Noriyuki Satoh

Publications of Noriyuki Satoh

• Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption.

  Authors: Toshifumi Minamoto, Shuji Hanai, Koji Kadota, Katsutaka Oishi, Hiromi Matsumae, Manabu Fujie, Kaoru Azumi, Noriyuki Satoh, Masanobu Satake, Norio Ishida

  Journal of biochemistry. 10/2009;

  The molecular mechanisms of the endogenous circadian clocks that allow most animals to adapt to environmental cycles have recently been uncovered. The draft genome of the ascidian, CionaThe molecular mechanisms of the endogenous circadian clocks that allow most animals to adapt to environmental cycles have recently been uncovered. The draft genome of the ascidian, Ciona intestinalis, a model animal that is close to vertebrates, has been described. However, the C. intestinalis genome lacks the canonical clock genes such as Per, Bmal and Clock that are shared by vertebrates and insects. Here, we found the circadian rhythms at the physiological and molecular levels. The oxygen consumption rate was lower during the light phase and higher during the dark phase during a day, and the rhythm highly damped and continued under constant darkness. From the microarray analysis, the 396 spots (1.8% of the total; corresponding to 388 clones) were extracted as candidates for circadian expression. We confirmed the circadian expression of several candidate genes by Northern blotting. Furthermore, three of four rhythmic expressed genes showed phase-shifts to prolonged light period. However, most of known clock genes did not oscillate. These data suggest that C. intestinalis have a unique molecular circadian clock and suggest that the daily environmental change is not so strong effect for sea squirt in its evolution when compared to vertebrates and insects.

• [Decoding of amphioxus genome and evolution of chordates]

  Authors: Noriyuki Satoh, Takeshi Kawashima, Eiichi Shoguchi

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 02/2009; 54(1):20-8.

• brachyury null mutant-induced defects in juvenile ascidian endodermal organs.

  Authors: Shota Chiba, Di Jiang, Noriyuki Satoh, William C Smith

  Development (Cambridge, England). 12/2008;

  We report the isolation of a recessive ENU-induced short-tailed mutant in the ascidian Ciona intestinalis that is the product of a premature stop in the brachyury gene. Notochord differentiation andWe report the isolation of a recessive ENU-induced short-tailed mutant in the ascidian Ciona intestinalis that is the product of a premature stop in the brachyury gene. Notochord differentiation and morphogenesis are severely disrupted in the mutant line. At the larval stage, variable degrees of ectopic endoderm staining were observed in the homozygous mutants, indicating that loss of brachyury results in stochastic fate transformation. In post-metamorphosis mutants, a uniform defect in tail resorption was observed, together with variable defects in digestive tract development. Some cells misdirected from the notochord lineage were found to be incorporated into definitive endodermal structures, such as stomach and intestine.

• A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae.

  Authors: Jr-Kai Yu, Ming-Chih Wang, Tadasu Shin-I, Yuji Kohara, Linda Holland, Noriyuki Satoh, Yutaka Satou

  Development genes and evolution. 10/2008;

  Cephalochordates are the basal invertebrate chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand theCephalochordates are the basal invertebrate chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the chordate body plan and the origin of vertebrates. Recently, the genome of the cephalochordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5'- and 3'-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5'- and 3'-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3'-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the "Branchiostoma floridae Gene Collection Release 1." We also constructed a database with a searchable interface for this EST dataset and the related information on "Branchiostoma floridae Gene Collection Release 1." This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.

• The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

  Authors: Linda Z Holland, Ricard Albalat, Kaoru Azumi, Elia Benito-Gutiérrez, Matthew J Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J Dishaw [......] Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M Zmasek, Pieter J de Jong, Kazutoyo Osoegawa, Nicholas H Putnam, Daniel S Rokhsar, Noriyuki Satoh, Peter W H Holland

  Genome research. 08/2008; 18(7):1100-11.

  Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, weCephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates-a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

• ERK- and JNK-signalling regulate gene networks that stimulate metamorphosis and apoptosis in tail tissues of ascidian tadpoles.

  Authors: Jean-Philippe Chambon, Akie Nakayama, Katsumi Takamura, Alex McDougall, Noriyuki Satoh

  Development (Cambridge, England). 04/2007; 134(6):1203-19.

