Table 1 Comparison of the three main currently used genome engineering platforms: ZFN, TALEN, and CRISPR/Cas9*
Aspect of comparison | ZFN | TALEN | CRISPR/Cas9 |
|---|---|---|---|
Origin | Eukaryotes | Bacteria | Bacteria/archaea |
Structure | Dimer | Dimer | Monomer |
Design simplicity | Moderate (ZFNs need customized protein for every DNA sequence) | Slightly complex (identical repeats are multiple, which creates technical issues of engineering and delivery into cells) | Simpler (available versions for crRNA can be easily designed) |
Engineering feasibility/affordability | Low/limited | Moderate/affordable but resource intensive | High |
Popularity/affordability | Low/limited | Moderate/affordable but resource intensive | High/highly affordable |
DNA-binding molecule/DNA recognition mechanism | Zinc finger protein/protein-DNA interactions that introduce DSB | Transcription activator-like effectors/protein-DNA interactions that introduce DSB | crRNA or sgRNA/RNA-guided protein-DNA interactions that introduce DSB |
Modification pattern | FokI nuclease | FokI nuclease | Cas9 nuclease |
Specificity-determining length of recognition site | Typically 9–18 bp per ZFN monomer, 18–36 bp per ZFN pair | Typically 14–20 bp per TALEN monomer, 28–40 bp per TALEN pair | 22 bp (20-bp guide sequence C 2-bp protospacer adjacent motif (PAM) for Cas9; up to 44 bp for double nicking |
Targeting/target specificity | Low/difficult to target non-G-rich sequences/high; G-rich sequence preference; only small positional mismatches are tolerated; re-targeting requires protein engineering | Higher/for each TALEN monomer targeted base sequence must start (5′) with a T and end with an A (3’) end. High, requires a T at each 5’-end of its target; small positional mismatches are tolerated; re-targeting requires complex molecular cloning | Highest/targeted sequence end with an NGG or NAG (lower activity) sequence (that is, PAM) Moderate: RNA-targeted sequence must precede the 2 base pairs recognized by PAM. Only small positional and multiple consecutive mismatches are tolerated. Re-targeting requires new RNA guide. Protein engineering is not required. |
Mechanism of action | Introduction of double-strand breaks (DSBs) in target DNA | Introduction of double-strand breaks (DSBs) in target DNA | Introduction of DSBs in target DNA by wtCas9 or single-strand nicks by Cas9 nickase |
Cleavage efficacy | Efficient | Efficient | Highly efficient |
Multiplex genome editing | Not easy (few models) | Not easy (few models) | Easy (high-yield multiplexing available (no need for obtaining embryonic stem cells)) |
Delivery vehicle | Easy via electroporation and viral vectors transduction | Easy in vitro delivery; difficult in vivo due to the large size of TALEN DNA and their high probability of recombination | Easy in vitro; moderate difficulty of delivery in vivo due to poor packaging of the large Cas9 by viral vectors. |
Use as gene activator | Yes; activation of endogenous genes; minimal off-target effects; may require engineering to target particular sequences | Yes; activation of endogenous genes; minimal off-target effects; no sequence limitations | Yes; activation of endogenous genes; minimal off-target effects; requires “NGG” PAM next to the target sequence |
Use as gene inhibitor | Yes; works by blocking transcription elongation via chromatin repression; minimal off-target effects; may require engineering to target particular sequences | Yes; works by blocking transcription elongation via chromatin repression; minimal off-target effects; no sequence limitations | Yes; works by blocking transcription elongation via chromatin repression; minimal off-target effects; requires “NGG” PAM next to target sequence. |
Success rate‡ | Low (~ 24%) | High (> 99%) | High (~ 90%) |
Average mutation rate§ | Low or variable (~ 10%) | High (~ 20%) | High (~ 20%) |
Off-target effects | Highly possible off-target activities | Low possible off-target activities | Variable; limited off-target activities, not fully studied in plants |
Programmable | Highly difficult | Difficult | Easy |
Cytotoxicity | Variable to high | Low | Low |
Cost | Low | High | Low |
Online resources for nuclease design | • The Zinc Finger Consortium includes software tools and protocols genome-wide tag scanner for nuclease off-sites • The Segal Laboratory software site • ZFN target site algorithm for identifying sites compatible with the Lawson-Wolfe modular assembly system • Zinc finger tools • ZiFiT Targeter software | • E-TALEN • Genome engineering resources • Scoring algorithm for predicting TALE(N) activity • ToolGen TALEN designer • ZiFiT Targeter software | • E-CRISP • Genome engineering resources • RGEN tools • ZiFiT Targeter software |
Suppliers Non-profit organizations *Companies | - Addgene (https://www.addgene.org/) *Sigma-Aldrich/ToolGen | - Addgene/TALEN library resource *Cellectis Bioresearch/Life Technologies/ToolGen/Transposagen Biopharmaceuticals | - Addgene *Life Technologies/Sigma-Aldrich/System Biosciences/ToolGen/Transposagen Biopharmaceuticals |