ArticleNucleic acids research2014
Effects of supercoiling on enhancer-promoter contacts.
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 19 papers.
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Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction.Science advances · 2025Article
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- All eukaryotic SMC proteins induce a twist of -0.6 at each DNA loop extrusion step.Science advances · 2024Article
- Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity.bioRxiv : the preprint server for biology · 2024Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 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
- Principles of genome folding into topologically associating domains.Science advances · 2019Review
- Are TADs supercoiled?Nucleic acids research · 2019Review
- Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Review
- DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?International journal of molecular sciences · 2018Review
- Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.Nucleic acids research · 2018Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Modeling chromosomes: Beyond pretty pictures.FEBS letters · 2015Review
- Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.Nucleic acids research · 2015Article
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer-promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains.
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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.