Kaoru S Imai

Kyoto University, Kyoto, Kyoto-fu, Japan

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Publications (23)168.48 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The function of bone morphogenetic protein (BMP) signaling in dorsoventral (DV) patterning of animal embryos is conserved among Bilateria. In vertebrates, the BMP ligand antidorsalizing morphogenetic protein (Admp) is expressed dorsally and moves to the opposite side to specify the ventral fate. Here, we show that Pinhead is an antagonist specific for Admp with a role in establishing the DV axis of the trunk epidermis in embryos of the ascidian Ciona intestinalis. Pinhead and Admp exist in tandem in the genomes of various animals from arthropods to vertebrates. This genomic configuration is important for mutually exclusive expression of these genes, because Pinhead transcription directly disturbs the action of the Admp enhancer. Our data suggest that this dual negative regulatory mechanism is widely conserved in animals.
    Science 08/2012; 337(6097):964-7. · 31.20 Impact Factor
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    ABSTRACT: Precise spatiotemporal gene expression during animal development is achieved through gene regulatory networks, in which sequence-specific transcription factors (TFs) bind to cis-regulatory elements of target genes. Although numerous cis-regulatory elements have been identified in a variety of systems, their global architecture in the gene networks that regulate animal development is not well understood. Here, we determined the structure of the core networks at the cis-regulatory level in early embryos of the chordate Ciona intestinalis by chromatin immunoprecipitation (ChIP) of 11 TFs. The regulatory systems of the 11 TF genes examined were tightly interconnected with one another. By combining analysis of the ChIP data with the results of previous comprehensive analyses of expression profiles and knockdown of regulatory genes, we found that most of the previously determined interactions are direct. We focused on cis-regulatory networks responsible for the Ciona mesodermal tissues by examining how the networks specify these tissues at the level of their cis-regulatory architecture. We also found many interactions that had not been predicted by simple gene knockdown experiments, and we showed that a significant fraction of TF-DNA interactions make major contributions to the regulatory control of target gene expression.
    Development 04/2010; 137(10):1613-23. · 6.60 Impact Factor
  • Atsushi Kubo, Kaoru S Imai, Yutaka Satou
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    ABSTRACT: Ascidians belong to the subphylum Urochordata or Tunicata, which is the sister group of the vertebrates. The simple architecture of the ascidian larva represents the basic chordate body plan. Recent analyses have shown many instances of developmental mechanisms conserved during evolution, while these studies have also revealed a much larger number of instances of divergence. However, to precisely determine the degree of conservation and divergence, that is, how many ways are used to make tadpole-like larvae, we need a systems-level understanding of development. Because animal development is organized by the genome and the minimal functional unit of development is a cell, comprehensiveness and single-cell resolution are necessary for a systems-biological understanding of the development. In the ascidian Ciona intestinalis, gene-regulatory networks responsible for the embryonic development have been studied on a genome-wide scale and at single-cell resolution. The simplicity and compactness of the genome facilitates genome-wide studies. In the Ciona genome, only approximately 670 transcription factor genes are encoded, and their expression profiles during the embryonic development have been analyzed. Gene-knockdown analyses of the transcription factor genes expressed during the embryonic development have been performed. The simplicity of the embryo permits these analyses to be done at single-cell resolution. Actually, these simple embryos are now being modeled in the computer, which allows us to understand the gene-regulatory networks very precisely in three dimensions.
    Briefings in Functional Genomics and Proteomics 07/2009; 8(4):250-5.
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    ABSTRACT: The tripartite organization of the central nervous system (CNS) may be an ancient character of the bilaterians. However, the elaboration of the more complex vertebrate brain depends on the midbrain-hindbrain boundary (MHB) organizer, which is absent in invertebrates such as Drosophila. The Fgf8 signaling molecule expressed in the MHB organizer plays a key role in delineating separate mesencephalon and metencephalon compartments in the vertebrate CNS. Here, we present evidence that an Fgf8 ortholog establishes sequential patterns of regulatory gene expression in the developing posterior sensory vesicle, and the interleaved ;neck' region located between the sensory vesicle and visceral ganglion of the simple chordate Ciona intestinalis. The detailed characterization of gene networks in the developing CNS led to new insights into the mechanisms by which Fgf8/17/18 patterns the chordate brain. The precise positioning of this Fgf signaling activity depends on an unusual AND/OR network motif that regulates Snail, which encodes a threshold repressor of Fgf8 expression. Nodal is sufficient to activate low levels of the Snail repressor within the neural plate, while the combination of Nodal and Neurogenin produces high levels of Snail in neighboring domains of the CNS. The loss of Fgf8 patterning activity results in the transformation of hindbrain structures into an expanded mesencephalon in both ascidians and vertebrates, suggesting that the primitive MHB-like activity predates the vertebrate CNS.
