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A small molecule enhances RNA interference and promotes microRNA processing

Nature Biotechnology volume 26, pages 933–940 (2008)Cite this article

Abstract

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are sequence-specific post-transcriptional regulators of gene expression. Although major components of the RNA interference (RNAi) pathway have been identified, regulatory mechanisms for this pathway remain largely unknown. Here we demonstrate that the RNAi pathway can be modulated intracellularly by small molecules. We have developed a cell-based assay to monitor the activity of the RNAi pathway and find that the small-molecule enoxacin (Penetrex) enhances siRNA-mediated mRNA degradation and promotes the biogenesis of endogenous miRNAs. We show that this RNAi-enhancing activity depends on the trans-activation-responsive region RNA-binding protein. Our results provide a proof-of-principle demonstration that small molecules can be used to modulate the activity of the RNAi pathway. RNAi enhancers may be useful in the development of research tools and therapeutics.

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Figure 1: Identification of a small molecule enhancing RNAi through a chemical screen.
Figure 2: Enoxacin potentiates additional synthetic siRNA-induced gene knockdown.
Figure 3: Determination of chemical structure required for RNAi-enhancing activity.
Figure 4: Enoxacin promotes the processing of miRNAs and the loading of siRNA duplexes onto RISCs.
Figure 5: Enoxacin facilitates the TRBP-RNA interaction, and the RNAi-enhancing activity is TRBP-dependent.
Figure 6: Enoxacin enhances RNAi in vivo.

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Acknowledgements

We would like to thank S. Warren, S. Chang, K. Garber and C. Strauss for their helpful discussions and critical reading of the manuscript and H. Ju for technical assistance. We thank I. Verma, J. Belasco and G. Hannon for providing us the plasmids. Q.L. is a Damon Runyon Scholar (DRS-43) and is supported by the Welch Foundation (I-1608). P.J. is supported by NIH grants (NS051630 and MH076090). P.J. is the recipient of a Beckman Young Investigator Award and a Basil O'Connor Scholar Research Award and is an Alfred P. Sloan Research Fellow in Neuroscience.

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Author notes

  1. Ge Shan and Yujing Li: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, 30322, Georgia, USA

    Ge Shan, Yujing Li, Wendi Li, Keith E Szulwach, Ranhui Duan, Anthony W S Chan & Peng Jin

  2. Department of Chemistry, The University of Chicago, 929 East 57th St., Chicago, 60637, Illinois, USA

    Junliang Zhang, Lianghua Lu & Chuan He

  3. Department of Molecular and Integrative Neurosciences, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, 33458, Florida, USA

    Mohammad A Faghihi, Ahmad M Khalil & Claes Wahlestedt

  4. Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, 75390, Texas, USA

    Zain Paroo & Qinghua Liu

  5. The College of Chemistry, Peking University, 202 Chengfu Rd., Beijing, 100871, P.R., China

    Zhangjie Shi

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  1. Ge Shan
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Contributions

P.J. designed the research. G.S. conducted the chemical screen and identified the small molecule presented in this paper. G.S. and Y.L. performed the majority of mechanistic experiments. J.Z., L.L., Z.S. and C.H. performed chemical synthesis. G.S., Y.L., W.L., M.A.F., A.M.K. and C.W. performed additional testing on the compound. K.E.S. and R.D. performed miRNA profiling and developed the reporter system. A.W.S.C., Z.P. and Q.L. provided some reagents used in this paper. G.S., Y.L. and P.J. wrote the paper.

Corresponding author

Correspondence to Peng Jin.

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Competing interests

P.J. is the scientific founder of Effigene Pharmaceuticals, Inc. Effigene is engaged in the development of RNAi modulators.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9, Tables 1–4, Methods (PDF 3440 kb)

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Shan, G., Li, Y., Zhang, J. et al. A small molecule enhances RNA interference and promotes microRNA processing. Nat Biotechnol 26, 933–940 (2008). https://doi.org/10.1038/nbt.1481

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