Histone octamer

FIGURE 11.23 A diagram of the histone octamer. Nucleosomes consist of two turns of DNA supercoiled about a histone core octamer. 

If chromatin is swelled suddenly in water and prepared for viewing in the electron microscope, the nucleosomes are evident as beads on a string, dsDNA being the string (Figure 12.28). The structure of the histone octamer core has been determined by X-ray crystallography without DNA by E. N. Moudrianakis s laboratory (Figure 12.29) and wrapped with DNA by T. J. 

FIGURE 12.31 A model for chromosome structure, human chromosome 4. The 2-um DNA helix is wound twice around histone octamers to form 10-um uucleosomes, each of which contains 160 bp (80 per turn). These uucleosomes are then wound in solenoid fashion with six uucleosomes per turn to form a 30-nm filament. In this model, the 30-nm filament forms long DNA loops, each containing about 60,000 bp, which are attached at their base to the nuclear matrix. Eighteen of these loops are then wound radially around the circumference of a single turn to form a miniband unit of a chromosome. Approximately 10 of these minibands occur in each chromatid of human chromosome 4 at mitosis. 

The nucleosome represents the first level of DNA condensation and is the basic building block of all chromatin structures. It was discovered in 1973 and consists of a central histone octamer with about 150 base pairs of DNA wrapped around. 

When the histone octamer is mixed with purified, double-stranded DNA, the same x-ray diffraction pattern is formed as that observed in freshly isolated chromatin. Electron microscopic studies confirm the existence of reconstituted nucleosomes. Furthermore, the reconsti-mtion of nucleosomes from DNA and histones H2A, H2B, H3, and H4 is independent of the organismal or cellular origin of the various components. The histone HI and the nonhistone proteins are not necessary for the reconstitution of the nucleosome core. 

In the nucleosome, the DNA is supercoiled in a left-handed helix over the surface of the disk-shaped histone octamer (Figure 36-2). The majority of core histone proteins interact with the DNA on the inside of the supercoil without protruding, though the amino terminal tails of all the histones probably protrude outside of this structure and are available for regulatory covalent modifications (see Table 36-1). 

Figure 36-2. Model for the structure of the nucleosome, in which DNA is wrapped around the surface of a flat protein cylinder consisting of two each of histones H2A, H2B, H3, and H4 that form the histone octamer. The 146 base pairs of DNA, consisting of 1.75 superhelical turns, are in contact with the histone octamer. This protects the DNA from digestion by a nuclease. The position of histone HI, when it is present, is indicated by the dashed outline at the bottom of the figure.

In the nuclei of all eukaryotic cells, DNA is tightly wrapped around an octamer of histone proteins and is compacted into a dense structure known as chromatin. In order to access the genetic information which is required in numerous essential cellular processes including DNA replication, gene expression and DNA repair, chromatin needs to be partially unwound. One important mechanism to regulate chromatin structure and thus to control the access of the genomic DNA is through histone modifications [1-6]. The histone octamer is composed of two copies of H2A, H2B, H3 and H4 core histone proteins. Their tails, that protrude out of the surface of the... 

Hyde and Walker, 1975a) indicate that there are two basic types of histone-histone interactions or contacts those within the nucleosome which result in the formation of histone octamers and those between nucleosomes which give rise to higher oligomers. 

The histone octamer of nucleosome core particles was cross-linked by dimethylsuberimidate and isolated from the DNA by precipitation in 3 M NaCl (0.05 M sodium phosphate buffer, pH 7.0). The cross-linked octamer, dissolved at low ionic strength, was reconstituted by mixing with DNA at 1.0 M NaCl (pH 8.0 Tris buffer) and dialyzed against 0.6 M NaCl in the same buffer. The reconstituted particle had properties similar to those of the cross-linked core particle. It sedi-... 

Upon increase in salt concentration to 2 M, histone octamers were obtained (Thomas and Butler, 1978). The octamer could be assembled from acid-extracted as well as from salt-extracted histones (Thomas and Butler, 1978). In a concentrated solution of the four core histones (prepared by acid extraction) at an ionic strength higher than 2 M NaCl (minimum 10 mg/ml histone concentration), there is a small fraction of assembled fibrous structures which can be observed in the electron microscope (Sperling and Bustin, 1976 Wachtel and Sperling, 1979). These fibers (see Fig. 3d) are 60 A in diameter and have a 330 A axial repeat, and were shown to be composed of the four core histones in an equimolar ratio (Wachtel and Sperling, 1979). The percentage of fibers in the solution of the four core histones is promoted by increase in histone and salt concentrations. 

