Chromosomes, eukaryotic nucleosomes

Shioda et al. [43,44] visualized by electron microscopy both regions of naked DNA and of DNA covered with particles in the chromosome of Halobacterium salinarium isolated from gently lysed cells. In a control experiment, they did not detect such particles in E. coli. They also reported the existence of nucleosome-like structures in S. acidocaldarius and methanogens (unpublished results cited in ref. [43]). The size of the particles detected in H. salinarium (9.5 nm) is similar to that of eukaryotic nucleosomes (10.3 nm) however, this putative archaebacterial chromatin is not as regular as eukaryotic chromatin, since not all of the DNA is covered with nucleosomes and since the length of the DNA spacer between the particles is not uniform. In contrast to these results, Bohrmann and coworkers [45] did not visualize nucleosome-like structures in isolated chromosome fibers of Thermoplasma acidophilum. These authors also reported that in situ the nucleoid of T. acidophilum appears to be highly dispersed in the cytoplasm. 

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

Kornberg RD, Lorch Y (1999). Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98 285-294. 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

Kim MS, Blake M, Baek JH, Kohlhagen G, Pommier Y, Carrier F (2003) Inhibition of histone deacetylase increases cytotoxicity to anticancer drugs targeting DNA. Cancer Res 63(21) 7291—7300 Komberg RD and Lorch Y (1999) Twenty-Five years of die nucleosome, fundamental particle of die eukaryote chromosome. Cell 98(3) 285—294... 

Nucleosomes are organized into 30 nm fibers, and the fibers are extensively folded to provide the 10,000-fold compaction required to fit a typical eukaryotic chromosome into a cell nucleus. The higher-order folding involves attachment to a nuclear scaffold that contains histone HI, topoisomerase II, and SMC proteins. 

In the chromatin of eukaryotic cells DNA forms a coiled-coil structure with an approximately equal weight of a mixture of five basic proteins known as histones. Four of these histones in pairs form an octa-mer around which the DNA duplex occurs in a left-handed helix. The DNA octamer complex is called a nucleosome. Each nucleosome contains about 140 base pairs of DNA in a nuclease-resistant nucleosome core and approximately 60 base pairs of spacer between core particles. Histone HI binds to the chromatin independently of the octamer and is the first histone to dissociate from the chromatin when the ionic strength is raised. Beyond the nucleosome the higher order structure of the chromosome involves coiled-coil structures with varying degrees of regularity. 

DNA in eukaryotic chromosomes is complexed with histone proteins in complexes called nucleosomes. These DNA-protein complexes are disassembled directly in front of the replication fork. The nucleosome disassembly may be rate-limiting for the migration of the replication forks, as the rate of migration is slower in eukaryotes than prokaryotes. The length of Okazaki fragments is also similar to the size of the DNA between nucleosomes (about 200 bp). One model that would allow the synthesis of new eukaryotic DNA and nucleosome formation would be the disassembly of the histones in front of the replication fork and then the reassembly of the histones on the two duplex strands. Histone synthesis is closely coupled to DNA replication. 

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