Potent effect of target structure on microRNA function

Abstract

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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Figure 1: A two-step model for hybridization between a structured mRNA and a partially complementary miRNA, illustrated for a single structural conformation of the target.
Figure 2: Target accessibility profiling by S fold.
Figure 3: The average ΣΔGtotal for miRNAs compared with that calculated for randomers, for positive miRNA-target interactions supported either by genetic epistasis evidence or by nongenetic evidence, and for the set of 12 putative lsy-6–target pairs predicted by conserved seed matching but having negative interactions in vivo27 (Table 2).
Figure 4: Linear regression prediction of in vivo repression sensitivity (measured by β-galactosidase (β-gal) expression ratios in adult and larval stages) by the ΣΔGtotal for the lin-41 3′ UTR mutant constructs (see Table 3).

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Acknowledgements

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.

Author information

D.L. and Y.D. designed the algorithm and performed computational modeling of RNA structure and thermodynamics, R.L. and V.A. analyzed lin-41 reporter genes in C. elegans, P.W. performed computational modeling and C.Y.C. developed the web interface.

Correspondence to Victor Ambros or Ye Ding.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Analysis of alternative initiation energy values. (PDF 65 kb)

Supplementary Table 1

Open blocks of nucleotides in lin-41 UTR constructs. (PDF 83 kb)

Supplementary Table 2

Analysis of published microRNA-target interactions. (PDF 54 kb)

Supplementary Table 3

Comparison of folding programs. (PDF 37 kb)

Supplementary Table 4

UTR sequences of lac-Z reporter constructs. (PDF 31 kb)

Supplementary Table 5

Spacer sequences. (PDF 26 kb)

Supplementary Data (PDF 112 kb)

Supplementary Methods (PDF 147 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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