ArticleProceedings of the National Academy of Sciences of the United States of America2014
DNA supercoiling: a regulatory signal for the λ repressor.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed, 59 citations in OpenAlex.
- The eukaryotic homology search complex distorts donor DNA structure to probe for homology.Genes & development · 2026Article
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- Force and the α-C-terminal domains bias RNA polymerase recycling.Nature communications · 2024Article
- Loops are geometric catalysts for DNA integration.Nucleic acids research · 2024Article
- Reciprocating RNA Polymerase batters through roadblocks.Nature communications · 2024Article
- Tuning Protein Hydrogel Mechanics through Modulation of Nanoscale Unfolding and Entanglement in Postgelation Relaxation.ACS nano · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- Article
- Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids.Science advances · 2021Article
- Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Emerging roles for R-loop structures in the management of topological stress.The Journal of biological chemistry · 2020Review
- In silico simulations of occurrence of transcription factor binding sites in bacterial genomes.BMC evolutionary biology · 2019Article
- Transcription factor regulation of RNA polymerase's torque generation capacity.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Article
- Influence of DNA sequence on the structure of minicircles under torsional stress.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling between them. Furthermore, in single DNA molecules stretched and twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops ranged from -15% or +11%. Finally, in DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation and was essential for DNA looping. Supercoiling-enhanced looping can influence the maintenance of lysogeny in the λ repressor system; it can encode sensitivity to the energy level of the cell and creates independent topological domains of distinct superhelical density.
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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.