---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '18778'
abstract:
- lang: eng
  text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
    RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
    repress transcription remains unclear. Here we present cryogenic-electron microscopy
    structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
    and RNA bind to Pol II during transcription elongation. Further, we show how distinct
    domains of the general transcription factor TFIIF control repressive activity.
    Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions
  and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding
  assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU
  data collection. We thank D. Slade (Max Perutz Laboratories and Medical University
  of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank
  N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of
  Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank
  C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
  by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The
  funders had no role in study design, data collection and analysis, decision to publish
  or preparation of the manuscript. This research was further supported by the Scientific
  Service Units of ISTA through resources provided by the Laboratory Support Facility,
  Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Katarina
  full_name: Tluckova, Katarina
  id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
  last_name: Tluckova
- first_name: Beata M
  full_name: Kaczmarek, Beata M
  id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
  last_name: Kaczmarek
- first_name: Anita P
  full_name: Testa Salmazo, Anita P
  id: 41F1F098-F248-11E8-B48F-1D18A9856A87
  last_name: Testa Salmazo
- first_name: Carrie A
  full_name: Bernecky, Carrie A
  id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
  last_name: Bernecky
  orcid: 0000-0003-0893-7036
citation:
  ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian
    transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular
    Biology</i>. 2025;32:607-612. doi:<a href="https://doi.org/10.1038/s41594-024-01448-7">10.1038/s41594-024-01448-7</a>
  apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025).
    Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature
    Structural &#38; Molecular Biology</i>. Springer Nature. <a href="https://doi.org/10.1038/s41594-024-01448-7">https://doi.org/10.1038/s41594-024-01448-7</a>
  chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie
    Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.”
    <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href="https://doi.org/10.1038/s41594-024-01448-7">https://doi.org/10.1038/s41594-024-01448-7</a>.
  ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism
    of mammalian transcriptional repression by noncoding RNA,” <i>Nature Structural
    &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 607–612, 2025.
  ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of
    mammalian transcriptional repression by noncoding RNA. Nature Structural &#38;
    Molecular Biology. 32, 607–612.
  mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression
    by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32,
    Springer Nature, 2025, pp. 607–12, doi:<a href="https://doi.org/10.1038/s41594-024-01448-7">10.1038/s41594-024-01448-7</a>.
  short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural
    &#38; Molecular Biology 32 (2025) 607–612.
corr_author: '1'
date_created: 2025-01-08T11:20:20Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-11-20T10:28:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41594-024-01448-7
external_id:
  isi:
  - '001390268000001'
  pmid:
  - '39762629'
file:
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  date_created: 2025-04-16T08:17:27Z
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intvolume: '        32'
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month: '04'
oa: 1
oa_version: Published Version
page: 607-612
pmid: 1
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
  grant_number: P34185
  name: Regulation of mammalian transcription by noncoding RNA
publication: Nature Structural & Molecular Biology
publication_identifier:
  eissn:
  - 1545-9985
  issn:
  - 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2025'
...
---
_id: '14644'
abstract:
- lang: eng
  text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
    RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
    repress transcription remains unclear. Here we present cryo-electron microscopy
    structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
    and RNA bind to Pol II during transcription elongation. Further, we show how domains
    of the general transcription factor TFIIF affect complex dynamics and control
    repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian
    gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: PreCl
acknowledgement: "We thank B. Kaczmarek and other members of the Bernecky lab for
  helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support
  with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid.
  We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank
  C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
  by Austrian Science Fund (FWF) grant P34185. This research was further supported
  by the Scientific Service Units (SSU) of IST Austria through resources provided
  by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific
  Computing (SciComp), and the Preclinical Facility (PCF)."
article_processing_charge: No
author:
- first_name: Katarina
  full_name: Tluckova, Katarina
  id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
  last_name: Tluckova
- first_name: Anita P
  full_name: Testa Salmazo, Anita P
  id: 41F1F098-F248-11E8-B48F-1D18A9856A87
  last_name: Testa Salmazo
- first_name: Carrie A
  full_name: Bernecky, Carrie A
  id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
  last_name: Bernecky
  orcid: 0000-0003-0893-7036
citation:
  ama: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
    repression by noncoding RNA. doi:<a href="https://doi.org/10.15479/AT:ISTA:14644">10.15479/AT:ISTA:14644</a>
  apa: Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of
    mammalian transcriptional repression by noncoding RNA. Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:14644">https://doi.org/10.15479/AT:ISTA:14644</a>
  chicago: Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism
    of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science
    and Technology Austria, n.d. <a href="https://doi.org/10.15479/AT:ISTA:14644">https://doi.org/10.15479/AT:ISTA:14644</a>.
  ieee: K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian
    transcriptional repression by noncoding RNA.” Institute of Science and Technology
    Austria.
  ista: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
    repression by noncoding RNA. <a href="https://doi.org/10.15479/AT:ISTA:14644">10.15479/AT:ISTA:14644</a>.
  mla: Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression
    by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href="https://doi.org/10.15479/AT:ISTA:14644">10.15479/AT:ISTA:14644</a>.
  short: K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).
