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


Authors: Ruby, J. G.; Stark, A.; Johnston, W. K.; Kellis, M.; Bartel, D. P.; Lai, E. C.
Article Title: Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
Abstract: 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.
Keywords: controlled study; genetics; nonhuman; comparative study; molecular genetics; methodology; animal; metabolism; animals; microrna; gene expression; biology; computational biology; gene function; physiology; evolution, molecular; gene expression regulation; prenatal development; gene expression regulation, developmental; biosynthesis; molecular evolution; conserved sequence; molecular sequence data; messenger rna; rna, messenger; gene identification; nucleotide sequence; base sequence; drosophila melanogaster; conformation; nucleic acid conformation; micrornas; mathematical computing; biogenesis; insect genetics; evolutionary homology
Journal Title: Genome Research
Volume: 17
Issue: 12
ISSN: 1088-9051
Publisher: Cold Spring Harbor Laboratory Press  
Date Published: 2007-12-01
Start Page: 1850
End Page: 1864
Language: English
DOI: 10.1101/gr.6597907
PUBMED: 17989254
PROVIDER: scopus
PMCID: PMC2099593
DOI/URL:
Notes: --- - "Cited By (since 1996): 110" - "Export Date: 17 November 2011" - "CODEN: GEREF" - "Source: Scopus"
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  1. Eric C Lai
    159 Lai