Accardo, Maria Carmela (2006) Un’analisi genomica per l’identificazione di nuovi geni che codificano piccoli RNA nucleolari in Drosophila melanogaster. [Tesi di dottorato] (Inedito)

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Abstract

In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly of the C/D and H/ACA families), which act as guides in the maturation or post-trascriptional modifications of target RNA molecules. We have performed a genome-wide analysis of Drosophila melanogaster genome searching for C/D snoRNA genes by a computational approach based on the use of the SNOSCAN program and the methylation sites conserved between yeast, human and Drosophila rRNAs, followed by experimental validation of the putative candidates. This analysis led to confirm the expression of 52 out of the 100 putative snoRNA genes identified by bioinformatic analysis. Organization of the Dm genome was found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and the exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Interestingly, this analysis led to identify not only snoRNAs able to target rRNA but also at least six molecules able to target snRNAs, while nine novel snoRNAs were classified as “orphans”. Searching in the Drosophila transcriptome for potential additional targets, we found that many mRNAs may potentially be modified by these orphan molecules.

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