Table 1. Chromatin marks.

Listed are chromatin marks discussed in this review

Chromatin mark	“Writers”	“Reader” domains & proteins	“Erasers”	Genomic distribution	Main function as epigenetic mark	Other features
DNA:
5mC	DNA methyltransferases (Dnmts 1, 3a, 3b)	Methyl-CpG Binding Domains (MBDs) (e.g. MeCP2, MBDs1-4) BTB/POZ domains (Kaiso, ZBTB4, ZBTB38)	Active demethylation (TET 1,2,3 proteins) Passive demethylation processes	CpG dinucleotides throughout the genome: intergenic regions, gene bodies, heterochromatin, satellite repeats. Excluded from CpG islands associated with promoters	Repressive mark Cellular memory	Essential for chromosome stability, silencing of transposons, genomic imprinting and X-inactivation
5hmC, 5fC, 5caC	Ten-eleven translocation enzymes (TET 1, 2, 3)	Unknown	TDG followed by base excision repair (BER) Passive processes	Oxidation products of 5mC; abundant levels of 5hmC in brain and ES cells	Unknown	Demethylation intermediates of 5mC; Mutations targeting TET genes frequently observed in human cancers
Histone tails:
H3K27me	Histone lysine methyltransferases - HMTs (EZH2)	Chromo and WD40 domains (e.g. Polycomb protein Pc, EED, CBX7)	Histone lysine demethylases- HDMs (KDM6a, KDM6b)	Repressive domains and silent developmental genes	Repressive mark Cellular memory	Established by polycomb complex activity; mark associated with bivalent chromatin*
H3K4me	Lysine HMT (e.g.SETD1a,b,SETD7, NSD3, MLL, PRDM9)	Chromo, PHD, Tudor, MBT, Zf-W domains (e.g. CHD1, ING2)	HDMs (e.g.KDM1A,5A,5D, PHF8)	H3K4me1: enhancers H3K4me2: promoters & enhancers H3K4me3: promoters & transcription start sites	Activating mark	H3K4me3 mark is enriched at CpG islands devoided of DNA methylation & associated with bivalent chromatin*
H3K9me	Lysine HMT (e.g. G9a/KTM1C, PRDM2, SETDB1-2; SUV39H1-H2/KTM1A-B)	Chromo, PHD, Tudor, WD40 domains, Ankyrin repeats (e.g. HP1, CDY, EED)	HDMs (e.g. KDM1A, 1B, 3A, 3B, 4A, 4C, 4D)	H3K9me2: heterochromatin H3K9me3: constitutive heterochromatin and repetitive elements	Repressive mark	The chromodomain of all HP1 isoforms binds to H3K9me3 and this interaction is important for the recruitment of HP1 proteins to heterochromatic areas of the genome.
H3K36me3	Lysine HMT (SETD2, NSD2)	Chromo, PWWP Domains (e.g. EAF3, MRG15, N-PAC)	HDMs (KDM4A, NO66)	Associated with transcribed portions of genes, with preference for 3’regions after intron1	Elongation mark associated with transcription	H3K36me3 regulates DNA mismatch repair (MMR) in human cells, being required to recruit MMR recognition proteins onto chromatin
H3K4ac	Histone acetyltransferases – HATs (KAT2A/GCN5)	Bromo Domains	Histone deacetylases-HDAC’s (HDAC3)	Enriched at transcription start sites (TSS) and along gene bodies	Activating mark (“Open” chromatin)
H3K9ac	HATs (e.g. KAT2A/GCN5, ELP3)	Bromo Domains (e.g. BRG1, BRD4, TAF1)	HDAC’s (SIRT1, SIRT6)	Preference for promoters (near TSS is related to transcriptional activation)	Activating mark (“Open” chromatin)	Mark of active regulatory elements
H3K27ac	HATs (P300, CREBBP/CBP)	Bromo Domains (e.g. BRG1, BRD4, TAF1)	HDACs (e.g. HDAC1)	Active regulatory elements (may distinguish between active promoters and enhancers from inactive ones)	Activating mark (“Open” chromatin)	Distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone

^*contains both activating and repressing marks in the same domain of chromatin; these bivalent domains are considered to “poise” expression of developmental genes, allowing timely activation while maintaining repression in the absence of differentiation signals; for extended information on the chromatin marks listed see review articles: Huang H et al. (2004) Snapshot: Histone modifications Cell, 159:p458; Li E and Zhang Y (2014) DNA methylation in mammals. CSH Perspect Biol 6:a019133; Yun M et al. (2015) Readers of histone modifications. Cell Research 21:564-578; see also main text for details)