There is abundant evidence that chemical modifications to histones, found in all eukaryotic organisms, play a direct role in the regulation of gene transcription. The N-terminus of each histone protein in a nucleosome protrudes outward from the nucleosome. These so-called histone tails are accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups, such as acetyl, methyl, and phosphate groups. Generally, histone acetylation—the addition of an acetyl group to an amino acid in a histone tail—appears to promote transcription by opening up the chromatin structure, while the addition of methyl groups to histones can lead to the condensation of chromatin and reduced transcription. Often, the addition of a particular chemical group may create a new binding site for enzymes that further modify chromatin structure in various ways.
Rather than modifying histone proteins, a different set of enzymes can methylate the DNA itself on certain bases, usually cytosine. Such DNA methylation occurs in most plants, animals, and fungi. Long stretches of inactive DNA, such as that of inactivated mammalian X chromosomes, are generally more methylated than regions of actively transcribed DNA (although there are exceptions). On a smaller scale, the DNA of individual genes is usually more heavily methylated in cells in which those genes are not expressed. Removal of the extra methyl groups can turn on some of these genes.
Once methylated, genes usually stay that way through successive cell divisions in a given individual. At DNA sites where one strand is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication. Methylation patterns are thus passed on to daughter cells, and cells forming specialized tissues keep a chemical record of what occurred during embryonic development. A methylation pattern maintained in this way also accounts for genomic imprinting in mammals, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development.
Urry, Lisa A.. Campbell Biology (p. 369). Pearson Education. Kindle Edition.