special feature | COMMENTARY method of the year Zinc-finger nucleases: how to play two good hands Mark Isalan © 2012 Nature America, Inc. All rights reserved. Zinc-finger nuclease dimers are more difficult to engineer than single DNA-binding domains, but the development of new methods could help. The potential of gene targeting with zinc-finger nucleases (ZFNs) was first explored by the groups of Carroll and Chandrasegaran1 and has resulted in the explosive growth of an exciting new field. In the typical implementation, pairs of artificial zinc-finger DNA-binding proteins (ZFPs) containing three or four zinc fingers apiece are linked to the FokI nuclease domain to create a sequence-specific nuclease upon dimerization (Fig. 1). The nuclease can then be used to mutate chromosomal targets, via a double-stranded DNA break, either by error-prone nonhomologous end joining (NHEJ)2 or by stimulation of homologous recombination with a donor DNA template3. Despite the growing number of publications attesting to the power of this method, there is an elephant in the room: it is very difficult for the average research group to build functional ZFNs for particular target DNAs. Successful projects either buy readymade ZFNs, employing the enormous resources of companies such as SigmaAldrich (CompoZr ZFNs), or collaborate with academic teams, using the opensource tools of the Zinc Finger Consortium (http://www.zincfingers.org)4. Commercial ZFNs were once expensive custom projects but now also include cheaper off-the-shelf reagents (although to use these one may need to compromise on the specific target site). Alternatively, the consortium provides convenient computational tools such as ZiFiT5 to help design constructs, although this can still be challenging for inexperienced users; building one or two ZFNs à la carte can often result in failure. EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation and UPF Barcelona, Spain. e-mail: [email protected] To G or not to G The reasons that ZFNs are challenging to build are outlined in Figure 1. The major limiting factor is that it is not possible to target just any desired DNA sequence. Although zinc-finger engineering has been extensively developed 6, it is no coincidence that the zinc fingers used as engineering scaffolds have G-rich consensus sequences (for example, Zif268: 5ʹ-GCG(G/T)GGGCG-3ʹ; Sp1: 5ʹ-GGGGCGGGG-3ʹ). My group and others have put great effort into targeting non–G-rich sequences (for instance, by using overlapping finger approaches 7,8), but the fact is that G-rich sequences are the natural preference of zinc fingers. Assembly of fingers for other types of targets is frequently unsuccessful 9, for two reasons. First, the strongest protein-DNA interactions are between arginine residues and guanine bases in the major groove10. Second, overlapping contacts between adjacent fingers have a configuration in which guanines are particularly stable at the first and third bases of each fingerrecognition site11. Therefore, perhaps the best advice for novice ZFN engineers is to choose a G-rich target from their computer-generated list of hits. This G preference puts a real constraint on the specific sequences that can be targeted by ZFNs, and it is related to the second problem: it is far easier to make a single designer DNA-binding domain than to join together two domains, in the appropriate orientation, with the correct spacing, to yield a functional nuclease. Given 1 kb of genome sequence, it is relatively straightforward to find a suitable patch to target the binding of a single ZFP domain, and this has been done routinely for over a decade 6 . However, 32 | VOL.9 NO.1 | JANUARY 2012 | nature methods for nucleases, the ‘easiest’ sequence to target is 5ʹ-MNNCNNCNNCNNCX 5– 7 GNNGNNGNNGNNK-3ʹ (where M = A,C; N = contacted bases (ideally G rich); X = uncontacted bases; and K = G,T), a consensus sequence derived from structural considerations and a wealth of phage-display experiments6. Furthermore, the ideal target will be unique in the genome, with few closely related sequences that could potentially draw off-target binding (targets and ‘off-targets’ should be at least 3 bp different and share less than two-thirds homology12,13). As can be seen, therefore, even before one begins to engineer a ZFN, target selection is quite restricted. It is best achieved with a web-based computer program5. Gaps, linkers and cutting-site position The 5- to 7-bp gap in the target between the sequences recognized by the two ZFP domains is another constraint for ZFN engineering and is determined by the design of the linker between each ZFP and the FokI nuclease. The constraint can be relaxed by using much longer linkers, but this comes at the expense of increasing binding promiscuity resulting from accommodating many different gap lengths1. For most applications, restrictive linkers are preferred: -LRGS-4 (5- to 6-bp gap), -QNKK-1 (6-bp gap) and -TGQKD(7-bp gap; K.A. Wilson and M.H. Porteus, personal communication) are all linkers that fit between the ZFP terminal histidine and the -QLV beginning of FokI. The restrictions on target choice have a bearing on the final application of the ZFN because it is sometimes desirable to target an exact base position. For example, for the purpose of integrating foreign DNA efficiently into a locus, the inserted cassette COMMENTARY | special feature ZFPs functional as a pair G-rich target Correct finger overlap Appropriate linkers 5–7-bp gap -N FokI C- M NN CNNC NN CNNC K NN GNNG NN GNNG Specificity, affinity, kinetics NN NNNN NN NNNN FokI G N N GN N GN N G N N K CNNCNN C NNCNN