Microarray analysis of zygotic expression of transcription factor genes and cell signaling molecule genes in early Ciona intestinalis embryos.

In ascidians, specification of embryonic cells takes place very early at the 16-, 32- and 64-cell stages, and this developmental event involves zygotic expression of various genes, some encoding transcription factors and some encoding cell signaling molecules. Previous studies have demonstrated that approximately 50 transcription factor genes and 25 signaling molecule genes commence their zygotic expression by the 64-cell stage of Ciona intestinalis embryos. With the aid of oligonucleotide-based microarray, we examined the zygotic expression profiles of developmental genes in early Ciona embryos. Although the microarray method had a tendency to barely detect zygotic expression of genes that are expressed maternally, the present results confirmed the results of previous studies. In addition, the present analysis demonstrated the zygotic expression of four genes that were not identified in previous studies, and this result was confirmed by whole-mount in situ hybridization. Our results therefore provide further information on the developmental genes that are zygotically expressed in early Ciona embryos, and demonstrate that the microarray is a powerful tool for future studies of the gene regulatory network in Ciona, a basal chordate with a body plan similar to that of vertebrates.