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In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub

Author

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  • Fang Liu

    (Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
    Institut Pasteur of Shanghai, Chinese Academy of Sciences)

  • Ziying Chen

    (Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
    Fudan University
    Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University)

  • Shuo Zhang

    (Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
    Institut Pasteur of Shanghai, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Kejing Wu

    (Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
    Institut Pasteur of Shanghai, Chinese Academy of Sciences)

  • Cheng Bei

    (Fudan University)

  • Chuan Wang

    (Fudan University)

  • Yanjie Chao

    (Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
    Institut Pasteur of Shanghai, Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences)

Abstract

Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3’UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.

Suggested Citation

  • Fang Liu & Ziying Chen & Shuo Zhang & Kejing Wu & Cheng Bei & Chuan Wang & Yanjie Chao, 2023. "In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43632-1
    DOI: 10.1038/s41467-023-43632-1
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    1. Michaela Huber & Anne Lippegaus & Sahar Melamed & Malte Siemers & Benjamin R. Wucher & Mona Hoyos & Carey Nadell & Gisela Storz & Kai Papenfort, 2022. "An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Nikolai Peschek & Roman Herzog & Praveen K. Singh & Marcel Sprenger & Fabian Meyer & Kathrin S. Fröhlich & Luise Schröger & Marc Bramkamp & Knut Drescher & Kai Papenfort, 2020. "RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. Pengbo Cao & Derek Fleming & Dina A. Moustafa & Stephen K. Dolan & Kayla H. Szymanik & Whitni K. Redman & Anayancy Ramos & Frances L. Diggle & Christopher S. Sullivan & Joanna B. Goldberg & Kendra P. , 2023. "A Pseudomonas aeruginosa small RNA regulates chronic and acute infection," Nature, Nature, vol. 618(7964), pages 358-364, June.
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