Table 3.
Epigenetic editing technologies for gene transcriptional repression
| Gene regulation: REPRESSION | Effector domain (ED) | Molecular function | Targeted genomic region | Epigenetic technology (direct ED fusion) | Epigenetic technology (ED recruitment) |
|---|---|---|---|---|---|
| Recruiters of endogenous transcriptional repressors | KRAB (Krüppel-associated box) | Recruitment of corepressor KAP1, HP1, SetDB1 and NuRD Increased H3K9me3 Decreased H3K9ac | Gene promoters and enhancers | ZFP (8,79,83,154,191,244) TALE (84) SpdCas9 (30,45,85,86,174) SadCas9 (245) LmoCascade (233) | Sp and Sa dCas9 (GAI/GID1) and (ABI/PYL1) (18) SpdCas9 (Com) (117) |
| SIN3A (SIN3 Transcription Regulator Family Member A) | Transcriptional corepressor hub Recruitment of HDACs Decreased H3ac | Gene promoters and enhancers | SpdCas9 (87) | TALE-LITE (120) | |
| FOG1 (Friend of GATA1) | Recruitment of NuRD, HDAC1 and 2 and PRC2 complex Increased H3K27me3 | Gene promoters | SpdCas9 (88) | ||
| HP1 (Heterochromatin protein 1) | Interacts with KMTs, e.g., Suv39h1, SetDB1, and G9a Increased H3K9me3 | Gene promoters | SpdCas9-FIRE (89) | ||
| KRAB and MeCP2 (Enhanced gene repression) | MeCP2 binds to DNA methyltransferase DNMT1 and the SIN3A–histone deacetylase co-repressor complex | Gene promoters | SpdCas9 (90) | ||
| Enzymes: DNA methylation (DNAme) | DNMT3A (catalytic domain or full-length) | DNA methyltransferase Increased cytosine methylation (writer) | Gene promoters and introns | ZFP (80,81,92,243,246) SpdCas9 (61,93–97,105) SadCas9 (20) | TALE (CRY2-CIB1) (125) SpdCas9-SunTag (106,107) |
| Major satellite repeats | SpdCas9 (GBP-GFP) (65) | ||||
| DNMT3B (catalytic domain) | DNA methyltransferase Increased cytosine methylation (writer) | Gene promoters | SpdCas9 (105) | ||
| DNMT3A and DNMT3L (Enhanced gene repression) | A: DNA methyltransferase (writer) L: regulatory factor | Gene promoters | ZFP (100) TALE (103) SpdCas9 (101,102) | ||
| MQ1 | Prokaryotic DNA methyltransferase (writer) | Gene promoters | SpdCas9 (98) | ||
| M.SssI | Prokaryotic DNA methyltransferase (writer) | Pericentromeres | TALE and SpdCas9 (104) | ||
| Multiple distinct EDs for epigenetic memory | DNMT3A, DNMT3L, and KRAB | Long-term gene silencing Increased DNAme and H3K9me3 Decreased H3K4me3 | Gene promoters | TALE (108,109) SpdCas9 (108) | |
| Enzymes: Histone lysine methylation | Ezh2 (catalytic domain) | Histone lysine methyltransferase (KMT) Increased H3K27me3 (writer) | Gene promoters | SpdCas9 (88,110,112) | SpdCas9 (PP7-PCP) (111) |
| G9a (EHMT2) (minimal catalytic domain) | Histone lysine methyltransferase (KMT) Increased H3K9me2 (writer) | Gene promoters | ZFP (28) | ||
| Multiple distinct EDs for epigenetic memory | Ezh2, DNMT3A, and DNMT3L (overexpressed) | Long-term gene silencing Increased DNAme and H3K27me3 Decreased H3K27ac | Gene promoters | SpdCas9 (112) (Ezh2 and DNMT3A) | |
| Enzymes: Histone lysine demethylation | LSD1 (Lysine Demethylase 1A) | Histone lysine demethylase (KDM) Decreased H3K4me2 Decreased H3K27ac (eraser) | Enhancers | TALE (113) NmedCas9 (114) SadCas9 (21) | |
| Enzymes: Histone lysine deacetylation | HDAC3 (full-length) | Histone deacetylase Decreased H3K27ac (eraser) | Gene promoters | SpdCas9 (115) | |
| HDAC8 (full-length) | Histone deacetylase Decreased H3K27ac (eraser) | Enhancers | SpdCas9 (116) | ||
| Sir2a (Sirtuin Type 1) | Histone deacetylase Decreased H3ac and H4ac (eraser) | Gene promoters | SpdCas9 (72) |
Abbreviations: KAP1: KRAB associated protein 1; HP1: heterochromatin protein 1; SetDB1: SET domain bifurcated histone lysine methyltransferase 1; NuRD: nucleosome remodeling and deacetylase; KMT: histone lysine methyltransferase; HDAC: histone lysine deacetylase; H3: histone 3; K: lysine; me2: di-methylated state; me3: tri-methylated state; ac: acetylation; ZFP: zinc-finger proteins; TALE: transcription activator-like effector; Sp: Streptococcus pyogenes; Sa: Staphylococcus aureus; dCas9: catalytically deactivated Cas9 protein; Lmo: Listeria monocytogenes; Cascade: CRISPR-associated complex for antiviral defense; GAI: gibberellin (GA) insensitive protein; GID1: gibberellin-insensitive dwarf1 protein; ABI: abscisic acid (ABA)-insensitive 1 protein; PYL1: abscisic acid receptor; Com: RNA aptamer Com-coat protein; LITE: light-inducible transcriptional effector; PRC2: polycomb repressive complex 2; Suv39h1: suppressor of variegation 3–9 homolog 1; G9a: histone-lysine N-methyltransferase EHMT2; EHMT2: euchromatic histone lysine methyltransferase 2; FIRE: Fkbp/Frb inducible recruitment for epigenome; FKBP: FK506-binding protein; FRB: FKBP–rapamycin binding; MeCP2: methyl-CpG binding protein 2; DNMT: DNA methyltransferase; CRY2: cryptochrome 2; CIB1: cryptochrome-2-interacting binding protein-1; SunTag: SUperNova tagging; GFP: green fluorescent protein; GBP: GFP-binding protein; Ezh2: enhancer of zeste 2 polycomb repressive complex 2 subunit; PP7: RNA aptamer; PCP: PP7-coat protein; Nme: Neisseria meningitidis.