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Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis
Tomoko Ishibashi1, Masumi Nakazawa, Hiroaki Ono
1Department of Biology, Faculty of Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi 780-8520, Japan.
Abstract:
Many chordate- and vertebrate-specific characteristics develop depending on retinoic acid (RA). Because the gene encoding the RA receptor exists only in chordates, RA function seems to be involved in chordate evolution. A cDNA microarray analysis of 9287 non-redundant cDNA clones was used to screen for RA target genes in the ascidian Ciona intestinalis. In addition, the spatial expression pattern of 94 candidate RA target genes was examined by in situ hybridization in RA-treated and control embryos. Strong RA-induced upregulation of Hox-1 and Cyp26 was observed, as is the case in vertebrates. In addition, a number of novel candidate target genes was identified. These included transcription factors and signaling molecules, suggesting that various differentiation and/or morphogenetic pathways are modulated by RA. The expression of cell adhesion molecules, cytoskeletal proteins and extracellular matrix components was affected by RA. Changes in the expression pattern of these genes may be a direct cause of abnormal morphogenesis of the anterior neural tissues. RA also affected the expression of genes that seemed to be involved in neuronal functions. Although obvious homeotic transformation has not been observed, the function of various neural cell types seemed to be impaired by RA. The microarray data are reliable and will contribute to comprehensive understanding of RA action in the development and evolution of chordates.
Insights
Retinoic acid (RA) influences chordate development and evolution. This study identified novel RA target genes in Ciona intestinalis, revealing its role in modulating differentiation, morphogenesis, and neural functions.
Area of Science:
- Developmental Biology
- Evolutionary Biology
- Molecular Biology
Background:
- Retinoic acid (RA) is crucial for chordate and vertebrate development.
- The RA receptor gene is unique to chordates, suggesting a role in their evolution.
- Understanding RA's molecular targets is key to deciphering its developmental and evolutionary roles.
Purpose of the Study:
- To identify retinoic acid (RA) target genes in the chordate Ciona intestinalis using cDNA microarray analysis.
- To investigate the spatial expression patterns of candidate RA target genes in response to RA treatment.
- To explore the involvement of RA in chordate development and evolution through gene expression analysis.
Main Methods:
- cDNA microarray analysis of 9287 non-redundant cDNA clones to screen for RA target genes.
- In situ hybridization to examine the spatial expression patterns of 94 candidate RA target genes.
- Treatment of Ciona intestinalis embryos with RA and comparison with control embryos.
Main Results:
- Identified significant RA-induced upregulation of Hox-1 and Cyp26, consistent with vertebrate studies.
- Discovered novel RA target genes, including transcription factors and signaling molecules, indicating modulation of diverse pathways.
- Observed RA's effect on cell adhesion molecules, cytoskeletal proteins, and extracellular matrix components, potentially impacting morphogenesis.
- Noted RA's influence on genes involved in neuronal functions, suggesting impairment of neural cell types.
Conclusions:
- RA plays a significant role in modulating differentiation and morphogenetic pathways in chordates.
- RA affects genes involved in neural development and function, potentially leading to abnormal morphogenesis.
- The identified RA target genes provide insights into the molecular mechanisms underlying RA action in chordate development and evolution.