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

Kaoru Azumi, Sorin V. Sabau, Manabu Fujie, Takeshi Usami, Ryo Koyanagi, Takeshi Kawashima, Shigeki Fujiwara, Michio Ogasawara, Masanobu Satake, Masaru Nonaka, Hong Gang Wang, Yutaka Satou, Nori Satoh

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Recent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, we made use of a large-scale oligo-DNA microarray to further investigate and identify genes with specific or correlated expression profiles, and we report global gene expression profiles for about 66% of all the C. intestinalis genes that are expressed during its life cycle. We succeeded in categorizing the data set into 5 large clusters and 49 sub-clusters based on the expression profile of each gene. This revealed the higher order of gene expression profiles during the developmental and aging stages. Furthermore, a combined analysis of microarray data with the EST database revealed the gene groups that were expressed at a specific stage or in a specific organ of the adult. This study provides insights into the complex structure of ascidian gene expression, identifies co-expressed gene groups and marker genes and makes predictions for the biological roles of many uncharacterized genes. This large-scale oligo-DNA microarray for C. intestinalis should facilitate the understanding of global gene expression and gene networks during the development and aging of a basal chordate.

Original languageEnglish (US)
Pages (from-to)572-582
Number of pages11
JournalDevelopmental biology
Volume308
Issue number2
DOIs
StatePublished - Aug 15 2007

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Ciona intestinalis
Urochordata
Life Cycle Stages
Transcriptome
Genes
Expressed Sequence Tags
Oligonucleotide Array Sequence Analysis
Chordata
Gene Expression
Gene Regulatory Networks
Microarray Analysis
Sequence Analysis
Genome
Databases

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Developmental Biology
  • Cell Biology

Cite this

Azumi, K., Sabau, S. V., Fujie, M., Usami, T., Koyanagi, R., Kawashima, T., ... Satoh, N. (2007). Gene expression profile during the life cycle of the urochordate Ciona intestinalis. Developmental biology, 308(2), 572-582. https://doi.org/10.1016/j.ydbio.2007.05.022
Azumi, Kaoru ; Sabau, Sorin V. ; Fujie, Manabu ; Usami, Takeshi ; Koyanagi, Ryo ; Kawashima, Takeshi ; Fujiwara, Shigeki ; Ogasawara, Michio ; Satake, Masanobu ; Nonaka, Masaru ; Wang, Hong Gang ; Satou, Yutaka ; Satoh, Nori. / Gene expression profile during the life cycle of the urochordate Ciona intestinalis. In: Developmental biology. 2007 ; Vol. 308, No. 2. pp. 572-582.
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Azumi, K, Sabau, SV, Fujie, M, Usami, T, Koyanagi, R, Kawashima, T, Fujiwara, S, Ogasawara, M, Satake, M, Nonaka, M, Wang, HG, Satou, Y & Satoh, N 2007, 'Gene expression profile during the life cycle of the urochordate Ciona intestinalis', Developmental biology, vol. 308, no. 2, pp. 572-582. https://doi.org/10.1016/j.ydbio.2007.05.022

Gene expression profile during the life cycle of the urochordate Ciona intestinalis. / Azumi, Kaoru; Sabau, Sorin V.; Fujie, Manabu; Usami, Takeshi; Koyanagi, Ryo; Kawashima, Takeshi; Fujiwara, Shigeki; Ogasawara, Michio; Satake, Masanobu; Nonaka, Masaru; Wang, Hong Gang; Satou, Yutaka; Satoh, Nori.

In: Developmental biology, Vol. 308, No. 2, 15.08.2007, p. 572-582.

Research output: Contribution to journalArticle

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T1 - Gene expression profile during the life cycle of the urochordate Ciona intestinalis

AU - Azumi, Kaoru

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AU - Usami, Takeshi

AU - Koyanagi, Ryo

AU - Kawashima, Takeshi

AU - Fujiwara, Shigeki

AU - Ogasawara, Michio

AU - Satake, Masanobu

AU - Nonaka, Masaru

AU - Wang, Hong Gang

AU - Satou, Yutaka

AU - Satoh, Nori

PY - 2007/8/15

Y1 - 2007/8/15

N2 - Recent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, we made use of a large-scale oligo-DNA microarray to further investigate and identify genes with specific or correlated expression profiles, and we report global gene expression profiles for about 66% of all the C. intestinalis genes that are expressed during its life cycle. We succeeded in categorizing the data set into 5 large clusters and 49 sub-clusters based on the expression profile of each gene. This revealed the higher order of gene expression profiles during the developmental and aging stages. Furthermore, a combined analysis of microarray data with the EST database revealed the gene groups that were expressed at a specific stage or in a specific organ of the adult. This study provides insights into the complex structure of ascidian gene expression, identifies co-expressed gene groups and marker genes and makes predictions for the biological roles of many uncharacterized genes. This large-scale oligo-DNA microarray for C. intestinalis should facilitate the understanding of global gene expression and gene networks during the development and aging of a basal chordate.

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Azumi K, Sabau SV, Fujie M, Usami T, Koyanagi R, Kawashima T et al. Gene expression profile during the life cycle of the urochordate Ciona intestinalis. Developmental biology. 2007 Aug 15;308(2):572-582. https://doi.org/10.1016/j.ydbio.2007.05.022