The T genes in embryogenesis.

Since its identification in 1927, the mouse T (Brachyury) locus has been implicated in mesoderm formation and notochord differentiation. Recent work has demonstrated that this gene encodes a putative transcription factor expressed specifically in nascent mesoderm and in the differentiating notochord. Homologous genes have been cloned from the frog Xenopus laevis, the zebrafish Brachydanio rerio and the ascidian Halocynthia roretzi. The T gene is an important tool for elucidating mesoderman and embryonic pattern formation.

Genomic organization of M line titin and its tissue-specific expression in two distinct isoforms.

Titin is a 3000 kDa large protein of vertebrate striated muscle which extends from Z discs to M lines. Within the segment of titin that locates in the I band, tissue-specific isoforms are expressed by differential splicing in correlation to the sarcomeric ultrastructure. We have now searched the M-line region of titin for differential expression. The 20 kb section from the 3' end of the gene has been sequenced and contains 23 exons. Exon/intron organization is correlated to the modular organization of the titin protein. The six exons at the 3' end of the gene encode the M-line section of titin and are referred to as Mex1 to Mex6. Analysis of the RNAs expressed in different rabbit striated muscles reveals that the exon Mex5 is either included or excluded in the titin mRNA during splicing. The levels of inclusion of Mex5 vary between different types of striated muscles. Heart expresses (Mex5+)-titin, skeletal muscles co-express tissue-specifically distinct ratios of (Mex5+) and (Mex5-)-titins. In situ hybridization of whole-mount mouse embryos with Mex5 antisense RNA provide no evidence for the exclusion of Mex5 during embryonic development. We speculate that the establishment of differential splicing pathways of M-line titin late during development may correlate with and explain the postnatal development of different M-line fine structures in the different muscles. Comparison of titin gene sequences from different vertebrates reveals that the intron sequences located upstream of Mex3 and Mex5, referred to as Min-2 and Min-4, respectively, have remained strongly conserved during evolution. While the conservation of Min-4 may be explained by its participation in the regulation of the differential skipping of Mex5, the functional significance of the conservation of the Min-2 intron located upstream of Mex3 is yet unknown.

Kidney-specific cadherin (cdh16) is expressed in embryonic kidney, lung, and sex ducts.

Cdh16 was initially described as a truncated cadherin expressed in the adult rabbit kidney. We have analyzed the expression pattern of cdh-16 during mouse embryogenesis, and show that cdh-16 transcripts are present in ureter-derived epithelia of the metanephric kidney. In addition, we demonstrate that cdh-16 is also transiently expressed in the epithelia of embryonic sex ducts and the lung of the embryo.

Large-scale screen for genes involved in gonad development.

The vertebrate gonad develops from the intermediate mesoderm as an initially bipotential organ anlage, the genital ridge. In mammals, Sry acts as a genetic switch towards testis development. Sox9 has been shown to act downstream of Sry in testis development, while Dax1 appears to counteract Sry. Few more genes have been implicated in early gonad development. However, the genetic networks controlling early differentiation events in testis and ovary are still far from being understood. In order to provide a broader basis for the molecular analysis of gonad development, high-throughput gene expression analysis was utilized to identify genes specifically expressed in the gonad. In total, among 138 genes isolated which showed tissue specific expression in the embryo, 79 were detected in the developing gonad or sex ducts. Twenty-seven have not been functionally described before, while 40 represent known genes and 12 are putative mouse orthologues. Forty-five of the latter two groups (86%) have not been described previously in the fetal gonad. In addition, 21 of the gonad specific genes showed sex-dimorphic expression suggesting a role in sex determination and/or gonad differentiation. Eighteen of the latter (86%) have not been described previously in the fetal gonad. In total we provide new data on 72 genes which may play a role in gonad or sex duct development and/or sex determination. Thus we have generated a large gene resource for the investigation of these processes, and demonstrate the suitability of high-throughput gene expression screening for the genetic analysis of organogenesis.

Distinct regulatory control of the Brachyury gene in axial and non-axial mesoderm suggests separation of mesoderm lineages early in mouse gastrulation.

Brachyury is required for the normal extension of the anteroposterior axis during mouse embryogenesis. A transgene comprising sequences from -500 to +150 relative to the start of Brachyury transcription, and the reporter gene lacZ, recapitulates some, but not all elements of Brachyury expression. Beta-Galactosidase expression is seen in the primitive streak from 6.5 d.p.c. but there is no detectable reporter expression in the node or notochord. Thus, the regulatory sequences required for the expression of Brachyury in the cells traversing the primitive streak are distinct from those required for the initiation of expression in the node. This suggests that different or additional signals are involved in activation of Brachyury in the node and notochord than those inducing Brachyury in the primitive streak. Additionally, the data suggest the possibility that axial and non-axial mesoderm are distinct from the earliest stages of Brachyury expression.

