Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development

Transcriptomes of a fast-developing chordate uncover drastic differences in transcription factors and localized maternal RNA composition compared with those of ascidians

The larvacean Oikopleura dioica is a fast-developing chordate because of its small number of cells (∼4500 in juveniles) and rapid development to complete morphogenesis by 10 h after fertilization. Strikingly, most of its blastomeres are restricted to give rise to a single cell-type by the 32-cell stage of embryogenesis, unlike cell fate determination at the 110-cell stage in ascidians. In this study, RNA-sequencing (RNA-seq) revealed non-canonical properties of O. dioica: (1) an initial zygotic gene expression of 950 genes at the 16- to 32-cell stage; (2) 25 transcription factors (TFs) are expressed in the 32-cell stage (fewer than half of the TFs underlying gene regulatory networks in ascidian embryogenesis were lost or not expressed); (3) five maternal mRNAs localized in the vegetal-posterior blastomeres in animal and vegetal hemispheres; and (4) three maternal mRNAs localized in the small vegetal pole region of unfertilized eggs. These observations indicate that this fast-developing chordate lacks the first phase of development in ascidians: fertilization-driven ooplasmic movements that drive postplasmic RNAs toward the vegetal pole. These data have been deposited in ANISEED (https://www.aniseed.fr/) as transcriptome resources.

H3K27me3 suppresses sister-lineage somatic gene expression in late embryonic germline cells of the ascidian, Halocynthia roretzi

Protection of the germline from somatic differentiation programs is crucial for germ cell development. In many animals, whose germline development relies on the maternally inherited germ plasm, such protection in particular at early stages of embryogenesis is achieved by maternally localized global transcriptional repressors, such as PIE-1 of Caenorhabditis elegans, Pgc of Drosophila melanogaster and Pem of ascidians. However, zygotic gene expression starts in later germline cells eventually and mechanisms by which somatic gene expression is selectively kept under repression in the transcriptionally active cells are poorly understood. By using the ascidian species Halocynthia roretzi, we found that H3K27me3, a repressive transcription-related chromatin mark, became enriched in germline cells starting at the 64-cell stage when Pem protein level and its contribution to transcriptional repression decrease. Interestingly, inhibition of H3K27me3 together with Pem knockdown resulted in ectopic expression in germline cells of muscle developmental genes Muscle actin (MA4) and Snail, and of Clone 22 (which is expressed in all somatic but not germline cells), but not of other tissue-specific genes such as the notochord gene Brachyury, the nerve cord marker ETR-1 and a heart precursor gene Mesp, at the 110-cell stage. Importantly, these ectopically expressed genes are normally expressed in the germline sister cells (B7.5), the last somatic lineage separated from the germline. Also, the ectopic expression of MA4 was dependent on a maternally localized muscle determinant Macho-1. Taken together, we propose that H3K27me3 may be responsible for selective transcriptional repression for somatic genes in later germline cells in Halocynthia embryos and that the preferential repression of germline sister-lineage genes may be related to the mechanism of germline segregation in ascidian embryos, where the germline is segregated progressively by successive asymmetric cell divisions during cell cleavage stages. Together with findings from C. elegans and D. melanogaster, our data for this urochordate animal support the proposal for a mechanism, conserved widely throughout the animal kingdom, where germline transcriptional repression is mediated initially by maternally localized factors and subsequently by a chromatin-based mechanism.

Wavy movements of epidermis monocilia drive the neurula rotation that determines left-right asymmetry in ascidian embryos

Tadpole larvae of the ascidian, Halocynthia roretzi, show morphological left-right asymmetry in the brain structures and the orientation of tail bending within the vitelline membrane. Neurula embryos rotate along the anterior-posterior axis in a counterclockwise direction, and then this rotation stops when the left side of the embryo is oriented downwards. Contact of the left-side epidermis with the vitelline membrane promotes nodal gene expression in the left-side epidermis. This is a novel mechanism in which rotation of whole embryos provides the initial cue for breaking left-right symmetry. Here we show that epidermal monocilia, which appear at the neurula rotation stage, generate the driving force for rotation. A ciliary protein, Arl13b, fused with Venus YFP was used for live imaging of ciliary movements. Although overexpression of wild-type Arl13b fusion protein resulted in aberrant movements of the cilia and abrogation of neurula rotation, mutant Arl13b fusion protein, in which the GTPase and coiled-coil domains were removed, did not affect the normal ciliary movements and neurula rotation. Epidermis cilia moved in a wavy and serpentine way like sperm flagella but not in a rotational way or beating way with effective stroke and recovery stroke. They moved very slowly, at 1/7 Hz, consistent with the low angular velocity of neurula rotation (ca. 43°/min). The tips of most cilia pointed in the opposite direction of embryonic rotation. Similar motility was also observed in Ciona robusta embryos. When embryos were treated with a dynein inhibitor, Ciliobrevin D, both ciliary movements and neurula rotation were abrogated, showing that ciliary movements drive neurula rotation in Halocynthia. The drug also inhibited Ciona neurula rotation. Our observations suggest that the driving force of rotation is generated using the vitelline membrane as a substrate but not by making a water current around the embryo. It is of evolutionary interest that ascidians use ciliary movements to break embryonic left-right symmetry, like in many vertebrates. Meanwhile, ascidian embryos rotate as a whole, similar to embryos of non-vertebrate deuterostomes, such as echinoderm, hemichordate, and amphioxus, while swimming.

Control of Pem protein level by localized maternal factors for transcriptional regulation in the germline of the ascidian, Halocynthia roretzi

Localized maternal mRNAs play important roles in embryogenesis, e.g. the establishment of embryonic axes and the developmental cell fate specification, in various animal species. In ascidians, a group of maternal mRNAs, called postplasmic/PEM RNAs, is localized to a subcellular structure, called the Centrosome-Attracting Body (CAB), which contains the ascidian germ plasm, and is inherited by the germline cells during embryogenesis. Posterior end mark (Pem), a postplasmic/PEM RNAs member, represses somatic gene expression in the germline during cleavage stages by inhibition of RNA polymerase II activity. However, the functions of other postplasmic/ PEM RNAs members in germline formation are largely unknown. In this study, we analyzed the functions of two postplasmic/PEM RNAs, Popk-1 and Zf-1, in transcriptional regulation in the germline cells. We show that Popk-1 contributes to transcriptional quiescence by controlling the size of the CAB and amount of Pem protein translated at the CAB. Our studies also indicated that zygotic expression of a germline gene starts around the onset of gastrulation and that the decrease of Pem protein is necessary and sufficient for the zygotic germline gene expression. Finally, further studies showed that the decrease of the Pem protein level is facilitated by Zf-1. Taken together, we propose that postplasmic/PEM RNAs such as Popk-1 and Zf-1 control the protein level of the transcriptional repressor Pem and regulate its transcriptional state in the ascidian germline.

DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica

The maternal contribution to the oocyte cytoplasm plays an important role during embryogenesis because it is involved in early cell fate specification and embryonic axis establishment. However, screening projects targeting maternal factors have only been conducted in a limited number of animal models, such as nematodes, fruit flies, and zebrafish, while few maternal genes have been analysed because of difficulties encountered in inhibiting gene products already expressed in the ovaries. Therefore, simple and efficient methods for large-scale maternal screening are necessary. The appendicularian Oikopleura dioica is a planktonic tunicate member of the chordates. Gonadal microinjection and a novel gene knockdown method, DNA interference (DNAi), have been developed for use in this animal with the aim of inhibiting gene functions during oogenesis within the gonad. In this study, we adapted these methods for large-scale maternal factor screening, and observed malformation phenotypes related to some maternal factors. Approximately 2000 (56.9%) ovary-enriched gene products were screened, of which the knockdown of seven encoding genes resulted in various abnormalities during embryonic development. Most of these were related to microtubules and cell adhesion-related proteins. We conclude that DNAi is a potentially powerful screening tool for the identification of novel maternal factors in chordates.

Asymmetric and Unequal Cell Divisions in Ascidian Embryos

Asymmetric cell division during embryogenesis contributes to cell diversity by generating daughter cells that adopt distinct developmental fates. In this chapter, we summarize current knowledge of three examples of asymmetric cell division occurring in ascidian early embryos: (1) Three successive cell divisions that are asymmetric in terms of cell fate and unequal in cell size in the germline lineage at the embryo posterior pole. A subcellular structure, the centrosome-attracting body (CAB), and maternal PEM mRNAs localized within it control both the positioning of the cell division planes and segregation of the germ cell fates. (2) Asymmetric cell divisions involving endoderm and mesoderm germ layer separation. Asymmetric partitioning of zygotically expressed mRNA for Not, a homeodomain transcription factor, promotes the mesoderm fate and suppresses the endoderm fate. This asymmetric partitioning is mediated by transient nuclear migration toward the mesodermal pole of the mother cell, where the mRNA is delivered. In this case, there is no special regulation of cleavage plane orientation. (3) Asymmetric cell divisions in the marginal region of the vegetal hemisphere. The directed extracellular FGF and ephrin signals polarize the mother cells, inducing distinct fates in a pair of daughter cells (nerve versus notochord and mesenchyme versus muscle). The directions of cell division are regulated and oriented but independently of FGF and ephrin signaling. In these examples, polarization of the mother cells is facilitated by localized maternal factors, by delivery of transcripts from the nucleus to one pole of each cell, and by directed extracellular signals. Two cellular processes-asymmetric fate allocation and orientation of the cell division plane-are coupled by a single factor in the first example, but these processes are regulated independently in the third example. Thus, various modes of asymmetric cell division operate even at the early developmental stages in this single type of organism.

Regulation of the number of cell division rounds by tissue-specific transcription factors and Cdk inhibitor during ascidian embryogenesis

Mechanisms that regulate the number of cell division rounds during embryogenesis have remained largely elusive. To investigate this issue, we used the ascidian, which develops into a tadpole larva with a small number of cells. The embryonic cells divide 11.45 times on average from fertilization to hatching. The number of cell division rounds varies depending on embryonic lineages. Notochord and muscle consist of large postmitotic cells and stop dividing early in developing embryos. Here we show that conversion of mesenchyme to muscle cell fates by inhibition of inductive FGF signaling or mis-expression of a muscle-specific key transcription factor for muscle differentiation, Tbx6, changed the number of cell divisions in accordance with the altered fate. Tbx6 likely activates a putative mechanism to halt cell division at a specific stage. However, precocious expression of Tbx6 has no effect on progression of the developmental clock itself. Zygotic expression of a cyclin-dependent kinase inhibitor, CKI-b, is initiated in muscle and then in notochord precursors. CKI-b is possibly downstream of tissue-specific key transcription factors of notochord and muscle. In the two distinct muscle lineages, postmitotic muscle cells are generated after 9 and 8 rounds of cell division depending on lineage, but the final cell divisions occur at a similar developmental stage. CKI-b gene expression starts simultaneously in both muscle lineages at the 110-cell stage, suggesting that CKI-b protein accumulation halts cell division at a similar stage. The difference in the number of cell divisions would be due to the cumulative difference in cell cycle length. These results suggest that muscle cells do not count the number of cell division rounds, and that accumulation of CKI-b protein triggered by tissue-specific key transcription factors after cell fate determination might act as a kind of timer that measures elapsed time before cell division termination.

The functions and regulatory principles of mRNA intracellular trafficking

The subcellular localization of RNA molecules is a key step in the control of gene expression that impacts a broad array of biological processes in different organisms and cell types. Like other aspects of posttranscriptional gene regulation discussed in this collection of reviews, the intracellular trafficking of mRNAs is modulated by a complex regulatory code implicating specific cis-regulatory elements, RNA-binding proteins, and cofactors that function combinatorially to dictate precise localization mechanisms. In this review, we first discuss the functional benefits of transcript localization, the regulatory principles involved, and specific molecular mechanisms that have been described for a few well-characterized mRNAs. We also overview some of the emerging genomic and imaging technologies that have provided significant insights into this layer of gene regulation. Finally, we highlight examples of human diseases where defective transcript localization has been documented.

Cytosolic subunits of ATP synthase are localized to the cortical endoplasmic reticulum-rich domain of the ascidian egg myoplasm

Previously, we revealed that p58, one of the ascidian maternal factors, is identical to the alpha-subunit of F1-ATP synthase (ATPα), a protein complex of the inner mitochondrial membrane. In the current study, we used immunological probes for ascidian mitochondria components to show that the ascidian ATPα is ectopically localized to the cytosol. Virtually all mitochondrial components were localized to the mitochondria-rich myoplasm. However, in detail, ATP synthase subunits and the matrix proteins showed different localization patterns. At least at the crescent stage, transmission electron microscopy (TEM) distinguished the mitochondria-less, endoplasmic reticulum (ER)-rich cortical region and the mitochondria-rich internal region. ATPα was enriched in the cortical region and MnSOD was limited to the internal region. Using subcellular fractionation, although all of the mitochondria components were highly enriched in the mitochondria-enriched fraction, a considerable amount of ATPα and F1-ATP synthase beta-subunit (ATPβ) were recovered in the insoluble cytoplasmic fraction. Even under these conditions, F1-ATP synthase gamma-subunit (ATPγ) and F0-ATP synthase subunit b (ATPb) were not recovered in the insoluble cytoplasmic fraction. This result strongly supports the exomitochondrial localization of both ATPα and ATPβ. In addition, the detergent extraction of eggs supports the idea that these cytosolic ATP synthase subunits are associated with the egg cytoskeleton. These results suggest that the subunits of ATP synthase might play dual roles at different subcellular compartments during early development.

Cytoplasmic localization and reorganization in ascidian eggs: role of postplasmic/PEM RNAs in axis formation and fate determination

Localization of maternal molecules in eggs and embryos and cytoplasmic movements to relocalize them are fundamental for the orderly cellular and genetic processes during early embryogenesis. Ascidian embryos have been known as 'mosaic eggs' because of their autonomous differentiation abilities based on localized cell fate determinants. This review gives a historical overview of the concept of cytoplasmic localization, and then explains the key features such as ooplasmic movements and cell lineages that are essential to grasp the process of ascidian development mediated by localized determinant activities. These activities are partly executed by localized molecules named postplasmic/PEM RNAs, originating from approximately 50 genes, of which the muscle determinant, macho-1, is an example. The cortical domain containing these RNAs is relocalized to the posterior-vegetal region of the egg by cytoskeletal movements after fertilization, and plays crucial roles in axis formation and cell fate determination. The cortical domain contains endoplasmic reticulum and characteristic granules, and gives rise to a subcellular structure called the centrosome-attracting body (CAB), in which postplasmic/PEM RNAs are highly concentrated. The CAB is responsible for a series of unequal partitionings of the posterior-vegetal cytoplasmic domain and the postplasmic/PEM RNAs at the posterior pole during cleavage. Some components of this domain, which is rich in granules, are eventually inherited by prospective germline cells with particular postplasmic/PEM RNAs such as vasa. The postplasmic/PEM RNAs are classified into two groups according to their final cellular destinations and localization pathways. Localization of these RNAs is regulated by specific nucleotide sequences in the 3' untranslated regions (3'UTRs).

