"Histones are highly conserved proteins that serve as the structural scaffold for the organization of nuclear DNA into chromatin. The histones have an amino terminal tail, a globular domain, and a carboxy-terminal tail. The four core histones, H2A, H2B, H3 and H4 assemble into the octamer (2 molecules of each). Subsequently, 146 base pairs of DNA are wrapped in a sequence-independent manner around the octamer, forming the basic subunit of chromatin, the nucleosome. The distance between nucleosomes varies from species to species but generally is between 180 and 200 base pairs for higher organisms. Histone H1, the most common form of linker histone, binds to nucleosomal DNA at the point from which the DNA exits the nucleosome, and is required for higher order packing of chromatin.
Histones are modified post-translationally by the actions of enzymes in both the nucleus and cytoplasm that deposit specific functional groups. These modifications help to regulate the processes that depend on DNA, such as transcription, DNA repair, recombination and replication. The most commonly studied and best understood modifications are acetylation, phosphorylation, methylation, and to a lesser extent ubiquitination. The modifications occur predominantly on the amino terminal tails that extend out beyond the nucleosome core particle, but certain modifications have also been identified on the C-terminal tails and globular domains of some histones. Acetylation occurs on the epsilon amino group of lysine residues of all four core histones, and increases in acetylation in are correlated strongly with increases in gene expression.
Indeed, many histone acetyltransfease enzymes (HATs) form the catalytic subunits of transcriptional activating protein complexes. Histone deacetylases (HDACs) remove acetyl marks, antagonizing the activity of HATs and lead to decreases in transcription (see above). Phosphorylation occurs on serine residues in the amino termini of all four core histones and in multiple regions of H1. Phosphorylation of serines 10 and 28 of H3 occur during chromosome condensation in mitosis, and antibodies to these sites are excellent mitotic markers. H2B is phosphorylated at serines 14 and 32 in cells undergoing apoptosis, and the histone variant H2A.X is phosphorylated at serine 139 in response to DNA damage. Histone methylation has recently become a popular research topic, and occurs on both lysine and arginine residues. Arginine methylation appears to be associated predominantly with transcriptional activation, whereas two specific lysine methylation events on histone H3 are hallmarks of either active chromatin (euchromatin) or silenced chromatin (heterochromatin). Ubiquitination is the least understood of the histone modifications and occurs on the C-terminal tails of H2A and H2B, and in some cases is a necessary precursor to specific histone methylation events.
Using a technique known as chromatin immunoprecipitation (ChIP), it is possible to analyze the variety of histone modifications present within a given promoter region or even an entire gene locus. Antibodies specific to the modification of interest are used to enrich for regions of chromatin (sheared to a manageable size and harvested from cells) that contain the modification, and various detection methods (Southern blot, PCR, microarray) are employed to detect specific DNA sequences within the enriched chromatin. This data is very useful in analyzing the involvement of a modification in specific biological processes."