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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

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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