Microarray analysis of localization of maternal transcripts in eggs and early embryos of the ascidian, Ciona intestinalis

Developmental Biology

Volumn 284, Issue 2, 2005, Pages 536-550

  Yamada, Lixy ^a   Kobayashi, Kenji ^a   Satou, Yutaka ^a   Satoh, Nori ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Ciona intestinalis; Localization; Maternal transcripts; Microarray

Indexed keywords

ANIMAL TISSUE; ARTICLE; ASCIDIACEA; BLASTOMERE; CELLULAR DISTRIBUTION; CIONA INTESTINALIS; CONTROLLED STUDY; DNA MICROARRAY; EGG; EMBRYO; EMBRYO DEVELOPMENT; GENE IDENTIFICATION; GENE LOCATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; IN SITU HYBRIDIZATION; MITOCHONDRIAL GENETICS; NONHUMAN; PRIORITY JOURNAL; ZYGOTE;

ANIMALIA; ASCIDIA; CIONA; CIONA INTESTINALIS;

EID: 23944515753     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2005.05.027     Document Type: Article

References (65)

1. K. Azumi, H. Takahashi, Y. Miki, M. Fujie, T. Usami, H. Ishikawa, A. Kitayama, Y. Satou, N. Ueno, and N. Satoh Construction of a cDNA microarray derived from the ascidian Ciona intestinalis Zool. Sci. 20 2003 1223 1229
2. J.N. Betley, M.C. Frith, J.H. Graber, S. Choo, and J.O. Deshler A ubiquitous and conserved signal for RNA localization in chordates Curr. Biol. 12 2002 1756 1761
3. A. Caracciolo, A. Di Gregorio, F. Aniello, R. Di Lauro, and M. Branno Identification and developmental expression of three Distal-less homeobox containing genes in the ascidian Ciona intestinalis Mech. Dev. 99 2000 173 176
4. S. Chiba, Y. Satou, T. Nishikata, and N. Satoh Isolation and characterization of cDNA clones for epidermis-specific and muscle-specific genes in Ciona savignyi embryos Zool. Sci. 15 1998 239 246
5. P. Chomczynski, and N. Sacchi Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction Anal. Biochem. 162 1987 156 159
6. E.G. Conklin The organization and cell lineage of ascidian egg J. Acad. Nat. Sci. 13 1905 1 119
7. E.H. Davidson Genomic Regulatory Systems-Development and Evolution 2001 Academic Press San Diego, CA
8. P. Dehal, Y. Satou, R.K. Campbell, J. Chapman, B. Degnan, A. De Tomaso, B. Davidson, A. Di Gregorio, M. Gelpke, D.M. Goodstein, N. Harafuji, K.E. Hastings, I. Ho, K. Hotta, W. Huang, T. Kawashima, P. Lemaire, D. Martinez, I.A. Meinertzhagen, S. Necula, M. Nonaka, N. Putnam, S. Rash, H. Saiga, M. Satake, A. Terry, L. Yamada, H.G. Wang, S. Awazu, K. Azumi, J. Boore, M. Branno, S. Chin-Bow, R. DeSantis, S. Doyle, P. Francino, D.N. Keys, S. Haga, H. Hayashi, K. Hino, K.S. Imai, K. Inaba, S. Kano, K. Kobayashi, M. Kobayashi, B.I. Lee, K.W. Makabe, C. Manohar, G. Matassi, M. Medina, Y. Mochizuki, S. Mount, T. Morishita, S. Miura, A. Nakayama, S. Nishizaka, H. Nomoto, F. Ohta, K. Oishi, I. Rigoutsos, M. Sano, A. Sasaki, Y. Sasakura, E. Shoguchi, T. Shin-i, A. Spagnuolo, D. Stainier, M.M. Suzuki, O. Tassy, N. Takatori, M. Tokuoka, K. Yagi, F. Yoshizaki, S. Wada, C. Zhang, P.D. Hyatt, F. Larimer, C. Detter, N. Doggett, T. Glavina, T. Hawkins, P. Richardson, S. Lucas, Y. Kohara, M. Levine, N. Satoh, and D.S. Rokhsar The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins Science 298 2002 2157 2167
9. D. Ding, and H.D. Lipshitz Localized RNAs and their functions BioEssays 15 1993 651 658
10. M. Fujimura, and K. Takamura 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 Dev. Genes Evol. 210 2000 64 72
