Microarray analysis of zygotic expression of transcription factor genes and cell signaling molecule genes in early Ciona intestinalis embryos

Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq

Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. Recently, single-cell RNA-seq has been applied to developing embryos, which offers great potential for finding and characterising genes controlling the course of development along with their expression patterns. In this study, we applied single-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computational search for cell-specific gene expression patterns. We recovered many known expression patterns from our single-cell RNA-seq data and despite extensive previous screens, we succeeded in finding new cell-specific patterns, which we validated by in situ and single-cell qPCR.

Gata is ubiquitously required for the earliest zygotic gene transcription in the ascidian embryo

In ascidian embryos, the earliest transcription from the zygotic genome begins between the 8-cell and 16-cell stages. Gata.a, a maternally expressed Gata transcription factor, activates target genes specifically in the animal hemisphere, whereas the complex of β-catenin and Tcf7 antagonizes the activity of Gata.a and activates target genes specifically in the vegetal hemisphere. Here, we show that genes zygotically expressed at the 16-cell stage have significantly more Gata motifs in their upstream regions. These genes included not only genes with animal hemisphere-specific expression but also genes with vegetal hemisphere-specific expression. On the basis of this finding, we performed knockdown experiments for Gata.a and reporter assays, and found that Gata.a is required for the expression of not only genes with animal hemisphere-specific expression, but also genes with vegetal hemisphere-specific expression. Our data indicated that weak Gata.a activity that cannot induce animal hemisphere-specific expression can allow β-catenin/Tcf7 targets to be expressed in the vegetal cells. Because genes zygotically expressed at the 32-cell stage also had significantly more Gata motifs in their upstream regions, Gata.a function may not be limited to the genes expressed specifically in the animal or vegetal hemispheres at the 16-cell stage, and Gata.a may play an important role in the earliest transcription of the zygotic genome.

Gene regulatory systems that control gene expression in the Ciona embryo

Transcriptional control of gene expression is one of the most important regulatory systems in animal development. Specific gene expression is basically determined by combinatorial regulation mediated by multiple sequence-specific transcription factors. The decoding of animal genomes has provided an opportunity for us to systematically examine gene regulatory networks consisting of successive layers of control of gene expression. It remains to be determined to what extent combinatorial regulation encoded in gene regulatory networks can explain spatial and temporal gene-expression patterns. The ascidian Ciona intestinalis is one of the animals in which the gene regulatory network has been most extensively studied. In this species, most specific gene expression patterns in the embryo can be explained by combinations of upstream regulatory genes encoding transcription factors and signaling molecules. Systematic scrutiny of gene expression patterns and regulatory interactions at the cellular resolution have revealed incomplete parts of the network elucidated so far, and have identified novel regulatory genes and novel regulatory mechanisms.

Transcriptional regulation in the early ectodermal lineage of ascidian embryos

In ascidian embryos, ectodermal tissues derive from blastomeres in the animal hemisphere. The animal hemisphere-specific gene expression is observed as early as the 16-cell stage. Here, we characterized animal hemisphere-specific enhancers of three genes, Ci-ephrin-Ad, Ci-TGFβ-NA1 and Ci-Fz4. Deletion analyses identified minimal essential elements. Although these elements contained multiple GATA sequences, electrophoretic mobility shift assays revealed that only some of them were strong binding sites for the transcription factor Ci-GATAa. On the other hand, the motif-searching software MEME identified an octamer, GA (T/G) AAGGG, shared by these enhancers. In Ci-ephrin-Ad and Ci-TGFβ-NA1, the octamer was GATAAGGG, which strongly bound Ci-GATAa. The 397-bp upstream region of Ci-ephrin-Ad contained two strong Ci-GATAa-binding sites, one of which was the octamer motif. Mutation in the octamer motif, but not the other Ci-GATAa-binding site, severely affected the enhancer activity. The 204-bp upstream region of Ci-TGFβ-NA1 contained four strong Ci-GATAa-binding sites, including the octamer motif. Mutation only in the octamer motif, leaving the other three Ci-GATAa-binding sites intact, abolished the enhancer activity. These results suggest a crucial role for the octamer motif.

