Drug discovery with engineered zinc-finger proteins
10.1038/nrd1087
Crossref journal-article
Springer Science and Business Media LLC
Nature Reviews Drug Discovery (297)
Bibliography

Jamieson, A. C., Miller, J. C., & Pabo, C. O. (2003). Drug discovery with engineered zinc-finger proteins. Nature Reviews Drug Discovery, 2(5), 361–368.

Authors 3
  1. Andrew C. Jamieson (first)
  2. Jeffrey C. Miller (additional)
  3. Carl O. Pabo (additional)
References 74 Referenced 229
  1. Tupler, R., Perini, G. & Green, M. R. Expressing the human genome. Nature 409, 832–833 (2001). (10.1038/35057011) / Nature by R Tupler (2001)
  2. Miller, J., McLachlan, A. D. & Klug, A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 1609–1614 (1985). (10.1002/j.1460-2075.1985.tb03825.x) / EMBO J. by J Miller (1985)
  3. Berg, J. M. Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc. Natl Acad. Sci. USA 85, 99–102 (1988). (10.1073/pnas.85.1.99) / Proc. Natl Acad. Sci. USA by JM Berg (1988)
  4. Lee, M. S. et al. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635–637 (1989). (10.1126/science.2503871) / Science by MS Lee (1989)
  5. Pavletich, N. P. & Pabo, C. O. Zinc finger-DNA recognition: crystal structure of a Zif268–DNA complex at 2. 1 A. Science 252, 809–817 (1991). The first crystal structure to give a detailed view of how ZFPs recognize DNA. This paper laid the foundation for the subsequent experiments in zinc finger protein engineering. (10.1126/science.2028256) / Science by NP Pavletich (1991)
  6. Houbaviy, H. B. et al. Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc. Natl Acad. Sci. USA 93, 13577–13582 (1996). (10.1073/pnas.93.24.13577) / Proc. Natl Acad. Sci. USA by HB Houbaviy (1996)
  7. Nolte, R. T. et al. Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc. Natl Acad. Sci. USA 95, 2938–2943 (1998). (10.1073/pnas.95.6.2938) / Proc. Natl Acad. Sci. USA by RT Nolte (1998)
  8. Fairall, L. et al. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature 366, 483–487 (1993). (10.1038/366483a0) / Nature by L Fairall (1993)
  9. Rebar, E. J. & Pabo, C. O. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263, 671–673 (1994). (10.1126/science.8303274) / Science by EJ Rebar (1994)
  10. 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). (10.1021/bi00185a004) / Biochemistry by AC Jamieson (1994)
  11. 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). One of several early phage display papers showing how ZFPs can be engineered to recognize different DNA target sequences. (10.1073/pnas.91.23.11163) / Proc. Natl Acad. Sci. USA by Y Choo (1994)
  12. Wolfe, S. A., Nekludova, L. & Pabo, C. O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183–212 (2000). (10.1146/annurev.biophys.29.1.183) / Annu. Rev. Biophys. Biomol. Struct. by SA Wolfe (2000)
  13. Smith, G. P. Surface presentation of protein epitopes using bacteriophage expression systems. Curr. Opin. Biotechnol. 2, 668–673 (1991). (10.1016/0958-1669(91)90032-Z) / Curr. Opin. Biotechnol. by GP Smith (1991)
  14. Rebar, E. J., Greisman, H. A. & Pabo, C. O. Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities. Methods Enzymol. 267, 129–149 (1996). (10.1016/S0076-6879(96)67010-4) / Methods Enzymol. by EJ Rebar (1996)
  15. Isalan, M., Choo, Y. & Klug, A. Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proc. Natl Acad. Sci. USA 94, 5617–5621 (1997). (10.1073/pnas.94.11.5617) / Proc. Natl Acad. Sci. USA by M Isalan (1997)
  16. Isalan, M., Klug, A. & Choo, Y. Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry 37, 12026–12033 (1998). (10.1021/bi981358z) / Biochemistry by M Isalan (1998)
  17. Segal, D. J. et al. 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). (10.1073/pnas.96.6.2758) / Proc. Natl Acad. Sci. USA by DJ Segal (1999)
  18. Dreier, B. et al. 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). (10.1074/jbc.M102604200) / J. Biol. Chem. by B Dreier (2001)
