A genomewide survey of developmentally relevant genes in Ciona intestinalis

Yagi, Keisuke; Satou, Yutaka; Mazet, Françoise; Shimeld, Sebastian M.; Degnan, Bernard M.; Rokhsar, Daniel S.; Levine, Michael; Kohara, Yuji; Satoh, Nori

doi:10.1007/s00427-003-0322-z

Cited by 140 publications

(85 citation statements)

References 28 publications

(21 reference statements)

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“…Even though some of the ligands for the 1H and 1I receptors, such as bile salts and vitamin D, are thought to be vertebrate innovations, orthologs to these receptors are found in C. intestinalis and other invertebrates. In addition to the Ciona LXR analyzed in this report, comparative genomics reveals an FXR ortholog and a single ortholog to VDR/PXR/CAR [11]. The preliminary draft of the purple sea urchin (Strongylocentrotus purpuratus) genome shows four NR1H-like genes, some of which have high expression in early embryogenesis, suggesting developmental and/or protective functions.…”

Section: Discussionmentioning

confidence: 84%

“…Sequencing of the Ciona intestinalis genome revealed two genes that have close sequence similarity to vertebrate NR1H genes [11]. By reciprocal BLAST analysis, one gene (ciLXR; Ensembl database accession no.…”

Section: Phylogenetic Analysis Of the Ciona Intestinalis Lxr Orthologmentioning

confidence: 99%

“…We also sought to probe the evolution of LXR in invertebrates by studying the chordate invertebrate sea squirt (Ciona intestinalis), a member of Urochordata, a subphylum that may contain the closest extant invertebrate relatives to modern vertebrates [10]. The completed genome of Ciona intestinalis revealed a gene that is an apparent ortholog to vertebrate LXRs [11]. From the Ghost database of Ciona intestinalis Genomic and cDNA Resources (http://ghost.zool.kyoto-u.ac.jp/indexr1.html), cDNA clone IDs cigd011h11 and cieg096k22 correspond to this putative 'Ciona LXR' (ciLXR).…”

Section: Introductionmentioning

confidence: 99%

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Ligand specificity and evolution of liver X receptors

Reschly

Ni²,

Welsh³

et al. 2008

The Journal of Steroid Biochemistry and Molecular Biology

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Liver X receptors (LXRs) are key regulators of lipid and cholesterol metabolism in mammals. Little is known, however, about the function and evolution of LXRs in non-mammalian species. The present study reports the cloning of LXRs from African clawed frog (Xenopus laevis), Western clawed frog (Xenopus tropicalis), and zebrafish (Danio rerio), and their functional characterization and comparison with human and mouse LXRs. Additionally, an ortholog of LXR in the chordate invertebrate Ciona intestinalis was cloned and functionally characterized. Ligand specificities of the frog and zebrafish LXRs were very similar to LXRα and LXRβ from human and mouse. All vertebrate LXRs studied were activated robustly by the synthetic ligands T-0901317 and GW3965 and by a variety of oxysterols. In contrast, Ciona LXR was not activated by T-0901317 or GW3965 but was activated by a limited number of oxysterols, as well as some androstane and pregnane steroids. Pharmacophore analysis, homology modeling, and docking studies of Ciona LXR predict a receptor with a more restricted ligand-binding pocket and less intrinsic disorder in the ligand-binding domain compared to vertebrate LXRs. The results suggest that LXRs have a long evolutionary history, with vertebrate LXRs diverging from invertebrate LXRs in ligand specificity.

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Section: Discussionmentioning

confidence: 84%

Section: Phylogenetic Analysis Of the Ciona Intestinalis Lxr Orthologmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ligand specificity and evolution of liver X receptors

Reschly

Ni²,

Welsh³

et al. 2008

The Journal of Steroid Biochemistry and Molecular Biology

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“…FoxF orthologs are highly conserved among diverse metazoans, and have been analyzed in vertebrates and Drosophila (Adell and Muller, 2004;Kaestner et al, 2000;Yagi et al, 2003). FoxF is one of the first genes to be activated in the anterior B7.5 lineage following FGF induction.…”

Section: Foxf Is Essential For Fgf-induced Migration Of Heart Progenimentioning

confidence: 99%

FoxFis essential for FGF-induced migration of heart progenitor cells in the ascidianCiona intestinalis

et al. 2007

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Heart development requires precise coordination of morphogenetic movements with progressive cell fate specification and differentiation. In ascidian embryos, FGF/MAPK-mediated activation of the transcription factor Ets1/2 is required for heart tissue specification and cell migration. We found that FoxF is one of the first genes to be activated in heart precursors in response to FGF signaling. We identified the FoxF minimal heart enhancer and used a cis-trans complementation test to show that Ets1/2 can interact with the FoxF enhancer in vivo. Next, we found that FoxF function is required downstream and in parallel to the FGF/MAPK/Ets cascade for cell migration. In addition, we demonstrated that targeted expression of a dominant-negative form of FoxF inhibits cell migration but not heart differentiation, resulting in a striking phenotype: a beating heart at an ectopic location within the body cavity of juveniles. Taken together, our results indicate that FoxF is a direct target of FGF signaling and is predominantly involved in the regulation of heart cell migration.

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“…The sequencing of the genome of the urochordate Ciona intestinalis allowed cataloguing of the Fox gene complement of this species, demonstrating FoxC, FoxF, and FoxQ1 genes but no FoxL1 orthologue Yagi et al, 2003). These genes are not closely linked in the C. intestinalis genome (Mazet et al, 2006).…”

Section: Comparison To Invertebrate Chordates and Clustered Fox Gene mentioning

confidence: 99%