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The nucleosome core contains four histone proteins: H2A, H2B, H3, and H4. These core histones form the protein octamer around which DNA wraps. In addition to these standard histones, eukaryotes possess variants of each histone type, except H4, which provide functional diversity in chromatin regulation and gene expression.

Histone acetylation increases negative charge on histones, weakening DNA-histone interactions and loosening chromatin structure, allowing greater DNA access. Conversely, methylation increases positive charge, strengthening DNA-histone affinity and promoting chromatin compaction. These opposing effects make acetylation associated with gene activation and methylation with gene silencing.

The histone code is a system where coordinated sets of histone modifications encode specific cellular signals. Different modification combinations signal DNA damage, gene expression, gene silencing, or chromatin modifications. Regulatory proteins called readers recognize these marks, bind to chromatin regions, and recruit additional protein complexes to execute specific biological functions.

Writer enzymes like methyltransferases, acetylases, and kinases catalyze histone modifications including acetylation, methylation, and phosphorylation. Eraser enzymes such as demethylases, deacetylases, and phosphatases remove these modifications. This dynamic system allows cells to rapidly alter chromatin states and regulate gene expression in response to developmental and environmental signals.

Histone modifications occur on the amino-terminal tails of core histones, which protrude from the nucleosome and comprise approximately 30 amino acids. These highly unstructured and mobile tails are subjected to covalent modifications including acetylation of lysines, phosphorylation of serines, and mono-, di-, or tri-methylation of lysines.

Histone modifications are epigenetically inherited, meaning they are not genetically coded but faithfully passed to daughter cells during cell division as epigenetic memory. This inheritance of chromatin structures allows cells to maintain gene expression patterns and chromatin states across generations without changes to DNA sequence.

Acetylated histones are associated with active gene expression, while hypoacetylated histones correlate with gene repression. For example, the beta-globin gene in erythroid cells is associated with acetylated histones that increase its expression, whereas in non-erythroid cells where the gene is inactive, it associates with nonacetylated histones.