IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43632-1.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43632-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-43632-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Alejandro Gomez Toledo & Eleni Bratanis & Erika Velásquez & Sounak Chowdhury & Berit Olofsson & James T. Sorrentino & Christofer Karlsson & Nathan E. Lewis & Jeffrey D. Esko & Mattias Collin & Oonagh , 2023. "Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43632-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.