Nuclear localization of beta-catenin by interaction with transcription factor LEF-1.

Vertebrate beta-catenin and Drosophila Armadillo share structural similarities suggesting that beta-catenin, like Armadillo, has a developmental signaling function. Both proteins are present as components of cell adherens junctions, but accumulate in the cytoplasm upon Wingless/Wnt signaling. beta-Catenin has axis-inducing properties like Wnt when injected into Xenopus blastomeres, providing evidence for participation of beta-catenin in the Wnt-pathway, but until now no downstream targets for beta-catenin have been identified. Here we demonstrate that beta-catenin binds to the HMG-type transcription factor lymphoid enhancer factor-1 (LEF-1), resulting in a nuclear translocation of beta-catenin both in cultured mouse cells and after ectopic expression of LEF-1 in two-cell mouse embryos. LEF-1/beta-catenin complexes bind to the promoter region of the E-cadherin gene in vitro, suggesting that this interaction could regulate E-cadherin transcription. As shown for beta-catenin, ectopic expression of LEF-1 in Xenopus embryos caused duplication of the body axis, indicating a regulatory role for a LEF-1-like molecule in dorsal mesoderm formation.

Brachyury is a target gene of the Wnt/beta-catenin signaling pathway.

To identify target genes of the Wnt/beta-catenin signaling pathway in early mouse embryonic development we have established a co-culture system consisting of NIH3T3 fibroblasts expressing different Wnts as feeder layer cells and embryonic stem (ES) cells expressing a green fluorescent protein (GFP) reporter gene transcriptionally regulated by the TCF/beta-catenin complex. ES cells specifically respond to Wnt signal as monitored by GFP expression. In GFP-positive ES cells we observe expression of Brachyury. Two TCF binding sites located in a 500 bp Brachyury promoter fragment bind the LEF-1/beta-catenin complex and respond specifically to beta-catenin-dependent transactivation. From these results we conclude that Brachyury is a target gene for Wnt/beta-catenin signaling.

Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos.

We have adapted the whole-mount in situ hybridization technique to perform high-throughput gene expression analysis in mouse embryos. A large-scale screen for genes showing specific expression patterns in the mid-gestation embryo was carried out, and a large number of genes controlling development were isolated. From 35760 clones of a 9.5 d.p.c. cDNA library, a total of 5348 cDNAs, enriched for rare transcripts, were selected and analyzed by whole-mount in situ hybridization. Four hundred and twenty-eight clones revealed specific expression patterns in the 9.5 d.p.c. embryo. Of 361 tag-sequenced clones, 198 (55%) represent 154 known mouse genes. Thirty-nine (25%) of the known genes are involved in transcriptional regulation and 33 (21%) in inter- or intracellular signaling. A large number of these genes have been shown to play an important role in embryogenesis. Furthermore, 24 (16%) of the known genes are implicated in human disorders and three others altered in classical mouse mutations. Similar proportions of regulators of embryonic development and candidates for human disorders or mouse mutations are expected among the 163 new mouse genes isolated. Thus, high-throughput gene expression analysis is suitable for isolating regulators of embryonic development on a large-scale, and in the long term, for determining the molecular anatomy of the mouse embryo. This knowledge will provide a basis for the systematic investigation of pattern formation, tissue differentiation and organogenesis in mammals.

Transgenic expression of oncogenic BRAF induces loss of stem cells in the mouse intestine, which is antagonized by ß-catenin activity.

Colon cancer cells frequently carry mutations that activate the ß-catenin and mitogen-activated protein kinase (MAPK) signaling cascades. Yet how oncogenic alterations interact to control cellular hierarchies during tumor initiation and progression is largely unknown. We found that oncogenic BRAF modulates gene expression associated with cell differentiation in colon cancer cells. We therefore engineered a mouse with an inducible oncogenic BRAF transgene, and analyzed BRAF effects on cellular hierarchies in the intestinal epithelium in vivo and in primary organotypic culture. We demonstrate that transgenic expression of oncogenic BRAF in the mouse strongly activated MAPK signal transduction, resulted in the rapid development of generalized serrated dysplasia, but unexpectedly also induced depletion of the intestinal stem cell (ISC) pool. Histological and gene expression analyses indicate that ISCs collectively converted to short-lived progenitor cells after BRAF activation. As Wnt/ß-catenin signals encourage ISC identity, we asked whether ß-catenin activity could counteract oncogenic BRAF. Indeed, we found that intestinal organoids could be partially protected from deleterious oncogenic BRAF effects by Wnt3a or by small-molecule inhibition of GSK3ß. Similarly, transgenic expression of stabilized ß-catenin in addition to oncogenic BRAF partially prevented loss of stem cells in the mouse intestine. We also used BRAF(V637E) knock-in mice to follow changes in the stem cell pool during serrated tumor progression and found ISC marker expression reduced in serrated hyperplasia forming after BRAF activation, but intensified in progressive dysplastic foci characterized by additional mutations that activate the Wnt/ß-catenin pathway. Our study suggests that oncogenic alterations activating the MAPK and Wnt/ß-catenin pathways must be consecutively and coordinately selected to assure stem cell maintenance during colon cancer initiation and progression. Notably, loss of stem cell identity upon induction of BRAF/MAPK activity may represent a novel fail-safe mechanism protecting intestinal tissue from oncogene activation.

