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Table 1 Main characteristics of programmable genome targeting domains suitable for directing epigenetic modifiers

From: Synthetic epigenetics—towards intelligent control of epigenetic states and cell identity

 

Zinc fingers

TAL effectors

CRISPR/Cas9

Origin

Eukaryotic species

Phytopathogenic bacteria

Bacterial and archaea species

Type of DNA recognition

Protein:DNA

Protein:DNA

RNP:DNA (Watson-Crick base pairing)

Function of the protein of origin

Transcription factors

Transcription factors

DNA nuclease (inactivated for use in epigenetic editing)

Sensitivity to DNA modification

Sensitive to DNA modification

Sensitive to DNA modification

Not sensitive to DNA modification state

Recognition sequence length

Potentially long, but not all sequences can be recognized, size restrictions apply

Potentially very long, constraints apply

17–20 bp, requires an adjacent PAM sequence

Specificity/off-target effects

Less specific than TALEs

Most specific

More relaxed sequence recognition than ZF and TALES

Size of protein

Variable—depends on length of recognized sequence, one protein unit (approximately 3 kDa) per 3 bp of recognition sequence

Variable—depends on length of recognized sequence. Typically 50-70 kDa

Holoenzyme (~160 kDa)

Immunogenicity

Similar to natural mammalian proteins, potentially low immunogenicity

Unknown, needs further investigation

Unnatural for mammals, potentially high immunogenicity, needs further studies

Multiplexing

Difficult and labour intensive

Difficult and labour intensive

Easy and possible