Evidence map›Paper›PMID 40204744›Full record

ArticleNature communications2025

DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase.

Jihee Hwang, Chun-Ying Lee, Sumitabha Brahmachari, Shubham Tripathi, Tapas Paul, Huijin Lee, Alanna Craig, Taekjip Ha, Sua Myong

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Review
  8. DNA topological regulation in RNA polymerase II transcription.Cellular & molecular biology letters · 2026
    Review
  9. The Roles of Topoisomerases in Transcriptional Regulation.International journal of molecular sciences · 2026
    Review
  10. Review
  11. Article
  12. Review
  13. Review
  14. Review
  15. Review
  16. Review
  17. Article
  18. Article
  19. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Jihee Hwang *Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
Chun-Ying Lee *Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
Sumitabha BrahmachariCenter for Theoretical Biological Physics, Rice University, Houston, TX, USA.
Shubham TripathiYale Center for Systems and Engineering Immunology & Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
Tapas PaulPrograms in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
Huijin LeeDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Alanna CraigBiophysics, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0009-0002-3821-3039
Taekjip HaPrograms in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2195-6258
Sua MyongPrograms in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA. sua.myong@childrens.harvard.edu.ORCID http://orcid.org/0000-0001-9098-3423

Funding

Gene Expression Modulated by G4, R-loop and DNA Supercoiling (Supplement for Equipment)R01GM149729 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI Sua Myong · 2023 to 2026
$1.6M
NIGMS NIH HHS R01 GM149729U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) GM149729-04
6 · The paper itself

Abstract

RNA polymerase (RNAP) is a processive motor that modulates DNA supercoiling and reshapes DNA structures. The feedback loop between the DNA topology and transcription remains elusive. Here, we investigate the impact of potential G-quadruplex forming sequences (PQS) on transcription in response to DNA supercoiling. We find that supercoiled DNA increases transcription frequency 10-fold higher than relaxed DNA, which lead to an abrupt formation of G-quadruplex (G4) and R-loop structures. Moreover, the stable R-loop relieves topological strain, facilitated by G4 formation. The cooperative formation of G4/R-loop effectively alters the DNA topology around the promoter and suppresses transcriptional activity by impeding RNAP loading. These findings highlight negative supercoiling as a built-in spring that triggers a transcriptional burst followed by a rapid suppression upon G4/R-loop formation. This study sheds light on the intricate interplay between DNA topology and structural change in transcriptional regulation, with implications for understanding gene expression dynamics.

Indexed as

DNA-Directed RNA PolymerasesDNA, SuperhelicalG-QuadruplexesR-Loop StructuresTranscription, GeneticEscherichia coliPromoter Regions, GeneticDNA-Directed RNA PolymerasesDNA, Superhelical

Identifiers

PMID40204744
PMCPMC11982182

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.