Transcriptome dynamics in early embryos of the ascidian, Ciona intestinalis

Maternally provided mRNAs and proteins direct early development and activate the zygotic genome. Using microarrays, we examined the dynamics of transcriptomes during the early development of a basal chordate, Ciona intestinalis. Microarray analysis of unfertilized eggs, as well as 8-, and 16- and 32-cell embryos revealed that nearly half of the genes encoded in the genome were expressed maternally, and that approximately only one-fourth of these genes were expressed at similar levels among eggs obtained from different individuals. Genes encoding proteins involved in protein phosphorylation were enriched in this latter group. More than 90% of maternal RNAs were not reduced before the 16-cell stage when the zygotic developmental program begins. Additionally we obtained gene expression profiles of individual blastomeres from the 8- and 16-cell embryos. On the basis of these profiles, we concluded that the posterior-most localization, which has been reported for over 20 different transcripts, is the only major localization pattern of maternal transcripts. Our data also showed that maternal factors establish only nine distinct patterns of zygotic gene expression at the 16-cell stage. Therefore, one of the main developmental functions of maternally supplied information is to establish these nine distinct expression patterns in the 16-cell embryo. The dynamics of transcriptomes in early-stage embryos provides a foundation for studying how maternal information starts the zygotic program.

A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis

We provide a new oligo-microarray for Ciona intestinalis, based on the NimbleGen 12-plex×135k format. The array represents 106,285 probes, which is more than double the probe number of the currently available 44k microarray. These probes cover 99.2% of the transcripts in the KyotoHoya (KH) models, published in 2008, and they contain 81.1% of the entries in the UniGene database that are not included in the KH models. In this paper, we show that gene expression levels measured by this new 135k microarray are highly correlated with those obtained by the existing 44k microarray for genes common to both arrays. We also investigated gene expression using samples obtained from the ovary and the neural complex of adult C. intestinalis, showing that the expression of tissue-specific genes is consistent with previous reports. Approximately half of the highly expressed genes identified in the 135k microarray are not included in the previous microarray. The high coverage of gene models by this microarray made it possible to identify splicing variants for a given transcript. The 135k microarray is useful in investigating the functions of genes that are not yet well characterized. Detailed information about this 135k microarray is accessible at no charge from supplemental materials, NCBI Gene Expression Omnibus (GEO), and http://marinegenomics.oist.jp.

Mechanism of DNA replication-dependent transcriptional activation of the acetylcholinesterase gene in the Ciona intestinalis embryo

The acetylcholinesterase-encoding gene in the ascidian Ciona intestinalis (Ci-AChE) is expressed in tail muscle cells from the gastrula stage. When the embryo was continuously treated with aphidicolin from the 32-cell stage, Ci-AChE was not expressed even when control embryos reached the tailbud stage. This result suggests that Ci-AChE acquires the competence to be transcribed after passing through a certain number of DNA replication cycles. A lacZ reporter gene containing the 5' flanking region of Ci-AChE was expressed in the tail muscle cells. Aphidicolin treatment from the 32-cell stage affected, but did not completely suppress, the expression of lacZ. A bisulfite sequencing analysis was carried out to examine the methylation status of four regions within the 5' flanking sequence and the first exon. However, all of these regions remained unmethylated from the 16-cell to 110-cell stages. The results suggested that the DNA of the Ci-AChE locus is not responsible for counting the rounds of replication. We examined the expression of the C. intestinalis MyoD (Ci-MyoD), a transcription factor that activates Ci-AChE. Aphidicolin treatment from the 32-cell stage suppressed the expression of Ci-MyoD, even when control embryos reached the gastrula stage. These results suggest that a lack of Ci-MyoD is critical to the suppression of Ci-AChE in aphidicolin-treated embryos.

Early zygotic expression of transcription factors and signal molecules in fully dissociated embryonic cells of Ciona intestinalis: A microarray analysis

Specification of early embryonic cells of animals is established by maternally provided factors and interactions of neighboring cells. The present study addressed a question of autonomous versus non-autonomous specification of embryonic cells by using the Ciona intestinalis embryo, in particular the genetic cascade of zygotic expression of transcription factor genes responsible for notochord specification. To examine this issue, we combined the classic experiment of continuous dissociation of embryonic cells with the modern technique of oligonucleotide-based microarrays. We measured early zygotic expression of 389 core transcription factors genes and 118 major signal molecule genes in embryonic cells that were fully dissociated from the first cleavage. Our results indicated that even if cells are free from contact with neighbors, the major transcription factor genes that have primary roles in embryonic cell specification commence their zygotic expression at the same time as in normal embryos. Dissociation of embryonic cells did not affect extracellular signal-regulated kinases (ERK) activity. Although normal embryos treated with U0126 failed to express Bra and Twist-like-1, dissociated embryonic cells treated with U0126 expressed the genes. These results are discussed in relation to the grade of autonomous versus non-autonomous genetic cascades that are responsible for the specification of early Ciona embryonic cells.