Identification of a novel vanadium-binding protein by EST analysis on the most vanadium-rich ascidian, Ascidia gemmata

Ascidians are known to accumulate extremely high levels of vanadium in their blood cells (up to 350 mM). The branchial sac and the intestine are thought to be the first tissues to contact the outer environment and absorb vanadium ions. The concentration of vanadium in the branchial sac and the intestine of the most vanadium-rich ascidian Ascidia gemmata were determined to be 32.4 and 11.9 mM, respectively. Using an expressed sequence tag (EST) analysis of a cDNA library from the intestine of A. gemmata, we determined 960 ESTs and found 55 clones of metal-related gene orthologs, 6 redox-related orthologs, and 18 membrane transporter orthologs. Among them, two genes, which exhibited significant similarity to the vanadium-binding proteins of other vanadium-rich ascidian species, were designated AgVanabin1 and AgVanabin2. Immobilized metal ion affinity chromatography revealed that recombinant AgVanabin1 bound to metal ions with an increasing affinity for Cu(II) > Zn(II) > Co(II) and AgVanabin2 bound to metal ions with an increasing affinity for Cu(II) > Fe(III) > V(IV). To examine the use of AgVanabins for a metal absorption system, we constructed Escherichia coli strains that expressed AgVanabin1 or AgVanabin2 fused to maltose-binding protein and secreted into the periplasmic space. We found that the strain expressing AgVanabin2 accumulated about 13.5 times more Cu(II) ions than the control TB1 strain. Significant accumulation of vanadium was also observed in the AgVanabin2-expressing strain as seen by a 1.5-fold increase.

A maternal factor unique to ascidians silences the germline via binding to P-TEFb and RNAP II regulation

Suppression of zygotic transcription in early embryonic germline cells is tightly linked to their separation from the somatic lineage. Many invertebrate embryos utilize localized maternal factors that are successively inherited by the germline cells for silencing the germline. Germline quiescence has also been associated with the underphosphorylation of Ser2 of the C-terminal domain (CTD-Ser2) of RNA polymerase II [1-3]. Here, using the ascidian Halocynthia roretzi, we identified a first deuterostome example of a maternally localized factor, posterior end mark (PEM), which globally represses germline transcription. PEM knockdown resulted in ectopic transcription and ectopic phosphorylation of CTD-Ser2 in the germline. Overexpression of PEM abolished all transcription and led to the underphosphorylation of CTD-Ser2 in the somatic cells. PEM protein was reiteratively detected in the nucleus of the germline cells and coimmunoprecipitated with CDK9, a component of posterior transcription elongation factor b (P-TEFb). These results suggest that nonhomologous proteins, PEM and Pgc of Drosophila [3-5] and PIE-1 of C. elegans [1, 6, 7], repress germline gene expression through analogous functions: by keeping CTD-Ser2 underphosphorylated through binding to the P-TEFb complex. The present study is an interesting example of evolutionary constraint on how a mechanism of germline silencing can evolve in diverse animals.

Polo-like kinase 1 is required for localization of Posterior End Mark protein to the centrosome-attracting body and unequal cleavages in ascidian embryos

In ascidian embryos, the posterior-localized maternal factor Posterior End Mark (PEM) is responsible for patterning embryos along the anterior-posterior axis with regard to both cleavage pattern involving unequal cell divisions and gene expression. Although PEM plays important roles in embryogenesis, its mechanism of action is still unclear because PEM has no known functional domain. In the present study, we explored the candidate of PEM partner proteins in Halocynthia roretzi using yeast two-hybrid screening. We isolated a homologue of Polo-like kinase 1 (Plk1), a key regulator of cell division and highly conserved in eukaryotes, as the first potential binding partner of PEM. We biochemically confirmed that interaction occurred between the Plk1 and PEM proteins. Immunostaining showed that Plk1 protein concentrates in the centrosome-attracting body (CAB) at the posterior pole, where PEM protein is also localized. The CAB is a subcellular structure that plays an important role in generating the posterior cleavage pattern. Plk1 localization to the CAB was dependent on the cell cycle phases during unequal cleavage. Inhibition of Plk1 with specific drugs resulted in failure of the nucleus to migrate towards the posterior pole and formation of a microtubule bundle between the CAB and a centrosome, similarly to inhibition of PEM function, suggesting that both proteins are involved in the same process of unequal cleavages. This interrupted nuclear migration was rescued by overexpression of PEM. In Plk1-inhibited embryos, the localization of PEM protein to the CAB was impaired, indicating that Plk1 is required for appropriate localization of PEM.

Differential localization of mRNAs during early development in the mollusc, Crepidula fornicata

Certain mRNAs have been shown to be segregated in different cells in various metazoan embryos. These events represent aspects of autonomous mechanisms that establish particular embryonic cell fates and axial properties associated with asymmetric cell divisions. The spiralian lophotrochozoans (which include molluscs, annelids, nemerteans, gnathostomulids, dicyemid mesozoans, entoprocts, and platyhelminthes) exhibit a highly conserved pattern of early development that involves stereotypical, asymmetric cell divisions (termed "spiral cleavage"). Recently, it was demonstrated that various mRNAs are dynamically localized to the centrosomes in specific cells during early development in the gastropod mollusc, Ilyanassa obsoleta. During subsequent cell divisions, these messages become segregated in particular daughter cells, and it has been proposed that these events distinguish the developmental potential of these cells within the early embryo of I. obsoleta. The molecular mechanisms underlying these events, however, are still unknown. Here we show for the first time in another spiralian lophotrochozoan (the gastropod Crepidula fornicata) that similar patterns of mRNA localization take place during early development. To characterize the transcriptome of early development, and identify candidate genes for the expression analyses, high-throughput sequencing was carried out, via GS FLX Titanium 454 pyrosequencing. The annotated sequences have been made available as a resource for the scientific community (www.life.illinoi.edu/henry/crepidula_databases.html). Presumably, specific proteins associated with centrosomes may be important for these mRNA localization events. In silico sequence comparisons with known centriolar/centrosomal, ciliary/basal body proteomes shows that a large number of those proteins are represented in the collection of expressed sequence tags of C. fornicata annotated in this study. These data should be useful for future studies of the role of specific mRNAs in controlling cell fate and axial specification in the spiralian Lophotrochozoa, and for dissecting the underlying molecular mechanisms that accomplish these events.

