Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Differential gene expression in notochord and nerve-cord fate segregation in the Ciona intestinalis embryo

ABSTRACT: Fertilized eggs are plulipotent and during early embryogenesis, embryonic cells gradually restrict their developmental potential and are eventually destined to give rise to one type of cells. Molecular mechanism underlying developmental fate restriction is one of the major research subjects of developmental biology. Here we address this question by combining a classical technique of blastomere isolation with a modern technique of microarray analysis. During the 6th cleavage of the Ciona intestinalis embryo, from the 32-cell to the 64-cell stage, four mother cells divide into daughter cells with two distinct fates, one giving rise to notochord and the other to nerve-cord precursor cells. Nearly 500 notochord or nerve-cord precursor cells each were isolated, and difference in the quality of mRNAs between them was compared by microarray. This analysis identified 111 and 69 genes that are differentially expressed in the notochord and nerve-cord precursor cells, respectively. These included not only genes for transcription factors and signalling molecules but also those with functions that many kinds of cells used. In addition, whole-mount in situ hybridization showed complex and dynamic profiles of spatial expression of these genes during the segregation of the two fates. The process is accomplished by that transcripts that have been already present in the mother cell are properly partitioned into either type of cells and that new and preferential expression of genes in either type of cells. Two kinds of sample, Dye Swap design with 2 arrays

ORGANISM(S): Ciona intestinalis

SUBMITTER: Lixy Yamada

PROVIDER: E-GEOD-25184 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Postplasmic/PEM RNAs constitute a large class of cortical maternal RNAs with include at least 2 determinants (Macho1 and PEM1) involved in muscle differentiation, unequal cleavage and posterior patterning of the embryo. Two main classes have been defined - type I (localized in oocytes) and type II (localizing in embryos). Based on the fact that Vasa RNA - the only type II recognized in Ciona - segregates into B8.12 (germ) and sister B8.11 cells, while many others (including Macho1 and PEM1) segregate only into B8.11 (somatic) cells a first attempts at re-classifying these RNAs has been made. We have analyzed the associations of postplasmic/PEM RNAs with cortical structures in 2 ascidians species Ciona intestinalis and Phallusia mammillata using: - very high resolution fluorescent in situ hybridization localization in eggs and embryos and in their cortical fragments, - comparisons of RNAs extracted from whole oocytes and from isolated cortices using microarray analysis â screening of the Ciona intestinalis genome for the presence in 3â UTR regions of repeats containing the tri-nucleotide CAC motif (xCACx) followed by localization of xCACx rich RNAs using in situ hybridization. Based on our combined approaches we observe that: - 1) the vast majority of Ciona intestinalis postplasmic/PEM RNAs (including Ci-Vasa) are cortically localized in the eggs (type I) - 2) postplasmic/PEM RNAs are much more likely to contain xCACx motifs in their 3âUTR than other transcripts. Using this criterion we have found 2 new postplasmic/PEM RNAs: MnK and PSD - 3) some postplasmic/PEM RNAs are anchored to cER while others are located into granules. We therefore come to the conclusion that there are at least 2 distinct categories of postplasmic/PEM RNAs based on their cortical anchorage and cell fate: I) cER sub-domain associated postplasmic/PEM RNAs (Macho1 like) which segregate in the somatic B8.11 cells. II) postplasmic/PEM RNAs associated with (putative germ) granules (Vasa like) which in addition to B8.11 cells segregate into B8.12 germ cells. Two kinds of sample, Dye Swap design with 2 arrays

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Differential gene expression in notochord and nerve-cord fate segregation in the Ciona intestinalis embryo

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