    Development 01/2009; 136(2):285-93. · 6.21 Impact Factor
  • Yutaka Satou, Nori Satoh, Kaoru S Imai
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    ABSTRACT: Ascidians, or sea squirts, are tunicates that diverged from the vertebrate lineage early in the chordate evolution. The compact and simple organization of the ascidian genome makes this organism an ideal model system for analyzing gene regulatory networks in embryonic development. Embryos contain relatively few cells and gene activities by individual cells have been determined. Here we review and discuss advances in our understanding of the ascidian embryogenesis emerging from genomic expression studies and analyses at the single cell level.
    Biochimica et Biophysica Acta 04/2008; 1789(4):268-73. · 4.66 Impact Factor
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    ABSTRACT: Ciona is an emerging model system for elucidating gene networks in development. Comprehensive in situ hybridization assays have identified 76 regulatory genes with localized expression patterns in the early embryo, at the time when naïve blastomeres are determined to follow specific cell fates. Systematic gene disruption assays provided more than 3000 combinations of gene expression profiles in mutant backgrounds. Deduced gene circuit diagrams describing the formation of larval tissues were computationally visualized. These diagrams constitute a blueprint for the Ciona embryo and provide a foundation for understanding the evolutionary origins of the chordate body plan.
    Science 06/2006; 312(5777):1183-7. · 31.20 Impact Factor
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    ABSTRACT: The ascidian embryonic mesenchyme, comprising about 900 cells, forms mesodermal tissues or organs of the adult body after metamorphosis. The mesenchyme originates from the A7.6 [trunk lateral cells (TLCs)], B7.7, and B8.5 blastomeres of the 110-cell stage embryo. Previous studies showed that FGF9/16/20 is required for specification of the mesenchyme in Ciona embryos and that two different (A7.6 and B8.5/B7.7) but partially overlapping molecular mechanisms are associated with the expression of a basic helix-loop-helix (bHLH) transcription factor gene, Twist-like1, in the mesenchymal precursors, which triggers the differentiation process of mesenchyme cells. In the present study, we examined whether the three embryonic lineages express the same mesenchyme-specific structural genes under the control of a common mechanism or whether the three lineages are characterized by the expression of genes specific to each of the lineages. We characterized nine mesenchyme-specific genes in Ciona embryos and found that five were expressed in A7.6/B8.5/B7.7, two in B8.5/B7.7, and two in B7.7 only. FGF9/16/20 and Twist-like1 were required for the expression of all the mesenchyme-specific genes, except for three A7.6/B8.5/B7.7-specific genes in A7.6 progenitors. Overexpression of FGF9/16/20 or Twist-like1 upregulated the expression of A7.6/B8.5/B7.7- and B8.5/B7.7-specific genes, while it downregulated the expression of B7.7-specific genes. These results provide evidence that the differentiation of each of the three mesenchyme lineages of Ciona embryos is characterized by the expression of a specific set of genes, whose expression is controlled differentially.
    Developmental Biology 11/2004; 274(1):211-24. · 3.87 Impact Factor
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    ABSTRACT: Achieving a real understanding of animal development obviously requires a comprehensive rather than partial identification of the genes working in each developmental process. Recent decoding of genome sequences will enable us to perform such studies. An ascidian, Ciona intestinalis, one of the animals whose genome has been sequenced, is a chordate sharing a basic body plan with vertebrates, although its genome contains less paralogs than are usually seen in vertebrates. In the present study, we discuss the genomewide approach to networks of developmental genes in Ciona embryos. We focus on transcription factor genes and some major groups of signal transduction genes. These genes are comprehensively listed and examined with regard to their embryonic expression by in situ hybridization (http://ghost.zool.kyoto-u.ac.jp/tfst.html). The results revealed that 74% of the transcription factor genes are expressed maternally and that 56% of the genes are zygotically expressed during embryogenesis. Of these, 34% of the transcription factor genes are expressed both maternally and zygotically. The number of zygotically expressed transcription factor genes increases gradually during embryogenesis. As an example, and taking advantage of this comprehensive description of gene expression profiles, we identified transcription factor genes and signal transduction genes that are expressed at the early gastrula stage and that work downstream of beta-catenin, FoxD and/or Fgf9/16/20. Because these three genes are essential for ascidian endomesoderm specification, transcription factor genes and signal transduction genes involved in each of the downstream processes can be deduced comprehensively using the present approach.
