Print Email Facebook Twitter DNA sequence encodes the position of DNA supercoils Title DNA sequence encodes the position of DNA supercoils Author Kim, S.H. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft) Ganji, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Ludwig Maximilians University; Max Planck Institute of Biochemistry) Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft) van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft) Abbondanzieri, E. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft; University of Rochester) Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft) Department BN/Bionanoscience Date 2018 Abstract The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA. Subject C. eleganschromosome organizationchromosomesD. melanogasterDNA structureDNA SupercoilE. colifluorescencegene expressionphysics of living systemsplectonemeS. cerevisiaesingle molecule To reference this document use: http://resolver.tudelft.nl/uuid:6844c52e-f388-4110-a385-8bc99b9c7422 DOI https://doi.org/10.7554/eLife.36557 ISSN 2050-084X Source eLife, 7 Part of collection Institutional Repository Document type journal article Rights © 2018 S.H. Kim, M. Ganji, E. Kim, J. van der Torre, E. Abbondanzieri, C. Dekker Files PDF elife_36557_v2.pdf 7.84 MB Close viewer /islandora/object/uuid:6844c52e-f388-4110-a385-8bc99b9c7422/datastream/OBJ/view