MicroRNAs (miRNAs) are small noncoding RNAs that repress protein synthesis by binding to target messenger RNAs. We investigated the effect of target secondary structure on the efficacy of repression by miRNAs. Using structures predicted by the Sfold program, we model the interaction between an miRNA and a target as a two-step hybridization reaction: nucleation at an accessible target site followed by hybrid elongation to disrupt local target secondary structure and form the complete miRNA-target duplex. This model accurately accounts for the sensitivity to repression by let-7 of various mutant forms of the Caenorhabditis elegans lin-41 3′ untranslated region and for other experimentally tested miRNA-target interactions in C. elegans and Drosophila melanogaster. These findings indicate a potent effect of target structure on target recognition by miRNAs and establish a structure-based framework for genome-wide identification of animal miRNA targets.
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We acknowledge the Computational Molecular Biology and Statistics Core at the Wadsworth Center for providing computing resources. This work was supported in part by US National Science Foundation grants DMS-0200970 and DBI-0650991 and US National Institutes of Health grant GM068726 to Y.D., and by US National Institutes of Health grants GM34028 and GM066826 to V.A. We thank F. Slack of Yale University for gifts of plasmids, and A. Lee, G. Ambros and members of the Ambros lab for technical help and advice.
The authors declare no competing financial interests.
Analysis of alternative initiation energy values. (PDF 65 kb)
Open blocks of nucleotides in lin-41 UTR constructs. (PDF 83 kb)
Analysis of published microRNA-target interactions. (PDF 54 kb)
Comparison of folding programs. (PDF 37 kb)
UTR sequences of lac-Z reporter constructs. (PDF 31 kb)
Spacer sequences. (PDF 26 kb)
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Long, D., Lee, R., Williams, P. et al. Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14, 287–294 (2007). https://doi.org/10.1038/nsmb1226
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