IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-03279-9.html
   My bibliography  Save this article

Dissecting super-enhancer hierarchy based on chromatin interactions

Author

Listed:
  • Jialiang Huang

    (Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health
    Harvard Medical School)

  • Kailong Li

    (University of Texas Southwestern Medical Center)

  • Wenqing Cai

    (Harvard Medical School)

  • Xin Liu

    (University of Texas Southwestern Medical Center)

  • Yuannyu Zhang

    (University of Texas Southwestern Medical Center)

  • Stuart H. Orkin

    (Harvard Medical School
    Howard Hughes Medical Institute)

  • Jian Xu

    (University of Texas Southwestern Medical Center)

  • Guo-Cheng Yuan

    (Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health)

Abstract

Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.

Suggested Citation

  • Jialiang Huang & Kailong Li & Wenqing Cai & Xin Liu & Yuannyu Zhang & Stuart H. Orkin & Jian Xu & Guo-Cheng Yuan, 2018. "Dissecting super-enhancer hierarchy based on chromatin interactions," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03279-9
    DOI: 10.1038/s41467-018-03279-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-03279-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-03279-9?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
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Andrea Wilderman & Eva D’haene & Machteld Baetens & Tara N. Yankee & Emma Wentworth Winchester & Nicole Glidden & Ellen Roets & Jo Dorpe & Sandra Janssens & Danny E. Miller & Miranda Galey & Kari M. B, 2024. "A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    2. Yanli Liu & Zhong Wu & Jin Zhou & Dinesh K. A. Ramadurai & Katelyn L. Mortenson & Estrella Aguilera-Jimenez & Yifei Yan & Xiaojun Yang & Alison M. Taylor & Katherine E. Varley & Jason Gertz & Peter S., 2021. "A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    3. Claire Marchal & Nivedita Singh & Zachary Batz & Jayshree Advani & Catherine Jaeger & Ximena Corso-Díaz & Anand Swaroop, 2022. "High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Salah-Eddine Lamhamedi-Cherradi & Mayinuer Maitituoheti & Brian A. Menegaz & Sandhya Krishnan & Amelia M. Vetter & Pamela Camacho & Chia-Chin Wu & Hannah C. Beird & Robert W. Porter & Davis R. Ingram , 2022. "The androgen receptor is a therapeutic target in desmoplastic small round cell sarcoma," Nature Communications, Nature, vol. 13(1), pages 1-16, 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_s41467-018-03279-9. 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.