Histone modification enzymes involved

In contrast, lysine methylation seems to be an exceptionally stable modification. Early studies showed that turnover of histone methyl groups was even slower than turnover of the histones themselves (e.g., [26,27]). No conclusive evidence has yet been found for histone demethylating enzymes, and they may not exist [28]. It may be that removal of methylated histones mostly occurs passively, through post-replication chromatin assembly and replacement of old, methylated histones with new, unmethylated ones. However, the possibility remains that local methylation patterns may be more dynamic and may involve novel mechanisms for removal of methylated tails [28]. 

In eukaryotes, DNA supercoiling is an essential step in forming the DNA histone complexes of chromatin, and thus, in organizing the chromosome. DNA supercoiUng is controlled by a class of enzymes called topoisomerases [22]. We could demonstrate that the topoisomerase I molecule may be a target for ADP-ribosylation and that this covalent modification inactivates this enzyme involved in chromosome organization [23]. 

Here we review current knowledge on the enzymes and related binding proteins that are involved in covalent modifications to histones. We begin with a brief overview of the field aimed at the non-expert, then focus on the covalent modifications themselves as catalysed by specific enzymes. We also focus on the consequences of these modifications for binding interactions with other proteins that modulate gene expression. The field is one that is rapidly evolving and we hope to convey some of the excitement that we feel about recent discoveries in histone science, particularly from a molecular perspective. Two inhibitors of histone modifying enzymes are in clinical use, with more likely to be introduced in the near future. Thus, the development of modifiers of histone biochemistry is of medicinal as well as basic interest. 

It is now a decade since evidence was first presented that the modification (acetylation) of particular residues on the histone tails was functionally significant [13,14]. Since then, it has been established beyond all reasonable doubt that specific modifications and combinations thereof, mediate protein-protein interactions crucial for the long-term and short-term regulation of transcriptional activity. Some of these interactions involve the modifying enzymes themselves, and recent data shows how particular histone tail modifications can interact, both to put in place defined patterns of modification and to control their recognition. Examples are presented in Table 1. But do these findings support the existence of a histone code ... 

Histones within transcriptionally active chromatin and heterochromatin also differ in their patterns of covalent modification. The core histones of nucleosome particles (H2A, H2B, H3, H4 see Fig. 24-27) are modified by irreversible methylation of Lys residues, phosphorylation of Ser or Thr residues, acetylation (see below), or attachment of ubiquitin (see Fig. 27-41). Each of the core histones has two distinct structural domains. A central domain is involved in histone-histone interaction and the wrapping of DNA around the nucleosome. A second, lysine-rich amino-terminal domain is generally positioned near the exterior of the assembled nucleosome particle the covalent modifications occur at specific residues concentrated in this amino-terminal domain. The patterns of modification have led some researchers to propose the existence of a histone code, in which modification patterns are recognized by enzymes that alter the structure of chromatin. Modifications associated with transcriptional activation would be recognized by enzymes that make the chromatin more accessible to the transcription machinery. 

In the recent literature, many examples of A/BPs containing benzophenones can be found. A first example concerns the study of HDACs. These enzymes catalyze the hydrolysis of acetylated lysine amine side chains in histones and are thus involved in the regulation of gene expression. There are approximately 20 human HDACs, which are divided into three classes (I, II, and III). Class I and II HDACs are zinc-dependent metallohydrolases that do not form a covalent bond with their substrates during their catalytic process, which is similar to MMPs. It has been found that hydroxamate 65 (SAHA, see Fig. 5) is a potent reversible inhibitor of class I and II HDACs. In 2007, Cravatt and coworkers reported the transformation of SAHA into an A/BP by installment of a benzophenone and an alkyne moiety, which resulted in SAHA-BPyne (66) [73]. They showed that the probe can be used for the covalent modification and enrichment of several class I and class II HDACs from complex proteomes in an activity-dependent manner. In addition, they identified several HDAC-associated proteins, possibly arising from the tight interaction with HDACs. Also, the probe was used to measure differences in HDAC content in human disease models. Later they reported the construction of a library of related probes and studied the differences in HDAC labeling [74], Their most... 

Recent experimental evidence has indicated a central role for ADP-ribosylation of chromosomal proteins as a response to DNA damage produced by chemicals and radiation (1-3). ADP-ribosylation is involved in the initial response to DNA damage, as this paper demonstrates, and in die final step in DNA repair, which is the ligation of broken DNA ends to produce a continuous double helix. Repair of DNA is accompanied by an increase in DNA ligase activity, which apparently results from the attachment of ADP-ribose to the enzyme. ADP-ribosylation could have other functions coimected with DNA repair. Since the histones are major acceptors of ADP-ribose units, the structure of nucleosomes and the 30 run chromatin fibers could be altered by the modification. A number of other nuclear proteins are also substrates for the modification, including the latnins of the peripheral lamina. 

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