---
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'
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has_accepted_license: '1'
intvolume: '        32'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
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'
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    status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
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  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
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...