corr_author: '1'
date_created: 2023-12-04T14:51:00Z
date_published: 2023-12-05T00:00:00Z
date_updated: 2025-11-20T10:28:37Z
day: '05'
ddc:
- '572'
doi: 10.15479/AT:ISTA:14644
file:
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  creator: dernst
  date_created: 2023-12-05T10:37:02Z
  date_updated: 2023-12-05T10:37:02Z
  file_id: '14646'
  file_name: 2023_Tluckova_etal_REx.pdf
  file_size: 4892920
  relation: main_file
  success: 1
file_date_updated: 2023-12-05T10:37:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
  grant_number: P34185
  name: Regulation of mammalian transcription by noncoding RNA
publication_status: draft
publisher: Institute of Science and Technology Austria
related_material:
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    relation: later_version
    status: public
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12051'
abstract:
- lang: eng
  text: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is
    a major determinant of cellular growth, and dysregulation is observed in many
    cancer types. Here, we present the purification of human Pol I from cells carrying
    a genomic GFP fusion on the largest subunit allowing the structural and functional
    analysis of the enzyme across species. In contrast to yeast, human Pol I carries
    a single-subunit stalk, and in vitro transcription indicates a reduced proofreading
    activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native
    state rationalizes the effects of disease-associated mutations and uncovers an
    additional domain that is built into the sequence of Pol I subunit RPA1. This
    “dock II” domain resembles a truncated HMG box incapable of DNA binding which
    may serve as a downstream transcription factor–binding platform in metazoans.
    Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase
    2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing
    factor UBF. These adaptations of the metazoan Pol I transcription system may allow
    efficient release of positive DNA supercoils accumulating downstream of the transcription
    bubble.
acknowledgement: "The authors especially thank Philip Gunkel for his contribution.
  We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn
  Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert
  Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert
  Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the
  Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the
  Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence
  microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant
  no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research
  Center 960 (TP-A8 to C Engel)."
article_number: e202201568
article_processing_charge: No
article_type: original
author:
- first_name: Julia L
  full_name: Daiß, Julia L
  last_name: Daiß
- first_name: Michael
  full_name: Pilsl, Michael
  last_name: Pilsl
- first_name: Kristina
  full_name: Straub, Kristina
  last_name: Straub
- first_name: Andrea
  full_name: Bleckmann, Andrea
  last_name: Bleckmann
- first_name: Mona
  full_name: Höcherl, Mona
  last_name: Höcherl
- first_name: Florian B
  full_name: Heiss, Florian B
  last_name: Heiss
- first_name: Guillermo
  full_name: Abascal-Palacios, Guillermo
  last_name: Abascal-Palacios
- first_name: Ewan P
  full_name: Ramsay, Ewan P
  last_name: Ramsay
- first_name: Katarina
  full_name: Tluckova, Katarina
  id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
  last_name: Tluckova
- first_name: Jean-Clement
  full_name: Mars, Jean-Clement
  last_name: Mars
- first_name: Torben
  full_name: Fürtges, Torben
  last_name: Fürtges
- first_name: Astrid
  full_name: Bruckmann, Astrid
  last_name: Bruckmann
- first_name: Till
  full_name: Rudack, Till
  last_name: Rudack
- first_name: Carrie A
  full_name: Bernecky, Carrie A
  id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
  last_name: Bernecky
  orcid: 0000-0003-0893-7036
- first_name: Valérie
  full_name: Lamour, Valérie
  last_name: Lamour
- first_name: Konstantin
  full_name: Panov, Konstantin
  last_name: Panov
- first_name: Alessandro
  full_name: Vannini, Alessandro
  last_name: Vannini
- first_name: Tom
  full_name: Moss, Tom
  last_name: Moss
- first_name: Christoph
  full_name: Engel, Christoph
  last_name: Engel
citation:
  ama: Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals
    an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>.
    2022;5(11). doi:<a href="https://doi.org/10.26508/lsa.202201568">10.26508/lsa.202201568</a>
  apa: Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B.,
    … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking
    domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance.
    <a href="https://doi.org/10.26508/lsa.202201568">https://doi.org/10.26508/lsa.202201568</a>
  chicago: Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl,
    Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase
    I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life
    Science Alliance</i>. Life Science Alliance, 2022. <a href="https://doi.org/10.26508/lsa.202201568">https://doi.org/10.26508/lsa.202201568</a>.
  ieee: J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an
    HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>,
    vol. 5, no. 11. Life Science Alliance, 2022.
  ista: Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios
    G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky
    C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase
    I structure reveals an HMG-like docking domain specific to metazoans. Life Science
    Alliance. 5(11), e202201568.
  mla: Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like
    Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no.
    11, e202201568, Life Science Alliance, 2022, doi:<a href="https://doi.org/10.26508/lsa.202201568">10.26508/lsa.202201568</a>.
  short: J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G.
    Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann,
    T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life
    Science Alliance 5 (2022).
date_created: 2022-09-06T18:45:23Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2024-10-21T06:01:48Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.26508/lsa.202201568
external_id:
  isi:
  - '000972702600001'
file:
- access_level: open_access
  checksum: 4201d876a3e5e8b65e319d03300014ad
  content_type: application/pdf
  creator: dernst
  date_created: 2022-09-08T06:41:14Z
  date_updated: 2022-09-08T06:41:14Z
  file_id: '12062'
  file_name: 2022_LifeScienceAlliance_Daiss.pdf
  file_size: 3183129
  relation: main_file
  success: 1
file_date_updated: 2022-09-08T06:41:14Z
has_accepted_license: '1'
intvolume: '         5'
isi: 1
issue: '11'
keyword:
- Health
- Toxicology and Mutagenesis
- Plant Science
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
- Ecology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Life Science Alliance
publication_identifier:
  issn:
  - 2575-1077
publication_status: published
publisher: Life Science Alliance
quality_controlled: '1'
scopus_import: '1'
status: public
title: The human RNA polymerase I structure reveals an HMG-like docking domain specific
  to metazoans
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...