Rainbow trout Sox24, a novel member of the Sox family, is a transcriptional regulator during oogenesis

Genome-wide identification and expression profiling of the SOX gene family in a bivalve mollusc Patinopecten yessoensis

SOX family is composed of transcription factors that play vital roles in various developmental processes. Comprehensive understanding on evolution of the SOX family requires full characterization of SOX genes in different phyla. Mollusca is the second largest metazoan phylum, but till now, systematic investigation on the SOX family is still lacking in this phylum. In this study, we conducted genome-wide identification of the SOX family in Yesso scallop Patinopecten yessoensis and profiled their tissue distribution and temporal expression patterns in the ovaries and testes during gametogenesis. Seven SOX genes were identified, including SOXB1, B2, C, D, E, F and H, representing the first record in protostomes with SOX members identical to that proposed to exist in the last common ancestor of chordates. Genomic structure analysis identified relatively conserved exon-intron structures, accompanied by intron insertion. Quantitative real-time PCR analysis revealed possible involvement of scallop SOX in various functions, including neuro-sensory cell differentiation, hematopoiesis, myogenesis and gametogenesis. This study represents the first systematic characterization of SOX gene family in Mollusca. It will assist in a better understanding of the evolution and function of SOX family in metazoans.

Molecular cloning, characterization and expression of Lc-Sox11a in large yellow croaker Larimichthys crocea

Sox genes play important roles in various developmental processes such as sex determination, embryogenesis, oogenesis, neurogenesis, and larval development. In order to clarify the roles of Sox genes in the developmental process of large yellow croaker, the full-length cDNA of the Sox11a gene (Lc-Sox11a) was cloned for the first time. Bioinformatics analysis indicated that Lc-Sox11a contains a protein of 366 amino acids with a Ser-rich region, a C-terminal conserved region, and a high mobility group box. The expression of Lc-Sox11a in different tissues of both sexes and in different developmental embryonic stages revealed that Lc-Sox11a were expressed with tissue and gender specificity, of which the expression level in female was ovary>brain>eye>gill; in male was brain>testis>gill. The gender differences occurred in the brain and eye with the male brain>female brain, female eye>male eye. Moreover, the expression of Lc-Sox11a in the gonad and brain at different growth stages was detected. Significant up-regulated expression of Lc-Sox11a was found in the ovary and the male brain at 1000dph (days post hatching) compared with 270dph and 635dph. However, significant down-regulated expression of Lc-Sox11a occurred in the testis with growth. Besides, the expression of Lc-Sox11a in the female brain showed a trend of first rising then falling, with the highest peak in 635dph. The results of in situ hybridization displayed that Lc-Sox11a was widely distributed only in cytoplasm of oocytes at each stage in oogenesis. In early stage of oocytes, Lc-Sox11a was expressed weakly and evenly. As the appearance of vacuoles and synthesis of yolks, positive signals of Lc-Sox11a distributed intensively in the residual cytoplasm. In spermatogenesis, Lc-Sox11a was distributed in cytoplasm of all male germ cells except spermatozoon with spermatogonium>spermatocyte>spermatid. During embryogenesis, Lc-Sox11a was expressed in most embryonic stages, the highest expression occurred in the formation-of-eye-lens stage, closely followed by the closure-of-blastopore stage, then the beginning-of-heart-pulsation stage. The results of whole mount in situ hybridization showed that the expression of Lc-Sox11a began to increase beginning with the multiple-cell stage, with the major distribution of Lc-Sox11a in the brain and eye areas in the pre-hatching stage.