11. S. Fujiwara, Y. Maeda, T. Shin-I, Y. Kohara, N. Takatori, Y. Satou, and N. Satoh Gene expression profiles in Ciona intestinalis cleavage-stage embryos Mech. Dev. 112 2002 115 127
12. D. Gautreau, C.A. Cote, and K.L. Mowry Two copies of a subelement from the Vg1 RNA localization sequence are sufficient to direct vegetal localization in Xenopus oocytes Development 124 1997 5013 5020
13. E.R. Gavis Expeditions to the pole: RNA localization in Xenopus and Drosophila Trends. Cell Biol. 7 1997 485 492
14. J.B. Glotzer, and A. Ephrussi mRNA localization and the cytoskeleton Semin. Cell Dev. Biol. 7 1996 357 365
15. T. Hibino, T. Nishikata, and H. Nishida Centrosome-attracting body: a novel structure closely related to unequal cleavages in the ascidian embryo Dev. Growth Differ. 40 1998 85 95
16. K. Imai, N. Takada, N. Satoh, and Y. Satou β-catenin mediates the specification of endoderm cells in ascidian embryos Development 127 2000 3009 3020
17. K.S. Imai, N. Satoh, and Y. Satou A twist-like bHLH gene is a downstream factor of an endogenous FGF and determines mesenchymal fate in the ascidian embryos Development 130 2003 4461 4472
18. K.S. Imai, K. Hino, K. Yagi, N. Satoh, and Y. Satou Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks Development 131 2004 4047 4058
19. W.R. Jeffery Determinants of cell and positional fate in ascidian embryos Int. Rev. Cytol. 203 2001 3 62
20. M. Kloc, N.R. Zearfoss, and L.D. Etkin Mechanisms of subcellular mRNA localization Cell 108 2002 533 544
21. K. Kobayashi, K. Sawada, H. Yamamoto, S. Wada, H. Saiga, and H. Nishida Maternal macho-1 is an intrinsic factor that makes cell response to the same FGF signal differ between mesenchyme and notochord induction in ascidian embryos Development 130 2003 5179 5190
22. T. Kusakabe Decoding cis-regulatory systems in ascidians Zool. Sci. 22 2005 129 146
23. T. Kusakabe, R. Yoshida, Y. Ikeda, and M. Tsuda Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona Dev. Biol. 276 2004 563 580
24. P.M. Macdonald, K. Kerr, J.L. Smith, and A. Leask RNA regulatory element BLE1 directs the early steps of bicoid mRNA localization Development 118 1993 1233 1243
25. K.W. Makabe, T. Kawashima, S. Kawashima, T. Minokawa, A. Adachi, H. Kawamura, H. Ishikawa, R. Yasuda, H. Yamamoto, K. Kondoh, S. Arioka, Y. Sasakura, A. Kobayashi, K. Yagi, K. Shojima, Y. Kondoh, S. Kido, M. Tsujinami, N. Nishimura, M. Takahashi, T. Nakamura, M. Kanehisa, M. Ogasawara, T. Nishikata, and H. Nishida Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development Development 128 2001 2555 2567
26. Y. Marikawa, S. Yoshida, and N. Satoh Development of egg fragments of the ascidian Ciona savignyi: the cytoplasmic factors responsible for muscle differentiation are separated into a specific fragment Dev. Biol. 162 1994 134 142
27. T. Miya, and H. Nishida An Ets transcription factor, HrEts, is target of FGF signaling and involved in induction of notochord, mesenchyme, and brain in ascidian embryos Dev. Biol. 261 2003 25 38
28. T. Miya, and H. Nishida Expression pattern and transcriptional control of SoxB1 in embryos of the ascidian Halocynthia roretzi Zool. Sci. 20 2003 59 67