  In ascidian tadpoles, metamorphosis is triggered by a polarized wave of apoptosis, via mechanisms that are largely unknown. We demonstrate that the MAP kinases ERK and JNK are both required for theIn ascidian tadpoles, metamorphosis is triggered by a polarized wave of apoptosis, via mechanisms that are largely unknown. We demonstrate that the MAP kinases ERK and JNK are both required for the wave of apoptosis and metamorphosis. By employing a gene-profiling-based approach, we identified the network of genes controlled by either ERK or JNK activity that stimulate the onset of apoptosis. This approach identified a gene network involved in hormonal signalling, in innate immunity, in cell-cell communication and in the extracellular matrix. Through gene silencing, we show that Ci-sushi, a cell-cell communication protein controlled by JNK activity, is required for the wave of apoptosis that precedes tail regression. These observations lead us to propose a model of metamorphosis whereby JNK activity in the CNS induces apoptosis in several adjacent tissues that compose the tail by inducing the expression of genes such as Ci-sushi.

• Axial patterning in cephalochordates and the evolution of the organizer.

  Authors: Jr-Kai Yu, Yutaka Satou, Nicholas D Holland, Tadasu Shin-I, Yuji Kohara, Noriyuki Satoh, Marianne Bronner-Fraser, Linda Z Holland

  Nature. 03/2007; 445(7128):613-7.

  The organizer of the vertebrate gastrula is an important signalling centre that induces and patterns dorsal axial structures. Although a topic of long-standing interest, the evolutionary origin ofThe organizer of the vertebrate gastrula is an important signalling centre that induces and patterns dorsal axial structures. Although a topic of long-standing interest, the evolutionary origin of the organizer remains unclear. Here we show that the gastrula of the cephalochordate amphioxus expresses dorsal/ventral (D/V) patterning genes (for example, bone morphogenetic proteins (BMPs), Nodal and their antagonists) in patterns reminiscent of those of their vertebrate orthlogues, and that amphioxus embryos, like those of vertebrates, are ventralized by exogenous BMP protein. In addition, Wnt-antagonists (for example, Dkks and sFRP2-like) are expressed anteriorly, whereas Wnt genes themselves are expressed posteriorly, consistent with a role for Wnt signalling in anterior/posterior (A/P) patterning. These results suggest evolutionary conservation of the mechanisms for both D/V and A/P patterning of the early gastrula. In light of recent phylogenetic analyses placing cephalochordates basally in the chordate lineage, we propose that separate signalling centres for patterning the D/V and A/P axes may be an ancestral chordate character.

• [Recent advances in developmental genomics of the ascidian Ciona intestinalis]

  Authors: Takeshi Kawashima, Eiichi Shoguchi, Yutaka Satou, Noriyuki Satoh

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 01/2006; 50(16 Suppl):2153-9.

• A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis.

  Authors: David N Keys, Byung-In Lee, Anna Di Gregorio, Naoe Harafuji, J Chris Detter, Mei Wang, Orsalem Kahsai, Sylvia Ahn, Cindy Zhang, Sharon A Doyle, Noriyuki Satoh, Yutaka Satou, Hidetoshi Saiga, Allen T Christian, Dan S Rokhsar, Trevor L Hawkins, Mike Levine, Paul M Richardson

  Proceedings of the National Academy of Sciences of the United States of America. 01/2005; 102(3):679-83.

  A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis.A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

• [Draft genome sequence of Ciona intestinalis and its meaning]

  Authors: Yutaka Satou, Noriyuki Satoh

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 08/2003; 48(9):1282-6.

• [Morpholino oligonucleotide-based screen of novel genes with developmental function]

  Authors: Shuichi Wada, Lixy Yamada, Kenji Kobayashi, Eiichi Shoguchi, Noriyuki Satoh

  Seikagaku. The Journal of Japanese Biochemical Society. 08/2003; 75(7):617-20.

• Expression of epidermis-specific antigens during embryogenesis of the ascidian, Halocynthia roretzi

  Authors: Takahito Nishikata, Izumi Mita-Miyazawa, Takuya Deno, Katsumi Takamura, Noriyuki Satoh

  Developmental Biology.