  19. Beerli, R. R. & Barbas, C. F. 3rd. Engineering polydactyl zinc-finger transcription factors. Nature Biotechnol. 20, 135–141 (2002). (10.1038/nbt0202-135) / Nature Biotechnol. by RR Beerli (2002)
  20. Pabo, C. O., Peisach, E. & Grant, R. A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 70, 313–340 (2001). A comprehensive review of zinc finger DNA recognition that will allow the reader to find detailed biochemical information as needed. (10.1146/annurev.biochem.70.1.313) / Annu. Rev. Biochem. by CO Pabo (2001)
  21. Choo, Y. & Klug, A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc. Natl Acad. Sci. USA 91, 11168–11172 (1994). (10.1073/pnas.91.23.11168) / Proc. Natl Acad. Sci. USA by Y Choo (1994)
  22. Jamieson, A. C., Wang, H. & Kim, S. H. A zinc finger directory for high-affinity DNA recognition. Proc. Natl Acad. Sci. USA 93, 12834–12839 (1996). (10.1073/pnas.93.23.12834) / Proc. Natl Acad. Sci. USA by AC Jamieson (1996)
  23. Liu, Q. et al. Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem. 277, 3850–3856 (2002). (10.1074/jbc.M110669200) / J. Biol. Chem. by Q Liu (2002)
  24. Liu, P. Q. et al. Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A. J. Biol. Chem. 276, 11323–11334 (2001). (10.1074/jbc.M011172200) / J. Biol. Chem. by PQ Liu (2001)
  25. 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). (10.1074/jbc.M005341200) / J. Biol. Chem. by L Zhang (2000)
  26. Beerli, R. R., Dreier, B. & Barbas, C. F. 3rd. Positive and negative regulation of endogenous genes by designed transcription factors. Proc. Natl Acad. Sci. USA 97, 1495–1500 (2000). A convincing account of how ZFPs can be engineered to regulate endogenous genes. (10.1073/pnas.040552697) / Proc. Natl Acad. Sci. USA by RR Beerli (2000)
  27. 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). (10.1126/science.275.5300.657) / Science by HA Greisman (1997)
  28. Isalan, M., Klug, A. & Choo, Y. A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nature Biotechnol. 19, 656–660 (2001). This paper shows how, using phage display, a comprehensive archive of zinc fingers can be made for DNA recognition. (10.1038/90264) / Nature Biotechnol. by M Isalan (2001)
  29. Bartsevich, V. V. & Juliano, R. L. Regulation of the MDR1 gene by transcriptional repressors selected using peptide combinatorial libraries. Mol. Pharmacol. 58, 1–10 (2000). (10.1124/mol.58.1.1) / Mol. Pharmacol. by VV Bartsevich (2000)
  30. 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). (10.1073/pnas.110149297) / Proc. Natl Acad. Sci. USA by JK Joung (2000)
  31. Blancafort, P., Magnenat, L. & Barbas, C. F. Scanning the human genome with combinatorial transcription factor libraries. Nature Biotechnol. 21, 269–274 (2003). (10.1038/nbt794) / Nature Biotechnol. by P Blancafort (2003)
  32. Liu, Q. et al. Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc. Natl Acad. Sci. USA 94, 5525–5530 (1997). (10.1073/pnas.94.11.5525) / Proc. Natl Acad. Sci. USA by Q Liu (1997)
  33. Kim, J. S. & Pabo, C. O. Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants. Proc. Natl Acad. Sci. USA 95, 2812–2817 (1998). (10.1073/pnas.95.6.2812) / Proc. Natl Acad. Sci. USA by JS Kim (1998)
  34. Nekludova, L. & Pabo, C. O. Distinctive DNA conformation with enlarged major groove is found in Zn- finger–DNA and other protein–DNA complexes. Proc. Natl Acad. Sci. USA 91, 6948–6952 (1994). (10.1073/pnas.91.15.6948) / Proc. Natl Acad. Sci. USA by L Nekludova (1994)
  35. Moore, M., Klug, A. & Choo, Y. Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc. Natl Acad. Sci. USA 98, 1437–1441 (2001). (10.1073/pnas.98.4.1437) / Proc. Natl Acad. Sci. USA by M Moore (2001)
  36. Pomerantz, J. L., Wolfe, S. A. & Pabo, C. O. Structure-based design of a dimeric zinc finger protein. Biochemistry 37, 965–970 (1998). (10.1021/bi972464o) / Biochemistry by JL Pomerantz (1998)
  37. Wolfe, S. A., Ramm, E. I. & Pabo, C. O. Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. Structure Fold. Des. 8, 739–750 (2000). (10.1016/S0969-2126(00)00161-1) / Structure Fold. Des. by SA Wolfe (2000)
