Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors

Nature Biotechnology

Volumn 21, Issue 10, 2003, Pages 1208-1214

  Park, Kyung Soon ^a   Lee, Dong Ki ^a   Lee, Horim ^a   Lee, Yangsoon ^a   Jang, Young Soon ^a   Kim, Yong Ha ^a   Yang, Hyo Young ^a   Lee, Sung Il ^a   Seol, Wongi ^a   Kim, Jin Soo ^a  

^a ToolGen Inc   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; DNA; DRUG DOSAGE; PROTEINS;

DRUG RESISTANCE;

BIOTECHNOLOGY;

ARTIFICIAL TRANSCRIPTION FACTOR; REGULATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ANALYTIC METHOD; ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; DNA BINDING; DRUG RESISTANCE; EUKARYOTIC CELL; GENE TARGETING; GENETIC TRANSFECTION; HEAT TOLERANCE; MAMMAL CELL; MOUSE; NEUROBLASTOMA CELL; NONHUMAN; OSMOSIS; PHENOTYPE; PRIORITY JOURNAL; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; YEAST CELL;

ANIMALS; CELLS, CULTURED; CLONING, MOLECULAR; DNA-BINDING PROTEINS; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; MICE; MUTAGENESIS, SITE-DIRECTED; MYOBLASTS; NEUROBLASTOMA; PEPTIDE LIBRARY; PHENOTYPE; PROTEIN ENGINEERING; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; VARIATION (GENETICS); ZINC FINGERS;

ANIMALIA; EUKARYOTA; MAMMALIA;

EID: 10744225041     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt868     Document Type: Article

References (44)