Widespread RNA segregation in a spiralian embryo

Asymmetric cell divisions are a crucial mode of cell fate specification in multicellular organisms, but their relative contribution to early embryonic patterning varies among taxa. In the embryo of the mollusc Ilyanassa, most of the early cell divisions are overtly asymmetric. During Ilyanassa early cleavage, mRNAs for several conserved developmental patterning genes localize to interphase centrosomes, and then during division they move to a portion of the cortex that will be inherited by one daughter cell. Here we report an unbiased survey of RNA localization in the Ilyanassa embryo, and examine the overall patterns of centrosomal localization during early development. We find that 3-4% of RNAs are specifically localized to centrosomes during early development, and the remainder are either ubiquitously distributed throughout the cytoplasm or weakly enriched on centrosomes compared with levels in the cytoplasm. We observe centrosomal localization of RNAs in all cells from zygote through the fifth cleavage cycle, and asymmetric RNA segregation in all divisions after the four-cell stage. Remarkably, each specifically localized message is found on centrosomes in a unique subset of cells during early cleavages, and most are found in unique sets of cells at the 24-cell stage. Several specifically localized RNAs are homologous to developmental regulatory proteins in other embryos. These results demonstrate that the mechanisms of localization and segregation are extraordinarily intricate in this system, and suggest that these events are involved in cell fate specification across all lineages in the early Ilyanassa embryo. We propose that greater reliance on segregation of determinants in early cleavage increases constraint on cleavage patterns in molluscs and other spiralian groups.

Postplasmic/PEM RNAs: a class of localized maternal mRNAs with multiple roles in cell polarity and development in ascidian embryos

Ascidian is a good model to understand the cellular and molecular mechanisms responsible for mRNA localization with the discovery of a large family of localized maternal mRNAs, called postplasmic/PEM RNAs, which includes more than 40 members in three different ascidian species (Halocynthia roretzi, Ciona intestinalis, and C. savignyi). Among these mRNAs, two types (Type I and Type II) have been identified and show two different localization patterns from fertilization to the eight-cell stage. At the eight-cell stage, both types concentrate to a macromolecular cortical structure called CAB (for Centrosome Attracting Body) in the posterior-vegetal B4.1 blastomeres. The CAB is responsible for unequal cleavages and the partitioning of postplasmic/PEM RNAs at the posterior pole of embryos during cleavage stages. It has also been suggested that the CAB region could contain putative germ granules. In this review, we discuss recent data obtained on the distribution of Type I postplasmic/PEM RNAs from oogenesis to late development, in relation to their localization and translational control. We have first regrouped localization patterns for Type I and Type II into a comparative diagram and included all important definitions in the field. We also have made an exhaustive classification of their embryonic expression profiles (Type I or Type II), and analyzed their functions after knockdown and/or overexpression experiments and the role of the 3'-untranslated region (3'UTR) controlling both their localization and translation. Finally, we propose a speculative model integrating recent data, and we also discuss the relationship between postplasmic/PEM RNAs, posterior specification, and germ cell formation in ascidians.

Localized PEM mRNA and protein are involved in cleavage-plane orientation and unequal cell divisions in ascidians

BACKGROUND

Orientation and positioning of the cell division plane are essential for generation of invariant cleavage patterns and for unequal cell divisions during development. Precise control of the division plane is important for appropriate partitioning of localized factors, spatial arrangement of cells for proper intercellular interactions, and size control of daughter cells. Ascidian embryos show complex but invariant cleavage patterns mainly due to three rounds of unequal cleavage at the posterior pole.

RESULTS

The ascidian embryo is an emerging model for studies of developmental and cellular processes. The maternal Posterior End Mark (PEM) mRNA is localized within the egg and embryo to the posterior region. PEM is a novel protein that has no known domain. Immunostaining showed that the protein is also present in the posterior cortex and the in centrosome-attracting body (CAB) and that the localization is extraction-resistant. Here we show that PEM of Halocynthia roretzi is required for correct orientation of early-cleavage planes and subsequent unequal cell divisions because it repeatedly pulls a centrosome toward the posterior cortex and the CAB, respectively, where PEM mRNA and protein are localized. When PEM activity is suppressed, formation of the microtubule bundle linking the centrosome and the posterior cortex did not occur. PEM possibly plays a role in anchoring microtubule ends to the cortex. In our model of orientation of the early-cleavage planes, we also amend the allocation of the conventional animal-vegetal axis in ascidian embryos, and discuss how the newly proposed A-V axis provides the rationale for various developmental events and the fate map of this animal.

CONCLUSIONS

The complex cleavage pattern in ascidian embryos can be explained by a simple rule of centrosome attraction mediated by localized PEM activity. PEM is the first gene identified in ascidians that is required for multiple spindle-positioning events.

Nuclear accumulation of β-catenin and transcription of downstream genes are regulated by zygotic Wnt5α and maternal Dsh in ascidian embryos

Nuclear beta-catenin plays crucial roles in the establishment of the embryonic axis and formation of mesendoderm tissues in ascidians and other animals. However, the cue responsible for nuclear accumulation of beta-catenin in the vegetal hemisphere is still unknown in ascidians. Here, we investigated the roles of Wnt5alpha and Dsh in the nuclear accumulation of beta-catenin and activation of its downstream genes in the ascidian Halocynthia roretzi. Wnt5alpha knockdown embryos lost nuclear accumulation of beta-catenin at the 64-cell stage but not at the 32-cell stage, and expression of Hr-lim, one of the targets of beta-catenin, was impaired in the anterior region of the embryo. Zygotic Wnt5alpha expression in the anterior-vegetal blastomeres was primarily responsible for these defects. Dsh knockdown showed no effect on nuclear localization of beta-catenin, but inhibited Hr-lim expression in the posterior region. These results suggest that maintenance of nuclear Hr-beta-catenin after the 64-cell stage is regulated by zygotic Hr-Wnt5alpha, and that expression of its target genes is modulated by both Hr-Wnt5alpha and Hr-Dsh. Our results also highlight the importance of nuclear accumulation of beta-catenin up to the 32-cell stage through a still unclarified mechanism.

From oocyte to 16-cell stage: Cytoplasmic and cortical reorganizations that pattern the ascidian embryo

The dorsoventral and anteroposterior axes of the ascidian embryo are defined before first cleavage by means of a series of reorganizations that reposition cytoplasmic and cortical domains established during oogenesis. These domains situated in the periphery of the oocyte contain developmental determinants and a population of maternal postplasmic/PEM RNAs. One of these RNAs (macho-1) is a determinant for the muscle cells of the tadpole embryo. Oocytes acquire a primary animal-vegetal (a-v) axis during meiotic maturation, when a subcortical mitochondria-rich domain (myoplasm) and a domain rich in cortical endoplasmic reticulum (cER) and maternal postplasmic/PEM RNAs (cER-mRNA domain) become polarized and asymmetrically enriched in the vegetal hemisphere. Fertilization at metaphase of meiosis I initiates a series of dramatic cytoplasmic and cortical reorganizations of the zygote, which occur in two major phases. The first major phase depends on sperm entry which triggers a calcium wave leading in turn to an actomyosin-driven contraction wave. The contraction concentrates the cER-mRNA domain and myoplasm in and around a vegetal/contraction pole. The precise localization of the vegetal/contraction pole depends on both the a-v axis and the location of sperm entry and prefigures the future site of gastrulation and dorsal side of the embryo. The second major phase of reorganization occurs between meiosis completion and first cleavage. Sperm aster microtubules and then cortical microfilaments cause the cER-mRNA domain and myoplasm to reposition toward the posterior of the zygote. The location of the posterior pole depends on the localization of the sperm centrosome/aster attained during the first major phase of reorganization. Both cER-mRNA and myoplasm domains localized in the posterior region are partitioned equally between the first two blastomeres and then asymmetrically over the next two cleavages. At the eight-cell stage the cER-mRNA domain compacts and gives rise to a macroscopic cortical structure called the Centrosome Attracting Body (CAB). The CAB is responsible for a series of unequal divisions in posterior-vegetal blastomeres, and the postplasmic/PEM RNAs it contains are involved in patterning the posterior region of the embryo. In this review, we discuss these multiple events and phases of reorganizations in detail and their relationship to physiological, cell cycle, and cytoskeletal events. We also examine the role of the reorganizations in localizing determinants, postplasmic/PEM RNAs, and PAR polarity proteins in the cortex. Finally, we summarize some of the remaining questions concerning polarization of the ascidian embryo and provide comparisons to a few other species. A large collection of films illustrating the reorganizations can be consulted by clicking on "Film archive: ascidian eggs and embryos" at http://biodev.obs-vlfr.fr/recherche/biomarcell/.

