IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-017-02525-w.html
   My bibliography  Save this article

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Author

Listed:
  • Fidel Ramírez

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Vivek Bhardwaj

    (Max Planck Institute of Immunobiology and Epigenetics
    Faculty of Biology, University of Freiburg)

  • Laura Arrigoni

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Kin Chung Lam

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Björn A. Grüning

    (University of Freiburg, Department of Computer Science)

  • José Villaveces

    (Max Planck Institute of Biochemistry and Computational Biology)

  • Bianca Habermann

    (Max Planck Institute of Biochemistry and Computational Biology)

  • Asifa Akhtar

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Thomas Manke

    (Max Planck Institute of Immunobiology and Epigenetics)

Abstract

Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de .

Suggested Citation

  • Fidel Ramírez & Vivek Bhardwaj & Laura Arrigoni & Kin Chung Lam & Björn A. Grüning & José Villaveces & Bianca Habermann & Asifa Akhtar & Thomas Manke, 2018. "High-resolution TADs reveal DNA sequences underlying genome organization in flies," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02525-w
    DOI: 10.1038/s41467-017-02525-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-017-02525-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-017-02525-w?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. Nicholas Sim & Jean-Michel Carter & Kamalakshi Deka & Benita Kiat Tee Tan & Yirong Sim & Suet-Mien Tan & Yinghui Li, 2024. "TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, 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_s41467-017-02525-w. 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.