Epigenetics and DNA methylation in cancer

Table 1 Most common chromatin modifications with their reader motifs and function

Chromatin modification	Nomenclature	Chromatin-reader motif	Attributed function
DNA modification
5-methylcytosine	5mC	MBD domain	Transcription
5-formylcytosine	5fC	Unknown	Unknown
5-hydroxymethylcytosine	5hmC	Unknown	Transcription
5-carboxylcytosine	5caC	Unknown	Unknown
Histone modification
Acetylation	K-ac	BromodomainTandem PHD fingers	Transcription, repair, replication, and condensation
Methylation (lysine)	K-me1, K-me2, K-me3	Chromodomain, tudor domain, MBT domain, PWWP domain, PHD fingers	Transcription and repair
Methylation (arginine)	R-me, R-me2s, R-me2a	Tudor domain	Transcription
Phosphorylation (serine and threonine)	S-ph, T-ph	14-3-3. BRCT	Transcription, repair and condensation
Phosphorylation (tyrosine)	Y-ph	SH2	Transcription and repair
Ubiquitylation	K-ub	UIM, IUIM	Transcription and repair
Sumoylation	K-su	SIM	Transcription and repair
ADP ribosylation	E-ar	Macro domain, PBZ domain	Transcription and repair
Deimination	R→Cit	Unknown	Transcription and decondensation
Propoline isomerisation	P-cis↔P-trans	Unknown	Transcription
Crotonylation	K-cr	Unknown	Transcription
Propionylation	K-pr	Unknown	Unknown
Butyrylation	K-bu	Unknown	Unknown
Formylation	K-fo	Unknown	Unknown
Hydroxylation	Y-oh	Unknown	Unknown
O-GIcNAcylation (serine and threonine)	S-GIcNAc; T-GIcNAc	Unknown	Transcription

Adapted by Dawson et al[2], 2012. 5mC: 5-methylcytosine; 5hmC: 5-hydroxymethylcytosine; 5caC: 5 carboxylcytosine; 5fC: 5 formylcytosine; me1: Monomethylation; me2: Dimethylation; me3: Trimethylation; me2s: Symmetrical dimethylation; me2a: Asymmetrical dimethylation; Cit: Citrulline; MBD: Methyl-CpG-binding domain; PHD: Plant homeodomain; MBT: Malignant brain tumor domain; PWWP: Proline-tryptophan-tryptophan-proline domain; BRCT: BRCA1 C terminus domain; UIM: Ubiquitin interaction motif; IUIM: Inverted ubiquitin interaction motif; SIM: Sumo interaction motif; PBZ: Poly ADP-ribose binding zinc finger; SH2: Src Homology 2.