ArticleNucleic acids research2018
DNA knots occur in intracellular chromatin.
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 28 papers.
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Who cites it
28 citing papers in PubMed, 57 citations in OpenAlex.
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Effects of Knotting on the Collapse of Active Ring Polymers.Macromolecules · 2025Article
- Topologically-crosslinked hydrogels based on γ-cyclodextrins.Communications chemistry · 2025Review
- Unzipping of knotted DNA via nanopore translocation.QRB discovery · 2025Article
- Metasurface-Enabled 3-in-1 Microscopy.ACS photonics · 2023Article
- DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase ii modulates catalytic function.eLife · 2022Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- Human topoisomerases and their roles in genome stability and organization.Nature reviews. Molecular cell biology · 2022Review
- Transcription-mediated supercoiling regulates genome folding and loop formation.Molecular cell · 2021Article
- Topoisomerase II deficiency leads to a postreplicative structural shift in all Saccharomyces cerevisiae chromosomes.Scientific reports · 2021Article
- Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana.Nucleic acids research · 2021Article
- Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo.The EMBO journal · 2021Article
- Effects of turn-structure on folding and entanglement in artificial molecular overhand knots.Chemical science · 2020Article
- Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening.Scientific reports · 2020Article
- Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways.DNA repair · 2020Review
- Chromatin Is Frequently Unknotted at the Megabase Scale.Biophysical journal · 2020Article
- Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.Nucleic acids research · 2019Review
- Defining and detecting links in chromosomes.Scientific reports · 2019Article
- Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA.Nucleic acids research · 2019Article
- The Rabl configuration limits topological entanglement of chromosomes in budding yeast.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription. We found also that in vivo DNA knotting probability does not scale proportionately with chromatin length: it reaches a value of ∼0.025 in domains of ∼20 nucleosomes but tends to level off in longer chromatin fibers. These figures suggest that, while high flexibility of nucleosomal fibers and clustering of nearby nucleosomes facilitate DNA knotting locally, some mechanism minimizes the scaling of DNA knot formation throughout intracellular chromatin. We postulate that regulation of topoisomerase II activity and the fractal architecture of chromatin might be crucial to prevent a potentially massive and harmful self-entanglement of DNA molecules in vivo.
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