  We have produced two monoclonal antibodies (Epi-1 and Epi-2) which specifically recognize epidermal cells and their derivative, the larval tunic, of developing embryos of the ascidian HalocynthiaWe have produced two monoclonal antibodies (Epi-1 and Epi-2) which specifically recognize epidermal cells and their derivative, the larval tunic, of developing embryos of the ascidian Halocynthia roretzi. The antigens, examined by indirect immunofluorescence staining, first appear at the early tailbud stage and are present until at least the swimming larval stage. There were distinct and separate puromycin and actinomycin D sensitivity periods for each antigen. Aphidicolin, a specific inhibitor of DNA synthesis, prevented the appearance of each antigen when embryos were exposed to the drug continuously from cleavage stages. These results suggest that the antigens are synthesized during embryogenesis by developing epidermal cells and that several rounds of DNA replication are required for the antigen expression. Early cleavage stage embryos, including fertilized but unsegmented eggs, in which cytokinesis had been blocked with cytochalasin B expressed the antigens, and blastomeres exhibiting the antigens were always of the epidermis lineage. In partial embryos produced by four separated blastomere pairs of the 8-cell embryos, the expression of antigens was seen only in those developed from the animal blastomere pairs, which are progenitors of epidermal cells. These observations indicate that differentiation of epidermal cells in ascidian embryos takes place in a typical “mosaic” fashion.

• Neural Tube Is Partially Dorsalized by Overexpression ofHrPax-37:The Ascidian Homologue ofPax-3andPax-7

  Authors: Hiroshi Wada, Peter W.H. Holland, Shigeru Sato, Hiroaki Yamamoto, Noriyuki Satoh

  Developmental Biology.

  The origin and elaboration of the central nervous system played an important role in chordate and vertebrate history. All chordates possess a dorsal tubular central nervous system, but elaboration ofThe origin and elaboration of the central nervous system played an important role in chordate and vertebrate history. All chordates possess a dorsal tubular central nervous system, but elaboration of dorsoventral and segmental pattern is far more pronounced in cephalochordates and vertebrates than in the more basal urochordates. Analysis of the urochordates, therefore, should allow deduction of the neural organization and neuronal patterning mechanisms that predated overt dorsoventral and segmental complexity. Here we report functional studies of the ascidianPaxgene (HrPax-37). The spatiotemporal expression pattern ofHrPax-37has suggested involvement in two distinct developmental processes: specification of dorsal cell fates of ectoderm during neurulation, and regional differentiation of the neural tube in later stages. Here we show thatHrPax-37is descendent from the precursor of thePax-3andPax-7genes implicated in specification of dorsal fate in the vertebrate neural tube. We also demonstrate that injection ofHrPax-37RNA into fertilized eggs causes ectopic expression of the dorsal neural marker tyrosinase gene in neurulae, confirming a regulatory role in dorsal patterning of the neural tube comparable to its vertebrate homologues. These results suggest that dorsal specification in the neural tube byPax-3/7subfamily genes was established in the ancestors of extant chordates during emergence of the dorsal tubular nervous system.

• Pattern of Brachyury gene expression in starfish embryos resembles that of hemichordate embryos but not of sea urchin embryos

  Authors: Eiichi Shoguchi, Noriyuki Satoh, Yoshihiko K Maruyama

  Mechanisms of Development.

  Echinoderms, hemichordates and chordates are deuterostomes and share a number of developmental features. The Brachyury gene is responsible for formation of the notochord, the most defining feature ofEchinoderms, hemichordates and chordates are deuterostomes and share a number of developmental features. The Brachyury gene is responsible for formation of the notochord, the most defining feature of chordates, and thus may be a key to understanding the origin and evolution of the chordates. Previous studies have shown that the ascidian Brachyury (As-T and Ci-Bra) is expressed in the notochord and that a sea urchin Brachyury (HpTa) is expressed in the secondary mesenchyme founder cells. A recent study by Tagawa et al. (1998), however, revealed that a hemichordate Brachyury (PfBra) is expressed in a novel pattern in an archenteron invagination region and a stomodaeum invagination region in the gastrula. The present study demonstrated that the expression pattern of Brachyury (ApBra) of starfish embryos resembles that of PfBra in hemichordate embryos but not of HpTa in sea urchin embryos. Namely, ApBra is expressed in an archenteron invagination region and a stomodaeum invagination region.

• posterior end mark 2 (pem-2),pem-4,pem-5, andpem-6: Maternal Genes with Localized mRNA in the Ascidian Embryo

  Authors: Yutaka Satou, Noriyuki Satoh

  Developmental Biology.

