits following standard protocols. Consequently, it was found by using Western blot analysis that polyclonal antibodies against DMRT4 and DMRT1 had high specificity. The relative expression levels of DMRT4 and DMRT1 mRNA were determined by fluorescent Real-time RT-PCR in female and male Oreochromis aurea with beta-actin as the internal standard. DMRT1 was expressed only in testis, whereas DMRT4 was over expressed in the ovary, but in both female and male, a slight expression in the brain was also detected. Statistical analysis showed that in the brain, mean DMRT4 mRNA levels in female were significantly higher than in male. Meanwhile, the expression of DMRT4 and DMRT1 protein was also analyzed using the purified antibodies through Western blot and immunohistochemistry. It was found that DMRT4 was exclusively expressed in the ovary and DMRT1 in the testis. Study on DMRT4 and DMRT1 expression facilitated the elucidation of their roles and the understanding of sex differentiation of fish.

Nuclear localization, DNA binding and restricted expression in neural and germ cells of zebrafish Dmrt3

BACKGROUND INFORMATION

The DM (doublesex and male aberrant-3) genes implicated in sexual development in diverse metazoan organisms have been proved to be involved in development of non-gonadal tissues. The aim of the present study was to identify and characterize Dmrt3 (DM-related transcription factor 3) of zebrafish.

RESULTS

Zebrafish Dmrt3 has a conserved DMA domain, besides a common DM domain, which clustered it into the DMRTA subfamily. During embryogenesis, Dmrt3 expression increases gradually to a high level at pharyngula stage, which is restricted to the olfactory placode and the neural tube. In the juvenile zebrafish, the gene expression is first detected in undifferentiated gonad on 17 dpf (day post-fertilization). In adult, Dmrt3 is expressed only in the developing germ cells of both gonads, mainly in spermatogonia, spermatocytes and developing oocytes. The Dmrt3 has a functional NLS (nuclear localization signal) K(41)GHKR(45) within the DM domain, which ensures that Dmrt3 exerts its role in the nucleus. Moreover, EMSA (electrophoretic mobility-shift assay) indicates that the Dmrt3-derived DM polypeptide binds to similar sites of both targets of DSX (doublesex) and MAB-3 (male aberrant-3).

CONCLUSION

These results suggest that as a DNA-binding protein, zebrafish Dmrt3 may function in the nucleus as a potential transcription factor to exert potential roles in the development of the olfactory placode, the neural tube and germ cells.

Fish specific duplication of Dmrt2: characterization of zebrafish Dmrt2b

The protein families with a conserved zinc finger-like DNA binding DM domain are putative transcription factors related to the sexual regulator Dsx of Drosophila and Mab-3 of Caenorhabditis elegans. Although several members have been cloned, there are still other members need to be identified, and origin and evolution of the gene family also remain unclear. We report here cloning, expression and synteny analysis of a duplicated copy of zebrafish Dmrt2a gene, the Dmrt2b which is fish specific, whereas Dmrt2a exists in all vertebrates. During embryogenesis, the Dmrt2b expression increased gradually from shield stage to hatching stage, and mainly localized in branchial arches from 24 hpf to 40 hpf, indicating that it has a potential role in the development of branchial arches. The duplicated Dmrt2b and Dmrt2a with structural variation and expression diversification during development revealed that a process of functional diploidization of gene function occurred during zebrafish lineage. DNA binding experiment indicated that Dmrt2b recognized similar DNA sequences to those of both DSX and MAB-3, indicating a conserved regulatory function. Synteny analysis among chromosomes containing Dmrt2a and Dmrt2b showed that zebrafish Dmrt2b and at least nine genes on chromosome 6 have respective homologues on chromosome 5 containing Dmrt2a. Further synteny search from genome information showed that Dmrt2b and its neighborhood existed only in the genome of teleosts. Dmrt2a and Dmrt2b were duplicated from the duplication event, which might be part of the third genome duplication, occurred during the evolution of ray-finned fishes, probably before the emergence of osteichthyes around 350 Myr. The duplicated Dmrt2b and Dmrt2a with structural variation and expression diversification suggested their diverse roles: Dmrt2b in specification of branchial arches while Dmrt2a in somitogenesis. These analyses undoubtedly help understanding functional divergence and evolution of the DM genes following gene duplication in fishes.

Expression of DMRT genes in the gonads of Rana rugosa during sex determination

Sex is determined by various transcription factors. Dmrt1, a gene that contains the DM domain (Doublesex/Mab-3 DNA-binding motif), is known to be one of the critical factors required for testicular development in vertebrates. Recently, other DM domain-containing genes (DMRT genes) were isolated in mice and fish. In mice, three of the seven known DMRT genes are expressed in the embryonic gonad. In amphibians, however, only Dmrt1 and Dmrt4 have been cloned. To clarify the role(s) of DMRT genes in sex determination in vertebrates, the molecular cloning of amphibian DMRT genes would be very helpful. In this study, we isolated Dmrt2, -3, and -5 from the frog Rana rugosa and analyzed by RT-PCR their expression during sex determination. The analysis revealed that all three genes are expressed in the developing gonad/mesonephros complex during sex determination with no dimorphism. The results suggest that Dmrt2, -3, and -5 may be involved in sexual development in R. rugosa and that they may function in both testicular and ovarian differentiation.