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

11 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 1

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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  • 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