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NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions

Author

Listed:
  • Shurong Liu

    (Sun Yat-sen University)

  • Junhong Huang

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Jie Zhou

    (Sun Yat-sen University)

  • Siyan Chen

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Wujian Zheng

    (Sun Yat-sen University)

  • Chang Liu

    (Sun Yat-sen University)

  • Qiao Lin

    (Sun Yat-sen University)

  • Ping Zhang

    (Sun Yat-sen University)

  • Di Wu

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Simeng He

    (Sun Yat-sen University)

  • Jiayi Ye

    (Sun Yat-sen University)

  • Shun Liu

    (The University of Chicago)

  • Keren Zhou

    (Beckman Research Institute of City of Hope)

  • Bin Li

    (Sun Yat-sen University)

  • Lianghu Qu

    (Sun Yat-sen University)

  • Jianhua Yang

    (Sun Yat-sen University
    Sun Yat-sen University)

Abstract

Up to 80% of the human genome produces “dark matter” RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.

Suggested Citation

  • Shurong Liu & Junhong Huang & Jie Zhou & Siyan Chen & Wujian Zheng & Chang Liu & Qiao Lin & Ping Zhang & Di Wu & Simeng He & Jiayi Ye & Shun Liu & Keren Zhou & Bin Li & Lianghu Qu & Jianhua Yang, 2024. "NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46596-y
    DOI: 10.1038/s41467-024-46596-y
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    References listed on IDEAS

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