Table 2.
Histone demethylase nomenclature and substrate specificity
| Standardized family name | Family member (mammalian) | Former names | Homologs referenced in this review | Substrate specificity | References |
|---|---|---|---|---|---|
| KDM1 | KDM1 | LSD1; AOF2; BHC110 | Sp: SpLsd1; Swm1 | H3K4me2/1 | (Rudolph et al., 2007; Shi et al., 2004) |
| Dm: SU(VAR)3-3 | H3K9me2/1 | ||||
| p53 | |||||
| KDM2 | KDM2A | JHDM1A; FBXL11 | H3K36me2/1 | (Tsukada et al., 2006) | |
| KDM2B | JHDM1B; FBXL10 | ||||
| KDM3 | KDM3A | JHDM2A; JMJD1A; TSGA | H3K9me2/1 | (Yamane et al., 2006) | |
| KDM3B | JHDM2B; JMJD1B | ||||
| KDM4 | KDM4A | JMJD2A; JHDM3A | Ce: JMJD-2 | H3K9me3/2 | (Whetstine et al., 2006) |
| KDM4B | JMJD2B | H3K36me3/2 | |||
| KDM4C | JMJD2C; GASC1 | ||||
| KDM4D | JMJD2D | ||||
| KDM5 | KDM5A | RBP2; JARID1A | Ce: RBR-2 | H3K4me3/2 | (Christensen et al., 2007; Iwase et al., 2007; Klose et al., 2007; Lee et al., 2007a; Liang et al., 2007) |
| KDM5B | PLU-1; JARID1B | Dm: LID | |||
| KDM5C | SMCX; JARID1C | Sc: Yjr119Cp; Jhd2p | |||
| KDM5D | SMCY; JARID1D | ||||
| KDM6 | KDM6A | UTX | Ce: F18E9.5 | H3K37me3/2 | (Agger et al., 2007; Lan et al., 2007a) |
| KDM6B | JMJD3 |
The substrate specificity column lists the nomenclature and known substrate specificities of each demethylase family and enzyme referenced in this review. In the text, the demethylases are referred to by both the standardized name and one former name (in bold). Many of these demethylases have been described by multiple groups; here we reference the first report to show in vitro demethylase activity for each enzyme. Ce, Caenorhabditis elegans; Dm, Drosophila melanogaster; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe