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Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

Author

Listed:
  • Silvi Rouskin

    (California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California)

  • Meghan Zubradt

    (California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California)

  • Stefan Washietl

    (Massachusetts Institute of Technology
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
    The Broad Institute)

  • Manolis Kellis

    (Massachusetts Institute of Technology
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology
    The Broad Institute)

  • Jonathan S. Weissman

    (California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California)

Abstract

Understanding how RNA structure influences its function has been hampered by a lack of approaches that can accurately quantify RNA structure in vivo; here, RNA structure is revealed on a global scale and with nucleotide-level resolution, showing that there is less structure within cells than expected from in vitro and in silico analyses.

Suggested Citation

  • Silvi Rouskin & Meghan Zubradt & Stefan Washietl & Manolis Kellis & Jonathan S. Weissman, 2014. "Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo," Nature, Nature, vol. 505(7485), pages 701-705, January.
    • Handle: RePEc:nat:nature:v:505:y:2014:i:7485:d:10.1038_nature12894
    DOI: 10.1038/nature12894
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    Citations

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    Cited by:

    1. Bo Yu & Pan Li & Qiangfeng Cliff Zhang & Lin Hou, 2022. "Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Tammy C. T. Lan & Matty F. Allan & Lauren E. Malsick & Jia Z. Woo & Chi Zhu & Fengrui Zhang & Stuti Khandwala & Sherry S. Y. Nyeo & Yu Sun & Junjie U. Guo & Mark Bathe & Anders Näär & Anthony Griffith, 2022. "Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Gongwang Yu & Yao Liu & Zizhang Li & Shuyun Deng & Zhuoxing Wu & Xiaoyu Zhang & Wenbo Chen & Junnan Yang & Xiaoshu Chen & Jian-Rong Yang, 2023. "Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Ryan Damme & Kongpan Li & Minjie Zhang & Jianhui Bai & Wilson H. Lee & Joseph D. Yesselman & Zhipeng Lu & Willem A. Velema, 2022. "Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Bin Shao & Jiawei Yan & Jing Zhang & Lili Liu & Ye Chen & Allen R. Buskirk, 2024. "Riboformer: a deep learning framework for predicting context-dependent translation dynamics," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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