IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-25433-6.html
   My bibliography  Save this article

Expanding the binding specificity for RNA recognition by a PUF domain

Author

Listed:
  • Wei Zhou

    (University of Washington, Seattle
    University of Washington, Seattle
    The Rockefeller University)

  • Daniel Melamed

    (University of Washington, Seattle
    University of Haifa
    University of Haifa)

  • Gabor Banyai

    (The Rockefeller University)

  • Cindy Meyer

    (The Rockefeller University)

  • Thomas Tuschl

    (The Rockefeller University)

  • Marvin Wickens

    (University of Wisconsin-Madison)

  • Junyue Cao

    (The Rockefeller University)

  • Stanley Fields

    (University of Washington, Seattle
    University of Washington, Seattle)

Abstract

The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.

Suggested Citation

  • Wei Zhou & Daniel Melamed & Gabor Banyai & Cindy Meyer & Thomas Tuschl & Marvin Wickens & Junyue Cao & Stanley Fields, 2021. "Expanding the binding specificity for RNA recognition by a PUF domain," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25433-6
    DOI: 10.1038/s41467-021-25433-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-25433-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-25433-6?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
    ---><---

    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:12:y:2021:i:1:d:10.1038_s41467-021-25433-6. 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.