29. Y. Nakamura, K.W. Makabe, and H. Nishida Localization and expression pattern of type I postplasmic mRNAs in embryos of the ascidian Halocynthia roretzi Gene Expr. Patterns 3 2003 71 75
30. H. Nishida Cell fate specification by localized cytoplasmic determinants and cell interactions in ascidian embryos Int. Rev. Cytol. 176 1997 245 306
31. H. Nishida Specification of developmental fates in ascidian embryos: molecular approach to maternal determinants and signaling molecules Int. Rev. Cytol. 217 2002 227 276
32. H. Nishida Patterning the marginal zone of early ascidian embryos: localized maternal mRNA and inductive interactions BioEssays 24 2002 613 624
33. H. Nishida, and K. Sawada macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis Nature 409 2001 724 729
34. T. Nishikata, T. Hibino, and H. Nishida The centrosome-attracting body, microtubule system, and posterior egg cytoplasm are involved in positioning of cleavage planes in the ascidian embryo Dev. Biol. 209 1999 72 85
35. T. Nishikata, L. Yamada, Y. Mochizuki, Y. Satou, T. Shin-i, Y. Kohara, and N. Satoh Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis Dev. Biol. 238 2001 315 331
36. T. Oka, R. Amikura, S. Kobayashi, H. Yamamoto, and H. Nishida Localization of mitochondrial large ribosomal RNA in the myoplasm of the early ascidian embryo Dev. Growth Differ. 41 1999 1 8
37. C. Sardet, H. Nishida, F. Prodon, and K. Sawada Maternal mRNAs of PEM and macho 1, the ascidian muscle determinant, associate and move with a rough endoplasmic reticulum network in the egg cortex Development 130 2003 5839 5849
38. C. Sardet, P. Dru, and F. Prodon Maternal determinants and mRNAs in the cortex of ascidian oocytes, zygotes and embryos Biol. Cell 97 2005 35 49
39. Y. Sasakura, and K.W. Makabe Identification of cis elements which direct the localization of maternal mRNAs to the posterior pole of ascidian embryos Dev. Biol. 250 2002 128 144
40. Y. Sasakura, M. Ogasawara, and K.W. Makabe HrWnt-5: a maternally expressed ascidian Wnt gene with posterior localization in early embryos Int. J. Dev. Biol. 42 1998 573 579
41. Y. Sasakura, M. Ogasawara, and K.W. Makabe Maternally localized RNA encoding a serine/threonine protein kinase in the ascidian, Halocynthia roretzi Mech. Dev. 76 1998 161 163
42. Y. Sasakura, M. Ogasawara, and K.W. Makabe Two pathways of maternal RNA localization at the posterior-vegetal cytoplasm in early ascidian embryos Dev. Biol. 220 2000 365 378
43. N. Satoh Genomic resources for ascidians: sequence/expression databases and genome projects Methods Cell Biol. 74 2004 759 774
44. N. Satoh, Y. Satou, B. Davidson, and M. Levine Ciona intestinalis: an emerging model for whole-genome analyses Trends Genet. 19 2003 376 381
45. Y. Satou Posterior end mark 3 (pem-3), an ascidian maternally expressed gene with localized mRNA encodes a protein with Caenorhabditis elegans MEX-3-like KH domains Dev. Biol. 212 1999 337 350
46. Y. Satou, and N. Satoh Posterior end mark 2 (pem-2), pem-4, pem-5, and pem-6: maternal genes with localized mRNA in the ascidian embryo Dev. Biol. 192 1997 467 481
47. Y. Satou, T. Kusakabe, I. Araki, and N. Satoh Timing of initiation of muscle-specific gene expression in the ascidian embryo precedes that of developmental fate restriction in lineage cells Dev. Growth Differ. 37 1995 319 327
48. Y. Satou, K.S. Imai, and N. Satoh Action of morpholinos in Ciona embryos Genesis 30 2001 103 106
