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

• Published in: Developmental biology Vol. 308; no. 2; pp. 572 - 582
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.08.2007
• Subjects: Aging; Animals; Ascidian; Chordata; Ciona intestinalis; Ciona intestinalis - embryology; Ciona intestinalis - genetics; Ciona intestinalis - growth & development; Ciona intestinalis - immunology; Clustering; Development; DNA microarray; Female; Gene expression; Gene Expression Profiling - statistics & numerical data; Gene Expression Regulation, Developmental; Immunity - genetics; Male; Multigene Family; Notochord - embryology; Notochord - metabolism; Oligonucleotide Array Sequence Analysis - statistics & numerical data; Organ Specificity; Organ-specific gene; Reproducibility of Results; DNA microarray; Ciona intestinalis; Ascidian; Development; Aging; Organ-specific gene; Gene expression; Clustering
• ISSN: 0012-1606; 1095-564X
• DOI: 10.1016/j.ydbio.2007.05.022

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.