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Genome-wide profiling of human cap-independent translation-enhancing elements

Nature Methods volume 10, pages 747–750 (2013)Cite this article

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Abstract

We report an in vitro selection strategy to identify RNA sequences that mediate cap-independent initiation of translation. This method entails mRNA display of trillions of genomic fragments, selection for initiation of translation and high-throughput deep sequencing. We identified >12,000 translation-enhancing elements (TEEs) in the human genome, generated a high-resolution map of human TEE-bearing regions (TBRs), and validated the function of a subset of sequences in vitro and in cultured cells.

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Figure 1: In vitro selection of RNA elements that mediate cap-independent translation.
Figure 2: Functional analysis of selected TEEs in human cells and in vitro.
Figure 3: Genomic landscape of human TEEs.

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References

  1. Sonenberg, N. & Hinnebusch, A.G. Cell 136, 731–745 (2009).

    Article  CAS  Google Scholar 

  2. Jackson, R.J., Hellen, C.U.T. & Pestova, T.V. Nat. Rev. Mol. Cell Biol. 10, 113–127 (2010).

    Article  Google Scholar 

  3. Shatsky, I.N., Dmitriev, S.E., Terenin, I.M. & Andreev, D.E. Mol. Cells 30, 285–293 (2010).

    Article  CAS  Google Scholar 

  4. Johannes, G., Carter, M.S., Eisen, M.B., Brown, P.O. & Sarnow, P. Proc. Natl. Acad. Sci. USA 96, 13118–13123 (1999).

    Article  CAS  Google Scholar 

  5. Spriggs, K.A., Stoneley, M., Bushell, M. & Willis, A.E. Biol. Cell 100, 27–38 (2008).

    Article  CAS  Google Scholar 

  6. Roberts, R.W. & Szostak, J.W. Proc. Natl. Acad. Sci. USA 94, 12297–12302 (1997).

    Article  CAS  Google Scholar 

  7. Salehi-Ashtiani, K., Luptak, A., Litovchick, A. & Szostak, J.W. Science 313, 1788–1792 (2006).

    Article  CAS  Google Scholar 

  8. Korbel, J.O. et al. Science 318, 420–426 (2007).

    Article  CAS  Google Scholar 

  9. Kasowski, M. et al. Science 328, 232–235 (2010).

    Article  CAS  Google Scholar 

  10. Gilbert, W.V., Zhou, K.H., Butler, T.K. & Doudna, J.A. Science 317, 1224–1227 (2007).

    Article  CAS  Google Scholar 

  11. Baranick, B.T. et al. Proc. Natl. Acad. Sci. USA 105, 4733–4738 (2008).

    Article  CAS  Google Scholar 

  12. Moss, B. Science 252, 1662–1667 (1991).

    Article  CAS  Google Scholar 

  13. Van Eden, M.E., Byrd, M.P., Sherrill, K.W. & Lloyd, R.E. RNA 10, 720–730 (2004).

    Article  CAS  Google Scholar 

  14. Mitchell, S.F. et al. Mol. Cell 39, 950–962 (2010).

    Article  CAS  Google Scholar 

  15. Mokrejs, M. et al. Nucleic Acids Res. 38, D131–D136 (2010).

    Article  CAS  Google Scholar 

  16. Sakharkar, M.K., Chow, V.T. & Kangueane, P. In Silico Biol. 4, 387–393 (2004).

    CAS  PubMed  Google Scholar 

  17. Akey, J.M. Genome Res. 19, 711–722 (2009).

    Article  CAS  Google Scholar 

  18. Sabeti, P.C. et al. Science 312, 1614–1620 (2006).

    Article  CAS  Google Scholar 

  19. Traynelis, S.F. et al. Pharmacol. Rev. 62, 405–496 (2010).

    Article  CAS  Google Scholar 

  20. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  21. Ji, H.K. et al. Nat. Biotechnol. 26, 1293–1300 (2008).

    Article  CAS  Google Scholar 

  22. Kin, T. & Ono, Y. Methods Biochem. Anal. 23, 2945–2946 (2007).

    CAS  Google Scholar 

  23. Thomas, P.D. et al. Genome Res. 13, 2129–2141 (2003).

    Article  CAS  Google Scholar 

  24. Auerbach, R.K. et al. Proc. Natl. Acad. Sci. USA 106, 1492–1493 (2009).

    Article  Google Scholar 

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Acknowledgements

We thank J. Szostak (Harvard Medical School) and J. Doudna (University of California–Berkeley) for providing the human genome library and luciferase vectors, respectively; N. Pakulis, M. Leon, J. Flores and K. Fenton for technical assistance; G. McInnes for initial bioinformatics analysis; and members of the Chaput laboratory for helpful discussions and comments on the manuscript. This work was supported by US National Institutes of Health to J.C.C. (Eureka Award; GM085530) and S.K. (HG002096-11).

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Authors and Affiliations

  1. Center for Evolutionary Medicine and Informatics in the Biodesign Institute, Arizona State University, Tempe, Arizona, USA

    Brian P Wellensiek, Andrew C Larsen, Bret Stephens, Kim Kukurba, Natalia Briones, Li Liu, Sudhir Kumar & John C Chaput

  2. Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA

    Kim Kukurba & John C Chaput

  3. Department of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, California, USA

    Karl Waern & Michael Snyder

  4. Center for Infectious Diseases and Vaccinology in the Biodesign Institute, Arizona State University, Tempe, Arizona, USA

    Bertram L Jacobs

  5. School of Life Sciences, Arizona State University, Tempe, Arizona, USA

    Bertram L Jacobs & Sudhir Kumar

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  1. Brian P Wellensiek
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  2. Andrew C Larsen
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Contributions

J.C.C. conceived the project. J.C.C., B.P.W., B.L.J., S.K. and L.L. designed the experiments. B.P.W., B.S., K.W., A.C.L., K.K. and N.B. performed the experiments. J.C.C., B.P.W., A.C.L., K.K., L.L., S.K. and M.S. analyzed the data. J.C.C. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to John C Chaput.

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Competing interests

B.L.J., S.K. and J.C.C. are named inventors on a patent application (PCT/US11/44198) on the technology described in this manuscript.

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Wellensiek, B., Larsen, A., Stephens, B. et al. Genome-wide profiling of human cap-independent translation-enhancing elements. Nat Methods 10, 747–750 (2013). https://doi.org/10.1038/nmeth.2522

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