Table 1.
Mechanisms involved in epigenetic control and related epigenetic enzymes. References
| Mechanism | Writer | Eraser | Reader |
|---|---|---|---|
| DNA methylation | DNA methyltransferases (DNMT1, DNMT3) [67, 68] | DNA demethylation enzymes (TET) [69] | Methyl-CpG binding domains (MECP2, MBD1, MBD2, and MBD4) [70] |
| Histone lysine acetylation | Histone acetyltransferases (GCN5/PCAF, MYST, P300/CBP, SRC/p160) [71] | Histone deacetylases (HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, HDAC10, HDAC11); Sir2-like proteins (SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, SIRT7) [72] | Bromodomain, tandem PHD [73, 74] |
| Histone arginine methylation | Histone arginine methyltransferases (PRMT1, PRMT2, PRMT3, PRMT5, PRMT6, PRMT7, CARM1) [75] | Histone arginine demethylase (bifunctional arginine demethylase and lysyl-hydroxylase JMJD6) [76] | Tudor, ADD, WD40 [73, 74] |
| Histone lysine methylation | Histone lysine methyltransferases (EZH, SET1, SET2, SMYD, SUV39, SUV4-20, RIZ, SET8/PR-SET7, SET7/9, PRDM) [77] | Histone lysine demethylases Lysine-specific demethylase (LSD1, LSD2); Jumonji histone demethylases (JHDM1, JHDM2, JHDM3/JMJD2, JARID, JMJC, PHF2/PHF8, UTX/UTY) [77] |
Chromodomain, ADD, ankyrin, BAH, chromobarrel Tudor, PHD fingers, MBT, ZF-CW, WD40, PWWP [73, 74] |
| Histone phosphorylation | Histone kinases (AGC, CaMK, CMGC, protein-tyrosine kinase, MEK) [78] | Histone phosphatases Serine/threonine phosphatases (PPP, PPM); tyrosine phosphatases (PTP, VH1-like dual-specificity phosphatase, cdc25) [79, 80] |
Chromoshadow, 14.3.3 proteins, BIR, BRCT [73, 74] |
| Histone lysine ubiquitination | Histone lysine ubiquitinases (E1 enzyme, E2 ubiquitin conjugases); E3 ubiquitin-protein ligases (HECT domain, RING finger domain) [81] | Histone lysine deubiquitinases (UCH, USP, MJD, OTU, JAMM) [82] | Unknown |
| Histone arginine citrullination | Histone arginine deiminases (PAD1, PAD2, PAD3, PAD4, PAD6) [83] | Unknown | Unknown |
| Histone lysine biotinylation | Histone lysine biotinases (HLCS) [84] | Unknown | Unknown |
| Histone lysine ribosylation | Histone lysine ribosylases (PARP1) [85] | Histone lysine deribosylase (PARG) [85] | Unknown |