IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-03694-y.html
   My bibliography  Save this article

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

Author

Listed:
  • G. Bonora

    (University of Washington)

  • X. Deng

    (University of Washington)

  • H. Fang

    (University of Washington)

  • V. Ramani

    (University of Washington)

  • R. Qiu

    (University of Washington)

  • J. B. Berletch

    (University of Washington)

  • G. N. Filippova

    (University of Washington)

  • Z. Duan

    (University of Washington
    University of Washington)

  • J. Shendure

    (University of Washington)

  • W. S. Noble

    (University of Washington
    University of Washington)

  • C. M. Disteche

    (University of Washington
    University of Washington)

Abstract

The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts, separated by a hinge region. Using Hi-C in edited mouse cells with allelic deletions or inversions within the hinge, here we show that the conserved Dxz4 locus is necessary to maintain this bipartite structure. Dxz4 orientation controls the distribution of contacts on the Xi, as shown by a massive reversal in long-range contacts after Dxz4 inversion. Despite an increase in CTCF binding and chromatin accessibility on the Xi in Dxz4-edited cells, only minor changes in TAD structure and gene expression were detected, in accordance with multiple epigenetic mechanisms ensuring X silencing. We propose that Dxz4 represents a structural platform for frequent long-range contacts with multiple loci in a direction dictated by the orientation of its bank of CTCF motifs, which may work as a ratchet to form the distinctive bipartite structure of the condensed Xi.

Suggested Citation

  • G. Bonora & X. Deng & H. Fang & V. Ramani & R. Qiu & J. B. Berletch & G. N. Filippova & Z. Duan & J. Shendure & W. S. Noble & C. M. Disteche, 2018. "Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome," Nature Communications, Nature, vol. 9(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03694-y
    DOI: 10.1038/s41467-018-03694-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-03694-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-018-03694-y?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. Christian Much & Erika L. Lasda & Isabela T. Pereira & Tenaya K. Vallery & Daniel Ramirez & Jordan P. Lewandowski & Robin D. Dowell & Michael J. Smallegan & John L. Rinn, 2024. "The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation," Nature Communications, Nature, vol. 15(1), pages 1-13, 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:9:y:2018:i:1:d:10.1038_s41467-018-03694-y. 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.