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Progress and challenges for chemical probing of RNA structure inside living cells

Nature Chemical Biology volume 11, pages 933–941 (2015)Cite this article

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Abstract

Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges.

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Figure 1: The functional and structural complexity of RNA.
Figure 2: Chemical methods to probe RNA structure.
Figure 3: Methods to measure RNA structure inside living cells.
Figure 4: icSHAPE is a novel chemical probing method that permits transcriptome-wide interrogation of RNA structure.
Figure 5: Outstanding challenges for understanding RNA structure inside living cells.

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Acknowledgements

We thank members of the Spitale laboratory and R. Flynn for helpful discussions. We also thank professors S. Woodson and A. Laederach for critical reading of the manuscript. The University of California, Irvine and the US National Institutes of Health Director's New Innovator Award (grant 1DP2GM119164-01) support RNA research in the Spitale lab.

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  1. Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA

    Miles Kubota, Catherine Tran & Robert C Spitale

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Correspondence to Robert C Spitale.

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Kubota, M., Tran, C. & Spitale, R. Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol 11, 933–941 (2015). https://doi.org/10.1038/nchembio.1958

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