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Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Author

Listed:
  • Vladyslava Gorbovytska

    (University of Bayreuth)

  • Seung-Kyoon Kim

    (Pohang University of Science and Technology (POSTECH)
    Chungnam National University)

  • Filiz Kuybu

    (University of Bayreuth)

  • Michael Götze

    (Institute of Molecular Systems Biology, ETH Zurich)

  • Dahun Um

    (Pohang University of Science and Technology (POSTECH))

  • Keunsoo Kang

    (Dankook University)

  • Andreas Pittroff

    (University of Bayreuth)

  • Theresia Brennecke

    (University of Bayreuth)

  • Lisa-Marie Schneider

    (University of Bayreuth)

  • Alexander Leitner

    (Institute of Molecular Systems Biology, ETH Zurich)

  • Tae-Kyung Kim

    (Pohang University of Science and Technology (POSTECH)
    Yonsei University)

  • Claus-D. Kuhn

    (University of Bayreuth)

Abstract

Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we here investigate the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We find eRNAs not to exert their function through common structural or sequence motifs. Instead, eRNAs that exhibit a length >200 nucleotides and that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release. By revealing the molecular determinants of eRNA function, our study establishes eRNAs as an important player in Pol II pause release, and it provides new insight into the regulation of metazoan transcription.

Suggested Citation

  • Vladyslava Gorbovytska & Seung-Kyoon Kim & Filiz Kuybu & Michael Götze & Dahun Um & Keunsoo Kang & Andreas Pittroff & Theresia Brennecke & Lisa-Marie Schneider & Alexander Leitner & Tae-Kyung Kim & Cl, 2022. "Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29934-w
    DOI: 10.1038/s41467-022-29934-w
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    References listed on IDEAS

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    1. Carrie Bernecky & Franz Herzog & Wolfgang Baumeister & Jürgen M. Plitzko & Patrick Cramer, 2016. "Structure of transcribing mammalian RNA polymerase II," Nature, Nature, vol. 529(7587), pages 551-554, January.
    2. Patrick Cramer, 2019. "Organization and regulation of gene transcription," Nature, Nature, vol. 573(7772), pages 45-54, September.
    3. Wenbo Li & Dimple Notani & Qi Ma & Bogdan Tanasa & Esperanza Nunez & Aaron Yun Chen & Daria Merkurjev & Jie Zhang & Kenneth Ohgi & Xiaoyuan Song & Soohwan Oh & Hong-Sook Kim & Christopher K. Glass & M, 2013. "Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation," Nature, Nature, vol. 498(7455), pages 516-520, June.
    4. Seychelle M. Vos & Lucas Farnung & Henning Urlaub & Patrick Cramer, 2018. "Structure of paused transcription complex Pol II–DSIF–NELF," Nature, Nature, vol. 560(7720), pages 601-606, August.
    5. Tae-Kyung Kim & Martin Hemberg & Jesse M. Gray & Allen M. Costa & Daniel M. Bear & Jing Wu & David A. Harmin & Mike Laptewicz & Kellie Barbara-Haley & Scott Kuersten & Eirene Markenscoff-Papadimitriou, 2010. "Widespread transcription at neuronal activity-regulated enhancers," Nature, Nature, vol. 465(7295), pages 182-187, May.
    6. Robin Andersson & Claudia Gebhard & Irene Miguel-Escalada & Ilka Hoof & Jette Bornholdt & Mette Boyd & Yun Chen & Xiaobei Zhao & Christian Schmidl & Takahiro Suzuki & Evgenia Ntini & Erik Arner & Eivi, 2014. "An atlas of active enhancers across human cell types and tissues," Nature, Nature, vol. 507(7493), pages 455-461, March.
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    1. Heeyoun Bunch & Deukyeong Kim & Masahiro Naganuma & Reiko Nakagawa & Anh Cong & Jaehyeon Jeong & Haruhiko Ehara & Hongha Vu & Jeong Ho Chang & Matthew J. Schellenberg & Shun-ichi Sekine, 2023. "ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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