  38. Beerli, R. R. et al. Chemically regulated zinc finger transcription factors. J. Biol. Chem. 275, 32617–32627 (2000). (10.1074/jbc.M005108200) / J. Biol. Chem. by RR Beerli (2000)
  39. Gross, D. S. & Garrard, W. T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988). (10.1146/annurev.bi.57.070188.001111) / Annu. Rev. Biochem. by DS Gross (1988)
  40. Bushman, F. D. & Miller, M. D. Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites. J. Virol. 71, 458–464 (1997). (10.1128/JVI.71.1.458-464.1997) / J. Virol. by FD Bushman (1997)
  41. Xu, G. L. & Bestor, T. H. Cytosine methylation targetted to pre-determined sequences. Nature Genet. 17, 376–378 (1997). (10.1038/ng1297-376) / Nature Genet. by GL Xu (1997)
  42. Kim, Y. G., Cha, J. & Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 1156–1160 (1996). (10.1073/pnas.93.3.1156) / Proc. Natl Acad. Sci. USA by YG Kim (1996)
  43. Kalderon, D. et al. A short amino acid sequence able to specify nuclear location. Cell 39, 499–509 (1984). (10.1016/0092-8674(84)90457-4) / Cell by D Kalderon (1984)
  44. Sadowski, I. et al. GAL4-VP16 is an unusually potent transcriptional activator. Nature 335, 563–564 (1988). (10.1038/335563a0) / Nature by I Sadowski (1988)
  45. Ruben, S. M. et al. Isolation of a rel-related human cDNA that potentially encodes the 65- kD subunit of NF-κB. Science 251, 1490–1493 (1991). (10.1126/science.2006423) / Science by SM Ruben (1991)
  46. Thiesen, H. J. et al. Conserved KRAB protein domain identified upstream from the zinc finger region of Kox 8. Nucleic Acids Res. 19, 3996 (1991). (10.1093/nar/19.14.3996) / Nucleic Acids Res. by HJ Thiesen (1991)
  47. Guan, X. et al. Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors. Proc. Natl Acad. Sci. USA 99, 13296–13301 (2002). (10.1073/pnas.192412899) / Proc. Natl Acad. Sci. USA by X Guan (2002)
  48. Ren, D. et al. PPARγ knockdown by engineered transcription factors: exogenous PPARγ2 but not PPARγ1 reactivates adipogenesis. Genes Dev. 16, 27–32 (2002). A 'target validation' paper showing how ZFPs can be used to elucidate the role of a receptor isoform in fat cell differentiation. (10.1101/gad.953802) / Genes Dev. by D Ren (2002)
  49. Falke, D. et al. Design of artificial transcription factors to selectively regulate the pro-apoptotic bax gene. Nucleic Acids Res. 31, E10–20 (2003). (10.1093/nar/gng010) / Nucleic Acids Res. by D Falke (2003)
  50. Hopkins, A. L. & Groom, C. R. The druggable genome. Nature Rev. Drug Discov. 1, 727–730 (2002). (10.1038/nrd892) / Nature Rev. Drug Discov. by AL Hopkins (2002)
  51. Aranda, A. & Pascual, A. Nuclear hormone receptors and gene expression. Physiol. Rev. 81, 1269–1304 (2001). (10.1152/physrev.2001.81.3.1269) / Physiol. Rev. by A Aranda (2001)
  52. Reik, A., Gregory, P. D. & Urnov, F. D. Biotechnologies and therapeutics: chromatin as a target. Curr. Opin. Genet. Dev. 12, 233–242 (2002). (10.1016/S0959-437X(02)00291-5) / Curr. Opin. Genet. Dev. by A Reik (2002)
  53. Snowden, A. W. et al. Gene-specific targeting of h3k9 methylation is sufficient for initiating repression in vivo. Curr. Biol. 12, 2159–2166 (2002). (10.1016/S0960-9822(02)01391-X) / Curr. Biol. by AW Snowden (2002)
  54. Minucci, S. et al. Histone deacetylases: a common molecular target for differentiation treatment of acute myeloid leukemias? Oncogene 20, 3110–3115 (2001). (10.1038/sj.onc.1204336) / Oncogene by S Minucci (2001)
  55. Rebar, E. J. et al. Induction of angiogenesis in a mouse model using engineered transcription factors. Nature Med. 8, 1427–1432 (2002). A state-of-the-art paper showing how ZFPs can be used to stimulate the growth of blood vessels in a mouse ear. (10.1038/nm1202-795) / Nature Med. by EJ Rebar (2002)
  56. Grunstein, J. et al. Isoforms of vascular endothelial growth factor act in a coordinate fashion to recruit and expand tumor vasculature. Mol. Cell. Biol. 20, 7282–7291 (2000). (10.1128/MCB.20.19.7282-7291.2000) / Mol. Cell. Biol. by J Grunstein (2000)