    Development 09/2004; 131(16):4047-58. · 6.21 Impact Factor
  • Yutaka Satou, Kaoru S Imai, Nori Satoh
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    ABSTRACT: Understanding the molecular basis of heart development is an important research area, because malformation of the cardiovascular system is among the most frequent inborn defects. Although recent research has identified molecules responsible for heart morphogenesis in vertebrates, the initial specification of heart progenitors has not been well characterized. Ascidians provide an appropriate experimental system for exploring this specification mechanism, because the lineage for the juvenile heart is well characterized, with B7.5 cells at the 110-cell stage giving rise to embryonic trunk ventral cells (TVCs) or the juvenile heart progenitors. Here, we show that Cs-Mesp, the sole ortholog of vertebrate Mesp genes in the ascidian Ciona savignyi, is specifically and transiently expressed in the embryonic heart progenitor cells (B7.5 cells). Cs-Mesp is essential for the specification of heart precursor cells, in which Nkx, HAND and HAND-like (NoTrlc) genes are expressed. As a result, knockdown of Cs-Mesp with specific morpholino antisense oligonucleotides causes failure of the development of the juvenile heart. Together with previous evidence obtained in mice, the present results suggest that a mechanism for heart specification beginning with Mesp through Nkx and HAND is conserved among chordates.
    Development 07/2004; 131(11):2533-41. · 6.21 Impact Factor
  • Kaoru S Imai, Nori Satoh, Yutaka Satou
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    ABSTRACT: Ascidian larvae develop mesenchyme cells in their trunk. A fibroblast growth factor (FGF9/16/20) is essential and sufficient for induction of the mesenchyme in Ciona savignyi. We have identified two basic helix-loop-helix (bHLH) genes named Twist-like1 and Twist-like2 as downstream factors of this FGF. These two genes are phylogenetically closely related to each other, and were expressed specifically in the mesenchymal cells after the 110-cell stage. Gene-knockdown experiments using a specific morpholino oligonucleotide demonstrated that Twist-like1 plays an essential role in determination of the mesenchyme and that Twist-like2 is a downstream factor of Twist-like1. In addition, both overexpression and misexpression of Twist-like1 converts non-mesenchymal cells to mesenchymal cells. We also demonstrate that the upstream regulatory mechanisms of Twist-like1 are different between B-line mesenchymal cells and the A-line mesenchymal cells called 'trunk lateral cells'. FGF9/16/20 is required for the expression of Twist-like1 in B-line mesenchymal precursor cells, whereas FGF, FoxD and another novel bHLH factor called NoTrlc are required for Twist-like1 to be expressed in the A-line mesenchymal precursor cells. Therefore, two different but partially overlapping mechanisms are required for the expression of Twist-like1 in the mesenchymal precursors, which triggers the differentiation of the mesenchyme in Ciona embryos.
    Development 10/2003; 130(18):4461-72. · 6.21 Impact Factor
  • Kaoru S Imai
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    ABSTRACT: Nuclear localization of beta-catenin is most likely the first step of embryonic axis formation or embryonic cell specification in a wide variety of animal groups. Therefore, the elucidation of beta-catenin target genes is a key research subject in understanding the molecular mechanisms of the early embryogenesis of animals. In Ciona savignyi embryos, nuclear accumulation of beta-catenin is the first step of endodermal cell specification. Previous subtractive hybridization screens of mRNAs between beta-catenin-overexpressed embryos and nuclear beta-catenin-depleted embryos have resulted in the identification of beta-catenin downstream genes in Ciona embryos. In the present study, I characterize seven additional beta-catenin downstream genes, Cs-cadherinII, Cs-protocadherin, Cs-Eph, Cs-betaCD1, Cs-netrin, Cs-frizzled3/6, and Cs-lefty/antivin. All of these genes were expressed in vegetal blastomeres between the 16-cell and 110-cell stages, although their spatial and temporal expression patterns were different from one another. In situ hybridizations and real-time PCR revealed that the expression of all of these genes was up-regulated in beta-catenin-overexpressed embryos, and down-regulated in beta-catenin-suppressed embryos. Therefore, the accumulation of beta-catenin in the nuclei of vegetal blastomeres activates various vegetally expressed genes with potentially important functions in the specification of these cells.
    Differentiation 09/2003; 71(6):346-60. · 2.86 Impact Factor
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    ABSTRACT: In the present survey, we identified most of the genes involved in the receptor tyrosine kinase (RTK), mitogen activated protein kinase (MAPK) and Notch signaling pathways in the draft genome sequence of Ciona intestinalis, a basal chordate. Compared to vertebrates, most of the genes found in the Ciona genome had fewer paralogues, although several genes including ephrin, Eph and fringe appeared to have multiplied or duplicated independently in the ascidian genome. In contrast, some genes including kit/flt, PDGF and Trk receptor tyrosine kinases were not found in the present survey, suggesting that these genes are innovations in the vertebrate lineage or lost in the ascidian lineage. The gene set identified in the present analysis provides an insight into genes for the RTK, MAPK and Notch signaling pathways in the ancient chordate genome and thereby how chordates evolved these signaling pathway.
