title: Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.
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.
authors.affiliation: School of Molecular and Biomedical Science (Biochemistry), University of Adelaide, Adelaide, SA 5005, Australia; and.
authors.forename: David G
authors.initials: DG
authors.lastname: Priest
authors.affiliation: Departments of Cell Biology.
authors.forename: Sandip
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Physics, and.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Departments of Cell Biology, Biology, Emory University, Atlanta, GA 30322.
authors.forename: David D
authors.initials: DD
authors.lastname: Dunlap
authors.affiliation: School of Molecular and Biomedical Science (Biochemistry), University of Adelaide, Adelaide, SA 5005, Australia; and ian.dodd@adelaide.edu.au.
authors.forename: Ian B
authors.initials: IB
authors.lastname: Dodd
authors.affiliation: School of Molecular and Biomedical Science (Biochemistry), University of Adelaide, Adelaide, SA 5005, Australia; and.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Shearwin
mesh_terms: D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D004278:DNA, Superhelical / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D007763:Lac Operon; D056968:Lac Repressors; D015233:Models, Statistical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000737:chemistry; D013314:Stress, Mechanical
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical; D056968:Lac Repressors; D012097:Repressor Proteins
keywords: Lac repressor; lambda CI; statistical mechanical modeling; tethered particle motion