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Table 1 Mechanisms involved in epigenetic control and related epigenetic enzymes. References

From: The quest for an effective and safe personalized cell therapy using epigenetic tools

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