Zinc fingers and a green thumb: Manipulating gene expression in plants

Current Opinion in Plant Biology

Volumn 6, Issue 2, 2003, Pages 163-168

  Segal, David J ^a,b   Stege, Justin T ^a,c   Barbas III, Carlos F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c DIVERSA CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA;

EID: 0037394848     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(03)00007-4     Document Type: Review

References (46)

1. Zuo J, Chua NH: Chemical-inducible systems for regulated expression of plant genes. Curr Opin Biotechnol 2000, 11:146-151.
2. ZF in contrast to cDNA-based overexpression methods.
3. Gottesfetd JM, Neely L, Trauger JW, Baird EE, Dervan PB: Regulation of gene expression by small molecules. Nature 1997, 387:202-205.
4. Cooney M, Czernuszewicz G, Postel EH, Flint SJ, Hogan ME: Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science 1988, 241:456-459.
5. Rosenberg UB, Preiss A, Seifert E, Jackle H, Knipple DC; Production of phenocopies by Kruppel antisense RNA injection into Drosophila embryos. Nature 1985, 313:703-706.
6. Cotten M, Birnstiel ML: Ribozyme mediated destruction of RNA in vivo. EMBO J 1989, 8:3861-3866.
7. Steinecke P, Herget T, Schreier PH: Expression of a chimeric ribozyme gene results in endonucleolytic cleavage of target mRNA and a concomitant reduction of gene expression in vivo. EMBO J 1992, 11:1525-1530.
8. Lu G, Fed RJ: Site-specific oligodeoxynucleotide binding to maize Adh1 gene promoter represses Adh1-GUS gene expression in vivo. Plant Mol Biol 1992, 19:715-723.
9. Oh TJ, May GD: Oligonucleotide-directed plant gene targeting. Curr Opin Biotechnol 2001, 12:169-172.
10. Cornelissen M, Vandewiele M: Both RNA level and translation efficiency are reduced by anti-sense RNA in transgenic tobacco. Nucleic Acids Res 1989, 17:833-843.
11. Chuang CF, Meyerowitz EM: Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc Natl Acad Sci USA 2000, 97:4985-4990.
12. Cowell IG: Repression versus activation in the control of gene transcription. Trends Biochem Sci 1994, 19:38-42.
13. Ptashne M, Gann A: Transcriptional activation by recruitment. Nature 1997, 386:569-577.
14. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
15. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100.
16. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR et al.: Arabidopsis transcription factors- genome-wide comparative analysis among eukaryotes. Science 2000, 290:2105-2110.
17. Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF III: Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 2001, 276:29466-29478.
18. Beerli RR, Dreier B, Barbas CF III: Positive and negative regulation of endogenous genes by designed transcription factors. Proc Natl Acad Sci USA 2000, 97:1495-1500.
19. Zhang L, Spratt SK, Liu Q, Johnstone B, Qi H, Raschke EE, Jamieson AC, Rebar EJ, Wolffe AP, Case CC: Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J Biol Chem 2000, 275:33850-33860.
20. Xu D, Ye D, Fisher M, Juliano RL: Selective inhibition of P-glycoprotein expression in multidrug-resistant tumor cells by a designed transcriptional regulator. J Pharmacol Exp Ther 2002, 302:963-971.
21. Ren D, Collingwood TN, Rebar EJ, Wolffe AP, Camp HS: PPARγ knockdown by engineered transcription factors: exogenous PPARγ2 but not PPARγ1 reactivates adipogenesis. Genes Dev 2002, 16:27-32. A six-finger TFZF represser, similar to that described in [18], was used to target the gene for PPARγ, a nuclear hormone receptor involved in adipogenesis. By selectively repressing one splice variant but not the other, the authors were able to differentiate unique roles for the two isoforms and showed that only the PPARγ2 isoform was responsible for ligand-independent adipogenesis.
22. Segal DJ, Barbas CF III: Design of novel sequence-specific DNA-binding proteins. Curr Opin Chem Biol 2000, 4:34-39.
23. Rhodes D, Klug A: Zinc fingers. Sci Am 1993, 268:56-59,62-65.
24. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al.: The sequence of the human genome. Science 2001, 291:1304-1351.
25. Takatsuji H: Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol Biol 1999, 39:1073-1078.
26. Pabo CO, Nekludova L: Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol 2000, 301:597-624.
27. Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO: Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 2001, 9:717-723. This article hammers the final nail into the coffin of a simple universal 'one amino acid to one base pair' zinc-finger recognition code. Several interactions between the protein and the DNA were observed that were not predicted by any code.
28. Wolfe SA, Greisman HA, Ramm El, Pabo CO: Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol 1999, 285:1917-1934.
29. Dreier B, Segal DJ, Barbas CF III: Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains. J Mol Biol 2000, 303:489-502.
30. Segal DJ, Dreier B, Beerli RR, Barbas CF III: Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc Natl Acad Sci USA 1999, 96:2758-2763.
31. Corbi N, Libd V, Fanciulli M, Passananti C: Binding properties of the artificial zinc fingers coding gene Sint1. Biochem Biophys Res Commun 1998, 253:686-692.
32. ZF that contrasts with the modular assembly described in the present review. They claim that the method can generate a new binding protein for virtually any DNA sequence within two weeks.
33. Beerli RR, Segal DJ, Dreier B, Barbas CF III: Toward controlling gene expression at will: specific regulation of the erbB-2/ HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc Nat/Acad Sci USA 1998, 95:14628-14633.
34. Greisman HA, Pabo CO: A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science 1997, 275:657-661.
35. Segal D, Barbas CF III: Custom DNA-binding proteins come of age: polydactyl zinc-finger proteins. Curr Opin Biotech 2001, 12:632-637.
36. ZF construction and their use to regulate endogenous genes in mammalian cells.
37. Segal DJ: The use of zinc finger peptides to study the role of specific factor binding sites in the chromatin environment. Methods 2002, 26:76-83. This article provides step-by-step instructions on building new modular zinc-finger proteins, along with critical parameters and considerations as determined by the Barbas laboratory. No phage display is required. Table 1 of this paper provides the most current list of recognition domains and the 3-bp sites that they recognize.
38. Sadowski I, Ma J, Triezenberg S, Ptashne M: GAL4-VP16 is an unusually potent transcriptional activator. Nature 1988, 335:563-564.
39. Fujita T, Nolan GP, Ghosh S, Baltimore D: Independent modes of transcriptional activation by the p50 and p65 subunits of NF-kappa B. Genes Dev 1992, 6:775-787.
40. Margolin JF, Friedman JR, Meyer WK, Vissing H, Thiesen HJ, Rauscher FJ III: Kruppel-associated boxes are potent transcriptional repression domains. Proc Natl Acad Sci USA 1994, 91:4509-4513.
41. Heinzel T, Lavinsky RM, Mullen TM, Soderstrom M, Laherty CD, Torchia J, Yang WM, Brard G, Ngo SD, Davie JR et al.: A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression. Nature 1997, 387:43-48.
42. ZF in plant cells. They demonstrate the effective repression and activation of reporter genes in plant cells and identify the human SID domain as a potent repression domain in plant cells. The authors also explore the effects of binding-site position and promoter strength on the regulation of gene expression by TFSzF.
43. ZF using tissue-specific promoters.
44. ZF. This is also the first demonstration of endogenous gene regulation through multiple generations in a multi-cellular organism.
45. Irish VF: Patterning the flower. Dev Biol 1999, 209:211-220.
46. ZF to be applied for forward genetics in cells and whole organisms.