For many years histone methylation was thought to be irreversible, due to the fact that the half-life of the histone methylation was approximately equal to the half-life of histones themselves. In 2004, Shi et al. published their discovery of the histone demethylase LSD1, a nuclearamine oxidase homolog. Since then many more histone demethylases have been found. Defined by their mechanisms, two main classes of histone demethylases exist: a flavin adenine dinucleotide -dependent amine oxidase, and an Fe and α-ketoglutarate-dependent hydroxylase. Both operate by hydroxylation of a methyl group, followed by dissociation of formaldehyde. Demethylation has implications for epigenetics. Histone demethylase proteins have a variety of domains that serve different functions. These functions include binding to the histone, recognizing the correct methylated amino acid substrate and catalyzing the reaction, and binding cofactors. Cofactors include: alpha-keto glutarate, CoREST, FAD, Fe or NOG. Domains include: There are several families of histone demethylases, which act on different substrates and play different roles in cellular function. A code has been developed to indicate the substrate for a histone demethylase. The substrate is first specified by the histone subunit and then the one letter designation and number of the amino acid that is methylated. Lastly, the level of methylation is sometimes noted by the addition of "me#", with the numbers being 1, 2, and 3 for monomethylated, dimethylated, and trimethylated substrates, respectively. For example, H3K9me2 is histone H3 with a dimethylated lysine in the ninth position. ;KDM1:The KDM1 family includes KDM1A and KDM1B. KDM1A can act on mono- and dimethylated H3K4 and H3K9, and KDM1B acts only on mono- and dimethylated H3K4. These enzymes can have roles critical in embryogenesis and tissue-specific differentiation, as well as oocyte growth. KDM1A was the first demethylase to be discovered and thus it has been studied most extensively.
;KDM2:The KDM2 family includes KDM2A and KDM2B. KDM2A can act on mono- and dimethylated H3K36 and trimethylated H3K4. KDM2B acts only on mono- and dimethylated H3K36. KDM2A has roles in either promoting or inhibiting tumor function, and KDM2B has roles in oncogenesis. ;KDM3:The KDM3 family includes KDM3A, KDM3B and JMJD1C. KDM3A can act on mono- and dimethylated H3K9. The substrates for KDM3B and JMJD1C are not known. The KDM3A has roles in spermatogenesis and metabolic functions; the roles are of KDM3B and JMJD1C are unknown. ;KDM4:The KDM4 family includes KDM4A, KDM4B, KDM4C, and KDM4D. These are also referred to as JMDM3A/JMJD2A, JMDM3B/JMJD2B, JMDM3C/JMJD2C, and JMDM3D/JMJD2D, respectively. These enzymes can act on di- and trimethylated H3K9, H3K36, H1K26. KDM4B and KDM4C have roles in tumorigenesis, and the role of KDM4D is unknown. ;KDM5:The KDM5 family includes KDM5A, KDM5B, KDM5C, and KDM5D. These are also referred to as JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, and JARID1D/SMCY, respectively. These enzymes can act on di- and trimethylated H3K4. ;KDM6:The KDM6 family includes KDM6A, KDM6B, and UTY. KDM6A and KDM6B act on di- and trimethylated H3K27 and have roles in development; the substrate and role of UTY is unknown. On the whole, both KDM6A and KDM6B possess tumor-suppressive characteristics. KDM6A knockdowns in fibroblasts lead to an immediate increase in fibroblast population. KDM6B expressed in fibroblasts induces oncogenes of the RAS_RAF pathway. Deletions and point mutations of KDM6A have been identified as one cause of Kabuki Syndrome, a congenital disorder resulting in intellectual disability.
Ester demethylation
Another example of a demethylase is protein-glutamate methylesterase, also known as CheB protein, which demethylates MCPs through hydrolysis of carboxylic ester bonds. The association of a chemotaxis receptor with an agonist leads to the phosphorylation of CheB. Phosphorylation of CheB protein enhances its catalytic MCP demethylating activity resulting in adaption of the cell to environmental stimuli. MCPs respond to extracellular attractants and repellents in bacteria like E. coli in chemotaxis regulation. CheB is more specifically termed a methylesterase, as it removes methyl groups from methylglutamate residues located on the MCPs through hydrolysis, producing glutamate accompanied by the release of methanol. CheB is of particular interest to researchers as it may be a therapeutic target for mitigating the spread of bacterial infections.