M -C Improved FokI mutants N- Precision of cleavage site Number of fingers Unique DNA target in genome, no related sites, accessible chromatin © 2012 Nature America, Inc. All rights reserved. Figure 1 | Overcoming the challenges for engineering functional zinc-finger nucleases. The schematic shows two four-finger pairs binding to DNA in a canonical mode and highlights the main engineering constraints and considerations. Zinc-finger binding sites are shaded in blue (darker for the main contacted DNA bases). should be introduced at the exact site of the ZFN cut, in between the two homology arms14. Exact positioning is required here because it is thought that the cleaved chromosomal DNA ends need to prime on the donor template DNA, so a nonadjacent integration cassette would not be as effective. For introducing or correcting point mutations by homologous recombination, there is slightly more flexibility. The mutations should still be as close to the cutting site as possible but can be anywhere within about 400 bp, as most recombination events will occur within this distance 15. It is also worth noting that one can introduce a few silent mutations on the donor plasmid (mutating guanines) to prevent ZFN cutting of the template DNA. Finally, introducing a knockout mutation by errorprone NHEJ (using ZFNs in the absence of a donor DNA) provides even more flexibility in cutting-site position. Cutting sites, and hence frame-shifting mutations, can be put anywhere in a coding sequence, although more N-terminal positions are usually preferable. Targeted libraries A consistent source of confusion in zincfinger design is the fact that zinc fingers defy convention and bind DNA ‘backward’, with the zinc finger N–C binding DNA 3ʹ–5ʹ. Therefore, one must constantly specify DNA direction, and it helps to ‘think’ in the 3ʹ–5ʹ direction when designing fingers and libraries. Library design and engineering strategies are too numerous to describe here but have been discussed at length elsewhere4,6. Briefly, the main restriction in building libraries to make new DNA-binding zinc fingers is a combinatorial problem: the number of possible variations in the DNA recognition helices rapidly increases beyond what is practical to screen, even when only five or six amino acid positions are randomized. Existing methods overcome this in various ways, for instance by engineering smaller parts bit-by-bit, resulting in validated archives of one- or two-finger modules. Although the modern user can simply use a computer-generated archive5 to build ZFNs from parts, they are still left with a problem when a ZFN simply fails to work. When fingers fail, in vitro cutting assays16 can rapidly identify whether one or both halves of the nuclease are working, and this can guide a researcher as to what to do next. When both halves fail it is probably simplest to choose another target site. However, when only one half of the nuclease fails, it is very tempting to build a mini-library to screen for variants that rescue the failed half-ZFN. Although there are several ways to do this, including dedicated bacterial one-hybrid17 and twohybrid systems4, my group reasoned that it would be convenient to have an option that uses commercially available components. We therefore recently adapted a commercial yeast one-hybrid kit to select zinc fingers from targeted mini-libraries and used this to rescue ‘orphan’ half-ZFNs, resulting in working ZFN pairs16. The key decisions for success in this type of effort relate to how one achieves limited randomization of the finger framework. The size of the library in such a screen for active ZFP monomers is dependent on the number of fingers in the construct: the more fingers there are, the more difficult it is to randomize, as larger libraries are required. Longer chains of zinc fingers will also have an impact on the affinity and interaction kinetics of the DNA-binding domains. Longer ZFPs have increased affinity but slow off rates, with half-lives of days (see references in ref. 6), and simply adding more fingers does not appear to make the best ZFNs. For instance, an analysis of off-target cutting has suggested that avoiding ZFPs with very high binding energy could improve overall specificity12. Intriguingly, it was recently reported that three- or four-finger pairs can cut better than five- or six-finger pairs 18 . Nonetheless, there are several examples in the literature in which five- or six-finger ZFN pairs have been used successfully, albeit with longer (six-amino-acid) linkers after every second finger (for example, TGSERP rather than canonical TGEKP). Noncanonical linkers can even be used to jump bases between finger subsites, but because this option is not included in programs such as ZiFiT, it is best avoided by the average user. As with other aspects of ZFN engineering, success depends on being careful with the details. Improving efficiency Protein design and library selection have not been limited to the DNA-binding domains of ZFNs. For several years now, obligate heterodimer mutations 19,20 in the FokI domain have been the constructs of choice, preventing promiscuous cutting from unwanted homodimers. More recently, a FokI ‘Sharkey’ mutant was engineered for improved activity 21. Other refinements to increase efficiency include using 30 °C cold shock to enhance NHEJ 22, using alternative promoters to express ZFP (for example, the phosphoglycerate kinase promoter, pPGK16), using replicating plasmids (with SV40 origins of replication and large T antigen), and waiting for 7 days after ZFN and donor plasmid transfection before assaying