Chen, S., Oikonomou, G., Chiu, C.N., Niles, B.J., Liu, J., Lee, D.A., Antoshechkin, I., and Prober, D.A. (2013) A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic acids research. 41(4):2769-2778.
Zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs) have been shown to induce targeted mutations, but they have
not been extensively tested in any animal model. Here, we describe a large-scale comparison of ZFN and TALEN mutagenicity
in zebrafish. Using deep sequencing, we found that TALENs are significantly more likely to be mutagenic and induce an average
of 10-fold more mutations than ZFNs. We observed a strong correlation between somatic and germ-line mutagenicity, and identified
germ line mutations using ZFNs whose somatic mutations rates are well below the commonly used threshold of 1%. Guidelines
that have previously been proposed to predict optimal ZFN and TALEN target sites did not predict mutagenicity in vivo. However, we observed a significant negative correlation between TALEN mutagenicity and the number of CpG repeats in TALEN
target sites, suggesting that target site methylation may explain the poor mutagenicity of some TALENs in vivo. The higher mutation rates and ability to target essentially any sequence make TALENs the superior technology for targeted
mutagenesis in zebrafish, and likely other animal models.