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Landscape and variation of RNA secondary structure across the human transcriptome

Author

Listed:
  • Yue Wan

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine
    Stem Cell and Development, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672)

  • Kun Qu

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

  • Qiangfeng Cliff Zhang

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

  • Ryan A. Flynn

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

  • Ohad Manor

    (Weizmann Institute of Science, Rehovet 76100, Israel)

  • Zhengqing Ouyang

    (Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine
    Present address: The Jackson Laboratory for Genomic Medicine, 263 Farmington Avenue, ASB Call Box 901 Farmington, Connecticut 06030, USA.)

  • Jiajing Zhang

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

  • Robert C. Spitale

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

  • Michael P. Snyder

    (Stanford University School of Medicine)

  • Eran Segal

    (Weizmann Institute of Science, Rehovet 76100, Israel)

  • Howard Y. Chang

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

Abstract

An RNA secondary structure (RSS) map of coding and noncoding RNA from a human family (two parents and their child) is produced; this reveals that approximately 15% of all transcribed single nucleotide variants (SNVs) alter local RNA structure, and these SNVs are depleted in certain locations, suggesting that particular RNA structures are important at those sites.

Suggested Citation

  • Yue Wan & Kun Qu & Qiangfeng Cliff Zhang & Ryan A. Flynn & Ohad Manor & Zhengqing Ouyang & Jiajing Zhang & Robert C. Spitale & Michael P. Snyder & Eran Segal & Howard Y. Chang, 2014. "Landscape and variation of RNA secondary structure across the human transcriptome," Nature, Nature, vol. 505(7485), pages 706-709, January.
    • Handle: RePEc:nat:nature:v:505:y:2014:i:7485:d:10.1038_nature12946
    DOI: 10.1038/nature12946
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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. Anneke Brümmer & Sven Bergmann, 2024. "Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Elzbieta Kierzek & Xiaoju Zhang & Richard M. Watson & Scott D. Kennedy & Marta Szabat & Ryszard Kierzek & David H. Mathews, 2022. "Secondary structure prediction for RNA sequences including N6-methyladenosine," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    4. 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.
    5. 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.

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