Cell type and function of neurons in the ascidian nervous system

Ascidians, or sea squirts, are primitive chordates, and their tadpole larvae share a basic body plan with vertebrates, including a notochord and a dorsal tubular central nervous system (CNS). The CNS of the ascidian larva is formed through a process similar to vertebrate neurulation, while the ascidian CNS is remarkably simple, consisting of about 100 neurons. Recent identification of genes that are specifically expressed in a particular subtype of neurons has enabled us to reveal neuronal networks at single-cell resolution. Based on the information on neuron subtype-specific genes, different populations of neurons have been visualized by whole-mount in situ hybridization, immunohistochemical staining using specific antibodies, and fluorescence labeling of cell bodies and neurites by a fluorescence protein reporter driven by neuron-specific promoters. Neuronal populations that have been successfully visualized include glutamatergic, cholinergic, gamma-aminobutyric acid/glycinergic, and dopaminergic neurons, which have allowed us to propose functional regionalization of the CNS and a neural circuit for locomotion. Thus, the simple nervous system of the ascidian larva can serve as an attractive model system for studying the development, function, and evolution of the chordate nervous system.

A novel biological role of tachykinins as an up-regulator of oocyte growth: identification of an evolutionary origin of tachykininergic functions in the ovary of the ascidian, Ciona intestinalis

Tachykinins (TKs) and their receptors have been shown to be expressed in the mammalian ovary. However, the biological roles of ovarian TKs have yet to be verified. Ci-TK-I and Ci-TK-R, characterized from the protochordate (ascidian), Ciona intestinalis, are prototypes of vertebrate TKs and their receptors. In the present study, we show a novel biological function of TKs as an inducible factor for oocyte growth using C. intestinalis as a model organism. Immunostaining demonstrated the specific expression of Ci-TK-R in test cells residing in oocytes at the vitellogenic stage. DNA microarray and real-time PCR revealed that Ci-TK-I induced gene expression of several proteases, including cathepsin D, chymotrypsin, and carboxy-peptidase B1, in the ovary. The enzymatic activities of these proteases in the ovary were also shown to be enhanced by Ci-TK-I. Of particular significance is that the treatment of Ciona oocytes with Ci-TK-I resulted in progression of growth from the vitellogenic stage to the post-vitellogenic stage. The Ci-TK-I-induced oocyte growth was blocked by a TK antagonist or by protease inhibitors. These results led to the conclusion that Ci-TK-I enhances growth of the vitellogenic oocytes via up-regulation of gene expression and enzymatic activities of the proteases. This is the first clarification of the biological roles of TKs in the ovary and the underlying essential molecular mechanism. Furthermore, considering the phylogenetic position of ascidians as basal chordates, we suggest that the novel TK-regulated oocyte growth is an "evolutionary origin" of the tachykininergic functions in the ovary.

Effects of 5-aza-2'-deoxycytidine on the gene expression profile during embryogenesis of the Ascidian ciona intestinalis: a microarray analysis

DNA methylation is an important epigenetic factor that participates in silencing genes. Genomic approaches to studying DNA methylation promise to be particularly fruitful, since DNA methylation is involved in global control of gene expression in many organisms. With its draft genome completed and a large quantity of available cDNA data, Ciona intestinalis is newly emerging as an invaluable model organism for investigating genome-wide gene expression and function. Here we examine the effects of 5-aza-2'-deoxycytidine (5-aza-CdR), a chemical that blocks CpG methylation, on the gene expression profile of early C. intestinalis embryos, using oligonucleotide-based microarray analysis. Embryos treated with 5-aza-CdR show delayed gastrulation and are developmentally arrested at the neurula stage. They subsequently lose cellular adhesion and finally die. Apoptosis was not detected in these embryos by TUNEL staining at 12 h, indicating that the defects observed did not result from 5-aza-CdR-induced apoptosis. Gene expression profiles of 12-h-old 5-aza-CdR-treated embryos compared to wild-type revealed 91 upregulated genes and 168 downregulated genes. Although nearly half of these encoded proteins with unknown functions, several encoded cell-signaling molecules and transcription factors. In addition, genes associated with the stress response and cell defense were upregulated, whereas genes involved in cell adhesion were downregulated.