Identification of Drosophila MicroRNA Targets

来自 EBSCO

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阅读量：

454

作者：

Stark, Alexander， Brennecke, Julius， Russell, Robert B.， Cohen, Stephen M.

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摘要：

MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression by binding to target messenger RNAs and by controlling protein production or causing RNA cleavage. To date, functions have been assigned to only a few of the hundreds of identified miRNAs, in part because of the difficulty in identifying their targets. The short length of miRNAs and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods. Here we screen conserved 3′ UTR sequences from theDrosophila melanogastergenome for potential miRNA targets. The screening procedure combines a sequence search with an evaluation of the predicted miRNA–target heteroduplex structures and energies. We show that this approach successfully identifies the five previously validatedlet-7,lin-4, andbantamtargets from a large database and predict new targets forDrosophilamiRNAs. Our target predictions reveal striking clusters of functionally related targets among the top predictions for specific miRNAs. These includeNotchtarget genes formiR-7, proapoptotic genes for themiR-2family, and enzymes from a metabolic pathway formiR-277. We experimentally verified three predicted targets each formiR-7and themiR-2family, doubling the number of validated targets for animal miRNAs. Statistical analysis indicates that the best single predicted target sites are at the border of significance; thus, target predictions should be considered as tentative until experimentally validated. We identify features shared by all validated targets that can be used to evaluate target predictions for animal miRNAs. Our initial evaluation and experimental validation of target predictions suggest functions for two miRNAs. For others, the screen suggests plausible functions, such as a role formiR-277as a metabolic switch controlling amino acid catabolism. Cross-genome comparison proved essential, as it allows reduction of the sequence search space. Improvements in genome annotation and increased availability of cDNA sequences from other genomes will allow more sensitive screens. An increase in the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection. While the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone. A bioinformatic approach suggests many new target genes for Drosophila microRNAs. A number of them are validated experimentally

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关键词：

Bioinformatics/Computational Biology Development Evolution Genetics/Genomics/Gene Therapy Molecular Biology/Structural Biology

DOI：

10.1371/journal.pbio.0000060

被引量：

3836

年份：

2003