High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.

We report here an efficient method for targeted mutagenesis of Arabidopsis genes through regulated expression of zinc finger nucleases (ZFNs)-enzymes engineered to create DNA double-strand breaks at specific target loci. ZFNs recognizing the Arabidopsis ADH1 and TT4 genes were made by Oligomerized Pool ENgineering (OPEN)-a publicly available, selection-based platform that yields high quality zinc finger arrays. The ADH1 and TT4 ZFNs were placed under control of an estrogen-inducible promoter and introduced into Arabidopsis plants by floral-dip transformation. Primary transgenic Arabidopsis seedlings induced to express the ADH1 or TT4 ZFNs exhibited somatic mutation frequencies of 7% or 16%, respectively. The induced mutations were typically insertions or deletions (1-142 bp) that were localized at the ZFN cleavage site and likely derived from imprecise repair of chromosome breaks by nonhomologous end-joining. Mutations were transmitted to the next generation for 69% of primary transgenics expressing the ADH1 ZFNs and 33% of transgenics expressing the TT4 ZFNs. Furthermore, approximately 20% of the mutant-producing plants were homozygous for mutations at ADH1 or TT4, indicating that both alleles were disrupted. ADH1 and TT4 were chosen as targets for this study because of their selectable or screenable phenotypes (adh1, allyl alcohol resistance; tt4, lack of anthocyanins in the seed coat). However, the high frequency of observed ZFN-induced mutagenesis suggests that targeted mutations can readily be recovered by simply screening progeny of primary transgenic plants by PCR and DNA sequencing. Taken together, our results suggest that it should now be possible to obtain mutations in any Arabidopsis target gene regardless of its mutant phenotype.

A transient assay for monitoring zinc finger nuclease activity at endogenous plant gene targets.

Advances in plant biology have been frustrated by the lack of an efficient means to create targeted mutations. Zinc finger nucleases (ZFNs) hold much promise for overcoming this limitation: they can be used to generate targeted gene knockouts through imprecise repair of broken chromosomes by non-homologous end joining (NHEJ), or they can stimulate the introduction of specific DNA sequence changes through homologous recombination. Critical to the function of ZFNs is their ability to access and cleave chromosomal target sites. Numerous factors may obscure cleavage, including packaging of DNA into chromatin, DNA methylation, or the presence of other proteins at the target site. Here we describe a transient assay that rapidly assesses ZFN function at chromosomal targets in plant cells. The assay monitors the ability of a ZFN to introduce mutations by imprecise repair through NHEJ, resulting in the loss of a restriction endonuclease recognition sequence. The requirement for the restriction endonuclease recognition sequence coincident with the ZFN spacer region has thus far not been a limiting factor in identifying ZFN target sites in genes of interest suitable for this assay.