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RNA SHAPE analysis in living cells

Nature Chemical Biology volume 9, pages 18–20 (2013)Cite this article

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Abstract

RNA structure has important roles in practically every facet of gene regulation, but the paucity of in vivo structural probes limits current understanding. Here we design, synthesize and demonstrate two new chemical probes that enable selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) in living cells. RNA structures in human, mouse, fly, yeast and bacterial cells are read out at single-nucleotide resolution, revealing tertiary contacts and RNA-protein interactions.

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Figure 1: Design and experimental evaluation of NAI and FAI.
Figure 2: 5S rRNA has different modification patterns in cells.

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Acknowledgements

We thank Y. Wan, G. Zheng and R. Das for comments. This work is supported by the US National Institutes of Health (R01 GM072705 to E.T.K. and R01-HG004361 to H.Y.C.), the A.P. Giannini Foundation (R.C.S.) and the Stanford MedScholars Program (R.A.F.). H.Y.C. is an Early Career Scientist of the Howard Hughes Medical Institute.

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Author notes

  1. Robert C Spitale, Pete Crisalli and Ryan A Flynn: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA

    Robert C Spitale, Ryan A Flynn, Eduardo A Torre & Howard Y Chang

  2. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA

    Robert C Spitale, Ryan A Flynn, Eduardo A Torre & Howard Y Chang

  3. Department of Chemistry, Stanford University, Stanford, California, USA

    Pete Crisalli & Eric T Kool

Authors
  1. Robert C Spitale
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  2. Pete Crisalli
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  3. Ryan A Flynn
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  4. Eduardo A Torre
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  5. Eric T Kool
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  6. Howard Y Chang
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Contributions

R.C.S., E.T.K. and H.Y.C. conceived the project. R.C.S., P.C., R.A.F. and E.A.T. performed the experiments. R.C.S., P.C., R.A.F., E.T.K. and H.Y.C. analyzed the data. R.C.S. and H.Y.C. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Eric T Kool or Howard Y Chang.

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The authors declare no competing financial interests.

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Spitale, R., Crisalli, P., Flynn, R. et al. RNA SHAPE analysis in living cells. Nat Chem Biol 9, 18–20 (2013). https://doi.org/10.1038/nchembio.1131

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