A mouse gene of the paired-related homeobox class expressed in the caudal somite compartment and in the developing vertebral column, kidney and nervous system.

During vertebrate embryonic development, pairs of metameric units, the somites, bud off at the cranial end of the paraxial mesoderm. The somites soon obtain cranio-caudal and dorso-ventral polarity. Establishment of dorso-ventral and medio-lateral polarity depends on multiple signals from the notochord, neural tube surface ectoderm and lateral mesoderm. The establishment of cranio-caudal polarity in the somite is less well understood. One molecule involved is the Dll1 gene product, a transmembrane protein expressed in the unsegmented paraxial mesoderm and in the caudal half of the somites. We have identified a gene, Uncx4.1, expressed in the caudal half of newly formed somites. It encodes a protein belonging to the paired-related class of homeodomain transcription factors. Uncx4.1 expression is first detected in the entire caudal half of the somites, is later down-regulated in the myotome and dermatome, and is maintained in the caudal sclerotome and its derivatives from which part of the vertebral column will form. Thus, Uncx4.1 may be involved in the establishment and maintenance of segment polarity and in vertebral column formation. Uncx4.1 is also expressed in the first branchial arch, the meso- and metanephric kidney, the central nervous system and the first digit of the forelimb, suggesting control functions of Uncx4.1 in multiple processes of embryogenesis.

Expression pattern of the Brachyury gene in whole-mount TWis/TWis mutant embryos.

The murine Brachyury (T) gene is required in mesoderm formation. Mutants carrying different T alleles show a graded severity of defects correlated with gene dosage along the body axis. The phenotypes range from shortening of the tail to the malformation of sacral vertebrae in heterozygotes, and to disruption of trunk development and embryonic death in homozygotes. Defects include a severe disturbance of the primitive streak, an early cessation of mesoderm formation and absence of the allantois and notochord, the latter resulting in an abnormality of the neural tube and somites. The T gene is expressed in nascent mesoderm and in the notochord of wild-type embryos. Here the expression of T in whole-mount mutant embryos homozygous for the T allele TWis is described. The TWis gene product is altered, but the TWis/TWis phenotype is very similar to that of T/T embryos which lack T. In early TWis/TWis embryos T expression is normal, but ceases prematurely during early organogenesis coincident with a cessation of mesoderm formation. The archenteron/node region is disrupted and the extension of the notochord precursor comes to a halt, followed by a decrease and finally a complete loss of T gene expression in the primitive streak and the head process/notochord precursor. It appears that the primary defect of the mutant embryo is the disruption of the notochord precursor in the node region which is required for axis elongation. Thus the T gene product is directly or indirectly involved in the organization of axial development.

Action of the Brachyury gene in mouse embryogenesis.

The murine developmental mutation T identifies a gene required in mesoderm formation. T/T mutant embryos develop normally to the primitive streak stage; during early organogenesis they show insufficient mesoderm and absence of the notochord. The mutants die at around 10 days of gestation because of the lack of the allantois. We have localized the T mutation relative to DNA markers and used a combination of genetic and molecular techniques to clone the T gene. Expression of the T gene is restricted to nascent mesoderm and to the notochord, the tissues most strongly affected by the mutation. Recent results suggest that the T gene encodes a nuclear factor involved in establishing notochord cell identity and differentiation, and is directly or indirectly involved in the organization of axial development.

The Brachyury gene encodes a novel DNA binding protein.

Brachyury (T) mutant embryos are deficient in mesoderm formation and do not complete axial development. The notochord is most strongly affected. The T gene is expressed transiently in primitive streak-derived nascent and migrating mesoderm cells and continuously in the notochord. Ectopic expression of T protein in the animal cap of Xenopus embryos results in ectopic mesoderm formation. The T protein is located in the nucleus. These and other data suggested that the T gene might be involved in the control of transcriptional regulation. In an attempt to demonstrate specific DNA binding of the T protein we have identified a consensus sequence among DNA fragments selected from a mixture of random oligomers. Under our experimental conditions T protein binds as a monomer to DNA. This property resides in the N-terminal domain of 229 amino acid residues which is strongly conserved between the mouse protein, and its Xenopus and zebrafish homologues. The latter proteins also recognize the consensus DNA binding site. We suggest that the T protein is involved in the control of genes required for mesoderm formation, and for the differentiation and function of chorda mesoderm.