49. Y. Satou, K. Yagi, K.S. Imai, L. Yamada, H. Nishida, and N. Satoh macho-1-related genes in Ciona embryos Dev. Genes Evol. 212 2002 87 92
50. Y. Satou, L. Yamada, Y. Mochizuki, N. Takatori, T. Kawashima, A. Sasaki, M. Hamaguchi, S. Awazu, K. Yagi, Y. Sasakura, A. Nakayama, H. Ishikawa, K. Inaba, and N. Satoh A cDNA resource from the basal chordate Ciona intestinalis Genesis 33 2002 153 154
51. Y. Satou, K.S. Imai, M. Levine, Y. Kohara, D. Rokhsar, and N. Satoh A genomewide survey of developmentally relevant genes in Ciona intestinalis: I. Genes for bHLH transcription factors Dev. Genes Evol. 213 2003 213 221
52. B.J. Schnapp, E.A. Arn, J.O. Deshler, and M.I. Highett RNA localization in Xenopus oocyte Semin. Cell Dev. Biol. 8 1997 529 540
53. T.L. Serano, and R.S. Cohen A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA Development 121 1995 3809 3818
54. Y. Shimauchi, S. Chiba, and N. Satoh Synergistic action of HNF-3 and Brachyury in the notochord differentiation of ascidian embryos Int. J. Dev. Biol. 45 2001 643 652
55. S. Wada, Y. Katsuyama, S. Yasugi, and H. Saiga Spatially and temporally regulated expression of the LIM class homeobox gene Hrlim suggests multiple distinct functions in development of the ascidian, Halocynthia roretzi Mech. Dev. 51 1995 115 126
56. S. Wada, M. Tokuoka, E. Shoguchi, K. Kobayashi, A. Di Gregorio, A. Spagnuolo, M. Branno, Y. Kohara, D. Rokhsar, M. Levine, H. Saiga, N. Satoh, and Y. Satou A genomewide survey of developmentally relevant genes in Ciona intestinalis: II. Genes for homeobox transcription factors Dev. Genes Evol. 213 2003 222 234
57. J.E. Wilhelm, and R.D. Vale RNA on the move: the mRNA localization pathway J. Cell Biol. 123 1993 269 274
58. K. Yagi, Y. Satou, F. Mazet, S.M. Shimeld, B. Degnan, D. Rokhsar, M. Levine, Y. Kohara, and N. Satoh A genomewide survey of developmentally relevant genes in Ciona intestinalis: III. Genes for Fox, ETS, nuclear receptors and NFκB Dev. Genes Evol. 213 2003 235 244
59. K. Yagi, N. Satoh, and Y. Satou Identification of downstream genes of the ascidian muscle determinant gene Ci-macho1 Dev. Biol. 274 2004 478 489
60. K. Yagi, N. Takatori, Y. Satou, and N. Satoh Ci-Tbx6b and Ci-Tbx6c are key mediators of the maternal effect gene Ci-macho1 in muscle cell differentiation in Ciona intestinalis embryos Dev. Biol. 282 2005 535 549
61. L. Yamada, K. Kobayashi, B. Degnan, N. Satoh, and Y. Satou A genomewide survey of developmentally relevant genes in Ciona intestinalis: IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail Dev. Genes Evol. 213 2003 245 253
62. L. Yamada, E. Shoguchi, S. Wada, K. Kobayashi, Y. Mochizuki, Y. Satou, and N. Satoh Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis Development 130 2003 6485 6495
63. S. Yoshida, Y. Marikawa, and N. Satoh Posterior end mark, a novel maternal gene encoding a localized factor in the ascidian embryo Development 122 1996 2005 2012
64. S. Yoshida, Y. Satou, and N. Satoh Maternal genes with localized mRNA and pattern formation of the ascidian embryo Cold Spring Harbor Symp. Quant. Biol. 62 1997 89 96
65. M. Zalokar, and C. Sardet Tracing of cell lineage in embryonic development of Phallusia mammillata (Ascidia) by vital staining of mitochondria Dev. Biol. 102 1984 195 205