Ascidian embryonic development: An emerging model system for the study of cell fate specification in chordates

The ascidian tadpole larva represents the basic body plan of all chordates in a relatively small number of cells and tissue types. Although it had been considered that ascidians develop largely in a determinative way, whereas vertebrates develop in an inductive way, recent studies at the molecular and cellular levels have uncovered several similarities in the way developmental fates are specified. In this review, we describe ascidian embryogenesis and its cell lineages, introduce several characteristics of ascidian embryos, describe recent advances in understanding of the mechanisms of cell fate specification, and discuss them in the context of what is known in vertebrates and other organisms.

Effects of U0126 and fibroblast growth factor on gene expression profile in Ciona intestinalis embryos as revealed by microarray analysis

Fibroblast growth factor (FGF) induces the notochord and mesenchyme in ascidian embryos, via extracellular signal-regulated kinase (ERK) that belongs to the mitogen-activated protein kinase (MAPK) family. A cDNA microarray analysis was carried out to identify genes affected by an inhibitor of MAPK/ERK kinase (MEK), U0126, in embryos of the ascidian Ciona intestinalis. Data obtained from the microarray and in situ hybridization suggest that the majority of genes are downregulated by U0126 treatment. Genes that were downregulated in U0126-treated embryos included Ci-Bra and Ci-Twist-like1 that are master regulatory genes of notochord and mesenchyme differentiation, respectively. The plasminogen mRNA was downregulated by U0126 in presumptive endoderm cells. This suggests that a MEK-mediated extracellular signal is necessary for gene expression in tissues whose specification does not depend on cell-to-cell interaction. Among 85 cDNA clusters that were not affected by U0126, 30 showed mitochondria-like mRNA localization in the nerve cord/muscle lineage blastomeres in the equatorial region. The expression level and asymmetric distribution of these mRNA were independent of MEK signaling.

Embryonic expression profiles and conserved localization mechanisms of pem/postplasmic mRNAs of two species of ascidian, Ciona intestinalis and Ciona savignyi

In many animals, the first cue for development is transcripts and/or proteins that are provided maternally and are localized at specific regions of fertilized eggs and early embryos. The ascidian is known to exhibit a mosaic mode of development, which is largely dependent on localized maternal factors. In early Ciona intestinalis embryos, the posterior-most localization appears to be the major specialized pattern of maternal transcripts. The present study examined the temporal and spatial expression pattern of 40 genes known as pem/postplasmic genes, for which maternal mRNAs are localized at the posterior-most region during early Ciona embryogenesis. Ten of these genes showed redistribution to B8.12-line cells, which are known to give rise to germ cells in ascidians. In addition 23 orthologues were newly identified in a related ascidian species, Ciona savignyi, and 16 of them showed the mRNA localization pattern at the posterior-most region. Furthermore, the localized pattern of exogenous mRNA, which comprised the 3' UTR of C. intestinalis pem/postplasmic genes conjugated with the LacZ ORF, showed the localization at the posterior-most region in C. savignyi embryos. Likewise, the 3' UTR of C. savignyi pem/postplasmic genes conjugated with the LacZ ORF showed localization at the posterior most region in C. intestinalis embryos, suggesting that localization mechanisms are conserved between the two species. The present study therefore provides basic information for future functional analyses of these pem/postplasmic genes and for exploring the mechanisms of localization of mRNAs.

Live imaging of fluorescent proteins in chordate embryos: from ascidians to mice

Although we have advanced in our understanding of the molecular mechanisms intrinsic to the morphogenesis of chordate embryos, the question of how individual developmental events are integrated to generate the final morphological form is still unresolved. Microscopic observation is a pivotal tool in developmental biology, both for determining the normal course of events and for contrasting this with the results of experimental and pathological perturbations. Since embryonic development takes place in three dimensions over time, to fully understand the events required to build an embryo we must investigate embryo morphogenesis in multiple dimensions in situ. Recent advances in the isolation of naturally fluorescent proteins, and the refinement of techniques for in vivo microscopy offer unprecedented opportunities to study the cellular and molecular events within living, intact embryos using optical imaging. These technologies allow direct visual access to complex events as they happen in their native environment, and thus provide greater insights into cell behaviors operating during embryonic development. Since most fluorescent protein probes and modes of data acquisition are common across species, we have chosen the mouse and the ascidian, two model organisms at opposite ends of the chordate clade, to review the use of some of the current genetically-encoded fluorescent proteins and their visualization in vivo in living embryos for the generation of high-resolution imaging data.

The functional analysis of Type I postplasmic/PEM mRNAs in embryos of the ascidian Halocynthia roretzi

Maternal factors, such as a muscle determinant macho-1 mRNA that is localized to the posterior-vegetal cortex (PVC) of fertilized ascidian eggs, are crucial for embryonic axis formation and cell fate specification. Maternal mRNAs that show an identical posterior localization pattern to that of macho-1 in eggs and embryos are called Type I postplasmic/PEM mRNAs. We investigated the functions of five of the nine Type I mRNAs so far known in Halocynthia roretzi: Hr-Wnt-5, Hr-GLUT, Hr-PEM3, Hr-PEN1, and Hr-PEN2. Suppression of their functions with specific antisense morpholino oligonucleotides (MOs) had effects on the formation of various tissues: Hr-Wnt-5 on notochord, muscle, and mesenchyme, although zygotic function of Hr-Wnt-5 is responsible for notochord formation; Hr-GLUT on notochord, mesenchyme, and endoderm; and Hr-PEN2 on muscle, mesenchyme, and endoderm. On the other hand, Hr-PEM3 and Hr-PEN1 MOs seemed to have no effect. We conclude that the functions of at least some localized maternal Type I postplasmic/PEM mRNAs are necessary for early embryonic patterning in ascidians.

