IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v7y2016i1d10.1038_ncomms10407.html
   My bibliography  Save this article

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression

Author

Listed:
  • Michal Brunwasser-Meirom

    (Technion—Israel Institute of Technology)

  • Yaroslav Pollak

    (Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology)

  • Sarah Goldberg

    (Technion—Israel Institute of Technology)

  • Lior Levy

    (Technion—Israel Institute of Technology)

  • Orna Atar

    (Technion—Israel Institute of Technology)

  • Roee Amit

    (Technion—Israel Institute of Technology
    Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology)

Abstract

We explore a model for ‘quenching-like’ repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model’s predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10–11 bp insertions or deletions (INDELs) and sensitive to 5–6 bp INDELs. We test this prediction on 61 σ54-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers’ sequences to the DNA’s helical repeat.

Suggested Citation

  • Michal Brunwasser-Meirom & Yaroslav Pollak & Sarah Goldberg & Lior Levy & Orna Atar & Roee Amit, 2016. "Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression," Nature Communications, Nature, vol. 7(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10407
    DOI: 10.1038/ncomms10407
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms10407
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms10407?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:7:y:2016:i:1:d:10.1038_ncomms10407. 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.