title: Tension-Dependent Free Energies of Nucleosome Unwrapping.
abstract: Nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproducesquantitativelythe forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.
authors.affiliation: Institute for Molecular Engineering, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Joshua
authors.initials: J
authors.lastname: Lequieu
authors.affiliation: Institute for Molecular Engineering, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Andrés
authors.initials: A
authors.lastname: Córdoba
authors.affiliation: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.affiliation: Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States; Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo