---
APC_amount: 12348 EUR
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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
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publication: Nature Structural & Molecular Biology
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---
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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
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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:
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publication_status: draft
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title: Mechanism of mammalian transcriptional repression by noncoding RNA
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