Histone tetramer

The core unit of the chromatin, the nucleosome, consists of histones arranged as an octamer consisting of a (H3/ H4)2-tetramer complexed with two histone H2A/H2B dimers. Accessibility to DNA-binding proteins (for replication, repair, or transcription) is achieved by posttranslational modifications of the amino-termini of the histones, the histone tails phosphorylation, acetylation, methylation, ubiquitination, and sumoyla-tion. Especially acetylation of histone tails has been linked to transcriptional activation, leading to weakened interaction of the core complexes with DNA and subsequently to decondensation of chromatin. In contrast, deacetylation leads to transcriptional repression. As mentioned above, transcriptional coactivators either possess HAT activity or recruit HATs. HDACs in turn act as corepressors. 

The histones interact with each other in very specific ways. H3 and H4 form a tetramer containing two mol-... 

Histone Dimer and Tetramer Obtained by Salt Dissociation... 

Specifically, when histones are dissociated from DNA in 2 M NaCl, and H3 H4 tetramer and H2A-H2B dimer may be identified after fractionation of the histones at pH 5.0 and cross-linking with dimethylsu-berimidate (Komberg and Thomas, 1974). The inference was drawn that these complexes exist as such in the intact nucleosome. Furthermore, since both the un-cross-linked H3 H4 tetramer, and the uncross-linked H2A-H2B dimer are stable complexes, it has proved possible to characterize their physical properties in solution. Some of these results are summarized here. 

Infrared and circular dichroism (CD) measurements (Moss et al., 1976b) are both consistent with a sizable fraction of the tetramer being in the a-helical configuration, —29% a-helix with negligible j3 structure. This is rather similar to the 25% a-helix and —0% /3 structure obtained for the tetramer prepared from acid-extracted histones (D Anna and Isenberg, 1974b). 

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. 

As to the stoichiometry of the H3-H4-DNA particle, two complexes were identified an H3-H4 tetramer and an H3-H4 octamer, each associated with about 140 base pairs of DNA. The complexing of 140 base pairs of DNA with H3 and H4 resulted in the formation of nucleosome-like particles, as observed by the EM, and reported to have an s20base pairs (Bina-Stein and Simpson, 1977 Bina-Stein, 1978). These results differ from those of Simon et al. (1978) who report that at least two complexes of H3 H4-DNA can be obtained upon reconstitution of H3, H4, and 150 bp DNA. In this experiment both an octamer and a tetramer of H3-H4 were found bound to 150 base pairs of DNA, having sM,w equal to 10.4 and 7.5 for the octamer and tetramer, respectively. The stoichiometry of the complexes obtained is dependent on the histone-to-DNA ratio. At low ratios of histone to DNA the predominant species contains an H3-H4 tetramer per 150 base pairs of DNA. At a histone-to-DNA ratio of 1 1 the octamer prevails. The nuclease and protease digestion experiments (Camerini-Otero et al., 1976 Sollner-Webb et al., 1976) were performed at a histone-to-DNA ratio of 0.5, conditions which for 140-base-pair DNA would lead primarily to a tetrameric complex. Therefore, it seems that a tetramer of H3 H4 is sufficient for the generation of nuclease-resistant fragments similar to those of complete nucleosomes. Upon addition of H2A and H2B to the tetrameric complex, nucleosomes are formed. Addition of H3-H4 to the tetrameric complex resulted in an octameric complex which is similar in compaction to nucleosomes. H3-H4 tetramers and octamers were similarly found complexed with about 140 base pairs of DNA upon reconstitution of H3-H4 with SV40 DNA. Both complexes were reported to be able to fold 140 base pairs of DNA (Thomas and Oudet, 1979). 

In experiments performed with chromatin or core particles depleted of histones except for H3 and H4 (Stockley and Thomas, 1979), two complexes were obtained, one containing an octamer and one a tetramer of H3 and H4 per 140 base pairs of DNA. The physical properties of the two core complexes were similar to those observed by... 

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. 

Sperling and Wachtel, 1979) containing a tetramer of histones and 1.75 turns of smoothly bent DNA (Finch et al., 1977). The superposition illustrates how an H3-H4 double-stranded fiber could form the core of the H3-H4 subnucleosomal particle as well as serving as the arginine-rich kernel of the histone core of closely packed nucleo-... 

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. 

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). 

FKBP H2A-H2B (dimer) H3-H4 (tetramer) Histone chaperone regulating rDNA silencing... 

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... 

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