TY - JOUR
T1 - Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF
AU - Gorbovytska, Vladyslava
AU - Kim, Seung Kyoon
AU - Kuybu, Filiz
AU - Götze, Michael
AU - Um, Dahun
AU - Kang, Keunsoo
AU - Pittroff, Andreas
AU - Brennecke, Theresia
AU - Schneider, Lisa Marie
AU - Leitner, Alexander
AU - Kim, Tae Kyung
AU - Kuhn, Claus D.
N1 - Funding Information:
We thank Elizabeth Duncan, Olaf Stemmann, and Alan Cheung for critically reading the manuscript. We thank Dr. Kunz and Marcel Bowens from the Bayerische Landesanstalt für Landwirtschaft (LfL) for access to pig thymus of unparalleled freshness. We thank Dr. Felix Klatt and Silke Spudeit for technical help, Chris Sarnowski for support with the xQuest software, and we are grateful to the Core Unit Systems Medicine of the University of Würzburg for next-generation sequencing. We thank Patrick Cramer, Seychelle Vos, and Carrie Bernecky for providing NELF expression plasmids and for helping in establishing the purification of mammalian Pol II. We further thank Birgitta Wöhrl for the DSIF expression plasmid and Norbert Eichner and Gunter Meister for access to a miSeq instrument. This work was supported by the German Research Foundation (DFG, grants KU 3514/1-1 and KU 3514/3-1), the Oberfrankenstiftung (P-Nr. 05474), the Elite Network of Bavaria, the University of Bayreuth and the Paul Ehrlich and Ludwig Darmstaedter Prize for Young Researchers (to C.-D.K.). This work was also supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT), 2019R1A2C2006740 (T.-K.K.), 2019R1A5A6099645 (T.-K.K.), 2017M3A9G7073033 (T.-K.K.), 2020H1D3A1A04104610 (T.-K.K.), and 2020R1I1A1A01067189 (S.-K.K.), the Brain Research Program of the National Research Foundation (NRF) funded by the Korean government (MSIT), 2019M3C7A1031537 (T.-K.K.), Samsung Science & Technology Foundation (SSTF-BA2102-09), and a Simons Foundation Autism Research Initiative-Pilot Award 575147 (T.-K.K.). A.L. acknowledges funding from an ETH Research Grant (ETH-24 16-2) and the ETH Domain Strategic Focus Area “Personalized Health and Related Technologies” (PHRT-503) and would like to thank Paola Picotti (ETH Zurich) for access to instrumentation and infrastructure. The Orbitrap Fusion Lumos mass spectrometer used in this work was purchased using funding from the ETH Scientific Equipment program and the European Union Grant ULTRA-DD (FP7-JTI 115766). Open Access publication is in part funded by the German Research Foundation (DFG, Project No. 491183248) and by the Open Access Publishing Fund of the University of Bayreuth.
Funding Information:
We thank Elizabeth Duncan, Olaf Stemmann, and Alan Cheung for critically reading the manuscript. We thank Dr. Kunz and Marcel Bowens from the Bayerische Landesanstalt für Landwirtschaft (LfL) for access to pig thymus of unparalleled freshness. We thank Dr. Felix Klatt and Silke Spudeit for technical help, Chris Sarnowski for support with the xQuest software, and we are grateful to the Core Unit Systems Medicine of the University of Würzburg for next-generation sequencing. We thank Patrick Cramer, Seychelle Vos, and Carrie Bernecky for providing NELF expression plasmids and for helping in establishing the purification of mammalian Pol II. We further thank Birgitta Wöhrl for the DSIF expression plasmid and Norbert Eichner and Gunter Meister for access to a miSeq instrument. This work was supported by the German Research Foundation (DFG, grants KU 3514/1-1 and KU 3514/3-1), the Oberfrankenstiftung (P-Nr. 05474), the Elite Network of Bavaria, the University of Bayreuth and the Paul Ehrlich and Ludwig Darmstaedter Prize for Young Researchers (to C.-D.K.). This work was also supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT), 2019R1A2C2006740 (T.-K.K.), 2019R1A5A6099645 (T.-K.K.), 2017M3A9G7073033 (T.-K.K.), 2020H1D3A1A04104610 (T.-K.K.), and 2020R1I1A1A01067189 (S.-K.K.), the Brain Research Program of the National Research Foundation (NRF) funded by the Korean government (MSIT), 2019M3C7A1031537 (T.-K.K.), Samsung Science & Technology Foundation (SSTF-BA2102-09), and a Simons Foundation Autism Research Initiative-Pilot Award 575147 (T.-K.K.). A.L. acknowledges funding from an ETH Research Grant (ETH-24 16-2) and the ETH Domain Strategic Focus Area “Personalized Health and Related Technologies” (PHRT-503) and would like to thank Paola Picotti (ETH Zurich) for access to instrumentation and infrastructure. The Orbitrap Fusion Lumos mass spectrometer used in this work was purchased using funding from the ETH Scientific Equipment program and the European Union Grant ULTRA-DD (FP7-JTI 115766). Open Access publication is in part funded by the German Research Foundation (DFG, Project No. 491183248) and by the Open Access Publishing Fund of the University of Bayreuth.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-022-29934-w
DO - 10.1038/s41467-022-29934-w
M3 - Article
C2 - 35508485
AN - SCOPUS:85129420289
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 2429
ER -