homologous recombination. A recent innovation uses an elegant trick to enrich for ZFN-modified cells indirectly23 (Fig. 2a). Co-transfection of an episomal reporter plasmid with a ZFN site between the coding sequences of an RFP and an out-of-frame GFP means that cells in which there was more effective ZFN activity show green fluorescence because the GFP is restored via NHEJ. These cells can be recovered by FACS. As the system uses transient transfection, the reporter dies away rapidly, leaving marker-free cells. Thus, the process can be nature methods | VOL.9 NO.1 | JANUARY 2012 | 33 special feature | COMMENTARY © 2012 Nature America, Inc. All rights reserved. Figure 2 | Screening for full zinc-finger nuclease activity. (a) In a scheme developed by the Kim group23, the fluorescence of an out-of-frame GFP is restored by a functional zinc-finger nuclease (ZFN). This was originally designed as an indirect marker for FACS of ZFN-modified cells. However, it could be adapted to screen candidates from ZFN libraries in mammalian cells, as schematized here. (b) For screening larger ZFN libraries in a eukaryotic chromatin environment, the yeast onehybrid system we recently described16 could be adapted. ZFN cleavage of a negative selection marker (URA3 + 5-FOA) would be required for growth on a plate. NHEJ, nonhomologous end joining. Fokl+ and Fokl– are obligate heterodimer variants19. a repeated for several rounds23 to enrich for genome-modified cells progressively, even using ZFNs with relatively low efficiency. The existence of such a generic eukaryotic screen for ZFN activity raises the possibility of screening randomized libraries of ZFNs directly in mammalian cells. As long as library sizes can be maintained within practical limits, an advantage of testing the ZFPs in their paired context would be the elimination of orphan half-ZFPs. Another advantage is that one would be testing in a more realistic chromatin environment, as the in vitro and in vivo activities of these nucleases do not always correspond 4. However, mammalian systems based on transient transfection would not allow the partitioning of one library member per cell, and so transfections would have to be carried out oneby-one in well formats (Fig. 2a). One c ou ld a lter nat ively imag ine adapting our yeast one-hybrid system 16 to screen for nucleases (Fig. 2b). This would have several potential advantages: full nuclease pairs would be selected in a eukaryotic chromatin environment (albeit in yeast), low-copy yeast plasmids would segregate as one library member per cell, and well-established yeast selection markers would allow for positive selection of transformants and counterselection of cells with inactive ZFN variants. One could begin with a lead ZFN design from ZiFiT and mutate around the DNAbinding helices 16 to screen directly for ZFN cleavage. The selective principle outlined in Figure 2b exploits the selective toxicity of 5-fluoroorotic acid (5-FOA) when the URA3 uracil biosynthesis gene ZFN library member b PCR ZF library–L Stop * RFP Target site PCR ZF library–R FokI+ Out-of-frame GFP FokI– TRP1 NHEJ Prey plasmids LEU2 ZFN excises URA3 STOP In-frame GFP Target site URA3 HIS3 Target site Bait plasmid Co-transform yeast and plate on SD _His _Leu _Trp + 5-FOA FACS sort and identify ZFN Positive selection for triple transformants (HIS3, LEU2, TRP1); negative selection for URA3 not excised by ZFN is active: only active ZFNs would excise URA3 and allow cell survival in medium containing 5-FOA. I emphasize that this is a thought experiment—which we currently have no intentions of implementing—but it would be interesting to see whether full ZFN-pair selection would lower failure rates in vivo. A tell-TALE sign of things to come As a multitude of methods exist for engineering zinc fingers, one could be forgiven for thinking that making ZFNs is a solved problem. I have tried here to redress the balance by highlighting the fact that there are still many issues that need to be considered on a case-by-case basis. But it should not be forgotten that when ZFNs do work, they work very well3, and so they should not be sidelined too quickly, even if there are promising new technologies such as meganucleases24 and transcription activator–like effector (TALE) nucleases on the horizon25. The latter are being rapidly embraced by the research community, and ZiFiT was recently updated (version 4.0) to allow TALE nuclease design5. Will TALE nucleases be the solution to the G problem and become the nucleases of choice? What will their specificity and toxicity profiles be like in vivo? Alternatively, will commercial sources of ZFNs become so accessible that no custom academic projects will need to be undertaken? Only time will tell. ACKNOWLEDGMENTS M.I. is funded by the European Research Council, FP7-ERC-201249-ZINC-HUBS, Ministerio de Ciencia e Innovacion grant MICINN BFU2010-17953, and The Ministerio de Educacion y Ciencia and European Molecular Biology Laboratory (MEC-EMBL) agreement. 34 | VOL.9 NO.1 | JANUARY 2012 | nature methods COMPETING FINANCIAL INTERESTS The author declares no competing financial interests. 1. Bibikova, M. et al. Mol. Cell. Biol. 21, 289–297 (2001). 2. Bibikova, M., Golic, M., Golic, K.G. & Carroll, D. Genetics 161, 1169–1175 (2002). 3. Urnov, F.D. et al. Nature 435, 646–651 (2005). 4. Maeder, M.L. et al. Mol. Cell 31, 294–301 (2008). 5. Sander, J.D. et al. Nucleic Acids Res. 38, W462– W468 (2010). 6. Pabo, C.O., Peisach, E. & Grant, R.A. Annu. Rev. Biochem. 70, 313–340 (2001). 7. Isalan, M., Klug, A. & Choo, Y. 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