ArticleNucleic acids research2014
Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 120 citations in OpenAlex.
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- Nucleus size and its effect on nucleosome stability in living cells.Biophysical journal · 2022Article
- Modeling the 3D genome of plants.Nucleus (Austin, Tex.) · 2021Article
- Transcription-mediated supercoiling regulates genome folding and loop formation.Molecular cell · 2021Article
- DNA-Topology Simplification by Topoisomerases.Molecules (Basel, Switzerland) · 2021Review
- Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids.Science advances · 2021Article
- Weak interactions in higher-order chromatin organization.Nucleic acids research · 2020Review
- Emerging roles for R-loop structures in the management of topological stress.The Journal of biological chemistry · 2020Review
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Integrating transposable elements in the 3D genome.Mobile DNA · 2020Article
- Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The role of 3D genome organization in disease: From compartments to single nucleotides.Seminars in cell & developmental biology · 2019Review
- Article
- Are TADs supercoiled?Nucleic acids research · 2019Review
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4 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.
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