title: A deformation energy-based model for predicting nucleosome dyads and occupancy.
abstract: Nucleosome plays an essential role in various cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to decode the mechanism of nucleosome positioning and identify nucleosome positions in the genome. In this paper, we present a model for predicting nucleosome positioning based on DNA deformation, in which both bending and shearing of the nucleosomal DNA are considered. The model successfully predicted the dyad positions of nucleosomes assembled in vitro and the in vitro map of nucleosomes in Saccharomyces cerevisiae. Applying the model to Caenorhabditis elegans and Drosophila melanogaster, we achieved satisfactory results. Our data also show that shearing energy of nucleosomal DNA outperforms bending energy in nucleosome occupancy prediction and the ability to predict nucleosome dyad positions is attributed to bending energy that is associated with rotational positioning of nucleosomes.
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.|Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Liu
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Xing
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.|State Key Laboratory for Utilization of Bayan Obo Multi-Metallic Resources, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Jianying
authors.initials: J
authors.lastname: Wang
authors.affiliation: Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.|College of Computer Science and Technology, Jilin University, Changchun, Jilin 130021, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shang
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Cai
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019281:Dimerization; D004331:Drosophila melanogaster / Q000235:genetics; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013816:Thermodynamics
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D004247:DNA