    Development Genes and Evolution 07/2003; 213(5-6):254-63. · 1.70 Impact Factor
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    ABSTRACT: The basic helix-loop-helix (bHLH) proteins are transcription factors that play important roles in many biological processes, including the development of various animals. We identified 46 genes encoding bHLH proteins in the draft genome sequence of the basal chordate Ciona intestinalis. These 46 genes represent an almost complete set of bHLH genes in this animal. This number is comparable to 39 and 58 bHLH genes in those of Caenorhabditis elegans and Drosophila melanogaster but is much smaller than the 125 in the human genome. Genes that encode NeuroD, Beta3, Oligo, SCL, NSCL, SRC, Clock and Bmal were not found in the Ciona genome. We could also identify groucho and CBP orthologues in the Ciona genome. In addition, the comparison between the numbers of orthologous human and Ciona bHLH factors reveals the simplicity of the Ciona genome, in accordance with its phylogenetic position within chordates. The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidians and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.
    Development Genes and Evolution 07/2003; 213(5-6):213-21. · 1.70 Impact Factor
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    ABSTRACT: In the present survey, we identified most of the genes involved in the receptor tyrosine kinase (RTK), mitogen activated protein kinase (MAPK) and Notch signaling pathways in the draft genome sequence of Ciona intestinalis, a basal chordate. Compared to vertebrates, most of the genes found in the Ciona genome had fewer paralogues, although several genes including ephrin, Eph and fringe appeared to have multiplied or duplicated independently in the ascidian genome. In contrast, some genes including kit/flt, PDGF and Trk receptor tyrosine kinases were not found in the present survey, suggesting that these genes are innovations in the vertebrate lineage or lost in the ascidian lineage. The gene set identified in the present analysis provides an insight into genes for the RTK, MAPK and Notch signaling pathways in the ancient chordate genome and thereby how chordates evolved these signaling pathway.
    Development Genes and Evolution 05/2003; 213(5):254-263. · 1.70 Impact Factor
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    ABSTRACT: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
    Science 01/2003; 298(5601):2157-67. · 31.20 Impact Factor
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    Kaoru S Imai, Nori Satoh, Yutaka Satou
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    ABSTRACT: The vertebrate brain is regionalized during development into forebrain, midbrain and hindbrain. Fibroblast growth factor 8 (FGF8) is expressed in the midbrain/hindbrain boundary (MHB) and functions as an organizer molecule. Previous studies demonstrated that the brain of basal chordates or ascidians is also regionalized at least into fore/midbrain and hindbrain. To better understand the ascidian brain regionalization, the expression of the Ciona Fgf8/17/18 gene was compared with the expression of Otx, En and Pax2/5/8 genes. The expression pattern of these genes resembled that of the genes in the vertebrate forebrain, midbrain, MHB and hindbrain, each of those domains being characterized by sole or combined expression of Otx, Pax2/5/8, En and Fgf8/17/18. In addition, the putative forebrain and midbrain expressed Ci-FgfL and Ci-Fgf9/16/20, respectively. Therefore, the regionalization of the ascidian larval central nervous system was also marked by the expression of Fgf genes.
    Mechanisms of Development 01/2003; 119 Suppl 1:S275-7. · 2.38 Impact Factor
  • Yutaka Satou, Kaoru S Imai, Nori Satoh
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    ABSTRACT: In vertebrates, a number of fibroblast growth factors (FGFs) have been shown to play important roles in developing embryos and adult organisms. However, the molecular relationships of the vertebrate FGFs are not yet completely understood, partly due to the divergence of their amino acid sequences. To solve this problem, we have identified six FGF genes in a basal chordate, the ascidian Ciona intestinalis. A phylogenetic analysis confidently assigned two of them to vertebrate FGF8/17/18 and FGF11/12/13/14, respectively. Based on the presence of the conserved domains within or outside of the FGF domains, we speculate that three of the other genes are orthologous to vertebrate FGF3/7/10/22, FGF4/5/6 and FGF9/16/20, respectively, although we cannot assign the sixth member to any of the vertebrate FGFs. A survey of the raw whole genome shotgun sequences of C. intestinalis demonstrated the presence of no FGF genes other than the six genes in the genome. The identification of these six FGF genes in the basal chordate gave us an insight into the diversification of specific subfamilies of vertebrate FGFs.
