IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-03675-1.html
   My bibliography  Save this article

Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes

Author

Listed:
  • Sidika Tapsin

    (Genome Institute of Singapore)

  • Miao Sun

    (Genome Institute of Singapore)

  • Yang Shen

    (Genome Institute of Singapore)

  • Huibin Zhang

    (Agency for Science, Technology, and Research (A*STAR))

  • Xin Ni Lim

    (Genome Institute of Singapore)

  • Teodorus Theo Susanto

    (Genome Institute of Singapore)

  • Siwy Ling Yang

    (Genome Institute of Singapore)

  • Gui Sheng Zeng

    (Proteos)

  • Jasmine Lee

    (Proteos)

  • Alexander Lezhava

    (Genome Institute of Singapore)

  • Ee Lui Ang

    (Agency for Science, Technology, and Research (A*STAR))

  • Lian Hui Zhang

    (Proteos)

  • Yue Wang

    (Proteos)

  • Huimin Zhao

    (Agency for Science, Technology, and Research (A*STAR)
    University of Illinois at Urbana-Champaign)

  • Niranjan Nagarajan

    (Genome Institute of Singapore)

  • Yue Wan

    (Genome Institute of Singapore)

Abstract

RNAs are well-suited to act as cellular sensors that detect and respond to metabolite changes in the environment, due to their ability to fold into complex structures. Here, we introduce a genome-wide strategy called PARCEL that experimentally identifies RNA aptamers in vitro, in a high-throughput manner. By applying PARCEL to a collection of prokaryotic and eukaryotic organisms, we have revealed 58 new RNA aptamers to three key metabolites, greatly expanding the list of natural RNA aptamers. The newly identified RNA aptamers exhibit significant sequence conservation, are highly structured and show an unexpected prevalence in coding regions. We identified a prokaryotic precursor tmRNA that binds vitamin B2 (FMN) to facilitate its maturation, as well as eukaryotic mRNAs that bind and respond to FMN, suggesting FMN as the second RNA-binding ligand to affect eukaryotic expression. PARCEL results show that RNA-based sensing and gene regulation is more widespread than previously appreciated in different organisms.

Suggested Citation

  • Sidika Tapsin & Miao Sun & Yang Shen & Huibin Zhang & Xin Ni Lim & Teodorus Theo Susanto & Siwy Ling Yang & Gui Sheng Zeng & Jasmine Lee & Alexander Lezhava & Ee Lui Ang & Lian Hui Zhang & Yue Wang & , 2018. "Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03675-1
    DOI: 10.1038/s41467-018-03675-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-03675-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-03675-1?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
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.

    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:9:y:2018:i:1:d:10.1038_s41467-018-03675-1. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.