IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v7y2016i1d10.1038_ncomms12249.html
   My bibliography  Save this article

Systematic identification of protein combinations mediating chromatin looping

Author

Listed:
  • Kai Zhang

    (Graduate Program in Bioinformatics and Systems Biology, University of California, La Jolla)

  • Nan Li

    (University of California, La Jolla
    University of California, La Jolla)

  • Richard I. Ainsworth

    (University of California, La Jolla
    University of California, La Jolla)

  • Wei Wang

    (Graduate Program in Bioinformatics and Systems Biology, University of California, La Jolla
    University of California, La Jolla
    University of California, La Jolla)

Abstract

Chromatin looping plays a pivotal role in gene expression and other biological processes through bringing distal regulatory elements into spatial proximity. The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in three-dimensional (3D) space. Previously, identification of DBP cooperation has been limited to those binding to neighbouring regions in the proximal linear genome (1D cooperation). Here we present the first study that integrates protein ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs. We develop a new network model that allows identification of cooperation between multiple DBPs and reveals cell-type-specific and -independent regulations. Using this framework, we retrieve many known and previously unknown 3D-cooperations between DBPs in chromosomal loops that may be a key factor in influencing the 3D organization of chromatin.

Suggested Citation

  • Kai Zhang & Nan Li & Richard I. Ainsworth & Wei Wang, 2016. "Systematic identification of protein combinations mediating chromatin looping," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12249
    DOI: 10.1038/ncomms12249
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms12249
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms12249?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. Alexandros Armaos & François Serra & Iker Núñez-Carpintero & Ji-Heui Seo & Sylvan C. Baca & Stefano Gustincich & Alfonso Valencia & Matthew L. Freedman & Davide Cirillo & Claudia Giambartolomei & Gian, 2023. "The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, 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:7:y:2016:i:1:d:10.1038_ncomms12249. 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.