Table 1.

CRISPR-based tools for epigenome editing and transcriptional modulation

Purpose	CRISPR fusion protein	Remark	Reference
transcriptional interference	dCas9	repress gene expression by interfering transcriptional elongation, RNA polymerase binding, or transcription factor binding	(Qi et al. 2013)
transcriptional repression	dCas9-KRAB	induce heterochromatin formation, decrease chromatin accessibility and induce histone H3K9me3 at the enhancer and promoter regions	(Gilbert et al. 2013; Thakore et al. 2015)
transcriptional repression	dCas9-KRAB-MeCP2	robust silencing of multiple genes	(Yeo et al. 2018)
transcriptional activation	dCas9-VP64	recruit multiple components of the transcription pre- initiation complex, including endogenous histone acetyltransferases to induce histone H3K27ac at the enhancer and promoter regions	(Maeder et al. 2013b; Perez-Pinera et al. 2013)
transcriptional activation	dCas9-VPR	VPR is a VP64-p65-Rta tripartite activator that is more potent than VP64	(Chavez et al. 2015)
transcriptional activation	dCas9–6TAL-VP128 (dCas9-TV)	dCas9-TV is more potent than dCas9-VP64	(Li et al. 2017)
transcriptional activation	dCas9VPH (a fusion of dCas9-VP192 and P65- HSF1 activator domains)	induce human pluripotent reprogramming by activating endogenous master reprogramming factor genes	(Weltner et al. 2018)
DNA methylation	dCas9-DNMT3A	targeted CpG methylation of the promoter silences gene expression; targeted methylation of a CTCF loop anchor site blocks CTCF binding and interferes DNA looping	(Liu et al. 2016; Vojta et al. 2016)
DNA methylation	dCas9-SunTag- DNMT3A	SunTag recruits multiple copies of antibody-fused DNMT3A to increase CpG methylation	(Huang et al. 2017)
DNA methylation	dCas9-DNMT3A- DNMT3L	multimerization of DNMT3A/DNMT3L complexes on the promoter to induce long term hypermethylation and gene silencing	(Saunderson et al. 2017; Stepper et al. 2017)
DNA methylation	triple dCas9-based ETR combination	triple engineered transcriptional repressors (ETRs) combination using dCas9-DNMT3A, dCas9-DNMT3L and dCas9-KRAB to promote long-term silencing of endogenous genes	(Amabile et al. 2016)
DNA demethylation	dCas9-TET1	targeted demethylation of the promoter or enhancer activates gene expression or promotes active chromatin state	(Liu et al. 2016; Liu et al. 2018b)
DNA demethylation	dCas9-SunTag-TET1	the linker length of original SunTag was changed to 22 amino acids to improve targeted demethylation efficiency by efficiently recruiting multiple copies of antibody-fused TET1	(Morita et al. 2016)
histone methylation	dCas9-PRDM9 dCas9-DOT1L	sustain re-expression of epigenetically silenced genes by inducing H3K4me3 (using PRDM9) and H3K79me (using DOT1L) marks	(Cano-Rodriguez et al. 2016)
histone methylation	dCas9-EZH2 dCas9-FOG1	repress chromatin state by inducing H3K27me3 marks on the promoter	(O’Geen et al. 2017)
histone demethylation	dCas9-LSD1	remove enhancer-associated chromatin modifications (loss of H3K4me2 and H3K27ac) to downregulate target gene expression	(Kearns et al. 2015)
histone acetylation	dCas9-P300	promote robust transcriptional activation by inducing H3K27ac at the enhancer and promoter regions	(Hilton et al. 2015)
histone deacetylation	dCas9-HDAC3	repress gene transcription by removing H3K27ac marks in the promoter	(Kwon et al. 2017)
chromatin remodeling	FIRE-dCas9 system using dCas9-MS2 anchor and Fkbp/Frb dimerizing fusion proteins	silence (Hp1/Suv39h1 heterochromatin complex recruitment) or activate [mSWI/SNF (BAF) complex recruitment] target gene expression by recruiting endogenous chromatin regulators to specific genomic loci; rapid washout of chromatin regulators to reverse manipulation of epigenetic states	(Braun et al. 2017)
chromatin remodeling	protein trans-splicing to ligate chemical moieties to dCas9	dCas9-IntN and IntC-cargo (e.g. IntC-JQ1 and IntC- UNC3866) were used to recruit endogenous chromatin regulators (e.g. Brd4T bromodomain and PRC1 chromodomain) to targeted genomic loci	(Liszczak et al. 2017)
chromatin looping	bivalent dCas9-Zip complexes	induce DNA looping between the promoter and distal enhancer by heterodimerization of dSpCas9-Zip and dStCas9-Zip upon binding to two DNA target sites	(Hao et al. 2017)
chromatin looping	CRISPR-dCas9 (CLOuD9)	dSpCas9-PYL1 and dSaCas9-ABI1 induce a chromatin loop formation through dimerization of PYL1 and ABI1 domains upon addition of abscisic acid	(Morgan et al. 2017)
chromatin opening	proximal CRISPR targeting	dSpCas9 binds the proximal target sites to induce the reconfiguring and opening of the local chromatin structure	(Chen et al. 2017)

Note: Brd4T, bromodomain containing 4T; CLOuD9, chromatin loop reorganization using CRISPR-dCas9; DNMT3A, DNA methyltransferase 3 alpha; DOT1L, DOT1 like histone lysine methyltransferase; EZH2, enhancer of zeste 2 polycomb repressive complex 2 subunit; FIRE, Fkbp/Frb inducible recruitment for epigenome editing; FOG1, zinc finger protein, FOG family member 1; HDAC3, histone deacetylase 3; JQ1, a small molecule; KRAB, Krüppel associated box; LSD1, lysine demethylase 1A; MS2, bacteriophage coat proteins; P300, E1A binding protein p300; PRC1, protein regulator of cytokinesis 1; PRDM9, PR/SET domain 9; TET1, tet methylcytosine dioxygenase 1; UNC3866, a modified peptide; VPR, VP64-p65-Rta