Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development.

The ascidian egg is a well-known mosaic egg. In order to investigate the molecular nature of the maternal genetic information stored in the egg, we have prepared cDNAs from the mRNAs in the fertilized eggs of the ascidian, Halocynthia roretzi. The cDNAs of the ascidian embryo were sequenced, and the localization of individual mRNA was examined in staged embryos by whole-mount in situ hybridization. The data obtained were stored in the database MAGEST (http://www.genome.ad.jp/magest) and further analyzed. A total of 4240 cDNA clones were found to represent 2221 gene transcripts, including at least 934 different protein-coding sequences. The mRNA population of the egg consisted of a low prevalence, high complexity sequence set. The majority of the clones were of the rare sequence class, and of these, 42% of the clones showed significant matches with known peptides, mainly consisting of proteins with housekeeping functions such as metabolism and cell division. In addition, we found cDNAs encoding components involved in different signal transduction pathways and cDNAs encoding nucleotide-binding proteins. Large-scale analyses of the distribution of the RNA corresponding to each cDNA in the eight-cell, 110-cell and early tailbud embryos were simultaneously carried out. These analyses revealed that a small fraction of the maternal RNAs were localized in the eight-cell embryo, and that 7.9% of the clones were exclusively maternal, while 40.6% of the maternal clones showed expression in the later stages. This study provides global insights about the genes expressed during early development.

[1]  N. Satoh,et al.  Histospecific acetylcholinesterase development in the presumptive muscle cells isolated from 16-cell-stage ascidian embryos with respect to the number of DNA replications. , 1985, Journal of embryology and experimental morphology.

[2]  M. Ogasawara,et al.  A maternal RNA encoding smad1/5 is segregated to animal blastomeres during ascidian development , 1999, Development, growth & differentiation.

[3]  W. Jeffery.  The follicular envelope of ascidian eggs: A site of messenger RNA and protein synthesis during early embryogenesis , 1980 .

[4]  Y. Kohara,et al.  A multi-well version of in situ hybridization on whole mount embryos of Caenorhabditis elegans. , 1996, Nucleic acids research.

[5]  G. Rubin,et al.  The Role of the Genome Project in Determining Gene Function: Insights from Model Organisms , 1996, Cell.

[6]  M. Boguski,et al.  dbEST — database for “expressed sequence tags” , 1993, Nature Genetics.

[7]  N. Satoh,et al.  Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. II. The 16- and 32-cell stages. , 1985, Developmental biology.

[8]  M. Ogasawara,et al.  Maternally localized RNA encoding a serine/threonine protein kinase in the ascidian, Halocynthia roretzi , 1998, Mechanisms of Development.

[9]  A. Sidow,et al.  Gene duplications and the origins of vertebrate development. , 1994, Development (Cambridge, England). Supplement.

[10]  N. Satoh,et al.  Developmental Biology of Ascidians , 1995 .

[11]  M. Hosobuchi,et al.  Maternal beta-catenin establishes a 'dorsal signal' in early Xenopus embryos. , 1996, Development.

[12]  H. Lipshitz,et al.  Localized RNAs and their functions , 1993, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[14]  J. Eppig,et al.  Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. , 2000, Development.

[15]  H. Nishida,et al.  macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis , 2001, Nature.

[16]  E. R. Gavis.  Expeditions to the pole: RNA localization in Xenopus and Drosophila. , 1997, Trends in cell biology.

[17]  M. Levine,et al.  Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. , 1997, Development.

[18]  E. Wieschaus,et al.  Embryonic transcription and the control of developmental pathways. , 1996, Genetics.

[19]  G. Stent,et al.  Cell lineage analysis by intracellular injection of a tracer enzyme. , 1978, Science.

[20]  B. Schnapp,et al.  RNA localization inXenopusoocytes , 1997 .

[21]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[22]  A. Sidow.  Gen(om)e duplications in the evolution of early vertebrates. , 1996, Current opinion in genetics & development.

[23]  Minoru Kanehisa,et al.  MAGEST: MAboya Gene Expression patterns and Sequence Tags , 2000, Nucleic Acids Res..

[24]  N. Satoh,et al.  The ascidian embryo: An experimental system for studying genetic circuitry for embryonic cell specification and morphogenesis , 1996, Development, growth & differentiation.

[25]  M W Simmen,et al.  Gene number in an invertebrate chordate, Ciona intestinalis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Kazuhiro W. Makabe,et al.  Introduction and Expression of Recombinant Genes in Ascidian Embryos , 1992 .

[27]  K. Takamura,et al.  Characterization of an ascidian DEAD-box gene, Ci-DEAD1: specific expression in the germ cells and its mRNA localization in the posterior-most blastomeres in early embryos , 2000, Development Genes and Evolution.

