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Journal of Electron Microscopy Advance Access published online on February 22, 2006
Journal of Electron Microscopy, doi:10.1093/jmicro/dfi076
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© The Author 2006. Published by Oxford University Press on behalf of Japanese Society of Microscopy. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 3, 2005
Accepted January 21, 2006

Full-length paper

Comparative structural biology of the genome: nano-scale imaging of single nucleus from different kingdoms reveals the common physicochemical property of chromatin with a 40 nm structural unit

Toshiro Kobori 1 *, Mami Kodama 2, Kohji Hizume 2, Shige H. Yoshimura 2, Toshio Ohtani 3, and Kunio Takeyasu 2

1 Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan; National Food Research Institute, 2-1-12 Kan-nondai, Tsukuba 305-8642, Japan
2 Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
3 National Food Research Institute, 2-1-12 Kan-nondai, Tsukuba 305-8642, Japan

* To whom correspondence should be addressed.
Toshiro Kobori, E-mail: kobori{at}lif.kyoto-u.ac.jp


  Abstract

Genome function is closely linked to the higher-order chromatin structures. To reveal a structural basis for the interphase chromatin organization, the ‘on-substrate’ lysis procedure was applied to nuclei isolated from human HeLa cells, chicken erythrocyte cells and yeast Schizosaccharomyces pombe, which possessed different intrinsic properties of the genomes such as histone composition and inter-nucleosomal distance. The isolated nuclei on a coverslip were successively treated with a detergent and a high-salt solution to extract the nuclear membrane and the nucleoplasm, and therefore, atomic force microscopy (AFM) visualized the structural changes in response to the lysis procedure. After the nucleoplasm was extracted, AFM clarified that chromatin fibers, ~40 nm in width, were partially released out of the nuclei and that the other chromatin still remaining in the nuclei was composed of granular structures with diameter of 80-100 nm. Thus, these results suggest that the ~40 nm fiber would be a stable structural unit and fold the 80-100 nm granules into a one-step higher unit. A common mechanism could be implied regardless of the intrinsic properties of the eukaryotic genomes.

Keywords: chromatin fiber; nuclear isolation; on-substrate lysis; atomic force microscopy.
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