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In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Author

Listed:
  • Yiliang Ding

    (Pennsylvania State University, University Park
    Pennsylvania State University, University Park
    Center for RNA Molecular Biology, Pennsylvania State University, University Park)

  • Yin Tang

    (Pennsylvania State University, University Park
    Center for RNA Molecular Biology, Pennsylvania State University, University Park
    Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park)

  • Chun Kit Kwok

    (Pennsylvania State University, University Park
    Center for RNA Molecular Biology, Pennsylvania State University, University Park)

  • Yu Zhang

    (Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park
    Pennsylvania State University, University Park)

  • Philip C. Bevilacqua

    (Pennsylvania State University, University Park
    Center for RNA Molecular Biology, Pennsylvania State University, University Park
    Plant Biology Graduate Program, Pennsylvania State University, University Park)

  • Sarah M. Assmann

    (Pennsylvania State University, University Park
    Center for RNA Molecular Biology, Pennsylvania State University, University Park
    Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park
    Plant Biology Graduate Program, Pennsylvania State University, University Park)

Abstract

RNA adopts vast and complicated secondary structures in the living cell; reported here is a new approach, structure-seq, that characterises RNA structure in vivo on a genome-wide scale at nucleotide resolution and should be applicable to any organism.

Suggested Citation

  • Yiliang Ding & Yin Tang & Chun Kit Kwok & Yu Zhang & Philip C. Bevilacqua & Sarah M. Assmann, 2014. "In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features," Nature, Nature, vol. 505(7485), pages 696-700, January.
    • Handle: RePEc:nat:nature:v:505:y:2014:i:7485:d:10.1038_nature12756
    DOI: 10.1038/nature12756
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    Cited by:

    1. Rui Mao & Praveen Kumar Raj Kumar & Cheng Guo & Yang Zhang & Chun Liang, 2014. "Comparative Analyses between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana Using Random Forest and Support Vector Machine," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-12, August.
    2. 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.
    3. Yan Li & Kristofer G. Reyes & Jorge Vazquez-Anderson & Yingfei Wang & Lydia M. Contreras & Warren B. Powell, 2018. "A Knowledge Gradient Policy for Sequencing Experiments to Identify the Structure of RNA Molecules Using a Sparse Additive Belief Model," INFORMS Journal on Computing, INFORMS, vol. 30(4), pages 750-767, November.

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