Table 1

Overview of major epigenetic DNA and chromatin modification systems

System

Abbreviation

Class

Substrate/mark


DNA modifications

DNA methyltransferases

DNMT

Writer

Cytosine

Candidate systems: methylcytosine hydroxylation, DNA glycosylation, base excision repair and deaminases?

-

Eraser

5-methyl-C, 5-OH-methyl-C

Methyl-CpG binding domain

MBD

Reader

5-methyl-C

Histone modifications

Histone lysine methyltransferases

KMT

Writer

Methylation (lysine)

Histone methyl-lysine demethylases

KDM

Eraser

Demethylation (methyl lysine)

Chromodomain, Tudor domain, MBT domain, PWWP domain, PHD fingers, WD40 domain

-

Reader

Methyl lysine

Protein arginine methyltransferases

PRMT

Writer

Arginine methylation

Protein arginine deiminases

PADI

Eraser

deimination

Tudor domain

-

Reader

Methyl-arginine

Histone lysine acetyltransferases

KAT

Writer

Acetylation (lysine)

Histone lysine deacetylases

HDAC

Eraser

Deacetylation (lysine)

Bromodomain

-

Reader

Acetyl-lysine


For further details and nomenclature used, see [26,91].

Oppermann Arthritis Research & Therapy 2013 15:209   doi:10.1186/ar4186