Transcriptomics

Dataset Information

18

Comparative analysis of gene expression profiles between whole oocytes and isolated cortices


ABSTRACT: 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 – screening of the Ciona intestinalis genome for the presence in 3’ 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 3’UTR 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. Overall design: Two kinds of sample, Dye Swap design with 2 arrays

INSTRUMENT(S): Ciona intestinalis 44k Oligoarray ver.2

ORGANISM(S): Ciona intestinalis  

SUBMITTER: Lixy Yamada  

PROVIDER: GSE15586 | GEO | 2010-03-31

SECONDARY ACCESSION(S): PRJNA115595

REPOSITORIES: GEO

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