IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-54740-x.html
   My bibliography  Save this article

Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription

Author

Listed:
  • Julio Cordero

    (Heidelberg University
    German Centre for Cardiovascular Research (DZHK)
    Max-Planck-Institute for Heart and Lung Research)

  • Guruprasadh Swaminathan

    (UMR 7365)

  • Diana G. Rogel-Ayala

    (Max-Planck-Institute for Heart and Lung Research
    UMR 7365)

  • Karla Rubio

    (Max-Planck-Institute for Heart and Lung Research
    UMR 7365
    Massachusetts General Hospital and Harvard Medical School
    Benemérita Universidad Autónoma de Puebla)

  • Adel Elsherbiny

    (Heidelberg University
    German Centre for Cardiovascular Research (DZHK))

  • Samina Mahmood

    (Max-Planck-Institute for Heart and Lung Research)

  • Witold Szymanski

    (Philipps-University Marburg)

  • Johannes Graumann

    (Philipps-University Marburg)

  • Thomas Braun

    (Max-Planck-Institute for Heart and Lung Research)

  • Stefan Günther

    (Max-Planck-Institute for Heart and Lung Research
    Max-Planck-Institute for Heart and Lung Research)

  • Gergana Dobreva

    (Heidelberg University
    German Centre for Cardiovascular Research (DZHK)
    Helmholtz-Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University)

  • Guillermo Barreto

    (Max-Planck-Institute for Heart and Lung Research
    UMR 7365)

Abstract

The dynamics of three-dimensional (3D) genome organization are essential to transcriptional regulation. While enhancers regulate spatiotemporal gene expression, chromatin looping is a means for enhancer-promoter interactions yielding cell-type-specific gene expression. Further, non-canonical DNA secondary structures, such as G-quadruplexes (G4s), are related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), and in chromatin looping has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by transforming growth factor beta 1 (TGFB1) signaling. Moreover, we find that miR-9 is required for formation of G4s, promoter-super-enhancer looping and broad domains of the euchromatin histone mark H3K4me3 at TGFB1-responsive genes. Our study places miR-9 in the same functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical signaling pathway in cancer and fibrosis.

Suggested Citation

  • Julio Cordero & Guruprasadh Swaminathan & Diana G. Rogel-Ayala & Karla Rubio & Adel Elsherbiny & Samina Mahmood & Witold Szymanski & Johannes Graumann & Thomas Braun & Stefan Günther & Gergana Dobreva, 2024. "Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54740-x
    DOI: 10.1038/s41467-024-54740-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-54740-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-54740-x?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:15:y:2024:i:1:d:10.1038_s41467-024-54740-x. 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.