IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-19962-9.html
   My bibliography  Save this article

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations

Author

Listed:
  • Olivera Grujic

    (University of California, Los Angeles
    University of California, Los Angeles)

  • Tanya N. Phung

    (University of California, Los Angeles)

  • Soo Bin Kwon

    (University of California, Los Angeles
    University of California, Los Angeles)

  • Adriana Arneson

    (University of California, Los Angeles
    University of California, Los Angeles)

  • Yuju Lee

    (University of California, Los Angeles)

  • Kirk E. Lohmueller

    (University of California, Los Angeles
    University of California, Los Angeles
    University of California, Los Angeles)

  • Jason Ernst

    (University of California, Los Angeles
    University of California, Los Angeles
    University of California, Los Angeles
    Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles)

Abstract

Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) that is predictive of those bases. We further characterize the nature of constrained non-exonic bases with low CNEP scores using additional types of information. CNEP and CSS-CNEP are resources for analyzing constrained non-exonic bases in the genome.

Suggested Citation

  • Olivera Grujic & Tanya N. Phung & Soo Bin Kwon & Adriana Arneson & Yuju Lee & Kirk E. Lohmueller & Jason Ernst, 2020. "Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19962-9
    DOI: 10.1038/s41467-020-19962-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-19962-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-19962-9?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:11:y:2020:i:1:d:10.1038_s41467-020-19962-9. 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.