Primary oocyte transcriptional activation of aqp1ab by the nuclear progestin receptor determines the pelagic egg phenotype of marine teleosts

In marine teleosts, the aqp1ab water channel plays a vital role in the development of the pelagic egg phenotype. However, the developmental control of aqp1ab activation during oogenesis remains to be established. Here, we report the isolation of the 5'-flanking region of the teleost gilthead seabream aqp1ab gene, in which we identify conserved cis-regulatory elements for the binding of the nuclear progestin receptor (Pgr) and members of the Sox family of transcription factors. Subcellular localization studies indicated that the Pgr, as well as sox3 and -8b transcripts, are co-expressed in seabream oogonia, whereas in meiosis-arrested primary growth (pre-vitellogenic) oocytes, when aqp1ab mRNA and protein are first synthesized, the Pgr appears to be completely translocated from the ooplasm into the nucleus. By contrast, sox9b is highly expressed in more advanced oocytes, coinciding with a strong depletion of aqp1ab transcripts in the oocyte. Functional characterization of wild-type and mutated aqp1ab promoter constructs, using mammalian cells and Xenopus laevis oocytes, demonstrated that aqp1ab transcription is initiated by the Pgr, which is activated by the progestin 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P), the natural ligand of the seabream Pgr. In vitro incubation of seabream primary ovarian explants with the follicle-stimulating hormone or 17,20β-P confirmed that progestin-activated Pgr enhanced Aqp1ab synthesis via the aqp1ab promoter. However, transactivation assays in heterologous systems showed that Sox transcription factors can potentially modulate this mechanism. These data uncover the existence of an endocrine pathway involved in the early activation of a water channel necessary for egg formation in marine teleosts.

Characterization of SoxB2 and SoxC genes in amphioxus (Branchiostoma belcheri): implications for their evolutionary conservation

Most Sox genes directly affect cell fate determination and differentiation. In this study, we isolated two Sox genes: SoxB2 and SoxC from amphioxus (Branchiostoma belcheri), the closest living invertebrate relative of the vertebrates. Alignments of SoxB2 and SoxC protein sequences and their vertebrate homologs show high conservation of their HMG domains. Phylogenic analysis shows that amphioxus SoxB2 and SoxC fall out of the vertebrate branches, suggesting that vertebrate homologs might arise from gene duplications during evolution. The two genes possess similar spatial and temporal expression patterns during embryogenesis and in adults. They are both maternally inherited. During neurulation, they are expressed in the neural ectoderm and archenterons. In adults, they are expressed not only in the nerve cord, but also in the gut, midgut diverticulum, gill and oocytes. These results suggest that amphioxus SoxB2 and SoxC might co-function and have conserved functions in the nervous system and gonads as their vertebrate homologs.

Different sox17 transcripts during sex differentiation in sea bass, Dicentrarchus labrax

Sox genes participate in several developmental processes, including sex determination and differentiation. In this study, the genomic structure of sox17 was characterized in the sea bass (sb). Two transcripts, one producing a normal protein (sb Sox17) and another producing a truncated protein (sb t-Sox17) were detected. A third, novel transcript, originated by intron retention (sb i-sox17) was also observed. Sb sox17 was widely distributed, whereas sb i-sox17 was predominantly found in skin and brain. In gonads, sb sox17 expression first increased at 150 days of age, coinciding with the onset of sex differentiation. At 250 days and onwards, sb sox17 expression was significantly higher in females, and mRNA levels correlated with those of gonadal aromatase. Thus, this study provides the first evidence for the presence of alternative splicing by intron retention in a Sox17 gene, and for sex-related differences in expression, implicating sox17 in ovarian development and function in fish.

Isolation and expression of a novel alligator gene belonging to the Sox gene family

