Table 1.
A comprehensive selection of effector domains for epigenome editing systems
| Effect | Domain | Consequence | Reference(s) |
|---|---|---|---|
| Activation | VP64 VP16 p65 SAM VPR |
Activates transcription by recruiting a transcription complex and can then recruit histone acetylation as a consequence of the induced transcription. Can recruit p300 to deposit H3K27ac | Seipel et al. [52] Beerli et al. [53] Konermann et al. [57, 84] Gilbert et al. [81, 87] Mali et al. [83] Perez-Pinera et al. [30] Kearns et al. [85] Hu et al. [95] Tanenbaum et al. [96] Gao et al. [54] Chakraborty et al. [90] Heller et al. [125] Zalatan et al. [88] Nihongaki et al. [102] Polstein and Gersbach [103] Chavez et al. [97] |
| Repression | KRAB SID Tbx3-RD |
Represses transcription by preventing transcription complex formation. May also recruit other repressive modifications | Margolin et al. [55] Ayer et al. [56] Cong et al. [17] Gilbert et al. [81, 87] Chen et al. [105] Kearns et al. [85] Hu et al. [95] Ma et al. [59] Gao et al. [54] Zalatan et al. [88] Telese et al. [89] |
| DNA methylation | DNMT3A DNMT3B M.EcoHK31I M.HhaI M.SssI DNMT3A-3L |
Represses transcription | Li et al. [63] Meister et al. [64] Chaikind et al. [66, 69] Rivenbark et al. [65] Siddique et al. [67] Nunna et al. [68] Stolzenburg et al. [70] Kungulovski et al. [71] Bernstein et al. [76] |
| DNA demethylation | TDG TET1 TET2 |
Activates transcription | Gregory et al. [72] Maeder et al. [73] Chen et al. [78] |
| H3K9me | G9a (EHMT) Suvar KYP GLP |
Represses transcription | Snowden et al. [61] Falahi et al. [62] Konermann et al. [57] Heller et al. [125] Kungulovski et al. [71] Cho et al. [74] |
| H3K9 demethylation | JMJD2B | Activates transcription | Hu et al. [95] |
| H3K9 deacetylation | Sin3a | Represses transcription | Konermann et al. [57] |
| H3K4me2 demethylation | LSD1 | Also leads to H3K27ac removal; both repress transcription. Ideal for enhancers | Mendenhall et al. [75] Kearns et al. [58] |
| H3K27me3 | NUE | Represses transcription | Konermann et al. [57] |
| H3K27 demethylation | JMJD3 | Activates transcription | Hu et al. [95] |
| H3K27ac | p300 | Activates transcription. Ideal for enhancers | Hu et al. [95] Hilton et al. [91] |
| H4K8 deacetylation | HDAC8 RPD3 Sir2a |
Represses transcription | Konermann et al. [57] |
| H4K20me3 | tgSET8 | Represses transcription | Konermann et al. [57] |
| Affinity enrichment | PrA FLAG |
Locus-specific chromatin enrichment for protein analysis | Byrum et al. [109, 113] Fujita et al. [110, 111] Waldrip et al. [112] |
| Cell imaging | GFP Cherry BFP |
Sub-nuclear visualization | Chen et al. [46] Anton et al. [106] Ma et al. [108] |