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Keth-seq for transcriptome-wide RNA structure mapping

Nature Chemical Biology volume 16, pages 489–492 (2020)Cite this article

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Abstract

RNA secondary structure is critical to RNA regulation and function. We report a new N3-kethoxal reagent that allows fast and reversible labeling of single-stranded guanine bases in live cells. This N3-kethoxal-based chemistry allows efficient RNA labeling under mild conditions and transcriptome-wide RNA secondary structure mapping.

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Fig. 1: N3-kethoxal and experimental evaluation of its selectivity, cell permeability and reversibility.
Fig. 2: Keth-seq method and the profile around rG4 regions.

Data availability

All genomic data sets have been deposited in the Gene Expression Omnibus under accession number GSE122096. Other data and materials are available from the authors upon reasonable request.

Code availability

All custom codes used in this study are available at https://github.com/Tsinghua-gongjing/Keth-seq.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (grant nos. 21572172, 21778040 and 21822704 to X.W.; 21432008, 91753201 and 21721005 to X.Z.; 31671355, 91740204 and 31761163007 to Q.C.Z.) and National Institutes of Health grant no. HG008935 (C.H.). C.H. is an investigator of the Howard Hughes Medical Institute. X.W. was supported by China Scholarship Council (CSC) during his visit to the University of Chicago. We acknowledge S. Frank, who edited the manuscript.

Author information

Author notes

  1. These authors contributed equally: Xiaocheng Weng, Jing Gong, Yi Chen, Tong Wu.

Authors and Affiliations

  1. Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA

    Xiaocheng Weng, Tong Wu, Fang Wang, Guanzheng Luo, Kai Chen, Lulu Hu, Honghui Ma, Pingluan Wang & Chuan He

  2. College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, China

    Xiaocheng Weng, Yi Chen, Shixi Yang, Yushu Yuan & Xiang Zhou

  3. MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China

    Jing Gong & Qiangfeng Cliff Zhang

  4. Wuhan University School of Pharmaceutical Sciences, Wuhan, China

    Fang Wang

Authors
  1. Xiaocheng Weng
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  15. Chuan He
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Contributions

X.W., Q.C.Z., X.Z. and C.H. conceived the project, designed the experiments and wrote the manuscript. X.W., Y.C. and T.W. performed the experiments with the help of F.W., S.Y., Y.Y., G.L., K.C., L.H., H.M. and P.W. J.G. and Q.C.Z. designed and performed the bioinformatics analysis.

Corresponding authors

Correspondence to Qiangfeng Cliff Zhang, Xiang Zhou or Chuan He.

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Competing interests

C.H. is a scientific founder and a member of the scientific advisory board of Accent Therapeutics, Inc., and a shareholder of Epican Genetech.

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Supplementary Information

Supplementary Figs. 1–15 and Notes 1 and 2.

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Weng, X., Gong, J., Chen, Y. et al. Keth-seq for transcriptome-wide RNA structure mapping. Nat Chem Biol 16, 489–492 (2020). https://doi.org/10.1038/s41589-019-0459-3

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