Sox genes share a highly conserved DNA-binding motif, the HMG (high mobility group)-box domain, and have diverse roles in vertebrate embryonic development. A novel SRY-related cDNA (temporarily called Sox33) isolated from the Chinese alligator (Alligator sinensis) is 1,819 bp in length, with an open reading frame from 220 to 1113 bp, encoding a protein of 298 amino acids. Two putative polyadenylation signal sequences (AATAAA) are present upstream of the poly(A) tail in the 3' UTR (at 1255-1260 and 1774-1779). The putative protein contains an HMG-box domain most closely related to hSox12, mSox4, rtSox11, and mSox11 homologs, indicating that alligator Sox33 belongs to group C in the Sox gene family. Alligator adult and developing tissues were tested for Sox33 mRNA by independent Northern blots using a 336-bp probe (at 907-1243) between the HMG-box and the poly(A) site I and a 277-bp probe (at 1477-1754) between the two polyadenylation sites. Two transcripts (1.3 kb and 1.8 kb) in developing brain and one (1.8 kb) in adult brain were identified by the 336-bp probe; only one transcript (1.8 kb) in developing and adult brains was detected by the 277-bp probe. The results suggest that alligator Sox33 may use a different polyadenylation mechanism in the developing brain and play a role in the development and maintenance of the nervous system.

Expression profiling of candidate genes during ovary-to-testis trans-differentiation in rainbow trout masculinized by androgens

Fish gonadal phenotype is very sensitive to sex steroid and functional masculinizations can be obtained in most species using androgen treatments. To gain insight into the molecular effects of androgen-induced masculinization we characterized, in the rainbow trout, the gonadal expression profiles of 103 candidate genes involved in sex differentiation and early gametogenesis. The androgen treatment (11beta-hydroxyandrostenedione, 10 mg/kg of food for 3 months) was administered in a genetic all-female population. Gonads were sampled at different time points in genetic all-male and all-female control populations and in the androgen-treated group. Gene expression profiles were recorded by real-time RT-PCR and biological samples and gene expressions were compared using a global clustering analysis. This analysis revealed that masculinization with androgens acts firstly by repressing granulosa cell related genes, including genes involved in ovarian differentiation (foxl2a, fst, cyp19a1a), and subsequently by repressing genes important for early oogenesis (gdf9, bcl2lb, fancl, gcl, fshb, lhb, sox23, sox24, nup62 and vtgr). However, this masculinizing treatment did not induce a testicular differentiation similar to what was observed in the control male population. This was especially noticeable for many Leydig cell genes encoding proteins involved in steroidogenesis or its control (hsd3b1, star, cyp17a1, cyp11b2.1 and nr5a1b) that were down-regulated in the androgen-treated group. Concomitantly some Sertoli cells marker genes were up-regulated by the androgen treatment (sox9a.1, nr0b1, cldn11, dmrt1) whereas others were down-regulated (amh, sox9a.2), suggesting a partial differentiation of the Sertoli cell lineage. Overall, this suggests that the crucial step of this masculinization process is the de-differentiation of the granulosa cells.

A homologue of Sox11 predominantly expressed in the ovary of the orange-spotted grouper Epinephelus coioides

Sox, a family of genes related to the mammalian sex-determining region Y (SRY) gene, are found throughout the animal kingdom and regulate diverse developmental processes including sex determination. The full-length Sox11b cDNA was cloned from the ovary of the orange-spotted grouper Epinephelus coioides. This sequence is highly homologous to SOX11 of other species and contained the signature features of mammalian SOX11 homologues, except for the absence of Pro-Glu rich region and presence of two Ser-rich regions. Southern blot analysis suggested that there is likely a single copy of Sox11b gene in the genome of this fish. The mRNA expression of Sox11b was detected in a wide range of tissues except the blood cells, and its expression is especially abundant in the ovary. During embryogenesis and larval development, the mRNA levels of Sox11b were high except at the eyed stage. During 17alpha-methyltestosterone (MT)-induced precocious sex change, the mRNA levels of Sox11b in the gonads were decreased significantly. Together, these results indicated that Sox11b may be involved in the oogenesis, embryogenesis, larval development, and sex change of the orange-spotted grouper.