Specification of embryonic axis and mosaic development in ascidians

Setting up future body axes is the first important event before and at the beginning of embryogenesis. The ascidian embryo is a classic model that has been used to gain insight into developmental processes for over a century. This review summarizes advances made in this decade in our understanding of the developmental processes involved in the specification of the embryonic axes and cell fates during early ascidian embryogenesis. Maternal factors, including mRNAs, are translocated to specific regions of the egg by cytoplasmic and cortical reorganization, so-called ooplasmic segregation, and specify the animal-vegetal axis and the one perpendicular to it, which is defined as the anteroposterior axis in ascidians. Some postplasmic/PEM RNAs that are anchored to cortical endoplasmic reticulum are brought to the future posterior pole of fertilized eggs, and play crucial roles in posterior development. Following specification of the animal-vegetal axis, nuclear localization of beta-catenin takes place in the vegetal blastomeres; this occurrence is important for the acquisition of the vegetal character of the blastomeres in later development. Positioning of these maternal factors lead to subsequent cell interactions and zygotic gene expression responsible for axis establishment and for cell fate specification. We describe how endoderm blastomeres in the vegetal pole region emanate inductive signals mainly attributable to fibroblast growth factor. Marginal blastomeres next to endoderm blastomeres respond differently in ways that are determined by intrinsic competence factors. Expression patterns of developmentally important genes, including key transcription factors of each tissue type, are also summarized.

Xenomics

Xenopus genomics, or Xenomics for short, is coming of age. Indeed, biological insight into processes such as growth factor signaling and patterning of the early embryo is now being gained by combining the value of Xenopus as a model organism for cell and developmental biology with genomic approaches. In this review I address these recent advances and explore future possibilities gained from combining this powerful experimental system with genomic approaches, as well as how our quest to understand basic biological principles will be greatly facilitated though the marriage of Xenopus and genomics.

Microarray analysis of localization of maternal transcripts in eggs and early embryos of the ascidian, Ciona intestinalis

The establishment of body axes and specification of early embryonic cells depend on maternally supplied transcripts and/or proteins, several of which are localized at specific regions of fertilized eggs and early embryos. The ascidian is known to exhibit a mosaic mode of development, and this mode is largely dependent on localized maternal factors. Using blastomere isolation, microarray and whole-mount in situ hybridization, the present study of Ciona intestinalis demonstrates that maternal transcripts of a total of 17 genes are localized at the posterior-most region of fertilized eggs and early embryos. Ten of them are newly identified in the present study, while the remaining seven genes have already been characterized in previous studies. In addition, maternal transcripts of two genes, in addition to 14 genes encoded by the mitochondrial genome, showed a mitochondria-like distribution. Despite the present comprehensive approach, we could not identify maternal transcripts that are clearly localized to the animal-pole side, the vegetal-pole side, the anterior-side or other specific regions of the early embryo. Therefore, we concluded that the posterior-most localization and mitochondria-like distribution appear to be major specialized patterns of maternal transcripts in early Ciona embryos.

Maternal determinants and mRNAs in the cortex of ascidian oocytes, zygotes and embryos

The peripheral region of ascidian oocytes and zygotes contains five determinants for morphogenesis and differentiation of the embryo. The determinant for the 24 primary muscle cells of the tadpole, macho1, is one of several cortical mRNAs localized in a gradient along the animal-vegetal axis in the oocyte. After fertilization these mRNAs, together with cortical endoplasmic reticulum (cER) and a subcortical mitochondria-rich domain (myoplasm), relocate in two major reorganization phases forming the posterior plasm (postplasm) of the zygote. At the 8-cell stage cortical mRNAs concentrate in a macroscopic cortical structure called the centrosome-attracting body (CAB), forming a characteristic posterior end mark (PEM) in the two posterior vegetal blastomeres. We propose to call the numerous mRNAs showing this particular cortical localization in the posterior region of the embryo postplasmic/PEM RNAs and suggest a nomemclature. We do not know how postplasmic/PEM RNAs reach their polarized distribution in the oocyte cortex but at least PEM1 and macho1 (and probably others) bind to the network of cER retained in isolated cortical fragments. We propose that after fertilization, these postplasmic/PEM mRNAs move in the zygote cortex together with the cER network (cER/mRNA domain) via microfilament- and microtubule-driven translocations. The cER/mRNA domain is localized posteriorly at the time of first cleavage and distributed equally between the first two blastomeres. After the third cleavage, the cER/mRNA domain and dense particles compact to form the CAB in posterior vegetal blastomeres of the 8-cell stage. We discuss the identity of postplasmic/PEM RNAs, how they localize, anchor, relocate and may be translated. We also examine their roles in unequal cleavage and as a source of posterior morphogenetic and differentiation factors.

Decoding cis-regulatory systems in ascidians

Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.

Screen for genes differentially expressed during regeneration of the zebrafish caudal fin

The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. The cascade of genes induced after amputation or injury, leading to restoration of the lost fin structures, include those responsible for wound healing, blastema formation, tissue outgrowth, and patterning. We carried out a systematic study to identify genes that are up-regulated during "initiation" (1 day) and "outgrowth and differentiation" (4 days) of fin regeneration by using two complementary methods, suppression subtraction hybridization (SSH) and differential display reverse transcriptase polymerase chain reaction (DDRT-PCR). We obtained 298 distinct genes/sequences from SSH libraries and 24 distinct genes/sequences by DDRT-PCR. We determined the expression of 54 of these genes using in situ hybridization. In parallel, gene expression analyses were done in zebrafish embryos and early larvae. The information gathered from the present study provides resources for further investigations into the molecular mechanisms of fin development and regeneration.

Global gene expression profiling and cluster analysis in Xenopus laevis

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.

The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.)

Here, we report the transcript profile of wheat egg cells and proembryos, just after the first cell division. Microdissected female gametophytes of wheat were used to isolate eggs and two-celled proembryos to construct cell type-specific cDNA libraries. In total, 1197 expressed sequence tags (ESTs) were generated. Analysis of these ESTs revealed numerous novel transcripts. In egg cells, 17.6% of the clustered ESTs represented novel transcripts, while 11.4% novel clusters were identified in the two-celled proembryo. Functional classification of sequences with similarity to previously characterized proteins indicates that the unfertilized egg cell has a higher metabolic activity and protein turnover than previously thought. Transcript composition of two-celled proembryos was significantly distinct from egg cells, reflecting DNA replication as well as high transcriptional and translational activity. Several novel transcripts of the egg cell are specific for this cell. In contrast, some fertilization induced novel mRNAs are abundant also in sporophytic tissues indicating a more general role in plant growth and development. The potential functions of genes based on similarity to known genes involved in developmental processes are discussed. Our analysis has identified numerous genes with potential roles in embryo sac function such as signaling, fertilization or induction of embryogenesis.

Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

We show that sequence comparisons at different levels of resolution can efficiently guide functional analyses of regulatory regions in the ascidians Ciona savignyi and Ciona intestinalis. Sequence alignments of several tissue-specific genes guided discovery of minimal regulatory regions that are active in whole-embryo reporter assays. Using the Troponin I (TnI) locus as a case study, we show that more refined local sequence analyses can then be used to reveal functional substructure within a regulatory region. A high-resolution saturation mutagenesis in conjunction with comparative sequence analyses defined essential sequence elements within the TnI regulatory region. Finally, we found a significant, quantitative relationship between function and sequence divergence of noncoding functional elements. This work demonstrates the power of comparative sequence analysis between the two Ciona species for guiding gene regulatory experiments.

