Profiles of Maternally Expressed Genes in Fertilized Eggs of Ciona intestinalis

Abstract

A set of 1,378 expressed sequence tags (ESTs), both the 5'-most and 3'-most ends, derived from Ciona intestinalis fertilized eggs was categorized into 1,003 independent clusters. When compared with sequences in databases, 452 of the clusters showed significant matches with reported proteins, while 190 showed matches with putative proteins for which there is not enough information to categorize their function, and 361 had no significant similarities to known proteins. Sequence similarity analyses of the 452 clusters in relation to the biological function as well as the structure of the message population at this stage demonstrated that 362 of them have functions that many kinds of cells use, 65 are associated with cell-cell communication, including a candidate cDNA for sonic hedgehog, and 25 are transcription factors. Sequence prevalence distribution analysis demonstrated that the great majority (78%) of the mRNAs are rare mRNAs or are represented by a single clone/cluster. All of the 1,003 clusters were subjected to whole-mount in situ hybridization to analyze the distribution of the maternal mRNAs in fertilized eggs, and a total of 329 genes showed localized distribution of the mRNAs: 16 showed cortical localization, 12 showed mitochondrial-like distribution, 99 crescent-like distribution, 63 partial localization, and 139 weak localization. When the distribution pattern of all the maternally expressed mRNAs was examined in the 8-cell stage embryos, it became evident that 248 genes which have localized mRNA patterns at the fertilized egg stage lose their localized distribution by the 8-cell stage. In contrast, 13 genes newly gain a localized pattern by the 8-cell stage. In addition, a total of 39 genes showed distinct in situ signals in the nucleus of blastomeres of the 8-cell stage embryo, suggesting early zygotic expression of these genes by this stage. These results suggest that complicated cytoplasmic movements are associated with the characteristic distribution of maternal mRNAs, which in turn support proper embryonic axis formation and establishment of the genetic network for embryonic cell specification.

Ci-Pem-1 localizes to the nucleus and represses somatic gene transcription in the germline of Ciona intestinalis embryos

“…In C. intestinalis embryos, most zygotic genes are transcribed only in the somatic blastomeres, although a small number of genes appear to be expressed in the germline blastomeres during the cleavage stages (Imai et al, 2004;Nishikata et al, 2001;. This suggests that the RNAPII-mediated transcription in germline blastomeres is significantly reduced, even though it is not completely blocked.…”

“…For example, although the postplasmic/PEM RNA that encodes a transcriptional factor for muscle cell fate determination, macho-1, is distributed with the postplasm during the cleavage stages, its target genes, such as ADMP, are never expressed in the germline blastomeres (Tomioka et al, 2002;Yagi et al, 2004). In addition, a comprehensive in situ hybridization analysis of C. intestinalis embryos in the ghost database (http://ghost.zool.kyoto-u.ac.jp/indexr1.html) suggested that very few zygotic genes are transcribed in germline blastomeres during the cleavage stages (Imai et al, 2004;Nishikata et al, 2001;Satou et al, 2002). Intriguingly, upon cleavage of the germline blastomere, the daughter cell that does not inherit the postplasm immediately starts the zygotic expression of genes involved in somatic development.…”

Optimized green fluorescent protein variants provide improved single cell resolution of transgene expression in ascidian embryos

“…The genomes of two closely related species have been completely sequenced (Dehal et al, 2002; and http://www-genome.wi.mit. edu/annotation/ciona), there is an extensive collection of over 650,000 expressed sequence tag (EST) sequences, and the expression patterns of several thousand genes have been examined by in situ hybridization (Nishikata et al, 2001;Satou et al, 2001;2002a,b;Fujiwara et al, 2002;Kusakabe et al, 2002). One of the strengths of using the ascidian embryo to study developmental gene regulation is the ability to create hundreds or thousands of transgenic embryos in a single day using a simple electroporation procedure (Corbo et al, 1997;Di Gregorio and Levine, 2002;Zeller, 2004).…”

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

“…Second, an extensive analysis of expression sequence tags (ESTs) has been carried out , and more than 240000 cDNA clones have been sequenced to date (http://ghost.zool.kyoto-u.ac.jp/indexr1.html). Third, profiles of gene expression have been determined in eggs, embryos, larvae and young adults (Nishikata et al 2001;Fujiwara et al 2002;Satou et al 2001;Kusakabe et al 2002;Ogasawara et al 2002) In the present study, we prepared a cDNA microarray containing 9287 independent cDNA clones obtained from the EST project. Using this DNA chip, we screened candidate embryonic RA target genes and examined their expression pattern in normal and RA-treated embryos.…”