Eukaryotic DNA is packed in the form of chromatin. Chromatin comprises DNA and DNA-binding proteins: histones and non-histone proteins. Histones are the major DNA-binding proteins involved in maintaining the compacted structure of chromatin; other DNA-binding proteins include transcription factors, nuclear enzymes, and hormone receptors. The binding of DNA to histones establishes a structure named nucleosome. Five major classes of histones have been identified in humans: H1, H2A, H2B, H3, and H4. The nucleosome core contains an octameric protein structure consisting of two subunits each of H2A, H2B, H3 and H4. Histone H1 associates with the internucleosomal DNA and completes the assembly of the nucleosome. Histones are basic proteins that play a critical role in the proper packing of DNA.
Histones are small proteins (11-22 kDa) containing > 20% positively charged amino acid residues (lysine and arginine) rendering them highly basic. The core histones interact in pairs via a “hand shake” motif with two H3/H4 dimers interacting to form a tetramer, while two H2A/H2B dimers associate with the H3-H4 tetramer to form the nucleosomal core. Core histones are highly conserved among all eukaryotes, whereas HI is the most divergent class of among histones.
Histones stabilize the nucleosome complex by electrostatic interactions between negatively charged phosphate groups of DNA and positively charged ε-amino groups (lysine residues) and guanidino groups (arginine residues) of histones. In chromatin, nucleosomes are arranged like beads on a string; these repetitive sequences are folded into structures of higher order to further compact the DNA.
Histones consist of a globular domain and a flexible and charged amino terminus. The N-terminus of core histones protrudes from the nucleosome surface, where lysine, arginine, and serine residues can be post-translationally modified by enzymes that covalently add or remove a number of different modifications. Although most known modifications are located in the flexible N-terminal tails of the histones, histone H2A has been shown to be modified at the C-terminal end; in addition, recent mass spectrometry studies have identified new histone modifications located at the globular histone core. These post-translational modifications include acetylation, methylation, phosphorylation, ubiquitination, poly (ADP-ribosylation), and biotinylation.
Post-translational modifications of histones are crucial to the regulation of chromatin, playing important roles in regulating transcriptional activity of DNA, DNA repair, cell proliferation, and spermatogenesis. For example, hyperacetylation of histones has been associated with transcriptionally active chromatin, while hypoacetylated histones have been linked with repression of transcription. These modifications, individually or in combination, alter the interaction of histone tails with DNA or with chromatin-associated proteins that is required for different downstream cellular processes. Recently it was proposed that the post-translational modifications on the histone tails create what has been named the histone code. The histone code hypothesis predicts that both type and pattern of different histone covalent modifications dictate a particular biological outcome, being involved in gene-specific regulation. For example, hypermethylation of lysine-4 in histones H3 is associated with transcriptionally active euchromatin, whereas hypermethylation of lysine-9 in histone H3 is associated with transcriptionally silent chromatin. It has been proposed that a given modification of a specific histone residue is a determinant for subsequent additional modifications of the same histone or another histone molecule; this effect mediated by chromatin remodeling complexes. For example, phosphorylation of serine-10 inhibits dimethylation of lysine-9 in histone H3, a heterochromatin marker, altering the transcriptional silent state of the gene.
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