Related Experiment Video
Updated: Aug 17, 2026
Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis
Published on: October 16, 2016
Oligonucleotide-based microarray analysis of retinoic acid target genes in the protochordate, Ciona intestinalis
Tomoko Ishibashi1, Takeshi Usami, Manabu Fujie
1Department of Materials Science, Faculty of Science, Kochi University, Kochi, Japan.
Abstract:
Oligonucleotide-based microarray analyses were carried out to identify retinoic acid target genes in embryos of the ascidian Ciona intestinalis. Of 21,938 spots, 50 (corresponding to 43 genes) showed over twofold up-regulation in retinoic acid-treated tail bud embryos. In situ hybridization verified retinoic acid-induced up-regulation of 23 genes. Many of them were expressed in the anterior tail region, where a retinaldehyde dehydrogenase homolog is expressed. Homologs of vertebrate genes involved in neurogenesis and/or neuronal functions (e.g., COUP-TF, Ci-Hox1, and SCO-spondin) were expressed in the central nervous system of Ciona embryos, and activated by retinoic acid. Genes encoding transcription factors (e.g., Ci-lmx1.2, vitamin D receptor, and Hox proteins) and apoptosis-related proteins (e.g., transglutaminase and an apoptosis-inducing factor homolog) were also activated by retinoic acid. Simultaneous treatment of embryos with retinoic acid and puromycin revealed a few direct targets, including genes encoding Ci-Hox1, Ci-Cyp26, and an Rnf126-like ring finger protein.
Insights
Retinoic acid activates many genes in Ciona intestinalis embryos, including those involved in neurogenesis and apoptosis. This study identified key retinoic acid target genes, providing insights into developmental pathways.
Area of Science:
- Developmental Biology
- Molecular Genetics
- Marine Biology
Background:
- Retinoic acid (RA) is a crucial signaling molecule in vertebrate development.
- Understanding RA's role in invertebrate development, like in the ascidian Ciona intestinalis, offers comparative insights.
- Gene expression patterns reveal conserved developmental pathways.
Purpose of the Study:
- To identify retinoic acid (RA) target genes in Ciona intestinalis embryos.
- To investigate the function of RA in ascidian development.
- To explore conserved roles of RA signaling in neurogenesis and apoptosis.
Main Methods:
- Oligonucleotide-based microarray analysis of 21,938 gene spots.
- In situ hybridization to verify gene expression.
- Simultaneous treatment with retinoic acid and puromycin to identify direct targets.
Main Results:
- 50 gene spots (43 genes) showed >2-fold upregulation by retinoic acid in tail bud embryos.
- 23 genes confirmed to be upregulated by RA, many in the anterior tail region.
- RA activated homologs of vertebrate neurogenesis genes (e.g., COUP-TF, Ci-Hox1) and apoptosis-related genes.
Conclusions:
- Retinoic acid (RA) regulates a significant number of genes in Ciona intestinalis development.
- RA targets include genes involved in neurogenesis, neuronal function, transcription regulation, and apoptosis.
- Direct RA targets include Ci-Hox1, Ci-Cyp26, and an Rnf126-like ring finger protein.
