IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v2y2011i1d10.1038_ncomms1324.html
   My bibliography  Save this article

Predicting sites of ADAR editing in double-stranded RNA

Author

Listed:
  • Julie M. Eggington

    (University of Utah)

  • Tom Greene

    (University of Utah Health Sciences Center)

  • Brenda L. Bass

    (University of Utah)

Abstract

ADAR (adenosine deaminase that acts on RNA) editing enzymes target coding and noncoding double-stranded RNA (dsRNA) and are essential for neuronal function. Early studies showed that ADARs preferentially target adenosines with certain 5′ and 3′ neighbours. Here we use current Sanger sequencing protocols to perform a more accurate and quantitative analysis. We quantified editing sites in an ∼800-bp dsRNA after reaction with human ADAR1 or ADAR2, or their catalytic domains alone. These large data sets revealed that neighbour preferences are mostly dictated by the catalytic domain, but ADAR2's dsRNA-binding motifs contribute to 3′ neighbour preferences. For all proteins, the 5′ nearest neighbour was most influential, but adjacent bases also affected editing site choice. We developed algorithms to predict editing sites in dsRNA of any sequence, and provide a web-based application. The predictive power of the algorithm on fully base-paired dsRNA, compared with biological substrates containing mismatches, bulges and loops, elucidates structural contributions to editing specificity.

Suggested Citation

  • Julie M. Eggington & Tom Greene & Brenda L. Bass, 2011. "Predicting sites of ADAR editing in double-stranded RNA," Nature Communications, Nature, vol. 2(1), pages 1-9, September.
    • Handle: RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1324
    DOI: 10.1038/ncomms1324
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms1324
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms1324?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. Suba Rajendren & Xiang Ye & William Dunker & Antiana Richardson & John Karijolich, 2023. "The cellular and KSHV A-to-I RNA editome in primary effusion lymphoma and its role in the viral lifecycle," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Karthika Devi Kiran Kumar & Shubhangi Singh & Stella Maria Schmelzle & Paul Vogel & Carolin Fruhner & Alfred Hanswillemenke & Adrian Brun & Jacqueline Wettengel & Yvonne Füll & Lukas Funk & Valentin M, 2024. "An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Orshay Gabay & Yoav Shoshan & Eli Kopel & Udi Ben-Zvi & Tomer D. Mann & Noam Bressler & Roni Cohen‐Fultheim & Amos A. Schaffer & Shalom Hillel Roth & Ziv Tzur & Erez Y. Levanon & Eli Eisenberg, 2022. "Landscape of adenosine-to-inosine RNA recoding across human tissues," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    4. Hugo C. Medina-Munoz & Eric Kofman & Pratibha Jagannatha & Evan A. Boyle & Tao Yu & Krysten L. Jones & Jasmine R. Mueller & Grace D. Lykins & Andrew T. Doudna & Samuel S. Park & Steven M. Blue & Brodi, 2024. "Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Marlon S. Zambrano-Mila & Monika Witzenberger & Zohar Rosenwasser & Anna Uzonyi & Ronit Nir & Shay Ben-Aroya & Erez Y. Levanon & Schraga Schwartz, 2023. "Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2," Nature Communications, Nature, vol. 14(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:2:y:2011:i:1:d:10.1038_ncomms1324. 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.