Maternal expression and function of the Drosophila sox gene Dichaete during oogenesis

Members of the Sox family of DNA-binding HMG domain proteins have been shown to regulate gene transcription in a wide range of developmental processes, including sex determination, neurogenesis, and chondrogenesis. However, little is known about their potential functions in developing germline tissues. In Drosophila, the Sox protein Dichaete (a.k.a., Fish-hook) is a member of the SoxB subgroup whose HMG domain shares strong sequence similarity to that of vertebrate Sox2. Dichaete exhibits dynamic expression in embryonic and larval stages and has pleiotropic functions in a variety of tissues. In this study, we extend analyses of Dichaete function and show that expression of Dichaete protein is detected in the developing oocyte during early to mid stages of oogenesis. Strikingly, Dichaete exhibits cytoplasmic distribution and is not detected in the oocyte nucleus. Germline mosaic analyses revealed that the Dichaete gene has maternal functions that influence dorsal/ventral patterning of the egg chamber. Dichaete mutant eggs exhibit defects in formation of the dorsal appendages, differentiation of dorsal/anterior follicle cells, and mislocalization of Gurken protein and gurken mRNA. Dichaete protein was shown to possess RNA-binding capabilities, suggesting a direct post-transcriptional role in regulating RNA functions.

Zebrafish sex determination and differentiation: involvement of FTZ-F1 genes

Sex determination is the process deciding the sex of a developing embryo. This is usually determined genetically; however it is a delicate process, which in many cases can be influenced by environmental factors. The mechanisms controlling zebrafish sex determination and differentiation are not known. To date no sex linked genes have been identified in zebrafish and no sex chromosomes have been identified. However, a number of genes, as presented here, have been linked to the process of sex determination or differentiation in zebrafish. The zebrafish FTZ-F1 genes are of central interest as they are involved in regulating interrenal development and thereby steroid biosynthesis, as well as that they show expression patterns congruent with reproductive tissue differentiation and function. Zebrafish can be sex reversed by exposure to estrogens, suggesting that the estrogen levels are crucial during sex differentiation. The Cyp19 gene product aromatase converts testosterone into 17 beta-estradiol, and when inhibited leads to male to female sex reversal. FTZ-F1 genes are strongly linked to steroid biosynthesis and the regulatory region of Cyp19 contains binding sites for FTZ-F1 genes, further linking FTZ-F1 to this process. The role of FTZ-F1 and other candidates for zebrafish sex determination and differentiation is in focus of this review.

Large-Scale Temporal Gene Expression Profiling During Gonadal Differentiation and Early Gametogenesis in Rainbow Trout1

The overall understanding of the sex differentiation cascade in vertebrates is still growing slowly, probably because of the variety of vertebrate models used and the number of molecular players yet to be discovered. Finding conserved mechanisms among vertebrates should provide a better view of the key factors involved in this process. To this end, we used real-time reverse transcription-polymerase chain reaction to produce a temporal map of fluctuations in mRNA expression of 102 genes during sex differentiation and early gametogenesis in the rainbow trout (Oncorhynchus mykiss). We used these 102 temporal gene expression patterns as a basis for a hierarchical clustering analysis to find characteristic clusters of coexpressed genes. Analysis of some of these gene clusters suggested a conserved overall expression profile between the sex differentiation cascade in fish and mammals. Among these conserved molecular mechanisms, sox9, dmrt1, amh, nr5a1, nr0b1, igf1, and igf1ra are, for instance, characterized as early expressed genes involved in trout testicular differentiation as it is known or suggested in mammals. On the contrary, foxl2, fst, and lhr are characterized as early expressed genes during trout ovarian differentiation, as also found in mammals. Apart from this high conservation, our analysis suggests some potential new players, such as the fshb subunit gene, which is detected here for the first time, to our knowledge, in the female differentiating gonad of a vertebrate species and displays a specific overexpression that coincides in timing with the occurrence of first oocyte meioses, or the pax2 gene, which displays an early and testis-specific expression profile.

