Atomic Force Microscopy Dissects the Hierarchy of Genome Architectures in Eukaryote, Prokaryote, and Chloroplast

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.

Nanoscale nucleosome dynamics assessed with time-lapse AFM

“…The application of AFM to the organization of DNA within bacteria revealed the role of RNA in assembly of the 30–40-nm nucleoid fiber. However, RNA is not involved into the assembly of eukaryotic 30-nm chromatin (Ohniwa et al 2007). …”

Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology

“…These lines of evidence suggest that the 30-to 40-nm thin fiber and the 70-to 80-nm granular fiber are the fundamental structural units of eukaryotic chromosomes; these fibers are relatively stable in a wide range of experimental conditions. Recent reports have demonstrated that these hierarchical structures exist in both eukaryotes and prokaryotes [35] and that nascent single-stranded RNAs are part of the 30-80 nm fiber structures [62,63].…”

The influence of ATP-dependent proteases on a variety of nucleoid-associated processes

“…Furthermore, some bacterial and mitochondrial man, 2010)). Recent reports suggest that in addition to topoisomerases and NAPs, RNA also plays an important role in the organization of nucleoid DNA-protein fibers (Ohniwa et al, 2007).…”