Abstracts - 2007
Systematic Discovery and Characterization of Fly microRNAs Using 12 Drosophila Genomes
Alexander Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Graham Ruby, Gregory Hannon, David Bartel & Manolis Kellis
microRNAs (miRNAs) are short RNA genes that direct the inhibition of target messenger-RNA expression via complementary binding sites in the targets' 3' untranslated region (UTR) [1-8] . Currently, miRNAs are estimated to comprise 1%-5% of animal genes [2,9,10], making them one of the most abundant classes of regulators. In addition, an average miRNA may regulate hundreds of genes , so that a large fraction of all genes are miRNA targets [11-15]. It is thus desirable to obtain a comprehensive view on all miRNAs in an animal genome, especially as knowledge of the sequence alone can allow the identification of the physiologically relevant target genes.
We used the 12 recently sequenced Drosophila species  to study structural and evolutionary properties of miRNA hairpins. We found that several distinct signatures can guide the de-novo discovery of miRNAs, revealing more than 50 novel miRNA genes, many of which we validate experimentally. Several of the novel miRNAs are clustered in genomic loci, and likely to be transcribed from a single precursor. Our analysis finds several additional members of existing families, and also many novel families.
We also find distinct evolutionary signals for the precise annotation of the start position of mature miRNAs. This allows us to correct the annotation and strand of previously known miRNA genes, sometimes leading to drastic corrections in their target genes. For example, we correct the Hox miRNA miR-10, and reveal that the new annotation now has a highly conserved target site in the Hox genes ultrabithorax and abdominal-B, a regulatory relationship typical for Hox miRNAs in flies and vertebrates. When a precise signal for the miRNA start does not exist, we find that indeed experimental information suggests that multiple starts are used in practice; similarly, when both strands score highly according to our evolutionary models, we find that indeed a mature product is found from both strands.
Finally, we find that the performance scales with the total divergence between the species under consideration. The divergence of neutrally evolving sequence allowed the genome-wide de novo discovery of miRNAs in12 Drosophila genomes, and will serve as a model for similar studies in human as dozens of mammalian genomes become available.
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