  57. Modrek, B. & Lee, C. A genomic view of alternative splicing. Nature Genet. 30, 13–19 (2002). (10.1038/ng0102-13) / Nature Genet. by B Modrek (2002)
  58. Rowen, L. et al. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 79, 587–597 (2002). (10.1006/geno.2002.6734) / Genomics by L Rowen (2002)
  59. Young, J. C., Hoogenraad, N. J. & Hartl, F. U. Molecular chaperones hsp90 and hsp70 deliver preproteins to the mitochondrial import receptor tom70. Cell 112, 41–50 (2003). (10.1016/S0092-8674(02)01250-3) / Cell by JC Young (2003)
  60. Pollock, R. et al. Regulation of endogenous gene expression with a small-molecule dimerizer. Nature Biotechnol. 20, 729–733 (2002). (10.1038/nbt0702-729) / Nature Biotechnol. by R Pollock (2002)
  61. Johnson, L. et al. Selectively replicating adenoviruses targeting deregulated E2F activity are potent, systemic antitumor agents. Cancer Cell 1, 325–337 (2002). (10.1016/S1535-6108(02)00060-0) / Cancer Cell by L Johnson (2002)
  62. Dranoff, G. GM-CSF-based cancer vaccines. Immunol. Rev. 188, 147–154 (2002). (10.1034/j.1600-065X.2002.18813.x) / Immunol. Rev. by G Dranoff (2002)
  63. Reynolds, L. et al. Repression of the HIV-1 5' LTR promoter and inhibition of HIV-1 replication by using engineered zinc-finger transcription factors. Proc. Natl Acad. Sci. USA 100, 1615–1620 (2003). (10.1073/pnas.252770699) / Proc. Natl Acad. Sci. USA by L Reynolds (2003)
  64. Papworth, M. et al. Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors. Proc. Natl Acad. Sci. USA 100, 1621–1626 (2003). (10.1073/pnas.252773399) / Proc. Natl Acad. Sci. USA by M Papworth (2003)
  65. Chandrasegaran, S. & Smith, J. Chimeric restriction enzymes: what is next? Biol. Chem. 380, 841–848 (1999). (10.1515/BC.1999.103) / Biol. Chem. by S Chandrasegaran (1999)
  66. Bibikova, M. et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 21, 289–297 (2001). (10.1128/MCB.21.1.289-297.2001) / Mol. Cell. Biol. by M Bibikova (2001)
  67. Bibikova, M. et al. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161, 1169–1175 (2002). (10.1093/genetics/161.3.1169) / Genetics by M Bibikova (2002)
  68. Porteus, M. H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science (in the press). (10.1126/science.1078395)
  69. Hacein-Bey-Abina, S. et al. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N. Engl. J. Med. 348, 255–256 (2003). (10.1056/NEJM200301163480314) / N. Engl. J. Med. by S Hacein-Bey-Abina (2003)
  70. Robertson, K. D. & Wolffe, A. P. DNA methylation in health and disease. Nature Rev. Genet. 1, 11–19 (2000). (10.1038/35049533) / Nature Rev. Genet. by KD Robertson (2000)
  71. McNamara, A. R. et al. Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships. Nucleic Acids Res. 30, 3818–3830 (2002). (10.1093/nar/gkf501) / Nucleic Acids Res. by AR McNamara (2002)
  72. Jouvenot, Y. et al. Targeted regulation of imprinted genes by synthetic zinc-finger transcription factors. Gene Ther. (in the press). (10.1038/sj.gt.3301930)
  73. Kim, J. H. et al. Dopamine neurons derived from embryonic stem cells function in an animal model of Parkinson's disease. Nature 418, 50–56 (2002). (10.1038/nature00900) / Nature by JH Kim (2002)
  74. Stix, G. Legal circumvention. Sci. Am. 287, 36 (2002). / Sci. Am. by G Stix (2002)
Dates
Type When
Created 22 years, 3 months ago (May 15, 2003, 1:19 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 11:42 p.m.)
Indexed 4 weeks ago (Aug. 2, 2025, 12:55 a.m.)
Issued 22 years, 3 months ago (May 1, 2003)
Published 22 years, 3 months ago (May 1, 2003)
Published Print 22 years, 3 months ago (May 1, 2003)
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@article{Jamieson_2003, title={Drug discovery with engineered zinc-finger proteins}, volume={2}, ISSN={1474-1784}, url={http://dx.doi.org/10.1038/nrd1087}, DOI={10.1038/nrd1087}, number={5}, journal={Nature Reviews Drug Discovery}, publisher={Springer Science and Business Media LLC}, author={Jamieson, Andrew C. and Miller, Jeffrey C. and Pabo, Carl O.}, year={2003}, month=may, pages={361–368} }