Transcript mapping and genome annotation of ascidian mtDNA using EST data

Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to analyze processing and mapping of the mitochondrial transcripts and to investigate the gene organization of a previously uncharacterized mitochondrial genome (mtDNA). This new strategy would greatly facilitate the sequencing and annotation of mtDNAs. In Ciona intestinalis, the assembled mt-ESTs covered 22 mitochondrial genes ( approximately 12,000 bp) and provided the partial sequence of the mtDNA and the prediction of its gene organization. Such sequences were confirmed by amplification and sequencing of the entire Ciona mtDNA. For Halocynthia roretzi, for which the mtDNA sequence was already available, the inferred mt transcripts allowed better definition of gene boundaries (16S rRNA, ND1, ATP6, and tRNA-Ser genes) and the identification of a new gene (an additional Phe-tRNA). In both species, polycistronic and immature transcripts, creation of stop codons by polyadenylation, tRNA signal processing, and rRNA transcript termination signals were identified, thus suggesting that the main features of mitochondrial transcripts are conserved in Chordata.

Neural expression of the Huntington's disease gene as a chordate evolutionary novelty

Huntington's disease is a progressive neuro-degenerative disorder in humans, which is scharacterized by onset of dementia, muscular ataxia, and death. Huntington's disease is caused by the expansion of the polyglutamine (polyQ) tract in the N-terminus of the HD protein (Huntingtin). CAG expansion is a dominant gain of function mutation that affects striated neurons in the brain (Cattaneo, 2003, News Physiol Sci 18:34). The evolutionary origins of the vertebrate Hd gene are not well understood. In order to address the evolutionary history of the Hd gene, we have cloned and characterized the expression of the Hd gene in two invertebrate deuterostomes, an echinoderm and an ascidian, and have examined the expression patterns in a phylogenetic context. Echinoderms are basal deuterostomes and ascidians are basal chordates; both are useful for understanding the origins of and evolutionary trends in genes important in vertebrates such as the Huntigton's disease gene. Expression of Hd RNA is detected at all stages of development in both the echinoderm and ascidian studied. In the echinoderm Heliocidaris erythrogramma, Hd is expressed in coelomic mesodermal tissue derivatives, but not in the central nervous system. In the ascidian Halocynthia roretzi expression is located in both mesoderm and nervous tissue. We suggest that the primitive deuterostome expression pattern is not neural. Thus, neural expression of the Hd gene in deuterostomes may be a novel feature of the chordate lineage, and the original role(s) of HD in deuterostomes may have been non-neural.

EST analysis of gene expression in the tentacle of Cyanea capillata

Jellyfish, Cyanea capillata, has an important position in head patterning and ion channel evolution, in addition to containing a rich source of toxins. In the present study, 2153 expressed sequence tags (ESTs) from the tentacle cDNA library of C. capillata were analyzed. The initial ESTs consisted of 198 clusters and 818 singletons, which revealed approximately 1016 unique genes in the data set. Among these sequences, we identified several genes related to head and foot patterning, voltage-dependent anion channel gene and genes related to biological activities of venom. Five kinds of proteinase inhibitor genes were found in jellyfish for the first time, and some of them were highly expressed with unknown functions.

15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis

A total of 15590 unique zebrafish EST clusters from two cDNA libraries have been identified. Most significantly, only 22% (3437) of the 15590 unique clusters matched 2805 (of 15200) clusters in the Danio rerio UniGene database, indicating that our EST set is complementary to the existing ESTs in the public database and will be invaluable in assisting the annotation of genes based on the upcoming zebrafish genome sequence. Blast search showed that 7824 of our unique clusters matched 6710 known or predicted proteins in the nonredundant database. A cDNA microarray representing approximately 3100 unique zebrafish cDNA clusters has been generated and used to profile the gene expression patterns across six different embryonic stages (cleavage, blastula, gastrula, segmentation, pharyngula, and hatching). Analysis of expression data using K-means clustering revealed that genes coding for muscle-specific proteins displayed similar expression patterns, confirming that the coordinate gene expression is important for myogenesis. Our results demonstrate that the combination of microarray technology with the zebrafish model system can provide useful information on how genes are coordinated in a genetic network to control zebrafish embryogenesis and can help to identify novel genes that are important for organogenesis.

Localization and expression pattern of type I postplasmic mRNAs in embryos of the ascidian Halocynthia roretzi

The posterior-vegetal cytoplasm (PVC) of fertilized ascidian eggs plays important roles in embryo development. It has been reported that some maternal RNAs are localized to the PVC. We identified four novel type I postplasmic mRNAs that are localized to the PVC through the use of data from a cDNA project of maternal mRNAs in the eggs of Halocynthia roretzi (MAGEST database). The mRNAs are HrGLUT, HrPEN-1, and HrPEM-3, which show similarity to a glucose transporter, a g1-related protein, and Ciona pem-3, respectively; and HrPEN-2, with no similarity. Maternal mRNAs of all four genes were identically localized to the PVC after ooplasmic segregation. During cleavage, they were concentrated in the centrosome-attracting body (CAB) and were then segregated into the small blastomeres located at the posterior pole. This localization pattern is common to all known type I postplasmic mRNAs found so far. HrGLUT, HrPEN-1, and HrPEM-3 were expressed zygotically in various tissues later in embryogenesis: HrGLUT and HrPEM-3 in the mesenchyme and nervous system, and HrPEN-1 in the ectodermal cells.

Identification of a gene encoding a typical gamma-carboxyglutamic acid domain in the tunicate Halocynthia roretzi

We report the identification of a gene capable of encoding a novel Gla (gamma-carboxyglutamic acid) protein from the tunicate Halocynthia roretzi, a primitive member of the phylum Chordata. We call this new hypothetical protein Gla-RTK; it has a Gla domain typical of human vitamin K-dependent coagulation factors, a transmembrane domain, and a receptor tyrosine kinase domain. The receptor tyrosine kinase domain is very similar to the ARK (adhesion-related kinase) family of receptor tyrosine kinases. The ARK family includes Axl, Tyro3, and c-Mer. This gene also encodes a propeptide that binds to the human gamma-glutamyl carboxylase within a range of affinities observed for mammalian propeptides. The cDNA for this putative protein is found distributed throughout the oocyte and embryo but the cDNA is apparently not transcribed except during oogenesis. One of the most interesting aspects of this hypothetical protein is that its Gla domain is highly homologous to the Gla domain of Gas6, a ligand for Axl, while its receptor tyrosine kinase domain is highly homologous to Axl.

Specification of developmental fates in ascidian embryos: molecular approach to maternal determinants and signaling molecules

Tadpole larvae of ascidians represent the basic body plan of chordates with a relatively small number and few types of cells. Because of their simplicity, ascidians have been intensively studied. More than a century of research on ascidian embryogenesis has uncovered many cellular and molecular mechanisms responsible for cell fate specification in the early embryo. This review describes recent advances in our understanding of the molecular mechanisms of fate specification mainly uncovered in model ascidian species--Halocynthia roretzi, Ciona intestinalis, and Ciona savignyi. One category of developmentally important molecules represents maternal localized mRNAs that are involved in cell-autonomous processes. In the second category, signaling molecules and downstream transcription factors are involved in inductive cell interactions. Together with genome-wide information, there is a renewed interest in studying ascidian embryos as a fascinating model system for understanding how single-celled eggs develop a highly organized chordate body plan.

