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

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.

Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis

“…It is furthermore interesting to note that Azumi et al reported that many of the genes contained in the maternal cluster of their study encoded proteins functioning in mitochondria and the cell cycle (Azumi et al, 2007), and that although we did not find any GO term strongly bias towards SL(+) UniGene genes, the GO terms "mitochondrion", "protein transport" and "cell cycle" were episodically observed. The studies of operon structures in C. elegans and C. intestinalis bring further support to the possible association of mitochodrion and transsplicing.…”

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata

“…Due to their ability to examine the transcription levels of thousands of genes simultaneously, gene expression microarray analyses have been used to characterize gene expression profiles during key transitions in the life cycle of a diverse range of organisms (Arbeitman et al, 2002;Azumi et al, 2007;Baldessari et al, 2005;Hill et al, 2000;Wei et al, 2006). However, few studies have focused on the transcriptional changes regulating metamorphosis in marine invertebrates.…”

Is aging an evolved developmental program?

“…For four months, Azumi et al [17] measured gene expression during the life cycle of Ciona intestinalis (sea squirt); an invertebrate chordate. The developmental stages of this animal consist of 13 embryonic stages, larval and juvenile stages, as well as four adult stages.…”