Epigenetics has been defined as a stable, differential state of gene expression. In order to accomplish this, the cell employs multiple mechanisms that establish alternate states of chromatin structure, histone modification, associated protein composition and transcriptional activity. Although epigenetic changes do not occur exclusively on histones, the remodeling of chromatin is an excellent example of the mechanism by which nucleosomes are modified resulting in “open” and “closed” forms of chromatin, leading to changes in the transcriptional activity of the associated gene. Potential modifications to the histones include acetylation, methylation, poly-ADP ribosylation, ubiquitinylation, sumoylation, carbonylation and glycosylation.
Acetylation and deacetylation of histone proteins requires two types of enzymes, both of which do not affect histones exclusively. Histone acetyltransferases (HATs) catalyze the addition of an acetyl group to lysine residues and histone deacetylases (HDACs) catalyze their removal. To date, eighteen unique HDACs have been identified in humans. They have been subdivided into four classes based on their enzymatic activities, homology to yeast HDACs, and subcellular localization. Class I HDACs (1, 2, 3 and 8) are homologous to yeast RPD3, occur ubiquitously in most tissues and their subcellular localization is generally nuclear. Class II HDACs (4, 5, 6, 7, 9 and 10) are homologous to the yeast protein Hda1 and can translocate between the cytoplasm and nucleus. Within Class II HDACs are two subclasses, IIa and IIb. The differences between the two are defined by the Class IIb HDACs 6 and 10; both are found in the cytoplasm and contain two deacetylase domains. HDAC6 is unique in that it displays substrate specificity for the cytoplasmic protein a-tubulin. The class III HDACs (SIRT1, 2, 3, 4, 5, 6 and 7) are yeast protein Sir2 homologues. They require NAD+ for their activity to regulate gene expression, and can be inhibited by the drug nicotinamide. The remaining HDAC member is HDAC11, and since it shares sequence identities with the catalytic core of both classes I and II without altogether resembling either class it is placed in class IV.
Enzymes that methylate DNA have been identified at a molecular level and their cell biology, genetics and biochemistry have been well-characterized. In 1983, Bestor and colleagues identified the first DNA methyltransferase, which is now known as Dnmtl. Although Dnmtl possesses robust de novo methytransferase activity, its preferred substrate is hemi-methylated DNA. Dnmtl, is responsible for maintaining established patterns of DNA methylation during DNA replication. The demonstration that Dnmtl can be found at the replication fork in a complex with proliferating cell nuclear antigen (PCNA), where it uses the parent strand as a template for methylating the newly synthesized daughter strand fulfilled the predictions of a DNA methylating enzyme capable of semi-conservative replication of methylation patterns. Dnmtl-deficient mice die during gastrulation and demonstrate ectopic X-inactivation, biallelic expression of imprinted genes and increased expression of retroviral elements in addition to genome-wide loss of methylation.