ArticleProceedings of the National Academy of Sciences of the United States of America2014
Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Engineering the Link: From Genome Interaction Maps to Functional Insight.Advanced biology · 2025Review
- Loops are geometric catalysts for DNA integration.Nucleic acids research · 2024Article
- Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications.iScience · 2023Article
- 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
- Engineering 3D genome organization.Nature reviews. Genetics · 2021Review
- The loopometer: a quantitative in vivo assay for DNA-looping proteins.Nucleic acids research · 2021Article
- 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
- 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
- The free-energy cost of interaction between DNA loops.Scientific reports · 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
- Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.PLoS computational biology · 2016Article
- Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops--that aid or inhibit enhancer-promoter contact--are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other's formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other's formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions.
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