Gene expression profile during the life cycle of the urochordate Ciona intestinalis

Developmental Biology

Volumn 308, Issue 2, 2007, Pages 572-582

  Azumi, Kaoru ^a,b   Sabau, Sorin V ^c   Fujie, Manabu ^b   Usami, Takeshi ^a   Koyanagi, Ryo ^a   Kawashima, Takeshi ^d   Fujiwara, Shigeki ^e   Ogasawara, Michio ^f   Satake, Masanobu ^g   Nonaka, Masaru ^h   Wang, Hong Gang ⁱ   Satou, Yutaka ^d   Satoh, Nori ^b,d  

^a HOKKAIDO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TOKAI UNIVERSITY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e KOCHI UNIVERSITY   (Japan)

^f CHIBA UNIVERSITY   (Japan)

^g TOHOKU UNIVERSITY   (Japan)

^h UNIVERSITY OF TOKYO   (Japan)

ⁱ UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

Aging; Ascidian; Ciona intestinalis; Clustering; Development; DNA microarray; Gene expression; Organ specific gene

Indexed keywords

AGING; ARTICLE; CIONA INTESTINALIS; DEVELOPMENT; DEVELOPMENTAL GENETICS; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; LIFE CYCLE; NONHUMAN; PRIORITY JOURNAL; UROCHORDATA;

ASCIDIA; CIONA INTESTINALIS;

EID: 34547700777     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2007.05.022     Document Type: Article

References (45)