[28]  H. Takeda,et al.  Dorsal specification in blastoderm at the blastula stage in the goldfish, Carassius auratus , 1998, Development, growth & differentiation.

[29]  A. Smit,et al.  Tiggers and DNA transposon fossils in the human genome. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. Gibbs,et al.  Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. , 1998, Genome research.

[31]  W. Jeffery,et al.  Requirement of the Manx Gene for Expression of Chordate Features in a Tailless Ascidian Larva , 1996, Science.

[32]  Toshimichi Ikemura,et al.  Codon usage tabulated from international DNA sequence databases: status for the year 2000 , 2000, Nucleic Acids Res..

[33]  N. Satoh,et al.  Posterior end mark, a novel maternal gene encoding a localized factor in the ascidian embryo. , 1996, Development.

[34]  N. Perrimon,et al.  Zygotic lethals with specific maternal effect phenotypes in Drosophila melanogaster. I. Loci on the X chromosome. , 1989, Genetics.

[35]  M. Ogasawara,et al.  HrWnt-5: a maternally expressed ascidian Wnt gene with posterior localization in early embryos. , 1998, The International journal of developmental biology.

[36]  W. Jeffery,et al.  Localization of actin messenger RNA during early ascidian development. , 1983, Developmental biology.

[37]  L. Hood,et al.  EST analysis of gene expression in early cleavage-stage sea urchin embryos. , 1999, Development.

[38]  H. Nishida.  Vegetal egg cytoplasm promotes gastrulation and is responsible for specification of vegetal blastomeres in embryos of the ascidian Halocynthia roretzi. , 1996, Development.

[39]  Arn.,et al.  RNA localization in Xenopus oocytes. , 1997, Seminars in cell & developmental biology.

[40]  M. Kanehisa,et al.  DBGET/LinkDB: an integrated database retrieval system. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[41]  H. Yamamoto,et al.  Localization of mitochondrial large ribosomal RNA in the myoplasm of the early ascidian embryo , 1999, Development, growth & differentiation.

[42]  H. Nishida,et al.  Cell fate specification by localized cytoplasmic determinants and cell interactions in ascidian embryos. , 1997, International review of cytology.

[43]  S. Meier-Ewert,et al.  Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting. , 1999, Genomics.

[44]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[45]  G. Reverberi.  Fenomeni di evocazione nello sviluppo dell'uovo di Ascidie. Risultati dell'indagine sperimentale sull'uovo di Ascidiella aspersa e di Ascidia malaca allo stadio di otto blastomeri , 1946 .

[46]  Martin Vingron,et al.  Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning , 1998, Mechanisms of Development.

[47]  T. Minokawa,et al.  A Large-Scale Whole-Mount in situ Hybridization System: Rapid One-Tube Preparation of DIG-Labeled RNA Probes and High Throughput Hybridization using 96-Well Silent Screen Plates , 2001 .

[48]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank. , 1991, Nucleic acids research.

[49]  Eric H. Davidson,et al.  Gene activity in early development , 1968 .

[50]  Hans-Werner Mewes,et al.  The PIR-International Protein Sequence Database , 1992, Nucleic Acids Res..

[51]  A. Ephrussi,et al.  mRNA localization and the cytoskeleton , 1996 .

[52]  N. Satoh,et al.  Isolation and Characterization of cDNA Clones for Epidermis-Specific and Muscle-Specific Genes in Ciona savignyi Embryos , 1998 .

[53]  E. Conklin.  Organ-forming substances in the eggs of ascidians , 1905 .

[54]  Edwin G. Conklin,et al.  Mosaic development in ascidian eggs , 1905 .

[55]  W. C. Barker,et al.  The PIR-International Protein Sequence Database. , 1998, Nucleic acids research.

[56]  H. Nishida,et al.  An FGF signal from endoderm and localized factors in the posterior-vegetal egg cytoplasm pattern the mesodermal tissues in the ascidian embryo. , 2000, Development.

[57]  R. Vale,et al.  RNA on the move: the mRNA localization pathway [published erratum appears in J Cell Biol 1993 Dec;123(6 Pt 1):1625] , 1993, The Journal of cell biology.

[58]  M. Ogasawara,et al.  Two pathways of maternal RNA localization at the posterior-vegetal cytoplasm in early ascidian embryos. , 2000, Developmental biology.

[59]  C. Hunter,et al.  The maternal par genes and the segregation of cell fate specification activities in early Caenorhabditis elegans embryos. , 1997, Development.

[60]  N. Satoh,et al.  Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. I. Up to the eight-cell stage. , 1983, Developmental biology.