Table 1 A comprehensive selection of effector domains for epigenome editing systems
From: Strategies for precision modulation of gene expression by epigenome editing: an overview
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] 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] 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] 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 | Waldrip et al. [112] |
Cell imaging | GFP Cherry BFP | Sub-nuclear visualization | Chen et al. [46] Anton et al. [106] Ma et al. [108] |