Identification of novel domains within Sox-2 and Sox-11 involved in autoinhibition of DNA binding and partnership specificity

Sox transcription factors play key regulatory roles throughout development, binding DNA through a consensus (A/T)(A/T)CAA(A/T)G sequence. Although many different Sox proteins bind to this sequence, it has been observed that gene regulatory elements are commonly responsive to only a small subset of the entire family, implying that regulatory mechanisms exist to permit selective DNA binding and/or transactivation by Sox family members. To identify and explore the mechanisms modulating gene activation by Sox proteins further, we compared the function of Sox-2 and Sox-11. This led to the discovery that Sox proteins are regulated differentially at multiple levels, including transactivation, protein partnerships with Pit-Oct-Unc (POU) transcription factors, and DNA binding autoregulation. Specifically, we determined that Sox-11 activates transcription more strongly than Sox-2 and that the transactivation domain of Sox-11 is primarily responsible for this capability. Additionally, we demonstrate that the Sox-11 DNA binding domain is responsible for selective cooperation with the POU factor Brn-2. This requirement cannot be replaced by the DNA binding domain of Sox-2, indicating that the DNA binding domain of Sox proteins is critical for Sox-POU partnerships. Interestingly, we have also determined that a conserved domain of Sox-11 has the novel capability of autoinhibiting its ability to bind DNA in vitro and to activate gene expression in vivo. Our findings suggest that the autoinhibitory domain can repress promiscuous binding of Sox-11 to DNA and plays an important role in regulating the recruitment of Sox-11 to specific genes.

Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators

Members of the SOX family of transcription factors are found throughout the animal kingdom, are characterized by the presence of a DNA-binding HMG domain, and are involved in a diverse range of developmental processes. Previous attempts to group SOX genes and deduce their structural, functional, and evolutionary relationships have relied largely on complete or partial HMG box sequence of a limited number of genes. In this study, we have used complete HMG domain sequence, full-length protein structure, and gene organization data to study the pattern of evolution within the family. For the first time, a substantial number of invertebrate SOX sequences have been included in the analysis. We find support for subdivision of the family into groups A-H, as has been suggested in some previous studies, and for the assignment of two new groups, I and J. For vertebrate genes, it appears that relatedness as suggested by HMG domain sequence is congruent with relatedness as indicated by overall structure of the full-length protein and intron-exon structure of the genes. Most of the SOX groups identified in vertebrates were represented by a single SOX sequence in each invertebrate species studied. We have named anonymous sequences and, where appropriate, have suggested systematic names for some previously identified sequences. In addition, we identify an HMG domain signature motif which may be considered representative of the SOX family. Based on our data, we propose a robust phylogeny of SOX genes that reflects their evolutionary history in metazoans.

Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development

To investigate the role of sox genes in vertebrate development, we have isolated sox11 from zebrafish (Danio rerio). Two distinct classes of sox11-related cDNAs were identified, sox11a and sox11b. The predicted protein sequences shared 75% identity. In a gene phylogeny, both sox11a and sox11b cluster with human, mouse, chick, and Xenopus Sox11, indicating that zebrafish, like Xenopus, has two orthologues of tetrapod Sox11. The work reported here investigates the evolutionary origin of these two gene duplicates and the consequences of their duplication for development. The sox11a and sox11b genes map to linkage groups 17 and 20, respectively, together with other loci whose orthologues are syntenic with human SOX11, suggesting that during the fish lineage, a large chromosome region sharing conserved syntenies with mammals has become duplicated. Studies in mouse and chick have shown that Sox11 is expressed in the central nervous system during development. Expression patterns of zebrafish sox11a and sox11b confirm that they are expressed in the developing nervous system, including the forebrain, midbrain, hindbrain, eyes, and ears from an early stage. Other sites of expression include the fin buds and somites. The two sox genes, sox11a and sox11b, are expressed in both overlapping and distinct sites. Their expression patterns suggest that sox11a and sox11b may share the developmental domains of the single Sox11 gene present in mouse and chick. For example, zebrafish sox11a is expressed in the anterior somites, and zebrafish sox11b is expressed in the posterior somites, but the single Sox11 gene of mouse is expressed in all the somites. Thus, the zebrafish duplicate genes appear to have reciprocally lost expression domains present in the sox11 gene of the last common ancestor of tetrapods and zebrafish. This splitting of the roles of Sox11 between two paralogues suggests that regulatory elements governing the expression of the sox11 gene in the common ancestor of zebrafish and tetrapods may have been reciprocally mutated in the zebrafish gene duplicates. This is consistent with duplicate gene evolution via a duplication-degeneration-complementation process.