    Development Genes and Evolution 11/2002; 212(9):432-8. · 1.70 Impact Factor
  • Kaoru S Imai, Nori Satoh, Yutaka Satou
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    ABSTRACT: A key issue for understanding the early development of the chordate body plan is how the endoderm induces notochord formation. In the ascidian Ciona, nuclear accumulation of beta-catenin is the first step in the process of endoderm specification. We show that nuclear accumulation of beta-catenin directly activates the gene (Cs-FoxD) for a winged helix/forkhead transcription factor and that this gene is expressed transiently at the 16- and 32-cell stages in endodermal cells. The function of Cs-FoxD, however, is not associated with differentiation of the endoderm itself but is essential for notochord differentiation or induction. In addition, it is likely that the inductive signal that appears to act downstream of Cs-FoxD does not act over a long range. It has been suggested that FGF or Notch signal transduction pathway mediates ascidian notochord induction. Our previous study suggests that Cs-FGF4/6/9 is partially involved in the notochord induction. The present experimental results suggest that the expression and function of Cs-FGF4/6/9 and Cs-FoxD are not interdependent, and that the Notch pathway is involved in B-line notochord induction downstream of Cs-FoxD.
    Development 08/2002; 129(14):3441-53. · 6.21 Impact Factor
  • Kaoru S Imai, Yutaka Satou, Nori Satoh
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    ABSTRACT: Multiple functions of a Zic-like zinc finger transcription factor gene (Cs-ZicL) were identified in Ciona savignyi embryos. cDNA clones for Cs-ZicL, a beta-catenin downstream genes, were isolated and the gene was transiently expressed in the A-line notochord/nerve cord lineage and in B-line muscle lineage from the 32-cell stage and later in a-line CNS lineage from the 110-cell stage. Suppression of Cs-ZicL function with specific morpholino oligonucleotide indicated that Cs-ZicL is essential for the formation of A-line notochord cells but not of B-line notochord cells, essential for the CNS formation and essential for the maintenance of muscle differentiation. The expression of Cs-ZicL in the A-line cells is downstream of beta-catenin and a beta-catenin-target gene, Cs-FoxD, which is expressed in the endoderm cells from the 16-cell stage and is essential for the differentiation of notochord. In spite of its pivotal role in muscle specification, the expression of Cs-ZicL in the muscle precursors is independent of Cs-macho1, which is another Zic-like gene encoding a Ciona maternal muscle determinant, suggesting another genetic cascade for muscle specification independent of Cs-macho1. Cs-ZicL may provide a future experimental system to explore how the gene expression in multiple embryonic regions is controlled and how the single gene can perform different functions in multiple types of embryonic cells.
    Development 07/2002; 129(11):2723-32. · 6.21 Impact Factor
  • Kaoru S Imai, Nori Satoh, Yutaka Satou
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    ABSTRACT: In early Ciona savignyi embryos, nuclear localization of beta-catenin is the first step of endodermal cell specification, and triggers the activation of various target genes. A cDNA for Cs-FGF4/6/9, a gene activated downstream of beta-catenin signaling, was isolated and shown to encode an FGF protein with features of both FGF4/6 and FGF9/20. The early embryonic expression of Cs-FGF4/6/9 was transient and the transcript was seen in endodermal cells at the 16- and 32-cell stages, in notochord and muscle cells at the 64-cell stage, and in nerve cord and muscle cells at the 110-cell stage; the gene was then expressed again in cells of the nervous system after neurulation. When the gene function was suppressed with a specific antisense morpholino oligo, the differentiation of mesenchyme cells was completely blocked, and the fate of presumptive mesenchyme cells appeared to change into that of muscle cells. The inhibition of mesenchyme differentiation was abrogated by coinjection of the morpholino oligo and synthetic Cs-FGF4/6/9 mRNA. Downregulation of beta-catenin nuclear localization resulted in the absence of mesenchyme cell differentiation due to failure of the formation of signal-producing endodermal cells. Injection of synthetic Cs-FGF4/6/9 mRNA in beta-catenin-downregulated embryos evoked mesenchyme cell differentiation. These results strongly suggest that Cs-FGF4/6/9 produced by endodermal cells acts an inductive signal for the differentiation of mesenchyme cells. On the other hand, the role of Cs-FGF4/6/9 in the induction of notochord cells is partial; the initial process of the induction was inhibited by Cs-FGF4/6/9 morpholino oligo, but notochord-specific genes were expressed later to form a partial notochord.
    Development 05/2002; 129(7):1729-38. · 6.21 Impact Factor