Alterations in Chromatin Structure

See also role of Epigenetic Modifications in Driving Th1/Th2 Development

The chromatin in the nucleus of eukaryotic cells is regulated to permit or exclude access of the enzymatic machinery for processes such as transcription and recombination. Specific regulatory sequences in the DNA are ultimately responsible for this regulation, serving as binding sites for proteins or protein complexes that recruit specific chromatin-modifying activities. In the case of transcriptional regulation, specific DNA-bindng activators or repressors recruit histone-modifying enzymes and nucleosome remodeling complexes, generating localized modifications of the chromatin that govern the access of the transcription machinery. In addition to such localized chromatin modificaitons, there are developmentally regulated large-scale reorganizations of chromatin structure into active and inactive domains.

The amino-terminal (NH₂₎ terminal tails of histones H3 and H4   protrude from nucleosomes and are subject to diverse modifications, including phosphorylation, methylation and acetylation. For instance, methylation of Lys 9 of histone H3 (K9/H3) is involved in the formation of stable repressive heterochromatin whereas methylation of K4/H3 is associated with transcriptional activity. These covalent modifications may alter the interaction of histone tails with DNA or serve as docking sites for chromatin associated proteins. Such modifications can loosen up or further condense chromatin or such post translational modifications can create recognition (binding) sites for other proteins that regulate gene expression. In this last process, deposition of a given modification on the histone tail is thought to specify a code that dictates the regulatory features of a gene (the "histone code" hypothesis).

Core histone actylation is a reversible post-translational modification, and transcriptional activators and repressors recruit histone acetyltransferases (HATs) and histone deacetylases (HDACs) to gene promoters and enhancers. Chromatin remodeling and histone acetylation at regulatory regions of IL4 and IFNG is also associated with T cell differentiation. Mechanisms and examples of such chromatin alteration are as follows:

• Histone acetyl transferases (HATs) add acetyl groups to histone (particulary H3 & H4) lysine residues which can eliminate higher order chromatin structures.  Histone acetylation tends to destablize chromatin structure, perhaps because adding an acetyl group removes the + charge from lysine, thereby making it difficult for histones to neutralize the charges on DNA. In addition to reducing the interaction between DNA and the histones, HATs may also provide binding sites for proteins that recognize acetylated lysines but not de-acetylated lysines. Decondensed or "open" chromatin is characterized by hyperacetylation of associated histones as well as by increased accessibility to restriction enzymes, nucleases and transcription factors.

• histone deacetylases (HDACs) removes acetyl groups from the the lysine residues of histone proteins, which has the reverse effect of above (condenses chromatin and prevents gene expression).Histone deacetylation is a major mechanism of methylated DNA silencing.  See US Patent No. 6,541,661 entitled "inhibitors of Histone Deacetylase" provides compounds and methods for inhibiting HDAC enzymes.

• Chromatin remodeling complexes which are protein machines that use ATP hydrolysis can also change the structure of nucleosomes temporarily so that DNA becomes less tightly bound to the histone core.

• Methylation and Demethylation

• Phosphorylation of serines.