Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors (original) (raw)
Pavletich, N.P. & Pabo, C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1Å. Science252, 809–817 (1991). ArticleCAS Google Scholar
Wolfe, S.A., Kekludova, L. & Pabo, C.O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct.29, 183–212 (2000). ArticleCAS Google Scholar
Lee, D.K., Seol, W. & Kim, J.-S. Custom DNA-binding proteins and artificial transcription factors. Curr. Top. Med. Chem.3, 645–657 (2003). ArticleCAS Google Scholar
Rebar, E.J. & Pabo, C.O. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science263, 671–673 (1994). ArticleCAS Google Scholar
Jamieson, A.C., Kim, S.H. & Wells, J.A. In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry33, 5689–5695 (1994). ArticleCAS Google Scholar
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. USA91, 11163–11167 (1994). ArticleCAS Google Scholar
Wu, H., Yang, W.P. & Barbas, C.F. III. Building zinc fingers by selection: toward a therapeutic application. Proc. Natl. Acad. Sci. USA92, 344–348 (1995). ArticleCAS Google Scholar
Greisman, H.A. & Pabo, C.O. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science275, 657–661 (1997). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Taylor, W.E. et al. Designing zinc-finger ADR1 mutants with altered specificity of DNA binding to T in UAS1 sequences. Biochemistry34, 3222–3230 (1995). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Kang, J.S. & Kim, J.-S. Zinc finger proteins as designer transcription factors. J. Biol. Chem.275, 8742–8748 (2000). ArticleCAS Google Scholar
Bae, K.H. et al. Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat. Biotechnol.21, 275–280 (2003). ArticleCAS Google Scholar
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. USA93, 2159–2164 (1996). ArticleCAS Google Scholar
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. Science257, 1946–1950 (1992). ArticleCAS Google Scholar
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. USA96, 2758–2763 (1999). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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. USA96, 5873–5877 (1999). ArticleCAS Google Scholar
Vanden Bossche, H. et al. Antifungal drug resistance in pathogenic fungi. Med. Mycol.36, 119–128 (1998). CASPubMed Google Scholar
Kadosh, D. & Struhl, K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell89, 365–371 (1997). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). Article Google Scholar
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). ArticleCAS Google Scholar
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. USA91, 4514–4518 (1994). ArticleCAS Google Scholar
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. USA95, 14628–14633 (1998). ArticleCAS Google Scholar
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. USA98, 9396–9400 (2001). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Mayer, T.U. et al. Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science286, 971–974 (1999). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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. Genomics66, 274–283 (2000). ArticleCAS Google Scholar
Kruger, M. et al. Identification of eIF2Bgamma and eIF2gamma as cofactors of hepatitis C virus internal ribosome entry site-mediated translation using a functional genomics approach. Proc. Natl. Acad. Sci. USA97, 8566–8571 (2000). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Ashrafi, K. et al. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature421, 268–272 (2003). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). Article Google Scholar
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. USA97, 7382–7387 (2000). ArticleCAS Google Scholar
Gordon, C.L. et al. Glucoamylase: green fluorescent protein fusions to monitor protein secretion in Aspergillus niger. Microbiology146, 415–426 (2000). ArticleCAS Google Scholar
Blancafort, P., Magnenat, L. & Barbas, C.F. III. Scanning the human genome with combinatorial transcription factor libraries. Nat. Biotechnol.21, 269–274 (2003). ArticleCAS Google Scholar
Tupler, R., Perini, G. & Green, M.R. Expressing the human genome. Nature409, 832–833 (2001). ArticleCAS Google Scholar