Table 2.

CRISPR innovations that can potentially be used in HD research

CRISPR system	PAM sequence	Origin	Application	References
Cpf1	TTN or TTTN	Identified from Francisella novicida U112	Smaller than SpCas9.	[75]
			Complements SpCas9 due to PAM sequence differences.
			Introduces a staggered double-strand break with- 4 to 5-nucleotide overhangs, rather than blunt ends
			Suitable for multiplexed genome editing.
CjCas9	NNNVRYM	Identified from Campylobacter jejuni	A smaller variant of Cas9.	[77]
			Shows comparable editing efficiency, but better specificity than SpCas9.
Cas12f	Varies	Identified from uncultivated archaea	Smallest variants of Cas9 identified to date (400–700 amino-acids). Similar editing efficiency and specificity to SpCas9.	[78]
PIN-dCas9	Not required	A chimeric protein by fusing nuclease-null dCas9 to the PIN RNA endonuclease domain from SMG6	Specifically targets RNA but not DNA.	[86]
			Efficiently eliminates microsatellite repeat expansion RNAs (CUG, CCUG, CAG, GGGGCC) when exogenously expressed and in patient cells
dCas9-VP64	NGG	A chimeric protein by fusing nuclease-null dCas9 to the VP64 transcriptional activation domain	Increases transcription of selected human genes (VEGFA and NTF3) by targeting the promoter sequences.	[88]
dCas9-KRAB	NGG	A chimeric protein by fusing nuclease-null dCas9 to the KRAB domain of Kox1	Stably suppresses the expression of endogenous eukaryotic genes by targeting the promoter sequences.	[89]
dCas9-DNMT3A	NGG	Chimeric proteins by fusing nuclease-null dCas9 to DNA methyltransferase 3 alpha or DNA methyltransferase 3 like	Transiently expressed in combinations to achieve long-term gene-silencing by modulating DNA methylation.	[90]
dCas9-DNMT3L
dCas9-Tet1	NGG	A chimeric protein by fusing nuclease-null dCas9 to the Tet1 enzymatic domain.	Activates transcription of selected genes (BDNF and MyoD) by targeted DNA demethylation.	[91]
dCas9p300 Core	NGG	A chimeric protein by fusing nuclease-null dCas9 to the catalytic histone acetyltransferase core domain of the human E1A-associated protein p300.	Activates transcription of endogenous genes from promoters and enhancers by catalyzing acetylation of histone.	[92]
dCas9-HDAC3	NGG	A chimeric protein by fusing nuclease-null dCas9 to full-length human HDAC3.	Modulates histone deacetylation and gene expression, which is critically dependent on the location of endogenous histone acetylation.	[93]
Adenine base editor (ABE)	NGG	A chimeric protein by fusing nuclease-null dCas9 to the TadA adenine deaminase.	Converts A·T base-pairs to G·C base-pairs, without causing DNA double-strand breaks.	[95]
Cytosine base editor (CBE)	NGG	A chimeric protein by fusing nuclease-null dCas9 to the rat APOBEC1 cytidine deaminase domain.	Converts C·G base-pairs to T·A base-pairs, without causing DNA double-strand breaks.	[96]

N, any nucleotide base; V, either A, G, or C; R, either A or G; Y, either T or C; M, either A or C.