The genome folding mechanism in yeast

Hajime Kimura, Yasutoshi Shimooka, Jun Ichi Nishikawa, Osamu Miura, Shigeru Sugiyama, Shuji Yamada, Takashi Ohyama

    Research output: Contribution to journalArticle

    9 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)137-147
    Number of pages11
    JournalJournal of Biochemistry
    Volume154
    Issue number2
    DOIs
    Publication statusPublished - 2013 Aug

    Fingerprint

    Chromosomes
    Yeast
    Interphase
    Genes
    Yeasts
    Chromatin
    Genome
    Nucleosomes
    Fibers
    Chromosomes, Human, Pair 16
    Saccharomycetales
    DNA
    DNA sequences
    Saccharomyces cerevisiae
    Physical properties

    Keywords

    • 10-nm chromatin fibre
    • DNA properties
    • interphase chromosome
    • persistence length
    • yeast genome

    ASJC Scopus subject areas

    • Biochemistry
    • Molecular Biology

    Cite this

    Kimura, H., Shimooka, Y., Nishikawa, J. I., Miura, O., Sugiyama, S., Yamada, S., & Ohyama, T. (2013). The genome folding mechanism in yeast. Journal of Biochemistry, 154(2), 137-147. https://doi.org/10.1093/jb/mvt033

    The genome folding mechanism in yeast. / Kimura, Hajime; Shimooka, Yasutoshi; Nishikawa, Jun Ichi; Miura, Osamu; Sugiyama, Shigeru; Yamada, Shuji; Ohyama, Takashi.

    In: Journal of Biochemistry, Vol. 154, No. 2, 08.2013, p. 137-147.

    Research output: Contribution to journalArticle

    Kimura, H, Shimooka, Y, Nishikawa, JI, Miura, O, Sugiyama, S, Yamada, S & Ohyama, T 2013, 'The genome folding mechanism in yeast', Journal of Biochemistry, vol. 154, no. 2, pp. 137-147. https://doi.org/10.1093/jb/mvt033
    Kimura H, Shimooka Y, Nishikawa JI, Miura O, Sugiyama S, Yamada S et al. The genome folding mechanism in yeast. Journal of Biochemistry. 2013 Aug;154(2):137-147. https://doi.org/10.1093/jb/mvt033
    Kimura, Hajime ; Shimooka, Yasutoshi ; Nishikawa, Jun Ichi ; Miura, Osamu ; Sugiyama, Shigeru ; Yamada, Shuji ; Ohyama, Takashi. / The genome folding mechanism in yeast. In: Journal of Biochemistry. 2013 ; Vol. 154, No. 2. pp. 137-147.
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