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Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

Nature Structural & Molecular Biology volume 18, pages 1139–1146 (2011)Cite this article

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Abstract

Most metazoan microRNAs (miRNAs) target many genes for repression, but the nematode lsy-6 miRNA is much less proficient. Here we show that the low proficiency of lsy-6 can be recapitulated in HeLa cells and that miR-23, a mammalian miRNA, also has low proficiency in these cells. Reporter results and array data indicate two properties of these miRNAs that impart low proficiency: their weak predicted seed-pairing stability (SPS) and their high target-site abundance (TA). These two properties also explain differential propensities of small interfering RNAs (siRNAs) to repress unintended targets. Using these insights, we expand the TargetScan tool for quantitatively predicting miRNA regulation (and siRNA off-targeting) to model differential miRNA (and siRNA) proficiencies, thereby improving prediction performance. We propose that siRNAs designed to have both weaker SPS and higher TA will have fewer off-targets without compromised on-target activity.

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Figure 1: Strengthening SPS while decreasing TA imparted typical targeting proficiency to lsy-6 and miR-23 miRNAs.
Figure 2: Separating the effects of SPS and TA on miRNA targeting proficiency.
Figure 3: Impact of TA and SPS on sRNA targeting proficiency, as determined using array data.
Figure 4: Predictive performance of the context+ model, which considers miRNA or siRNA proficiency in addition to site context.

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Acknowledgements

We thank D. Didiano and O. Hobert (Columbia University) for lsy-6 target constructs and V. Auyeung, R. Friedman, C. Jan and H. Guo for helpful discussions and for sharing data sets before publication. This work was supported by US National Institutes of Health grant GM067031 (D.P.B.) and a Research Settlement Fund for the new faculty of SNU (D.B.). D.P.B. is an investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Andrew Grimson

    Present address: Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.,

  2. David M Garcia and Daehyun Baek: These authors contributed equally to this work.

Authors and Affiliations

  1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA

    David M Garcia, Daehyun Baek, Chanseok Shin, George W Bell, Andrew Grimson & David P Bartel

  2. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    David M Garcia, Daehyun Baek, Chanseok Shin, Andrew Grimson & David P Bartel

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    David M Garcia, Daehyun Baek, Chanseok Shin, Andrew Grimson & David P Bartel

  4. School of Biological Sciences, Seoul National University, Seoul, Republic of Korea

    Daehyun Baek

  5. Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea

    Daehyun Baek

  6. Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea

    Chanseok Shin

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Contributions

D.M.G. carried out most reporter assays and associated experiments and analyses. D.B. carried out all the computational analyses except for reporter analyses. G.W.B. implemented revisions to the TargetScan site. C.S. and A.G. carried out assays and analyses involving miR-23. D.M.G., D.B. and D.P.B. wrote the paper.

Corresponding authors

Correspondence to Daehyun Baek or David P Bartel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Tables 1–5. (PDF 2239 kb)

Supplementary Data 1

175 microarrays analyzed in this study. (XLSX 24 kb)

Supplementary Data 2

Human and C. elegans miRNA families, conserved in vertebrates and nematodes, respectively. (XLSX 22 kb)

Supplementary Data 3

Reference mRNAs. (ZIP 17965 kb)

Supplementary Data 4

mRNA fold-change values. (XLSX 17534 kb)

Supplementary Data 5

Predicted SPS and TA values for all heptamers in C. elegans, human and HeLa, mouse, and D. melanogaster. (XLSX 3972 kb)

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Garcia, D., Baek, D., Shin, C. et al. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18, 1139–1146 (2011). https://doi.org/10.1038/nsmb.2115

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