Core histones structure

Fig. 9. Accessory helices in core histone structures, (a) Accessory H3 helix, shown in a ribbon Ca model, interacts with the DNA entering and leave the nucleosome. A short helix in the tail of H2A is seen between the accessory and medial helix of H3. (b) Solvent accessible surface representation of the C-terminal residues of H2A showing the contribution of these residues to the ventral surface of the NCP.

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). 

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... 

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. 

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. 

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. 

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). 

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.)...

Simpson RT, Thoma F, Brubaker JM (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones a model system for study of higher order structure. Cell 42 799-808 Sugiyama S, Yoshino T, Kanahara H, Kobori T, Ohtani T (2003) Atomic force microscopic imaging of 30 nm chromatin fiber from partially relaxed plant chromosomes. Scanning 25 132-136 Sugiyama S, Yoshino T, Kanahara H, Shichiri M, Fukushi D, Ohtani T (2004) Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy. Anal Biochem 324 39 4... 

Zheng C, Hayes JJ (2003) Structures and interactions of the core histone tail domains. Biopolymers 68 539-546... 

The genome of the eukaryotic cell is packaged in a topologically complex, fibrous superstructure known as chromatin. The nucleosome core particle is the fundamental building block of chromatin and contains 146 bp of DNA wrapped in roughly two super helical turns around an octamer of four core histones (H3, H2B, H2A and H4) resulting in a beads on a string structure. This 10 nm structure further folds and... 

Jenkins T (2000) Targeting multi-stranded DNA structures. Curr Med Chem 7 99-115 Jenuwein T, AlUs CD (2001) Translating the histone code. Science 293(5532) 1074-1080 Juan LJ, Utley RT, Adams CC, Vettese-Dadey M, Workman JL (1994) Differential repression of transcription factor binding by histone HI is regulated by the core histone amino termini. EMBO J 15 6031-6040... 

Hansen JC, Tse C, Wolffe AP (1998) Structure and function of the core histone N-termini more than meets the eye. Biochemistry 37 17637-17641... 

It is not widely appreciated that the major aspects of core histone interactions were well understood even before the development of the nucleosome model. Evidence for strong H2A H2B dimer interactions and an FI3 H4 tetramer was available in the early seventies (see Ref. [1], Chapter 2). By 1978, the rigorous sedimentation equilibrium studies from Moudrianakis laboratory had elucidated the thermodynamics of octamer formation [7]. What was missing, of course, was any structural information concerning these interactions. This was overcome by arduous X-ray diffraction studies, culminating in the elegantly detailed structures we have today [15,17,18], see also Flarp et al., this volume, p. 13. We now know how the core... 

The nucleosome is the fundamental repeating structural unit of chromatin. It is composed of two molecules of the core histones H2A, H2B, H3, H4, approximately two superhelical turns of double-stranded DNA, and linker histone HI (H5). In addition to biochemical studies, the existence of the nucleosome was established in electron micrographs (Fig. la) [1,2], and the name nucleosome, coined to incorporate the concept of the spherical nu-bodies [3]. Micrococcal nuclease limit digestion of chromatin established the nucleosome core particle (NCP) as the portion of the nucleosome containing only the core histones surrounded by 1.75 superhelical turns of double-stranded DNA [4,5]. 

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