title: Computational predictions of structures of multichromosomes of budding yeast.
abstract: Knowledge of the global architecture of the cell nucleus and the spatial organization of genome is critical for understanding gene expression and nuclear function. Single-cell imaging techniques provide a wealth of information on the spatial organization of chromosomes. Computational tools for modelling chromosome structure have broad implications in studying the effect of cell nucleus on higher-order genome organization. Here we describe a multichromosome constrained self-avoiding chromatin model for studying ensembles of genome structural models of budding yeast nucleus. We successfully generated a large number of model genomes of yeast with appropriate chromatin fiber diameter, persistence length, and excluded volume under spatial confinement. By incorporating details of the constraints from single-cell imaging studies, our method can model the budding yeast genome realistically. The model developed here provides a general computational framework for studying the overall architecture of budding yeast genome.
authors.forename: Gamze
authors.initials: G
authors.lastname: Gürsoy
authors.forename: Yun
authors.initials: Y
authors.lastname: Xu
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D015825:Chromosomes, Fungal / Q000737:chemistry*; D016678:Genome; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D004718:Saccharomycetales / Q000235:genetics*
chemical_list: D002843:Chromatin