ArticleNucleic acids research2018
Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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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.
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Who cites it
70 citing papers in PubMed, 111 citations in OpenAlex.
- The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options.Molecular cancer · 2026Review
- Enhancer RNA transcription near segmentation gene enhancers can be analyzed in situ using FISH.G3 (Bethesda, Md.) · 2026Article
- Active processes shape and move the genome and nucleoplasm.Current opinion in genetics & development · 2026Review
- PAF1c depletion confers chemoresistance to topoisomerase inhibitors.Cell insight · 2026Article
- Actively Induced Supercoiling Can Slow Down Plasmid Solutions by Trapping the Threading Entanglements.ACS nano · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction.Science advances · 2025Article
- Bridging spatial and temporal scales of developmental gene regulation.Current opinion in genetics & development · 2025Review
- A Multiscale Perspective on Chromatin Architecture through Polymer Physics.Physiology (Bethesda, Md.) · 2025Review
- Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations.Genome research · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Article
- All eukaryotic SMC proteins induce a twist of -0.6 at each DNA loop extrusion step.Science advances · 2024Article
- Transcribing RNA polymerases: Dynamics of twin supercoiled domains.Biophysical journal · 2024Article
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.bioRxiv : the preprint server for biology · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 2024Article
- DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity.Nucleic acids research · 2024Article
- Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.Nature structural & molecular biology · 2024Article
- Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity.bioRxiv : the preprint server for biology · 2024Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres. The pushing direction is such that within each topologically associating domain (TAD) cohesin rings forming handcuffs move from the source of supercoiling, constituted by RNA polymerase with associated DNA topoisomerase TOP1, towards borders of TADs, where supercoiling is released by topoisomerase TOPIIB. Cohesin handcuffs are pushed by continuous flux of supercoiling that is generated by transcription and is then progressively released by action of TOPIIB located at TADs borders. Our model explains what can be the driving force of chromatin loop extrusion and how it can be ensured that loops grow quickly and in a good direction. In addition, the supercoiling-driven loop extrusion mechanism is consistent with earlier explanations proposing why TADs flanked by convergent CTCF binding sites form more stable chromatin loops than TADs flanked by divergent CTCF binding sites. We discuss the role of supercoiling in stimulating enhancer promoter contacts and propose that transcription of eRNA sends the first wave of supercoiling that can activate mRNA transcription in a given TAD.
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Registered trials
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.