title: Using deformation energy to analyze nucleosome positioning in genomes.
abstract: By modulating the accessibility of genomic regions to regulatory proteins, nucleosome positioning plays important roles in cellular processes. Although intensive efforts have been made, the rules for determining nucleosome positioning are far from satisfaction yet. In this study, we developed a biophysical model to predict nucleosomal sequences based on the deformation energy of DNA sequences, and validated it against the experimentally determined nucleosome positions in the Saccharomyces cerevisiae genome, achieving very high success rates. Furthermore, using the deformation energy model, we analyzed the distribution of nucleosomes around the following three types of DNA functional sites: (1) double strand break (DSB), (2) single nucleotide polymorphism (SNP), and (3) origin of replication (ORI). We have found from the analyzed energy spectra that a remarkable "trough" or "valley" occurs around each of these functional sites, implying a depletion of nucleosome density, fully in accordance with experimental observations. These findings indicate that the deformation energy may play a key role for accurately predicting nucleosome positions, and that it can also provide a quantitative physical approach for in-depth understanding the mechanism of nucleosome positioning.
authors.affiliation: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063009, China. Electronic address: chenweiimu@gmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: School of Public Health, North China University of Science and Technology, Tangshan 063000, China. Electronic address: fengpengmian@gmail.com.
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, and Center for Information in Biomedicine, School of Life Scienceand Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: hding@uestc.edu.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, and Center for Information in Biomedicine, School of Life Scienceand Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address: hlin@uestc.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
authors.affiliation: Gordon Life Science Institute, Boston, MA 02478, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: kcchou@gordonlifescience.org.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D053903:DNA Breaks, Double-Stranded; D016681:Genome, Fungal; D008954:Models, Biological; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D018741:Replication Origin; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism
chemical_list: D009707:Nucleosomes
keywords: DSB site; Deformation energy; Nucleosome; ORI; SNP site