ADD: The ADD domain of the DNMT3a DNA methyltransferase has been shown to interact with H4R3me2s, promoting silencing of the human β-globin locus. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    Ankyrin: Owing to extensive intermolecular contacts, the ankyrin repeats of G9a and GLP and the BAH domain of ORC1 show high specificity for di- or monomethylated H3K9 and H4K20me2, respectively. The H3K9me2 peptide is sandwiched between the β-turns and α-helices of the fourth and fifth ankyrin repeats, whereas K9me2 fits into the aromatic cage also containing a glutamate. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    BAH: Owing to extensive intermolecular contacts, the ankyrin repeats of G9a and GLP and the BAH domain of ORC1 show high specificity for di- or monomethylated H3K9 and H4K20me2, respectively. The H3K9me2 peptide is sandwiched between the β-turns and α-helices of the fourth and fifth ankyrin repeats, whereas K9me2 fits into the aromatic cage also containing a glutamate. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    Chromo-Barrel: Chromo-Barrel, as the other member of the Royal family, shows some specificity, preferring tri- or dimethylated H3K36 and monomethylated H4K20 (H4K20me1); however, they bind rather weakly. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    Chromodomain: The chromodomain is the smallest member, consisting of four curved β-strands and an α-helix. The chromodomains of HP1 and Polycomb were found to recognize histone H3 trimethylated at K9 (H3K9me3) and H3K27me3, respectively, and these proteins were the first examples of readers specific for methyllysine. Chromodomains generally prefer trimethylated lysine, though some have been shown to bind dimethylated species. The aromatic cage of the chromodomain of mouse and fly HP1 contains an aspartate or glutamate residue, accounting for its ability to interact well with H3K9me3 and dimethylated H3K9 (H3K9me2). (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    DCD: In the double chromodomain (DCD), both chromodomains share their general secondary structure elements with those previously seen in HP1 and Polycomb chromodomains. The linker segment forms a novel helix–turn–helix structure that juxtaposes the two chromodomains to form a continuous surface. A total of 350 Å is buried at the interface of these tandem chromodomains. (1)

Reference
1. John F. Flanagan, Li-Zhi Mi, Maksymilian Chruszcz, Marcin Cymborowski, Katrina L. Clines, Youngchang Kim, Wladek Minor, Fraydoon Rastinejad & Sepideh Khorasanizadeh.Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature.2005;438:1181–1185. PMID: 16372014.

    MBT: MBT reads lower methylation states, recognizing mono- and dimethylated lysines. All MBTs characterized at present contain two to four repeats of ~100 amino acids. The most common three-repeat 3MBT module folds in a propeller-like structure, and the four-repeat 4MBT module has an asymmetric rhombus architecture29-32. Notably, although each MBT repeat contains an aromatic cage, which also includes an acidic residue, only the second repeat binds methyllysine. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    PHD: Distinct from the Royal family is the PHD finger, a well-characterized reader of H3K4me3. It contains a C4HC3 motif that coordinates two zinc ions in a cross-brace manner. Such an arrangement produces a globular domain with a small β-sheet and an α-helix. PHD fingers make extensive contacts with H3K4me3, imparting a high degree of specificity. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    PWWP: PWWP, as one of the members of the Royal family, shows some specificity, preferring tri- or dimethylated H3K36 and monomethylated H4K20 (H4K20me1); however, they bind rather weakly. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    TTD: The structurally related TTD module possess a characteristic β-barrel topology and comprise the Royal superfamily. The single Tudor domains of PHF1 and PHF19 have been shown to recognize H3K36me3, whereas the canonical TTD of 53BP1 associates with H4K20me2, and the hybrid TTD of JMJD2A binds H3K4me3 and H4K20me3. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    Tudor: Tudor can exist as a single domain or in tandem, containing two β-barrels. The single Tudor domains of PHF1 and PHF19 have been shown to recognize H3K36me3, whereas the canonical TTD of 53BP1 associates with H4K20me2, and the hybrid TTD of JMJD2A binds H3K4me3 and H4K20me3. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    WD40: The WD40 domain of EED binds trimethylated lysines through an aromatic cage positioned at the top of the channel of a seven-bladed β-propeller. It is fairly promiscuous and interacts with H3K27me3, H3K9me3, H4K20me3 and H1K26me3. The structure of the EED WD40 in complex with H3K27me3 reveals an important role for the residues flanking K27me3. (1)

Reference
1. Musselman CA, Lalonde ME, Cote J, Kutateladze TG.Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol.2012;19(12):1218-27. PMID: 23211769.

    ZF-CW: The zinc finger CW (ZF-CW) domain is a motif of about 60 residues that is frequently found in proteins involved in epigenetic regulation. The ZF-CW domain adopts a new fold in which a zinc ion is coordinated tetrahedrally by four conserved Cys ligand residues. The tertiary structure of the ZF-CW domain partially resembles that adopted by the plant homeo domain (PHD) finger bound to the histone tail, suggesting that the ZF-CW domain and the PHD finger have similar functions. (1)

Reference
1. He F, Umehara T, Saito K, Harada T, Watanabe S, Yabuki T, Kigawa T, Takahashi M, Kuwasako K, Tsuda K, Matsuda T, Aoki M, Seki E, Kobayashi N, Güntert P, Yokoyama S, Muto Y.Structural insight into the zinc finger CW domain as a histone modification reader. Structure.2010;18:1127–1139. PMID: 20826339 .