Two distinct subgroups of Group B Sox genes for transcriptional activators and repressors: their expression during embryonic organogenesis of the chicken

Group B Sox genes, Sox1, -2 and -3 are known to activate crystallin genes and to be involved in differentiation of lens and neural tissues. Screening of chicken genomic sequences for more Group B Sox genes identified two additional genes, Sox14 and Sox21. Proteins encoded by Sox14 and Sox21 genes are similar to each other but distinct from those coded by Sox1-3 (subgroup B1) except for the HMG domain and Group B homology immediately C-proximal of the HMG domain. C-terminal domains of SOX21 and SOX14 proteins function as strong and weak repression domains, respectively, when linked to the GAL4 DNA binding domain. These SOX proteins strongly (SOX21) or moderately (SOX14) inhibited activation of delta1-crystallin DC5 enhancer by SOX1 or SOX2, establishing that Sox14 and Sox21 are repressing subgroup (B2) of Group B Sox genes. This provides the first evidence for the occurrence of repressor SOX proteins. Activating (B1) and repressing (B2) subgroups of Group B Sox genes display interesting overlaps of expression domains in developing tissues (e.g. optic tectum, spinal cord, inner ear, alimentary tract, branchial arches). Within each subgroup, most expression domains of Sox1 and -3 are included in those of Sox2 (e.g. CNS, PNS, inner ear), while co-expression of Sox14 and Sox21 occurs in highly restricted sites of the CNS, with the likely temporal order of Sox21 preceding Sox14 (e.g. interneurons of the spinal cord). These expression patterns suggest that target genes of Group B SOX proteins are finely regulated by the counterbalance of activating and repressing SOX proteins.

Altered gene expression in fetal Down syndrome brain as revealed by the gene hunting technique of subtractive hybridization

Information on gene expression in brain of patients with Down Syndrome (DS, trisomy 21) is limited and molecular biological research is focussing on mapping and sequencing chromosome 21. The information on gene expression in DS available follows the current concept of a gene dosage effect due to a third copy of chromosome 21 claiming overexpression of genes encoded on this chromosome. Based upon the availability of fetal brain and recent technology of gene hunting, we decided to use subtractive hybridization to evaluate differences in gene expression between DS and control brains. Subtractive hybridization was applied on two fetal brains with DS and two age and sex matched controls, 23rd week of gestation, and mRNA steady state levels were evaluated generating a subtractive library. Subtracted sequences were identified by gene bank and assigned by alignments to individual genes. We found a series of up- and downregulated sequences consisting of chromosomal transcripts, enzymes of intermediary metabolism, hormones, transporters/channels and transcription factors (TFs). We show that trisomy 21 or aneuploidy leads to the deterioration of gene expression and the derangement of transcripts describes the impairment of transport, carriers, channels, signaling, known metabolic and hormone imbalances. The dys-coordinated expression of transcription factors including homeobox genes, POU-domain TFs, helix-loop-helix-motifs, LIM domain containing TFs, leucine zippers, forkhead genes, maybe of pathophysiological significance for abnormal brain development and wiring found in patients with DS. This is the first description of the concomitant expression of a large series of sequences indicating disruption of the concerted action of genes in this disorder.

Further complexity of the human SOX gene family revealed by the combined use of highly degenerate primers and nested PCR

SOX proteins contain a conserved HMG-related DNA-binding domain. They fulfill essential functions during the development of animals. Mutations in several SOX genes have been implicated in human diseases. We present here a new set of PCR primers designed to amplify a broad range of SOX HMG-box sequences. These primers facilitated the cloning of several new SOX HMG boxes from human genomic DNA, revealing unexpected complexity of the SOX gene family.