Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote, and chloroplast

R. L. Ohniwa, K. Morikawa, J. Kim, T. Kobori, K. Hizume, R. Matsumi, H. Atomi, T. Imanaka, T. Ohta, C. Wada, S. H. Yoshimura, K. Takeyasu

Research output: Contribution to journalArticle

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Abstract

Because of its applicability to biological specimens (nonconductors), a single-molecule-imaging technique, atomic force microscopy (AFM), has been particularly powerful for visualizing and analyzing complex biological processes. Comparative analyses based on AFM observation revealed that the bacterial nucleoids and human chromatin were constituted by a detergent/salt-resistant 30-40-nm fiber that turned into thicker fibers with beads of 70-80 nm diameter. AFM observations of the 14-kbp plasmid and 110-kbp F plasmid purified from Escherichia coli demonstrated that the 70-80-nm fiber did not contain a eukaryotic nucleosome-like "beads-on-a-string" structure. Chloroplast nucleoid (that lacks bacterial-type nucleoid proteins and eukaryotic histones) also exhibited the 70-80-nm structural units. Interestingly, naked DNA appeared when the nucleoids from E. coli and chloroplast were treated with RNase, whereas only 30-nm chromatin fiber was released from the human nucleus with the same treatment. These observations suggest that the 30-40-nm nucleoid fiber is formed with a help of nucleoid proteins and RNA in E. coli and chroloplast, and that the eukaryotic 30-nm chromatin fiber is formed without RNA. On the other hand, the 70-80-nm beaded structures in both E. coli and human are dependent on RNA.

Original languageEnglish
Pages (from-to)3-12
Number of pages10
JournalMicroscopy and Microanalysis
Volume13
Issue number1
DOIs
Publication statusPublished - Feb 1 2007

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prokaryotes
eukaryotes
chloroplasts
genome
hierarchies
Atomic force microscopy
Genes
atomic force microscopy
Escherichia coli
chromatin
fibers
Fibers
RNA
plasmids
beads
proteins
Proteins
electrical insulation
detergents
Detergents

All Science Journal Classification (ASJC) codes

  • Instrumentation

Cite this

Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote, and chloroplast. / Ohniwa, R. L.; Morikawa, K.; Kim, J.; Kobori, T.; Hizume, K.; Matsumi, R.; Atomi, H.; Imanaka, T.; Ohta, T.; Wada, C.; Yoshimura, S. H.; Takeyasu, K.

In: Microscopy and Microanalysis, Vol. 13, No. 1, 01.02.2007, p. 3-12.

Research output: Contribution to journalArticle

Ohniwa, RL, Morikawa, K, Kim, J, Kobori, T, Hizume, K, Matsumi, R, Atomi, H, Imanaka, T, Ohta, T, Wada, C, Yoshimura, SH & Takeyasu, K 2007, 'Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote, and chloroplast', Microscopy and Microanalysis, vol. 13, no. 1, pp. 3-12. https://doi.org/10.1017/S1431927607070055
Ohniwa, R. L. ; Morikawa, K. ; Kim, J. ; Kobori, T. ; Hizume, K. ; Matsumi, R. ; Atomi, H. ; Imanaka, T. ; Ohta, T. ; Wada, C. ; Yoshimura, S. H. ; Takeyasu, K. / Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote, and chloroplast. In: Microscopy and Microanalysis. 2007 ; Vol. 13, No. 1. pp. 3-12.
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