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Type: Journal article
Title: Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells
Author: Priest, D.
Kumar, S.
Yan, Y.
Dunlap, D.
Dodd, I.
Shearwin, K.
Citation: Proceedings of the National Academy of Sciences of USA, 2014; 111(42):E4449-E4457
Publisher: National Academy of Sciences
Issue Date: 2014
ISSN: 1091-6490
Statement of
David G. Priest, Sandip Kumar, Yan Yan, David D. Dunlap, Ian B. Dodd, and Keith E. Shearwin
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.
Keywords: Lac repressor; lambda CI; statistical mechanical modeling; tethered particle motion
Rights: © PNAS
RMID: 0030009882
DOI: 10.1073/pnas.1410764111
Grant ID:
Appears in Collections:Molecular and Biomedical Science publications

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