Gene expression profiles in Ciona intestinalis cleavage-stage embryos

Expression of Raldh2, Cyp26 and Hox-1 in normal and retinoic acid-treated Ciona intestinalis embryos

Spatially regulated synthesis and degradation of retinoic acid (RA) organize embryonic pattern formation in vertebrate embryos. Here, we show expression pattern of genes encoding Ciona intestinalis homologs of the retinaldehyde dehydrogenase, RALDH2, and the cytochrome P450 RA-degrading enzyme, CYP26, in normal and RA-treated embryos. The Ciona homolog of Raldh2, Ci-Raldh2, was expressed in a few muscle-lineage blastomeres in the middle gastrula. Strong expression was then restricted to the anterior-most three muscle cells on each side of the tailbud embryo. The Ciona homolog of Cyp26, Ci-Cyp26, was expressed in the presumptive brain cells in the middle gastrula. The expression was then upregulated in the neck region. The posterior end of the tail was also weakly stained. Non-overlapping expression domains of Ci-Raldh2 and Ci-Cyp26 look similar to those in vertebrates, although the expression of both genes was restricted to a small number of cells in Ciona embryos. RA upregulated Ci-Cyp26 expression and slightly downregulated Ci-Raldh2 expression in the tailbud embryo. We also show expression pattern of a Hox-1 ortholog (CiHox-1) in the Ciona embryo. CiHox-1 was expressed in two separated regions of the nerve cord and neck epidermis at the neurula stage. Expression pattern of these three genes are essentially similar to that in vertebrates.

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

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.

Large scale EST analyses in Ciona intestinalis: its application as Northern blot analyses

We have conducted large-scale EST analyses of transcripts expressed in the basal chordate Ciona intestinalis. The cDNA libraries examined were from fertilized eggs, cleaving embryos, gastrulae/neurulae, tailbud embryos, larvae and whole young adults, and the gonad (ovary and testis), endostyle, neural complex, heart, and blood cells of the adult. Because the libraries were not normalized or amplified, the occurrence of cDNA clones or EST counts in each library may reflect the quantity of transcripts of the corresponding genes. Thus, comparison of the EST counts of a certain gene at the six developmental stages may reflect the temporal expression pattern of the gene, while the comparison of EST counts in different tissues of the adult may reflect the spatial expression pattern of the gene. Here we present evidence that this is the case, and that the EST count can therefore be used like "Northern blot analysis" of Ciona genes.

Hemocytes of Ciona intestinalis express multiple genes involved in innate immune host defense

Ascidians, which are classified as urochordata, appear to employ a primitive system of host defense that is considered to be a prototype of vertebrate innate immunity. We performed a cDNA/EST study to identify the genes expressed in the hemocytes of Ciona intestinalis. We obtained 3357 one-path reads that were then grouped into 1889 independent clusters. Although two thirds of the clusters could not be assigned to any particular gene, the remaining 530 clusters had significant homology to genes with known function. Of these, 62 clusters appeared to be related to host defense mechanisms. These include transcripts whose products are probably involved in cytotoxicity, detoxification, inflammation, and apoptosis. As expected, elements of acquired immunity were not detected. Thus, Ciona hemocytes appear to express a number of host defense-related genes involved in innate immune mechanisms.

Retinoic acid affects gene expression and morphogenesis without upregulating the retinoic acid receptor in the ascidian Ciona intestinalis

Many chordate-specific morphological features develop depending on retinoic acid (RA). We isolated cDNA clones encoding a retinoic acid receptor (CiRAR) and a retinoid X receptor (CiRXR) in the ascidian Ciona intestinalis. CiRAR mRNA was detected in the anterior ectoderm and endoderm during gastrulation. The expression persists in the head endoderm and two discrete regions of the nerve cord in the tailbud embryo. CiRXR mRNA was ubiquitously expressed. RA affected closure of the neural tube and formation of the adhesive papillae. However, no obvious upregulation in CiRAR expression was observed. Expression of some, but not all, of the neural and papilla-specific genes was reduced in the RA-treated embryo. These results suggest limited roles of CiRAR in ascidian embryos.

Early embryonic expression ofFGF4/6/9gene and its role in the induction of mesenchyme and notochord inCiona savignyiembryos

In early Ciona savignyi embryos, nuclear localization of β-catenin is the first step of endodermal cell specification, and triggers the activation of various target genes. A cDNA for Cs-FGF4/6/9, a gene activated downstream of β-catenin signaling, was isolated and shown to encode an FGF protein with features of both FGF4/6 and FGF9/20. The early embryonic expression of Cs-FGF4/6/9 was transient and the transcript was seen in endodermal cells at the 16- and 32-cell stages, in notochord and muscle cells at the 64-cell stage, and in nerve cord and muscle cells at the 110-cell stage; the gene was then expressed again in cells of the nervous system after neurulation. When the gene function was suppressed with a specific antisense morpholino oligo, the differentiation of mesenchyme cells was completely blocked, and the fate of presumptive mesenchyme cells appeared to change into that of muscle cells. The inhibition of mesenchyme differentiation was abrogated by coinjection of the morpholino oligo and synthetic Cs-FGF4/6/9 mRNA. Downregulation of β-catenin nuclear localization resulted in the absence of mesenchyme cell differentiation due to failure of the formation of signal-producing endodermal cells. Injection of synthetic Cs-FGF4/6/9 mRNA in β-catenin-downregulated embryos evoked mesenchyme cell differentiation. These results strongly suggest that Cs-FGF4/6/9 produced by endodermal cells acts an inductive signal for the differentiation of mesenchyme cells. On the other hand, the role of Cs-FGF4/6/9 in the induction of notochord cells is partial; the initial process of the induction was inhibited by Cs-FGF4/6/9 morpholino oligo, but notochord-specific genes were expressed later to form a partial notochord.

Gene expression profiles in tadpole larvae of Ciona intestinalis

A set of 12,779 expressed sequence tags (ESTs), both the 5'-most and 3'-most ends, derived from Ciona intestinalis tadpole larvae was categorized into 3521 independent clusters, from which 1013 clusters corresponding to 9424 clones were randomly selected to analyze genetic information and gene expression profiles. When compared with sequences in databases, 545 of the clusters showed significant matches (P < E-15) with reported proteins, while 153 showed matches with putative proteins for which there is not enough information to categorize their function, and 315 had no significant sequence similarities to known proteins. Sequence-similarity analyses of the 545 clusters in relation to the biological functions demonstrated that 407 of them have functions that many kinds of cells use, 104 are associated with cell-cell communication, and 34 are transcription factors or other gene-regulatory proteins. Sequence prevalence distribution analysis demonstrated that more than one-half of the mRNAs are rare mRNAs. All of the 1013 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profile in the tadpole larva. A total of 361 clusters showed expression specific to a certain tissue or organ: 96 showed epidermis-specific expression, 60 were specific to the nervous system, 108 to endoderm, 34 to mesenchyme, 5 to trunk lateral cells, 4 to trunk ventral cells, 23 to notochord, 28 to muscle, and 3 to siphon rudiments. In addition, 190 clusters showed expression in multiple tissues. Moreover, nervous system-specific genes showed intriguing expression patterns dependent on the cluster. The present study highlights a broad spectrum of genes that are used in the formation of one of the most primitive chordate body plans as well as for the function of various types of tissue and organ and also provides molecular markers for individual tissues and organs constituting the Ciona larva.