Core histones

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

Acetylation of core histones is associated with chromosomal assembly during DNA replication. 

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). 

Interestingly, post integration latency in microglial cells seems to be the result of the concerted action of both HDACs as well as HMTs on core histone H3 in nuc-1 (Marban et al. 2007). COUP-TF interacting protein 2 (CTIP2), a transcriptional repressor interacts with HDACl and HDAC2 via its N-terminus to repress... 

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... 

Fig. 10.2. FSPIM analysis of the interaction between maize transcriptional coactivators—GCN5 and ADA2—fused to CFP and YFP. GCN5 is a histone acetyltransferase that, in conjunction with adaptor protein ADA2, modulates transcription in diverse eukaryotes by affecting the acetylation status of the core histones in nucleosomes [63]. CFP- and YFP-tagged proteins, expressed in protoplasts, were excited by the 458 nm and the 514 nm laser lines sequentially. CFP fluorescence was selectively detected by an FIFT 458 dichroic mirror and BP 470-500 band pass emission filter while YFP fluorescence was selectively detected by using an HFT 514 dichroic mirror and...

The purpose of this article is to correlate the rather unique structural aspects of the five histone molecules—the differences among them as well as their similarities—with their biological function. Such an analysis is best approached, we believe, via a study of the many protein-protein (Section II) and protein-DNA (Section III) interactions in which the histones participate. Emphasis will be placed on the four core histones H2A, H2B, H3, and H4 HI will be discussed briefly, mainly in relation to its interaction with DNA. In no sense is the bibliography meant to be exhaustive. 

The similarity of the various histone fibers is probably correlated with the similarity in the distribution of the amino acids in the sequences of the four core histones and reflects their function as the skeleton or backbone of chromatin. However, from the presence of a specific pattern of interactions of the core histones and the existence of histone variants and histone postsynthetic modifications, one can anticipate modulations in the basic general pattern of histone structure. In Section V, a possible mechanism for histone microheterogeneity influencing chromatin structure is suggested. Analogous to other assembly systems, small subunit modifications may be amplified to produce major changes in the assembled superstructure. 

Cross-linking of chromatin in 2 M NaCl at pH 8.0 results in the formation of a cross-linked octamer (Thomas and Komberg, 1975a) which contains the four core histones in equimolar ratios (Thomas and Komberg, 1975b). A non-cross-linked complex of histones isolated in 2 M NaCl at pH 7.0 also was found to contain an equimolar ratio of the four core histones but had a molecular weight determined to be near that... 

As noted above, salt-extracted H2A H2B will form higher oligomers, fibers could be obtained from salt-extracted histones (Fig. 3c), and even octamers are now known to associate into superstructures at very high salt concentration (Wachtel and Sperling, 1979). It would therefore seem that self-assembly is a general property of histones. The pattern of complex formation of the core histones is shown schematically in Fig. 4. 

When the four core histones are mixed in equimolar ratio at low ionic strength a single sedimentation velocity peak is observed with Sjo.w = 2.0. Gel filtration and cross-linking with dimethylsuberimi-date showed that the peak contained a mixture of dimers (Sperling... 

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. 

During nucleosome reconstitution, performed by mixing core histones and DNA in 2 M NaCl with slow back-dialysis to low salt con-... 

B. DNA-Core Histone Interactions Involved in Formation of the Nucleosome... 

Two types of subnucleosomal particles which retain many, if not all, of the properties of the intact nucleosome have been identified. The first type contains only H3 and H4, either as a tetramer (Bina-Stein and Simpson, 1977) or an octamer (Simon et al., 1978 Stockley and Thomas, 1979), while the second contains all core histones, each lacking up to 30 amino-terminal residues which have been digested away by trypsin (Whitlock and Simpson, 1977). The fact that other subnucleosomal particles have not been isolated does not necessarily mean that they cannot exist it indicates only that the proper reconstitution or dissociation conditions have not been found. Nevertheless, results to date point to H3-H4 on the one hand, and the trypsin-resistant carboxy-terminal regions of all the core histones on the other hand, as playing controlling structural roles in the formation of the nucleosome and the consequent folding of the DNA. 

HI forms a microheterogeneous group of very lysine-rich histones. In nucleated avian erythrocytes H5 is also present (for references, see Cole, 1977), bearing a similarity in sequence and stoichiometry to HI. Histone HI does not interact with the other core histones in solution... 

Fig. 5. Schematic model of the nucleosome, with histone HI shown as stabilizing the fold of the DNA molecule around the core histones [based on results of Sperling and Sperling (1978)]. The nucleosome dimensions are derived from X-ray (Finch et al., 1977) and neutron (Baldwin et al., 1975 Pardon et al., 1977 Suauet al., 1977) scattering experiments. The histone core dimensions are derived from electron microscopic and X-ray studies (Sperling and Amos, 1977 Wachtel and Sperling, 1979 Sperling and Wachtel, 1979). The regions of the DNA molecule indicated by dashed lines indicate those base pairs which are not present in nucleosome core particles.

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. 

Structural studies were also performed on other histone fibers, in particular H3-H4 fibers and fibers prepared from all four core histones mixed in equimolar ratios. Bundles of fibers from both systems have also been obtained. The optical diffraction patterns from electron micrographs again showed dominant axial spacings of 55, 37, and 27 A, indicating a fundamental similarity of organization for all the histone fibers (Sperling and Wachtel, 1979). 

In arrays of closely packed nucleosomes composed of all four core histones, strands of H2A-H2B dimers could be incorporated in the grooves between the two H3-H4 strands, producing a four-stranded polymer. Alternatively, they could bind to the H3-H4 double-stranded fiber to give an octamer of the histones per nucleosome. This latter model is supported by the photochemical cross-linking of histones to DNA which have shown that within the nucleosome core the four core histones are not equivalently positioned with respect to... 

The topic of histone acetylation has been the subject of extensive reviews (Dixon et al., 1975 Dixon, 1976 Allfrey, 1977 Isenberg, 1979). Acetylation occurs at specific lysine residues. In the case of the four core histones the acetylation sites are all located in the amino-terminal half of the molecule. 

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