Evidence map›Paper›PMID 42105766›Full record

ArticleMolecular cell2026

Apical localization of RNA polymerases modulates 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 read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Structural principles of transcriptional collisions.bioRxiv : the preprint server for biology · 2026
    Article
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, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
Cristhian Cañari-ChumpitazCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
Jianfang LiuThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Bibiana OnoaCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
Sinead de CleirDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Enze ChengDepartment of Physics, University of California, Berkeley, Berkeley, CA, USA.
Katherinne I RequejoCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
Carlos BustamanteCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA, USA; Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, CA, USA. Electronic address: carlosb@berkeley.edu.

Funding

THE PHYSICAL CHEMISTRY OF NUCLEIC ACIDSR01GM032543 · NIGMS · UNIVERSITY OF OREGON · PI CARLOS Jose BUSTAMANTE · 1985 to 2026
$6.4M
Howard Hughes Medical InstituteNIGMS NIH HHS R01 GM032543
6 · The paper itself

Abstract

Protein interactions with canonical B-form DNA are well characterized, yet the effect of torsionally constrained DNA on these interactions-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 such as 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 and 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.

Indexed as

DNA, BacterialDNA-Directed RNA PolymerasesDNA, SuperhelicalEscherichia coliEscherichia coli ProteinsTranscription, GeneticCryoelectron MicroscopyDNA Topoisomerases, Type IElectron Microscope TomographyNucleic Acid ConformationProtein BindingDNA, BacterialDNA-Directed RNA PolymerasesDNA, SuperhelicalDNA Topoisomerases, Type IEscherichia coli Proteinsapical binding localizationconvergent transcriptioncryo-electron tomographydCas9divergent transcriptionDNA supercoilingRNA polymerasetopoisomerasetorsional blocktwin supercoiling domains

Identifiers

PMID42105766
PMCPMC13344188

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Registered trials

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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.