Microarray analysis of embryonic retinoic acid target genes in the ascidian <i>Ciona intestinalis</i>

Ishibashi, Tomoko; Nakazawa, Masumi; Ono, Hiroaki; Satoh, Nori; Gojobori, Takashi; Fujiwara, Shigeki

doi:10.1046/j.1524-4725.2003.694.x

Cited by 30 publications

(26 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The strong activation of Hox-1 and Cyp26 was similar to that in vertebrates Ishibashi et al, 2003). As previously shown by in situ hybridization analysis , RAR expression was not activated by RA .…”

Section: Variation Of the Repertoire Of Ra-target Genes In Some Chordsupporting

confidence: 84%

Acquisition of Retinoic Acid Signaling Pathway and Innovation of the Chordate Body Plan

Fujiwara

Kawamura

2003

Zoological Science

Self Cite

View full text Add to dashboard Cite

-Retinoic acid (RA) regulates many of the chordate-specific and vertebrate-specific characters. These include the anteroposterior pattern of the dorsally located central nervous system, pharynx with gill slits, neural crest cells, limb morphogenesis and anteroposteriorly organized vertebrae. The necessity of endogenous RA and the RA receptor (RAR) has been demonstrated by mutant analyses, vitamin Adeficient animals and various other methods. Since RAR has been identified only in chordates, the acquisition of the RAR-mediated RA signaling pathway is thought to be an important event for the innovation of the chordate body plan. RA-synthesizing aldehyde dehydrogenases and RA-degrading enzymes also seem to be chordate-specific. The expression pattern of these genes in ascidian embryos is similar to that in vertebrate embryos. These results suggest that the RA signaling cascade, with various regulators and modifiers, had been already well established in the common chordate ancestor. RA also regulates morphogenesis during the asexual reproduction of ascidians, suggesting that RA may also have played a part in producing diversity within the chordate groups.

show abstract

Section: Variation Of the Repertoire Of Ra-target Genes In Some Chordsupporting

confidence: 84%

Acquisition of Retinoic Acid Signaling Pathway and Innovation of the Chordate Body Plan

Fujiwara

Kawamura

2003

Zoological Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…For example, the RA receptor corepressor RIP140 is RA-induced, and silencing its induction enhances RA responsiveness (White et al, 2003). While over 500 other genes have been reported to be directly or indirectly regulated by RA in some context (Arima et al, 2005; Bouillet et al, 1995; Freemantle et al, 2002; Ishibashi et al, 2003), the potential functions of these genes in feedback regulation of RA signaling in the embryo has not been investigated directly.…”

Section: Introductionmentioning

confidence: 99%

Dhrs3a regulates retinoic acid biosynthesis through a feedback inhibition mechanism

Feng

Hernandez

Waxman

et al. 2010

Developmental Biology

122

148

View full text Add to dashboard Cite

Retinoic acid (RA) is an important developmental signaling molecule responsible for the patterning of multiple vertebrate tissues. RA is also a potent teratogen, causing multi-organ birth defects in humans. Endogenous RA levels must therefore be tightly controlled in the developing embryo. We used a microarray approach to identify genes that function as negative feedback regulators of retinoic acid signaling. We screened for genes expressed in early somite-stage embryos that respond oppositely to treatment with RA versus RA antagonists, and validated them by RNA in situ hybridization. Focusing on genes known to be involved in RA metabolism, we determined that dhrs3a, which encodes a member of the short-chain dehydrogenase/reductase protein family, is both RA dependent and strongly RA inducible. Dhrs3a is known to catalyze the reduction of the RA precursor all-trans retinaldehyde to vitamin A, however a developmental function has not been demonstrated. Using morpholino knock down and mRNA over-expression, we demonstrate that Dhrs3a is required to limit RA levels in the embryo, primarily within the central nervous system. Dhrs3a is thus an RA-induced feedback inhibitor of RA biosynthesis. We conclude that retinaldehyde availability is an important level at which RA biosynthesis is regulated in vertebrate embryos.

show abstract

“…cDNA microarray studies have been carried out in embryos of various organisms, including C. elegans (Hill et al, 2000), Drosophila (White et al, 1999;Furlong et al, 2001;Arbeitman et al, 2002), Ciona (Azumi et al, 2003;Ishibashi et al, 2003), zebrafish (Lo et al, 2003) and mouse (Tanaka et al, 2000;Miki et al, 2001;Mody et al, 2001;Bono et al, 2003). Among vertebrates, Xenopus has the advantage that it permits to easily collect preparative quantities of embryos from all stages, parts of embryos, as well as embryos manipulated by drug treatment or mRNA injection.…”

Section: Introductionmentioning

confidence: 99%

Global gene expression profiling and cluster analysis in Xenopus laevis

Baldessari

Shin

Krebs

et al. 2005

Mechanisms of Development

View full text Add to dashboard Cite

We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.

show abstract

Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis

Cited by 30 publications

References 56 publications

Acquisition of Retinoic Acid Signaling Pathway and Innovation of the Chordate Body Plan

Acquisition of Retinoic Acid Signaling Pathway and Innovation of the Chordate Body Plan

Dhrs3a regulates retinoic acid biosynthesis through a feedback inhibition mechanism

Global gene expression profiling and cluster analysis in Xenopus laevis

Contact Info

Product

Resources

About