  The posterior–vegetal cytoplasm of an ascidian egg contains maternal factors required for pattern formation and cell specification of the embryo. We report here the isolation and characterization ofThe posterior–vegetal cytoplasm of an ascidian egg contains maternal factors required for pattern formation and cell specification of the embryo. We report here the isolation and characterization of cDNA clones for novel maternal genes,posterior end mark 2(pem-2),pem-4,pem-5, andpem-6. We obtained these clones from a cDNA library ofCiona savignyifertilized egg mRNAs subtracted with gastrula mRNAs by examining the localization of the corresponding mRNAs of randomly selected clones by whole-mountin situhybridization. As in the case ofpem, all of these mRNAs were localized in the posterior–vegetal cytoplasm of the egg, and they later marked the posterior end of early embryos. The predicted amino acid sequence suggested that PEM-2 contains a signal for nuclear localization, an src homology 3 (SH3) domain, and a consensus sequence of the CDC24 family guanine nucleotide dissociation stimulators (GDSs). PEM-4 has a signal for nuclear localization and three C2H2-type zinc finger motifs, while PEM-5 and PEM-6 show no similarity to known proteins. These results provide further evidence that the ascidian egg contains maternal messages that are localized in the posterior–vegetal cytoplasm.

• Specification of notochord cells in the ascidian embryo analysed with a specific monoclonal antibody

  Authors: Takahito Nishikata, Noriyuki Satoh

  Cell Differentiation and Development.

  Among 40 notochord cells of an ascidian tadpole larva, 32 notochord cells originate from the anterior-vegetal blastomeres (the A4.1 pair) of an 8-cell embryo and eight cells originate from theAmong 40 notochord cells of an ascidian tadpole larva, 32 notochord cells originate from the anterior-vegetal blastomeres (the A4.1 pair) of an 8-cell embryo and eight cells originate from the posterior-vegetal blastomeres (the B4.1 pair), but the animal blastomeres (the a4.2 and b4.2 pairs) are not engaged in the formation of the notochord. If four pairs of cells, separated from an 8-cell embryo, were allowed to develop into quarter embryos, expression of the notochord-specific antigen was evident in the A4.1 and B4.1 quarter embryos. Embryos, in which cytokinesis had been permanently blocked at the 8-cell and later stages with cytochalasin B, were found to develop the notochord-specific antigen only in the presumptive notochord cells. These findings suggest the developmental autonomy of presumptive notochord cells in the ascidian embryo.

• Periodic appearance and disappearance of microvilli associated with cleavage cycles in the egg of the ascidian, Halocynthia roretzi

  Authors: Noriyuki Satoh, Takuya Deno

  Developmental Biology.

  The surface of eggs of the ascidian Halocynthia roretzi, observed with SEM, is essentially smooth until immediately before cell division when numerous microvilli appear and remain during cytokinesis.The surface of eggs of the ascidian Halocynthia roretzi, observed with SEM, is essentially smooth until immediately before cell division when numerous microvilli appear and remain during cytokinesis. As the divided blastomeres become closely adherent, however, the microvilli disappear and the eggs recover their smooth surface. This periodic appearance-disappearance of microvilli is repeated at each cleavage cycle up to at least the 32-cell stage. During blastomere adhesion, microvilli that have appeared near the plane of the first cleavage or of the bilateral symmetry seem to fuse together across the plane to form a zipper-like complex of cytoplasmic processes, which might be responsible for attachment of the two halves of these bilaterally symmetrical embryos via the blastomeres bordering the plane of symmetry.

• Isolation and characterization of cDNA clones for epidermis-specific and muscle-specific genes in Ciona savignyi embryos

  Authors: Shota Chiba, Yutaka Satou, Takahito Nishikata, Noriyuki Satoh

  Ascidian eggs and embryos have provided an appropriate experimental system to explore the cellular and molecular mechanisms involved in the embryonic cell specification and pattern formation of theAscidian eggs and embryos have provided an appropriate experimental system to explore the cellular and molecular mechanisms involved in the embryonic cell specification and pattern formation of the embryo. In Japan, most of the studies of ascidian embryology have been carried out with the large eggs of Halocynthia roretzi. However, for future studies, Ciona species may provide a better experimental system, in particular with respect to the incorporation of genetic approaches. In order to establish Ciona as an experimental system, molecular markers with which to examine cellular differentiation are required. In the present study, we isolated and characterized cDNA clones for two epidermis-specific genes (CsEpi-1 and CsEpi-2) and for two muscle-specific genes (CsMA-1 and CsMu-1). CsEpi-1 encodes a polypeptide with three trefoil domains, while CsMA-1 encodes a muscle-type actin from C. savignyi Although CsEpi-2 and CsMu-1 transcripts seem to have a poly(A) tail at the 3' end, we could not find a distinct open reading frame in the sequences. Probes for CsEpi-1, CsMA-1 and CsMu-1 cross-reacted with C. intestinalis embryos. These cDNAs are useful as molecular markers for the specification of epidermis and muscle of Ciona embryos.