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12 Drosophila Genomes/Letter

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

¹ Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; ² Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ³ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ⁴ Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA; ⁵ Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA

MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.

E-mail dbartel{at}wi.mit.edu; fax (617) 258-6768.

[Supplemental material is available online at www.genome.org. The small RNA sequence data from this study have been submitted to GEO under accession nos. GPL5061 and GSE7448. Computational tools for miRNA prediction (MiRscan3) are available for anonymous download at http://web.wi.mit.edu/bartel/pub/.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6597907

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