Evidence map›Paper›PMID 41929223›Full record

ArticlebioRxiv : the preprint server for biology2026

Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET.

Meng Zhang, Cristhian Cañari-Chumpitaz, Jianfang Liu, Bibiana Onoa, Sinead de Cleir, Enze Cheng, Katherinne I Requejo, Carlos Bustamante

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Meng ZhangCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, USA.
Cristhian Cañari-ChumpitazCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, USA.
Jianfang LiuThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA.
Bibiana OnoaCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, USA.
Sinead de CleirDepartment of Molecular and Cell Biology, University of California, Berkeley, USA.
Enze ChengDepartment of Physics, University of California, Berkeley, USA.
Katherinne I RequejoCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, USA.
Carlos BustamanteCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, USA.ORCID 0000-0002-2970-0073

Funding

THE PHYSICAL CHEMISTRY OF NUCLEIC ACIDSR01GM032543 · NIGMS · UNIVERSITY OF OREGON · PI CARLOS Jose BUSTAMANTE · 1985 to 2026
$6.4M
PHYSICAL CHEMISTRY OF NUCLEIC ACIDSR37GM032543 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI BUSTAMANTE, CARLOS JOSE · 1999 to 2008
$2.4M
NIGMS NIH HHS R01 GM032543NIGMS NIH HHS R37 GM032543
6 · The paper itself

Abstract

Protein interactions with canonical B-form DNA are well-characterized, yet the effect on these interactions of torsionally constrained DNA-ubiquitous in cells-remains underexplored. Using cryo-electron tomography (cryo-ET), we 3D-reconstructed entire negatively supercoiled DNA substrates bound to active RNA polymerase (RNAP), revealing diverse DNA supercoiling conformations and their interplay with transcription. RNAP preferentially localizes at plectoneme apices in a swiveled, pause-prone state. RNAP, along with other DNA-melting proteins like dCas9, can act as torsional roadblocks that segregate "twin-supercoiling domains" during active transcription, independent of external DNA/RNAP tethering. Co-transcribing RNAPs further intensify this domain separation: tandem oriented RNAPs relieve negative supercoiling more effectively than opposing ones, promote greater RNAP accumulation and enhanced elongation, both in vitro and in vivo. Topoisomerase I relieves torsional stress and facilitates RNAP escape from apical stalls, thereby supporting apical transcription regulation. Together, these findings support a load-and-release mechanism at plectoneme apices that may underlie supercoiling-dependent transcriptional bursting.

Identifiers

PMID41929223
PMCPMC13041910

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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 OpenQuestion graph.