The histone octamer is the histone unit of the nucleosome. As discussed in Section II, it has been shown that at high salt concentration (7 > 2 M) the core histones can assemble on their own, in the absence of DNA, to form histone octamers (this assembly occurs with both acid- and salt-extracted histones). Furthermore, the secondary and tertiary structures of core histones at high salt concentration are similar to the structures they have in the intact nucleosome. The basic units of the assembly of the four core histones are histone dimers which are obtained at low salt concentration. Upon increase in salt concentration, tetramers, hexamers, and octamers are obtained. The cross-linking pattern of histones in high salt concentration is similar to that in chromatin, again supporting the idea that the assembly of core histones at high salt concentration is similar to that in chromatin. 

Note added IN Proof Klug et al. (1980) obtained regular fibers by the assembly of histone octamers at high salt. From image reconstruction of these histone fibers a 22-A resolution model was proposed for the histone octamer, which has a 2-fold axis of symmetry and is wedge-shaped. From this structure and the results of various cross-linking data an arrangement of the individual histones within the octamer has been proposed. 

There is good agreement between the overall dimensions of the histone octamer found by Klug et al. and data obtained from other types of histone fibers discussed here. Similarity of cross-linking data of histone octamer fibers, octamer free in solution, and octamer in nucleosomes makes the extrapolation from the octamer model in the fibers to the octameric core of nucleosome valid (Klug et al., 1980). This further substantiates the idea that histones are part of an assembly system, and therefore the histone core of the nucleosome can be regarded as a truncated histone fiber (see Section IV). 

Figure 1. Hierarchical model of chromosome structure, (a) In interphase cells, DNA is packed in a nucleus as forming nucleosome and chromatin, (b) DNA forms nucleosome structure together with core histone octamer, which is then folded up into 30nm fiber with a help of linker histone HI. This 30 nm fiber is further folded into 80 nm fiber and 300 nm loop structures in a nucleus. In mitosis, chromosome is highly condensed. Proteins which are involved in each folding step are indicated above and non-protein factors are indicated below, (c) The amino acid sequences of histone tails (H2A, H2B, H3 and H4) are shown to indicate acetylation, methylation and phosphorylation sites. (See Colour Plate 1.)...

Linker histones (HI, H5 and others) are also major components of metaphase chromosome, and occupy 5.8% of the total protein amount (Uchiyama et al, 2005). They play an important role in the formation of the 30 nm fiber (see also section 2.3). These linker histones carry more lysine residues ( 30% of the total amino acids) than the core histones and have a core domain in the middle part that binds to a nucleosome. The linker histones could be easily extracted from the chromatin with 0.5 M NaCl, whereas the core histone octamers need more than 0.8 M NaCl to dissociate from nucleosomes. 

Figure 3. The stability of the nucleosome is affected by the length and the superhelicity of DNA. (a-b) The chromatin fibers were reconstituted from the purified plasmids and the histone octamers by a salt-dialysis method and observed under AFM. The 3 kb (a) or 106 kb (e) supercoiled circular plasmid was used as a template, (c) Relationship between the plasmid length and the frequency of nucleosome formation in the reconstitution process. The nucleosome frequency is represented as the number of base pairs per nucleosome and plotted against the length of the template DNA in supercoiled (filled circle) and linear (open circle) forms, (d) AFM image of the chromatin fiber reconstituted on the topoisomerase 1-treated plasmid, (e) Chromatin fiber reconstituted with Drosophila embryo extract. The chromatin fiber was reconstituted from plasmid DNA of 10kband the embryo extract of Drosophila, and was observed by AFM...

Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN (1991) The nucleosomal core histone octamer at 3.1 A resolution a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A 88 10148-10152... 

DNA is packaged in the nucleus into the form of chromatin. Chromatin is a nucleoprotein complex composed of histone and non-histone proteins, DNA and RNA and it exhibits a repeating structure (van Holde, 1988). The basal unit of chromatin, the nucleosome, is composed of a histone octamer (two each of H2A, H2B, H3 and H4) around which two superhelical turns of DNA are wrapped (van Holde, 1988). The structure of both the histone octamer (Arents et al, 1991)... 

The histone variants of H2A form the largest family of identified histone variants (Redon et al, 2002 Sarma and Reinberg, 2005). This could be associated with both the strategic position that has the histone H2A within the histone octamer and the less stable interaction of the H2A-H2B dimmer with both DNA and the (H3-H4)2 tetramer within the nucleosome (Luger et al, 1997). Most of the histone H2A variants exhibit a unique property in addition to the N-terminal tail domain, they also posses an unstructured C-terminal tail. To date four variants of histone H2A have been discovered. These include, H2AZ, H2A.X, macroH2A and H2A.Bbd. The highest differences in the primary structure of these H2A variants are observed in their C-terminal portion. Each of these variants could be efficiently incorporated in the nucleosome in vitro and in vivo. The presence of these variants alter the structural and functional properties of the nucleosome distinctly. 

Arents G, Moudrianakis EN (1993) Topography of the histone octamer surface repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci U S A 90 10489-10493... 

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). 

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