ReviewJournal of bacteriology2013
DNA looping in prokaryotes: experimental and theoretical approaches.
Review in Journal of bacteriology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 84 citations in OpenAlex.
- PhuS conformational dynamics are essential for DNA binding and heme-responsive control of the prrF operon in Pseudomonas aeruginosa.The Journal of biological chemistry · 2026Article
- Repression via DNA looping by the Gram-positive global transcriptional regulator ScoC from Geobacillus.Communications biology · 2025Article
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization.Nucleic acids research · 2025Article
- Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori.Nucleic acids research · 2024Article
- Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet.Briefings in bioinformatics · 2024Article
- Nanoscale Interaction of Endonuclease APE1 with DNA.International journal of molecular sciences · 2024Article
- Global Effects of the Developmental Regulator BldB in Streptomyces venezuelae.Journal of bacteriology · 2023Article
- Non-specific and specific DNA binding modes of bacterial histone, HU, separately regulate distinct physiological processes through different mechanisms.Molecular microbiology · 2023Article
- A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.Acta crystallographica. Section D, Structural biology · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes.FEBS letters · 2022Article
- Molecular insights into the role of heme in the transcriptional regulatory system AppA/PpsR.Biophysical journal · 2022Article
- A chromosomal loop anchor mediates bacterial genome organization.Nature genetics · 2022Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- DNA looping by protamine follows a nonuniform spatial distribution.Biophysical journal · 2021Article
- Anticipating response function in gene regulatory networks.Journal of the Royal Society, Interface · 2021Article
- Lsr2 and Its Novel Paralogue Mediate the Adjustment of Mycobacterium smegmatis to Unfavorable Environmental Conditions.mSphere · 2021Article
- The loopometer: a quantitative in vivo assay for DNA-looping proteins.Nucleic acids research · 2021Article
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional regulation is at the heart of biological functions such as adaptation to a changing environment or to new carbon sources. One of the mechanisms which has been found to modulate transcription, either positively (activation) or negatively (repression), involves the formation of DNA loops. A DNA loop occurs when a protein or a complex of proteins simultaneously binds to two different sites on DNA with looping out of the intervening DNA. This simple mechanism is central to the regulation of several operons in the genome of the bacterium Escherichia coli, like the lac operon, one of the paradigms of genetic regulation. The aim of this review is to gather and discuss concepts and ideas from experimental biology and theoretical physics concerning DNA looping in genetic regulation. We first describe experimental techniques designed to show the formation of a DNA loop. We then present the benefits that can or could be derived from a mechanism involving DNA looping. Some of these are already experimentally proven, but others are theoretical predictions and merit experimental investigation. Then, we try to identify other genetic systems that could be regulated by a DNA looping mechanism in the genome of Escherichia coli. We found many operons that, according to our set of criteria, have a good chance to be regulated with a DNA loop. Finally, we discuss the proposition recently made by both biologists and physicists that this mechanism could also act at the genomic scale and play a crucial role in the spatial organization of genomes.
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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.