A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny

Although data are available from only vertebrates, urochordates, and three nonchordate animals, there are definite differences in the structures of classic cadherins between vertebrates plus urochordates and nonchordates. In this study we examined structural diversity of classic cadherins among bilaterian animals by obtaining new data from an amphioxus (Cephalochordata, Chordata), an acorn worm (Hemichordata), a sea star (Echinodermata), and an oyster (Mollusca). The structures of newly identified nonchordate cadherins are grouped together with those of the known sea urchin and Drosophila cadherins, whereas the structure of an amphioxus (Branchiostoma belcheri) cadherin, designated BbC, is differently categorized from those of other known chordate cadherins. BbC is identified as a cadherin by its cytoplasmic domain whose sequence is highly related to the cytoplasmic sequences of all known classic cadherins, but it lacks all of the five repeats constituting the extracellular homophilic-binding domain of other chordate cadherins. The ectodomains of BbC match the ectodomains found in nonchordate cadherins but not present in other chordate cadherins. We show that the BbC functions as a cell-cell adhesion molecule when expressed in Drosophila S2 cells and localizes to adherens junctions in the ectodermal epithelia in amphioxus embryos. We argue that BbC is the amphioxus homologue of the classic cadherins involved in the formation of epithelial adherens junctions. The structural relationships of the cadherin molecules allow us to propose a possibility that cephalochordates might be basal to the sister-groups vertebrates and urochordates.

Identification of cis Elements Which Direct the Localization of Maternal mRNAs to the Posterior Pole of Ascidian Embryos

During ascidian embryogenesis, some mRNAs show clear localization at the posterior-most region. These postplasmic mRNAs are divided into two groups (type I and type II) according to their pattern of localization. To elucidate how these localization patterns are achieved, we attempted to identify the localization elements of these mRNAs. When in vitro synthesized postplasmic mRNAs were introduced into eggs, these mRNAs showed posterior localization similar to the endogenous mRNAs. The posterior localization of these mRNAs was mediated by their 3' untranslated regions (3' UTRs), as is the case for several localized Drosophila and Xenopus mRNAs. We identified smaller fragments of the 3' UTRs of HrWnt-5 and HrPOPK-1 mRNAs (type I) and HrPet-3 mRNA (type II) that were sufficient to direct green fluorescent protein mRNA to the posterior pole. For the localization of HrWnt-5 mRNA, two UG dinucleotide repetitive elements were essential. Motifs similar to these small elements also exist within the HrPOPK-1 mRNA localization element and 3' UTR of HrZF-1 mRNA, suggesting the conservation of localization elements among type I mRNAs. In contrast, the smallest sequence that suffices for the posterior localization of HrPet-3 (a type II mRNA) has different features from those of type I mRNAs; indeed, it does not have an identifiable critical element. This difference may distinguish type II mRNAs from type I mRNAs. These findings, especially the identification of the small localization element of HrWnt-5 mRNA, provide new insights into the localization of mRNAs during ascidian embryogenesis.

EST analysis of gene expression in testis of the ascidian Ciona intestinalis

To explore the gene expression underlying spermatogenesis, a large-scale analysis has been done on the cDNAs from testis of the ascidian, Ciona intestinalis. A set of 5,461 expressed sequence tags was analyzed and grouped into 2,806 independent clusters. Approximately 30% of the clusters showed significant sequence matches to the proteins reported in DDBJ/GenBank/EMBL database including a set of proteins closely related to the gene regulation during spermatogenesis, functional and morphological changes of spermatogenic cells during spermiogenesis, and physiological functions of sperm, as well as those with housekeeping functions commonly expressed in other cells. Some clones show similarities to the proteins present in vertebrate lymphocytes, suggesting a primitive immune system in ascidians. We have also found some genes that are known to participate in hormonal regulation of spermatogenesis in vertebrates. The large majority of the genes expressed in Ciona testis show no significant matches to known proteins and the further analysis of these genes may shed new light on the molecular mechanism of spermatogenesis and sperm functions.

Patterning the marginal zone of early ascidian embryos: localized maternal mRNA and inductive interactions

Early animal embryos are patterned by localized egg cytoplasmic factors and cell interactions. In invertebrate chordate ascidians, larval tail muscle originates from the posterior marginal zone of the early embryo. It has recently been demonstrated that maternal macho-1 mRNA encoding transcription factor acts as a localized muscle determinant. Other mesodermal tissues such as notochord and mesenchyme are also derived from the vegetal marginal zone. In contrast, formation of these tissues requires induction from endoderm precursors at the 32-cell stage. FGF-Ras-MAPK signaling is involved in the induction of both tissues. The responsiveness for induction to notochord or mesenchyme depends on the inheritance of localized egg cytoplasmic factors. Previous studies also point to critical roles of directed signaling in polarization of induced cells and in subsequent asymmetric divisions resulting in the formation of two daughter cells with distinct fates. One cell adopts an induced fate, while the other assumes a default fate. A simple model of mesoderm patterning in ascidian embryos is proposed in comparison with that of vertebrates.

A chromodomain-containing nuclear protein, MRG15 is expressed as a novel type of dendritic mRNA in neurons

On the basis of a hypothesis that proteins encoded by the mRNAs that are transported to and translated at the dendrites/synapses may play key roles in synaptic plasticity, this study reports on attempts to isolate mRNAs which are localizing at the dendrites/synapses from mouse cerebellar synaptosomal fractions. Among 100 pieces of dendritic mRNA candidates, 10 pieces of mRNAs were found to contain the cytoplasmic polyadenylation element (CPE)-like sequences which were contained in certain mRNAs translated in dendrites. We next examined the issue of whether the CPE-like sequence-containing mRNAs (CPERs) were localized in the synapses/dendrites by means of in situ hybridization. The findings indicate that CPER9 was actually localized at the apical dendrites of a portion of cerebral cortex layer V pyramidal cells, as well as at the proximal dendrites of some of the cerebellar Purkinje cells. CPER9 was found to encode a mouse homolog of MRG15, a nuclear protein which contains a chromodomain identified in several proteins that act as regulators of transcription. Immunohistochemistry with anti-MRG15 antibodies revealed that MRG15 was localized in dendrites as well as in the nuclei of Purkinje cells. These results suggest that MRG15 may serve as a link between synaptic activity and gene expression.

Repression of zygotic gene expression in the putative germline cells in ascidian embryos

In germline cells of early C. elegans and Drosophila embryos, repression of zygotic gene expression appears to be essential to maintain the germ cell fate. In these animals, specific residues in the carboxy-terminal domain (CTD) of RNA polymerase II large subunit (RNAP II LS) are dephosphorylated in the germline cells, whereas they are phosphorylated in the somatic cells. We investigated, in early embryos of the ascidian Halocynthia roretzi, the expression patterns of three genes that are essentially expressed in the entire embryo after the 32-cell stage. We found that the expression of these genes was inactive in the putative germline cells during the cleavage stages. Once cells were separated from the germline lineage by cleavages, the expression of the genes was initiated in the cells. These results suggest that repression of transcription in germline cells may also be common in chordate embryos. We then examined the phosphorylation state of the CTD of RNAP II using a phosphoepitope-specific antibody. At cleavage stages after the 32-cell stage, CTD was phosphorylated in every blastomere, including the germline cells. Therefore, in the ascidian, the inactivation of zygotic transcription is not correlated with dephosphorylation of the CTD. These observations indicate that zygotic transcription is inactivated in ascidian germline cells, but the mechanism of the repression may differ from that in C. elegans and Drosophila.