1. Arbeitman M.N., Furlong E.E.M., Imam F., Johnson E., Null B.H., Baker B.S., Krasnow M.A., Scott M.P., Davis R.W., and White K.P. Gene expression during the life cycle of Drosophila melanogaster. Science 297 (2002) 2270-2275
2. Azumi K., Takahashi H., Miki Y., Fujie M., Usami T., Ishikawa H., Kitayama A., Satou Y., Ueno N., and Satoh N. Construction of a cDNA microarray derived from the ascidian Ciona intestinalis. Zool. Sci. 20 (2003) 1223-1229
3. Azumi K., De Santis R., De Tomaso A., Rigoutsos I., Yoshizaki F., Pinto M.R., Marino R., Shida K., Ikeda M., Ikeda M., et al. Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics 55 (2003) 570-581
4. Azumi K., Fujie M., Usami T., Miki Y., and Satoh N. A cDNA microarray technique applied for analysis of global gene expression profiles in tributyltin-exposed ascidians. Mar. Environ. Res. 58 (2004) 543-546
5. Azumi K., Sasaki T., Okochi K., Yamasaki S., Saito T., Takayama H., and Yokosawa H. Differential display analysis reveals the expression of glutathione S-transferase omega and novel genes through an ITAM-containing receptor in ascidian immunocytes. Immunogenetics 57 (2005) 444-452
6. Baldessari D., Shin Y., Krebs O., Konig R., Koide T., Vinayagam A., Fenger U., Mochii M., Terasaka C., Kitayama A., et al. Global gene expression profiling and cluster analysis in Xenopus laevis. Mech. Dev. 122 (2005) 441-475
7. Carter M.G., Hamatani T., Sharov A.A., Carmack C.E., Qian Y., Aiba K., Ko N.T., Dudekula D.B., Brzoska P.M., Hwang S.S., et al. In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Res. 13 (2003) 1011-1021
8. Chiba S., Awazu S., Itoh M., Chin-Bow S.T., Satoh N., Satou Y., and Hastings K.E.M. A genomewide survey of developmentally relevant genes in Ciona intestinalis: IX. Genes for muscle structural proteins. Dev. Genes Evol. 213 (2003) 291-302
9. Chiba S., Sasaki A., Nakayama A., Takamura K., and Satoh N. Development of Ciona intestinalis juveniles (through 2nd ascidian stage). Zool. Sci. 21 (2004) 285-298
10. Chomczynski P., and Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162 (1987) 156-159
11. Corbo J.C., Di Gregorio A., and Levine M. The ascidian as a model organism in developmental and evolutionary biology. Cell 106 (2001) 535-538
12. Dehal P., Satou Y., Campbell R.K., Chapman J., Degnan B., De Tomaso A., Davidson B., Di Gregorio A., Gelpke M., Goodstein D., et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298 (2002) 2157-2167
13. Furlong E.E.M., Andersen E.C., Null B., White K.P., and Scott M.P. Patterns of gene expression during Drosophila mesoderm development. Science 293 (2001) 1629-1633
14. Hill A.A., Hunter C.P., Tsung B.T., Tucker-Kellogg G., and Brown E.L. Genomic analysis of gene expression in C. elegans. Science 290 (2000) 809-812
15. Hino K., Satou Y., Yagi K., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: VI. Genes for Wnt, TGFbeta, Hedgehog and JAK/STAT signaling pathways. Dev. Genes Evol. 213 (2003) 264-272
16. Hotta K., Takahashi H., Asakura T., Saitoh B., Takatori N., Satou Y., and Satoh N. Characterization of Brachyury-downstream notochord genes in the Ciona intestinalis embryo. Dev. Biol. 224 (2000) 69-80
17. Imai K.S., Levine M., Satoh N., and Satou Y. Regulatory blueprint for a chordate embryo. Science 312 (2006) 1183-1187
18. Ishibashi T., Nakazawa M., Ono H., Satoh N., Gojobori T., and Fujiwara S. Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis. Dev. Growth Differ. 45 (2003) 249-259
19. Ishibashi T., Usami T., Fujie M., Azumi K., Satoh N., and Fujiwara S. Oligonucleotide-based microarray analysis of retinoic acid target genes in the protochordate, Ciona intestinalis. Dev. Dyn. 233 (2005) 1571-1578
20. Kawashima T., Tokuoka M., Awazu S., Satoh N., and Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis: VIII. Genes for PI3K signaling and cell cycle. Dev. Genes Evol. 213 (2003) 284-290
21. Kawashima T., Satou Y., Murakami S.D., and Satoh N. Dynamic changes in developmental gene expression in the basal chordate Ciona intestinalis. Dev. Growth Differ. 47 (2005) 187-199
22. Lo J., Lee S., Xu M., Liu F., Ruan H., Eun A., He Y., Ma W., Wang W., Wen Z., et al. 15 000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res. 13 (2003) 455-466
23. Miki R., Kadota K., Bono H., Mizuno Y., Tomaru Y., Carninci P., Itoh M., Shibata K., Kawai J., Konno H., et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 2199-2204
24. Nonaka M., and Yoshizaki F. Primitive complement system of invertebrates. Immunol. Rev. 198 (2004) 203-215
25. Ogasawara M., Satoh N., Shimada Y., Wang Z., Tanaka T., and Noji S. Rapid and stable buffer exchange system using InSitu Chip suitable for multicolor and large-scale whole-mount analyses. Dev. Genes Evol. 216 (2006) 100-104
26. Sasakura Y., Yamada L., Takatori N., Satou Y., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: VII. Molecules involved in the regulation of cell polarity and actin dynamics. Dev. Genes Evol. 213 (2003) 273-283
27. Sasakura Y., Shoguchi E., Takatori N., Wada S., Meinertzhagen I.A., Satou Y., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: X. Genes for cell junctions and extracellular matrix. Dev. Genes Evol. 213 (2003) 303-313
28. Sasakura Y., Nakashima K., Awazu S., Matsuoka T., Nakayama A., Azuma J., and Satoh N. Transposon-mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 15134-15139
29. Satoh N. Developmental Biology of Ascidians (1994), Cambridge Univ Press, NY
30. Satoh N. Ascidian embryos as a model system to analyze expression and function of developmental genes. Differentiation 68 (2001) 1-12
31. Satoh N., Satou Y., Davidson B., and Levine M. Ciona intestinalis: an emerging model for whole-genome analyses. Trends Genet. 19 (2003) 376-381
32. Satou Y., Takatori N., Fujiwara S., Nishikata T., Saiga H., Kusakabe T., Shin-i T., Kohara Y., and Satoh N. Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287 (2002) 83-96
33. Satou Y., Yamada L., Mochizuki Y., Takatori N., Kawashima T., Sasaki A., Hamaguchi M., Awazu S., Yagi K., Sasakura Y., et al. A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33 (2002) 153-154
34. Satou Y., Imai K.S., Levine M., Kohara Y., Rokhsar D., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: I. Genes for bHLH transcription factors. Dev. Genes Evol. 213 (2003) 213-221
35. Satou Y., Sasakura Y., Yamada L., Imai K.S., Satoh N., and Degnan B. A genomewide survey of developmentally relevant genes in Ciona intestinalis: V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev. Genes Evol. 213 (2003) 254-263
36. Tanaka T.S., Jaradat S.A., Lim M.K., Kargul G.J., Wang X., Grahovac M.J., Pantano S., Sano Y., Piao Y., and Nagaraja R. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 9127-9132
37. Ton C., Stamatiou D., Dzau V.J., and Liew C.-C. Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochem. Biophys. Res. Commun. 296 (2002) 1134-1142
38. Wada S., Tokuoka M., Shoguchi E., Kobayashi K., Di Gregorio A., Spagnuolo A., Branno M., Kohara Y., Rokhsar D., Levine M., et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis: II. Genes for homeobox transcription factors. Dev. Genes Evol. 213 (2003) 222-234
39. Wei Z., Angerer R.C., and Angerer L.M. A database of mRNA expression patterns for the sea urchin embryo. Dev. Biol. 300 (2006) 476-484
40. White K.P., Rifkin S.A., Hurban P., and Hogness D.S. Microarray analysis of Drosophila development during metamorphosis. Science 286 (1999) 2179-2184
41. Yagi K., Satou Y., Mazet F., Shimeld S.M., Degnan B., Rokhsar D., Levine M., Kohara Y., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev. Genes Evol. 213 (2003) 235-244
42. Yagi K., Satou Y., and Satoh N. A zinc finger transcription factor, ZicL, is a direct activator of Brachyury in the notochord specification of Ciona intestinalis. Development 131 (2004) 1279-1288
43. Yamada L., Kobayashi K., Degnan B., Satoh N., and Satou Y. 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
44. Yamada L., Shoguchi E., Wada S., Kobayashi K., Mochizuki Y., Satou Y., and Satoh N. Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis. Development 130 (2003) 6485-6495
45. Yamada L., Kobayashi K., Satou Y., and Satoh N. Microarray analysis of localization of maternal transcripts in eggs and early embryos of the ascidian, Ciona intestinalis. Dev. Biol. 284 (2005) 536-550