title: The genome folding mechanism in yeast.
abstract: The structure of the nucleosome has been solved at atomic resolution, and the genome-wide nucleosome positions have been clarified for the budding yeast Saccharomyces cerevisiae. However, the genome-wide three-dimensional arrangement of nucleosomal arrays in the nucleus remains unclear. Several studies simulated overall interphase chromosome architectures by introducing the putative persistence length of the controversial 30-nm chromatin fibres into the modelling and using data-fitting approaches. However, the genome-folding mechanism still could not be linked with the chromosome shapes, to identify which structures or properties of chromatin fibres or DNA sequences determine the overall interphase chromosome architectures. Here we demonstrate that the paths of nucleosomal arrays and the chromatin architectures themselves are determined principally by the physical properties of genomic DNA and the nucleus size in yeast. We clarified the flexibilities and persistence lengths of all linker DNAs of the organism, deduced their spatial expanses and simulated the architectures of all 16 interphase chromosomes in the nucleus, at a resolution of beads-on-a-string chromatin fibre. For the average spatial distance between two given loci in a chromosome, the model predictions agreed well with all experimental data reported to date. These findings suggest a general mechanism underlying the folding of eukaryotic genomes into interphase chromosomes.
authors.affiliation: Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Kimura
authors.forename: Yasutoshi
authors.initials: Y
authors.lastname: Shimooka
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Nishikawa
authors.forename: Osamu
authors.initials: O
authors.lastname: Miura
authors.forename: Shigeru
authors.initials: S
authors.lastname: Sugiyama
authors.forename: Shuji
authors.initials: S
authors.lastname: Yamada
authors.forename: Takashi
authors.initials: T
authors.lastname: Ohyama
mesh_terms: D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D015825:Chromosomes, Fungal / Q000235:genetics / Q000378:metabolism*; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism*; D016681:Genome, Fungal / Q000502:physiology*; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes
keywords: 10-nm chromatin fibre; DNA properties; interphase chromosome; persistence length; yeast genome