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Genome-wide measurement of RNA secondary structure in yeast

Author

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  • Michael Kertesz

    (Weizmann Institute of Science
    Present address: Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California 94305, USA.)

  • Yue Wan

    (Howard Hughes Medical Institute, Program in Epithelial Biology, Stanford University School of Medicine)

  • Elad Mazor

    (Weizmann Institute of Science)

  • John L. Rinn

    (The Broad Institute of Harvard and Massachusetts Institute of Technology)

  • Robert C. Nutter

    (Life Technologies)

  • Howard Y. Chang

    (Howard Hughes Medical Institute, Program in Epithelial Biology, Stanford University School of Medicine)

  • Eran Segal

    (Weizmann Institute of Science
    Weizmann Institute of Science)

Abstract

RNA in close-up Despite the importance of RNA structure for its regulation and function, relatively few RNA structures are known experimentally and there is no experimental method for high-throughput measurement of RNA structure. Instead, computational methods are the norm for genome-wide applications. Recent technologies have allowed RNA structure to be calculated on a larger scale, however. Kertesz et al. use a deep-sequencing approach to determine the structure of the entire transcriptome of the yeast Saccharomyces cerevisiae. The results provide interesting hints about the role of secondary structure in translation, and set the stage for examination of how such structures can change in response to environmental conditions.

Suggested Citation

  • Michael Kertesz & Yue Wan & Elad Mazor & John L. Rinn & Robert C. Nutter & Howard Y. Chang & Eran Segal, 2010. "Genome-wide measurement of RNA secondary structure in yeast," Nature, Nature, vol. 467(7311), pages 103-107, September.
    • Handle: RePEc:nat:nature:v:467:y:2010:i:7311:d:10.1038_nature09322
    DOI: 10.1038/nature09322
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    Cited by:

    1. 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.
    2. Jun Inamo & Akari Suzuki & Mahoko Takahashi Ueda & Kensuke Yamaguchi & Hiroshi Nishida & Katsuya Suzuki & Yuko Kaneko & Tsutomu Takeuchi & Hiroaki Hatano & Kazuyoshi Ishigaki & Yasushi Ishihama & Kazu, 2024. "Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms," Nature Communications, Nature, vol. 15(1), pages 1-19, 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.
    4. Shivali Patel & Alec N. Sexton & Madison S. Strine & Craig B. Wilen & Matthew D. Simon & Anna Marie Pyle, 2023. "Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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