Immunohistochemical analysis of the Brachyury protein in wild-type and mutant mouse embryos.

The murine Brachyury (T) gene is required in posterior mesoderm formation and axial development. Mutant embryos lacking T gene function are deficient in notochord differentiation and posterior mesoderm formation, but make anterior mesoderm. Posterior axial development requires increasing T activity along the rostrocaudal axis. The T gene is transiently transcribed in nascent and migrating mesoderm and continuously in the notochord. The maintenance of T expression in the notochord depends, directly or indirectly, on wild-type T activity. In Xenopus it has been shown that the onset of T expression occurs in response to mesoderm-inducing growth factors. The T protein is binding to DNA and is probably involved in the control of gene expression. Here we show that the T protein is located in the nucleus. We have analyzed the expression pattern of T protein in wild-type and mutant embryos from early primitive streak formation to the end of the tail bud stage. Throughout all stages of mesoderm formation T protein is transiently present in nascent and migrating mesoderm. In the notochord T protein persists to the end of the tail bud stage. It is also transiently detectable in the forming gut endoderm and in prospective neuroectoderm of later embryos. This shows that T expression is not strictly correlated with a commitment of cells to mesoderm. The analysis of the tail development of TWis/+ mutant embryos demonstrated that the formation of the neural tube, gut, and somites from the tail bud proceeds in the absence of a notochord. The maintenance and differentiation of these structures, however, seems to depend on signals from the notochord.

Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.

The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans. Mutations in Brachyury and other T-box genes result in drastic embryonic phenotypes, indicating that T-box gene products are essential in tissue specification, morphogenesis and organogenesis. The T-box encodes a DNA-binding domain of about 180 amino-acid residues, the T domain. Here we report the X-ray structure of the T domain from Xenopus laevis in complex with a 24-nucleotide palindromic DNA duplex. We show that the protein is bound as a dimer, interacting with the major and the minor grooves of the DNA. A new type of specific DNA contact is seen, in which a carboxy-terminal helix is deeply embedded into an enlarged minor groove without bending the DNA. Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix. Thus the structure of this T domain complex with DNA reveals a new way in which a protein can recognize DNA.

Rescue of the tail defect of Brachyury mice.

The mouse Brachyury (T) gene is required for normal development of axial structures. Embryos homozygous for the T mutation show severe deficiencies in mesoderm formation. They lack the notochord and allantois, have abnormal somites, and die at approximately 10 days postcoitum probably as a result of the allantois defect. Mice heterozygous for the T mutation exhibit a variable short-tailed phenotype. The T gene has been cloned and shown to be expressed in the tissues most strongly affected by the mutation. In this paper, we show that a single-copy transgene representing the wild-type T allele is able to rescue the T-associated tail phenotype. In addition, we show that increasing dosage of the T gene in Tc/+ mice causes an increased extension of the axis. These data show the correlation of the level of T product with the extension of the anteroposterior axis, directly demonstrating the involvement of the T product in this process.

The chick Brachyury gene: developmental expression pattern and response to axial induction by localized activin.

The mouse Brachyury gene (T) is required in notochord differentiation and posterior mesoderm formation during axial development. We have isolated the chick homologue of T(Ch-T) and determined its putative protein sequence and expression pattern during embryogenesis. Ch-T is expressed in the epiblast close to and within the primitive streak, in early migrating mesoderm and in the notochord. In later stages Ch-T expression is found in the tail bud and in the entire notochord. The notochord expression ceases in an anterior-posterior wave when the formation of the body anlage is completed. This pattern is consistent with those reported for the expression of the mouse T gene and the T homologues of Xenopus laevis and zebrafish, suggesting that the mechanisms of embryonic pattern formation are highly conserved in all vertebrates. The N-terminal half of Ch-T shows a very high degree of sequence identity with the corresponding region of mouse T which has DNA-binding activity, and with the N-terminal half of Xenopus (Xbra) and zebrafish (Ntl) T protein. Finally, we have analyzed the effects of activin A on Ch-T induction and axis formation. Localized activin A treatment of prestreak blastoderms results in ectopic Ch-T expression that correlates with formation of second primitive streaks or with repositioning of the site of single streak origin (Cooke et al., 1994). These results strengthen the previous evidence that Brachyury activation is an early response to axis-inducing signals in vivo.