ArticleNucleic acids research2018
Protein-mediated loops in supercoiled DNA create large topological domains.
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 20 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
20 citing papers in PubMed, 18 citations in OpenAlex.
- Insights on the effect of macromolecular crowding on transcription and its regulation.QRB discovery · 2025Article
- Transcribing RNA polymerases: Dynamics of twin supercoiled domains.Biophysical journal · 2024Article
- The nucleolar shell provides anchoring sites for DNA untwisting.Communications biology · 2024Article
- Article
- Women's contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization.Frontiers in molecular biosciences · 2023Article
- Article
- Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli.Nucleic acids research · 2022Article
- Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops.Nucleic acids research · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time.Nucleic acids research · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- Transcription-mediated supercoiling regulates genome folding and loop formation.Molecular cell · 2021Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome.Biophysical journal · 2020Article
- Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling.Biophysical journal · 2020Article
- Emerging roles for R-loop structures in the management of topological stress.The Journal of biological chemistry · 2020Review
- Architecture of the Escherichia coli nucleoid.PLoS genetics · 2019Article
- DNA supercoiling and transcription in bacteria: a two-way street.BMC molecular and cell biology · 2019Review
- Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays.The Journal of biological chemistry · 2019Article
- Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure. To characterize the extent of constrained supercoiling, 400 bp, lac repressor-secured loops were formed in extensively over- or under-wound DNA under gentle tension in a magnetic tweezer. The protein-mediated loops constrained variable amounts of supercoiling that often exceeded the maximum writhe expected for a 400 bp plectoneme. Loops with such high levels of supercoiling appear to be entangled with flanking domains. Thus, loop-mediating proteins operating on supercoiled substrates can establish topological domains that may coordinate gene regulation and other DNA transactions across spans in the genome that are larger than the separation between the binding sites.
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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.