ArticleProceedings of the National Academy of Sciences of the United States of America2014
Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors.
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 31 papers.
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Who cites it
31 citing papers in PubMed, 47 citations in OpenAlex.
- 3D Genome Engineering Using CRISPR/dCas Systems.International journal of molecular sciences · 2026Review
- Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor.Nucleic acids research · 2024Article
- Detecting DNA Loops Using Tethered Particle Motion.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Robustness of DNA looping across multiple cell divisions in individual bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- GpsB Coordinates Cell Division and Cell Surface Decoration by Wall Teichoic Acids in Staphylococcus aureus.Microbiology spectrum · 2022Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops.Nucleic acids research · 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
- Engineering 3D genome organization.Nature reviews. Genetics · 2021Review
- The loopometer: a quantitative in vivo assay for DNA-looping proteins.Nucleic acids research · 2021Article
- Instability of CII is needed for efficient switching between lytic and lysogenic development in bacteriophage 186.Nucleic acids research · 2020Article
- Conditional Recruitment to a DNA-Bound CRISPR-Cas Complex Using a Colocalization-Dependent Protein Switch.ACS synthetic biology · 2020Article
- Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus.Scientific reports · 2019Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Programmable DNA looping using engineered bivalent dCas9 complexes.Nature communications · 2017Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Proteins mediating DNA loops effectively block transcription.Protein science : a publication of the Protein Society · 2017Article
- Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Efficient and specific interactions between proteins bound to the same DNA molecule can be dependent on the length of the DNA tether that connects them. Measurement of the strength of this DNA tethering effect has been largely confined to short separations between sites, and it is not clear how it contributes to long-range DNA looping interactions, such as occur over separations of tens to hundreds of kilobase pairs in vivo. Here, gene regulation experiments using the LacI and λ CI repressors, combined with mathematical modeling, were used to quantitate DNA tethering inside Escherichia coli cells over the 250- to 10,000-bp range. Although LacI and CI loop DNA in distinct ways, measurements of the tethering effect were very similar for both proteins. Tethering strength decreased with increasing separation, but even at 5- to 10-kb distances, was able to increase contact probability 10- to 20-fold and drive efficient looping. Tethering in vitro with the Lac repressor was measured for the same 600-to 3,200-bp DNAs using tethered particle motion, a single molecule technique, and was 5- to 45-fold weaker than in vivo over this range. Thus, the enhancement of looping seen previously in vivo at separations below 500 bp extends to large separations, underlining the need to understand how in vivo factors aid DNA looping. Our analysis also suggests how efficient and specific looping could be achieved over very long DNA separations, such as what occurs between enhancers and promoters in eukaryotic cells.
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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.