Core histones post-translational modifications

Several steps were needed to determine the structure of the core particle to higher resolution (Fig. Id). The X-ray phases of the low-resolution models were insufficient to extend the structure to higher resolution, since the resolution of the early models of the NCP was severely limited by disorder in the crystals. The disorder was presumed to derive from both the random sequences of the DNA and from heterogeneity of the histone proteins caused by variability in post-translational modification of the native proteins. One strategy for developing an atomic position model of the NCP was to develop a high-resolution structure of the histone core. This structure could then be used with molecular replacement techniques to determine the histone core within the NCP and subsequently identify the DNA in difference Fourier electron density maps. 

Fig. 6. Post-translational modifications of core and linker histones. The sites of acetylation, phosphorylation, poly-ADP ribosylation, methylation, and ubiquitination are incficated by numbers that correspond to the amino acid position from the N-termini of the molecules. The nomenclature of histone HI variants is as in Fig. 3. The length of C- and N-terminal tails is in relative scale between core histones to illustrate primary structural differences between these proteins.

Fig. 1. Histone modifications on the nucleosome core particle. The nucleosome core particle showing 6 of the 8 core histone N-terminal tail domains and 2 C-terminal tails. Sites of post-translational modification are indicated by coloured symbols that are defined in the key (lower left) acK = acetyl lysine, meR = methyl arginine, mcK = methyl lysine, PS = phosphoryl serine, and uK = ubiquitinated lysine. Residue numbers are shown for each modification. Note that H3 lysine 9 can be either acetylated or methylated. The C-terminal tail domains of one H2A molecule and one H2B molecule are shown (dashed lines) with sites of ubiquitination at H2A lysine 119 (most common in mammals) and H2B lysine 123 (most common in yeast). Modifications are shown on only one of the two copies of histones H3 and H4 and only one tail is shown for H2A and H2B. Sites marked by green arrows are susceptible to cutting by trypsin in intact nucleosomes. Note that the cartoon is a compendium of data from various organisms, some of which may lack particular modifications e.g., there is no H3meK9 in S. cerevisiae. (From Ref [7].)...

Histones are basic proteins that are made up by a globular domain and an N-terminal tail that protrudes from the nucleosome. Nucleosomes form the basic unit of chromatin and are made up by a complex of DNA wrapped around an octamer of histones formed by pairs of the histones H2A, H2B, H3, and H4 (45,46) (Fig. 1). Post-translational modification of the core histone tails by methylation, acetylation, phosphorylation, ubiquitina-tion, or sumoylation can alter the structure of the nucleosomes and thus alter gene expression. These post-translational modifications determine the structure and pattern of chromatin condensation and determine the histone code that drives gene transcriptional regulation (47,48). Below are briefly described the factors determining the histone acetylation and methylation. 

Acetylation and acylation. Acetylation of e-amino groups on conserved Lys residues in the N-terminal domains of the core histones, H2A, H2B, H3 and H4, is the most common post-translational modification of chromatin. Acetylation substantially weakens the constraints on DNA imposed by the core histones and provides molecular mechanism by which DNA becomes accessible to transacting factors while maintaining a nucleosome architecture (Wade et al, 1997). Histone acetylation is reversible and is controlled by a group of acetyltransferases and deacetylases. The balance between histone acetyltransferases and deacetylases determines the accessibility of the chromatin to the transcriptional machinery. Thus the acetylation status of histones is a key determinant of transcriptional activity. Transcription activators are often associated with histone acetyltransferases and repressors can interact with histone deacetylases (Ng and Bird, 2000). 

Histones are core proteins which form nucleosomes with DNA, in which an octamer of two copies of each of four different histones H2A, H2B, H3, and H4 are wrapped by DNA. This nucleosome is a basic unit of chromatin. Post-translational modifications of histones, such as acetylation, methylation, and phosphorylation, play an important role in gene regulation [90]. Although the synthesis of histones H2B [91] and H4 [92, 93], which contain no Cys residues, has been reported based on the combination of NCL and a desulfurization strategy by several groups, the synthesis of the Cys residue-containing histone H3 is difficult and has enjoyed limited success [72, 92, 94]. Recently, one-pot synthesis of H3 using peptide hydrazide as a peptide thioester precursor was reported [95]. 

Figure 5.3 Selected post-translational modifications of human histones. Methylation, acetylation, phosphorylation, biotinylation and ubiquitylation sites have been identified on all four core histones. The modifications shown here should not be regarded as a complete or final list.

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