Histone modification phosphorylation

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. 

Figure 3. Histone modification cross-talk between histone H2A phosphorylation on T119 and another histones methylation or acetylation in nhk-1 mutants (a) Histone H3 (K14) and (b) Histone H4 (K5) are not acetylated in the nhk-1 mutant, (c) Histone H4 (K12) is acetylated in the nhk-1 mutant (Ivanovska et al. 2005). Phosphorylation is represented by the blue flag, and acetylation is represented by the black flag...

These studies demonstrate that H2A (T119) phosphorylation by NHK-1 regulates mitotic and meiotic progression. However, it remains unclear what is the biological function of other histone H2A posphorylation sites and how they impact the many other histone modifications. 

We have discussed phosphorylation of histone H3, which has been studied in many organisms. Phosphorylation of histone H3 (SIO) has two opposite main functions. One is necessary to initiate chromosome condensation during mitosis and meiosis, while the other is transcriptional activation. Current evidence shows that a combination of phosphorylation of H3 (SIO) and methylation of H3 (K9) or acetylation H3 (K9, K14) play important roles in these phenomena including cell cycle related chromosome dynamics and transcriptional activation. These results suggest that a combination of different histone modifications excute different biological outcomes. 

Recent studies have demonstrated that histone H4 (SI) phosphorylation is also a key role in the response to DNA double-strand breaks, cell-cycle progression and gene expression. In particular, this modification may have important roles during mitosis and S-phase-associated events in the cell-cycle and its phosphorylation found on newly synthesized histones during S-phase. However this phosphorylated residue is a novel histone modification site, and the details of this mechanism will be made evident by future experimentation. 

The phenylselenocysteine has also been used successfully to chemically append analogues of methyl- or acetyl-lysine, important histone modifications that can contribute to chromatin structure and accessibility of transcriptional machinery in eukaryotes. By introducing phenylselenocysteine into the Xenopus histone H3, both acetyl-lysine and mono-, di-, and trimethyl-lysine analogues were appended to the purified unnatural amino acid-containing FI 3 protein (Figure 10). " Additionally, the H3 protein with a modification mimicking acetylation of lysine 9 can be deactylated by a histone deacetylation complex and is also a substrate for phosphorylation by Aurora B kinase. Such purified and chemically labeled histones are likely functional in nucleosomes, and preparation of specifically modified histones for comprehensive analysis of chromatin structure and accessibility is particularly suited to this chemical labeling technique. 

Fig. 1. Core histone modifications. Human histone N-terminal and in some cases C-terminal amino acid sequences are shown. The modifications include methylation (M), acetylation (Ac), phosphorylation (P), ubiquitination (U), and ADP ribosylation (step ladder). The sites of trypsin digestion of histones in nucleosomes are indicated (T).

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].)...

Figure 1 Histone modifications. The best-characterized human histone modifications are shown which include the acetylation of lysines (Ac), the methylation of lysines and arginines (Me)/ the phosphorylation of serine and threonines (Ph), and the ubiquitination of lysines (Ub). The vast majority of modifications are within the N-terminal domain of the histone tail/ but ubiquitination occurs at the C-terminal domain.

The phosphorylation of histone H3 can have a repressive or activating effect on transcription. Members of the MAP kinases (see Chapter 10) that are responsible for this phosphorylation have been identified, providing a link between growth factor stimulation and transcription activation at the level of histone modification. H3 phosphorylation has been also recognized as part of a complex signaling mechanism that operates in the condensation/decondensation of chromatin during the cell cycle. Furthermore, histone HI phosphorylation has been linked to the relief of transcription repression. 

In contrast, methylation at K4 of H3 is correlated with transcriptionally active states of chromatin. The K4 methylation appears to be absent from histones with methylation at K9, but colocalizes with acetylation at K9, indicating a positive cooperation of acetylation and methylation of distinct Lys residues during the establishment of a transcriptionally active state. For yeast histones, a link between methylation and acetylation at Lys residues and phosphorylation at Ser residues of histone H3 has been discovered (Nakayamaet al.,., 2001), defining a conserved pathway of sequential histone modifications during heterochromatin assembly. These modifications are recognized by specific proteins that are part of multiprotein assemblies in heterochromatin. 

Histone modifications, such as phosphorylation, acetylation, and methylation, regulate gene expression. " Histone lysine methylation was considered a static modification, until relatively recently, when histone demethylases were discovered." One such enzyme is ESDI, which belongs to the amine oxidase superfamily. ESDI catalyzes the demethylation of mono- and disubstituted Eys 4 of histone H3" in a reductive halfreaction very similar to those catalyzed by DAAO and MAO by oxidizing the amino group of the methylated lysine to the corresponding imino product, which hydrolyzes nonenzymatically to formaldehyde (Equation (2)). 

A number of histone modifications have been demonstrated but acetylation appears to be one of the most dynamic. Acetylation is most commonly on the e amino groups of lysine residues near the histone A -termini within histone tails that extend from the core of the nucleosome and beyond the DNA wrapped around the outer face of the histone octamer. The location of these modifications allows histone deacetylases to modulate chromatin structure and interaaion or remove binding platforms for regulatory factors (reviewed in ref. 5). The deacetylases themselves may be related by phosphorylation and, in the case of the class II... 

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