1. Pavletich, N.P. & Pabo, C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1Å. Science 252, 809-817 (1991).
2. Wolfe, S.A., Kekludova, L. & Pabo, C.O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183-212 (2000).
3. Lee, D.K., Seol, W. & Kim, J.-S. Custom DNA-binding proteins and artificial transcription factors. Curr. Top. Med. Chem. 3, 645-657 (2003).
4. Rebar, E.J. & Pabo, C.O. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263, 671-673 (1994).
5. Jamieson, A.C., Kim, S.H. & Wells, J.A. In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry 33, 5689-5695 (1994).
6. Choo, Y. & Klug, A. Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc. Natl. Acad. Sci. USA 91, 11163-11167 (1994).
7. Wu, H., Yang, W.P. & Barbas, C.F. III. Building zinc fingers by selection: toward a therapeutic application. Proc. Natl. Acad. Sci. USA 92, 344-348 (1995).
8. Greisman, H.A. & Pabo, C.O. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science 275, 657-661 (1997).
9. Desjarlais, J.R. & Berg, J.M. Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach. Proteins. Struct. Funct. Genet. 12, 101-104 (1992).
10. Nardelli, J., Gibson, T. & Charnay, P. Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. Nucl. Acids Res. 20, 4137-4144 (1992).
11. Taylor, W.E. et al. Designing zinc-finger ADR1 mutants with altered specificity of DNA binding to T in UAS1 sequences. Biochemistry 34, 3222-3230 (1995).
12. Kim, J.-S. & Pabo, C.O. Transcriptional repression by zinc finger peptides: exploring the potential for applications in gene therapy. J. Biol. Chem. 272, 29795-29800 (1997).
13. Kang, J.S. & Kim, J.-S. Zinc finger proteins as designer transcription factors. J. Biol. Chem. 275, 8742-8748 (2000).
14. Bae, K.H. et al. Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat. Biotechnol. 21, 275-280 (2003).
15. Gogos, J.A., Jin, J., Wan, H., Kokkinidis, M. & Kafatos, F.C. Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements. Proc. Natl. Acad. Sci. USA 93, 2159-2164 (1996).
16. Hsu, T., Gogos, J.A., Kirsh, S.A. & Kafatos, F.C. Multiple zinc finger forms resulting from developmentally regulated alternative splicing of a transcription factor gene. Science 257, 1946-1950 (1992).
17. Segal, D.J., Dreier, B., Beerli, R.R. & Barbas, C.F. 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 96, 2758-2763 (1999).
18. Dreier, B., Beerli, R.R., Segal, D.J., Flippin, J.D. & Barbas, C.F. 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. 276, 29466-29478 (2001).
19. Zhang, L. et al. Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J. Biol. Chem. 275, 33850-33860 (2000).
20. Liu, P.Q. et al. Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. J. Biol. Chem. 276, 11323-11334 (2001).
21. Lee, J.H., Van Montagu, M. & Verbruggen, N. A highly conserved kinase is an essential component for stress tolerance in yeast and plant cells. Proc. Natl. Acad. Sci. USA 96, 5873-5877 (1999).
22. Vanden Bossche, H. et al. Antifungal drug resistance in pathogenic fungi. Med. Mycol. 36, 119-128 (1998).
23. Kadosh, D. & Struhl, K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89, 365-371 (1997).
24. Mendez-Vidal, C., Wilhelm, M.T., Hellborg, F., Qian, W. & Wiman, K.G. The p53-induced mouse zinc finger protein wig-1 binds double-stranded RNA with high affinity. Nucl. Acids Res. 30, 1991-1996 (2002).
25. Morii, E., Oboli, K., Kataoka, T.R., Iagarashi, K. & Kitamura, Y. Interaction and cooperation of mi transcription factor (MITF) and myc-associated zinc-finger protein-related factor (MAZR) for transcription of mouse mast cell protease 6 gene. J. Biol. Chem. 277, 8566-8571 (2002).
26. Sanglard, D. et al. Mechanisms of resistance to azole antifungal agents in Candida albicans isolates from AIDS patients involve specific multidrug transporters. Antimicrob. Agents Chemother. 39, 2378-2386 (1998).
27. Moore, P.A., Ruben, S.M. & Rosen, C.A. Conservation of transcriptional activation functions of the NF-kappa B p50 and p65 subunits in mammalian cells and Saccharomyces cerevisiae. Mol. Cell Biol. 13, 1666-1674 (1993).
28. Witzgall, R., O'Leary, E., Leaf, A., Onaldi, D. & Bonventre, J.V. The Kruppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression. Proc. Natl. Acad. Sci. USA 91, 4514-4518 (1994).
29. Beerli, R.R., Segal, D.J., Drier, B. & Barbas, C.F. 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. Natl. Acad. Sci. USA 95, 14628-14633 (1998).
30. Wainwright, L.J., Lasorella, A. & Lavarone, A. Distinct mechanisms of cell cycle arrest control the decision between differentiation and senescence in human neuroblastoma cells. Proc. Natl. Acad. Sci. USA 98, 9396-9400 (2001).
31. Katagiri, T. et al. Bone morphogenic protein-2 converts the differentiation pathway of C2C12 myoblasts into the osteoblast lineage. J. Cell. Biol. 127, 1755-1766 (1994).
32. Campling, B.G., Pym, J., Galbraith, P.R. & Cole, S.P. Use of the MTT assay for rapid determination of chemosensitivity of human leukemic blast cells. Leuk. Res. 12, 823-831 (1988).
33. Mayer, T.U. et al. Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science 286, 971-974 (1999),
34. De Backer, M.D. et al. An antisense-based functional genomics approach for identification of genes critical for growth of Candida albicans. Nat. Biotechnol. 19, 235-241 (2001).
35. Welch, P.J. et al. Identification and validation of a gene involved in anchorage-independent cell growth control using a library of randomized hairpin ribozymes. Genomics 66, 274-283 (2000).
36. Kruger, M. et al. Identification of elF2Bgamma and elF2gamma as cofactors of hepatitis C virus internal ribosome entry site-mediated translation using a functional genomics approach. Proc. Natl. Acad. Sci. USA 97, 8566-8571 (2000).
37. Pierce, M.L. & Ruffner, D.E. Construction of a directed hammerhead ribozyme library; toward the identification of optimal target sites for antisense-mediated gene inhibition. Nucl. Acids Res. 26, 5093-5101 (1998).
38. Ashrafi, K. et al. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421, 268-272 (2003).
39. Stege, J.T., Guan, X., Ho, T., Beachy, R.N. & Barbas, C.F. III. Controlling gene expression in plants using synthetic zinc finger transcription factors. Plant J. 32, 1077-1086 (2002).
40. Sanches, J.P., Ullman, C., Moore, M., Choo, Y. & Chua, N.H. Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465-1472 (2002).
41. Joung, J.K., Ramm, E.I. & Pabo, C.O. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl. Acad. Sci. USA 97, 7382-7387 (2000).
42. Gordon, C.L. et al. Glucoamylase: green fluorescent protein fusions to monitor protein secretion in Aspergillus niger. Microbiology 146, 415-426 (2000).
43. Blancafort, P., Magnenat, L. & Barbas, C.F. III. Scanning the human genome with combinatorial transcription factor libraries. Nat. Biotechnol. 21, 269-274 (2003).
44. Tupler, R., Perini, G. & Green, M.R. Expressing the human genome. Nature 409, 832-833 (2001).