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Enhancer loops appear stable during development and are associated with paused polymerase

Author

Listed:
  • Yad Ghavi-Helm

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

  • Felix A. Klein

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

  • Tibor Pakozdi

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

  • Lucia Ciglar

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

  • Daan Noordermeer

    (Swiss Federal Institute of Technology, School of Life Sciences, CH-1015 Lausanne, Switzerland)

  • Wolfgang Huber

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

  • Eileen E. M. Furlong

    (European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany)

Abstract

A high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis shows that although local regulatory interactions are frequent, long-range interactions are also very common; unexpectedly, most interactions appear unchanged between tissues and across development and are formed prior to gene expression, indicating that transcription initiates from preformed enhancer–promoter loops, which are associated with paused polymerase.

Suggested Citation

  • Yad Ghavi-Helm & Felix A. Klein & Tibor Pakozdi & Lucia Ciglar & Daan Noordermeer & Wolfgang Huber & Eileen E. M. Furlong, 2014. "Enhancer loops appear stable during development and are associated with paused polymerase," Nature, Nature, vol. 512(7512), pages 96-100, August.
    • Handle: RePEc:nat:nature:v:512:y:2014:i:7512:d:10.1038_nature13417
    DOI: 10.1038/nature13417
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    Cited by:

    1. Maëlle Bellec & Jérémy Dufourt & George Hunt & Hélène Lenden-Hasse & Antonio Trullo & Amal Zine El Aabidine & Marie Lamarque & Marissa M. Gaskill & Heloïse Faure-Gautron & Mattias Mannervik & Melissa , 2022. "The control of transcriptional memory by stable mitotic bookmarking," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Vivekanandan Ramalingam & Xinyang Yu & Brian D. Slaughter & Jay R. Unruh & Kaelan J. Brennan & Anastasiia Onyshchenko & Jeffrey J. Lange & Malini Natarajan & Michael Buck & Julia Zeitlinger, 2023. "Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Dahong Chen & Catherine E. McManus & Behram Radmanesh & Leah H. Matzat & Elissa P. Lei, 2021. "Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    4. Joyce J. Thompson & Daniel J. Lee & Apratim Mitra & Sarah Frail & Ryan K. Dale & Pedro P. Rocha, 2022. "Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Jingyao Wang & Shihe Zhang & Hongfang Lu & Heng Xu, 2022. "Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Annkatrin Bressin & Olga Jasnovidova & Mirjam Arnold & Elisabeth Altendorfer & Filip Trajkovski & Thomas A. Kratz & Joanna E. Handzlik & Denes Hnisz & Andreas Mayer, 2023. "High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Christopher T. Rhodes & Joyce J. Thompson & Apratim Mitra & Dhanya Asokumar & Dongjin R. Lee & Daniel J. Lee & Yajun Zhang & Eva Jason & Ryan K. Dale & Pedro P. Rocha & Timothy J. Petros, 2022. "An epigenome atlas of neural progenitors within the embryonic mouse forebrain," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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