Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

• Type of Material: Article
• Authors: David G. Priest, University of Adelaide; Sandip Kumar, Emory University; Yan Yan, Emory University; David Dunlap, Emory University; Ian B. Dodd, University of Adelaide; Keith E. Shearwin, University of Adelaide
• Language: English
• Date: 2014-10-21
• Publisher: National Academy of Sciences
• Publication Version: Final Published Version
• Copyright Statement: © 2014, National Academy of Sciences. All rights reserved.
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.1410764111
• Title of Journal or Parent Work: Proceedings of the National Academy of Sciences
• Volume: 111
• Issue: 42
• Start Page: E4449
• End Page: E4457
• Grant/Funding Information: Support was provided by Human Frontiers Scientific Program Grant RGP0051 (to K.E.S. and D.D.D.), a University of Adelaide PhD scholarship (to D.G.P.), Australian Research Council Grants DP110100824 and DP11010470, the W. H. Elliott Fellowship in Biochemistry (to I.B.D.), Australian National Healthy and Medical Research Council Grant GNT1025549 (to I.B.D.), National Institutes of Health Grant RGM084070A, and the Center for Pediatric Nanomedicine in the Department of Biomedical Engineering, Georgia Institute of Technology and Children's Healthcare of Atlanta (D.D.D.).
• Keywords: LAMBDA CI REPRESSOR; IN-VIVO; PROMOTER INTERACTIONS; TRANSCRIPTIONAL ACTIVATION; BACTERIOPHAGE-LAMBDA; lambda CI; statistical mechanical modeling; Lac repressor; Science & Technology; GENE-REGULATION; REGULATORY LANDSCAPE; SITE JUXTAPOSITION; TOPOLOGICAL DOMAINS; Multidisciplinary Sciences; tethered particle motion; Science & Technology - Other Topics; CHROMATIN INSULATORS
• Research Categories: Biology, Genetics

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.