Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis

A set of 1,378 expressed sequence tags (ESTs), both the 5'-most and T-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 19 0 showed matches with putative proteins for which there is not enough infor mation to categorize their function, and 361 had no significant similaritie s to known proteins. Sequence similarity analyses of the 452 clusters in re lation to the biological function as well as the structure of the message p opulation at this stage demonstrated that 362 of them have functions that m any kinds of cells use, 65 are associated with cell-cell communication, inc luding a candidate cDNA for sonic hedgehog, and 25 are transcription factor s. Sequence prevalence distribution analysis demonstrated that the great ma jority (78%) of the mRNAs are rare mRNAs or are represented by a single clo ne/cluster. All of the 1,003 clusters were subjected to whole-mount in situ hybridization to analyze the distribution of the maternal mRNAs in fertili zed eggs, and a total of 329 genes showed localized distribution of the mRN As: 16 showed cortical localization, 12 showed mitochondrial-like distribut ion, 99 crescent-like distribution, 63 partial localization, and 139 weak l ocalization. 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 t heir localized distribution by the 8-cell stage. In contrast, 13 genes newl y 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 ar e associated with the characteristic distribution of maternal mRNAs, which in turn support proper embryonic axis formation and establishment of the ge netic network for embryonic cell specification. (C) 2001 Academic Press.