DNA-Binding Specificity of NGFI-A and Related Zinc Finger Transcription Factors

REFERENCES

• Ackerman, S. L., A. G. Minden, G. T. Williams, C. Bobonis, and C. Yeung. 1991. Functional significance of an overlapping consensus binding motif for Sp1 and Zif268 in the murine adenosine deaminase gene promoter. Proc. Natl. Acad. Sci. USA 88:7523–7527.
   PubMedGoogle Scholar
• Applied Biosystems, Inc. 1992. Evaluating and isolating synthetic oligonu-cleotides, the complete guide. Applied Biosystems, Inc., Foster City, Calif.
   Google Scholar
• Berg, J. M. 1990. Zinc finger domains: hypotheses and current knowledge. Annu. Rev. Biophys. Biophys. Chem. 19:405–421.
   PubMedGoogle Scholar
• Brown, R. S., C. Sander, and P. Argos. 1985. The primary structure of transcription factor TFIIIA has 12 consecutive repeats. FEBS Lett. 186:271–274.
   PubMed Web of Science ®Google Scholar
• Camier, S., N. Kacherovsky, and E. T. Young. 1992. A mutation outside the two zinc fingers of ADR1 can suppress defects in either finger. Mol. Cell. Biol. 12:5758–5767.
   PubMedGoogle Scholar
• Chavrier, P., C. Vesque, B. Galliot, M. Vigneron, P. Dolle, D. Duboule, and P. Charnay. 1990. The segment-specific gene Krox-20 encodes a transcription factor with binding sites in the promoter region of the Hox-1.4 gene. EMBO J. 9:1209–1218.
   PubMed Web of Science ®Google Scholar
• Chavrier, P., M. Zerial, P. Lemaire, J. Almendral, R. Bravo, and P. Charnay. 1988. A gene encoding a protein with zinc fingers is activated during G0/G1 transition in cultured cells. EMBO J. 7:29–35.
   PubMed Web of Science ®Google Scholar
• Christy, B., and D. Nathans. 1989. DNA binding site of the growth factor-inducible protein Zif268. Proc. Natl. Acad. Sci. USA 86:8737–8741.
   PubMed Web of Science ®Google Scholar
• Christy, B. A., L. F. Lau, and D. Nathans. 1988. A gene activated in mouse 3T3 cells by serum growth factors encodes a protein with ‘‘zinc finger’’ sequences. Proc. Natl. Acad. Sci. USA 85:7857–7861.
   PubMed Web of Science ®Google Scholar
• Crosby, S., R. A. Veile, H. Donis-Keller, J. M. Baraban, R. V. Bhat, K. S. Simburger, and J. Milbrandt. 1992. Neural-specific expression, genomic structure, and chromosomal localization of the gene encoding the zinc-finger transcription factor NGFI-C. Proc. Natl. Acad. Sci. USA 89:4739–4743.
   PubMedGoogle Scholar
• Crosby, S. D., J. J. Puetz, K. S. Simburger, T. J. Fahrner, and J. Milbrandt. 1991. The early response gene NGFI-C encodes a zinc finger transcriptional activator and is a member of the GCGGGGGCG (GSG) element-binding protein family. Mol. Cell. Biol. 11:3835–3841.
   PubMed Web of Science ®Google Scholar
• Day, M. L., T. J. Fahrner, S. Aykent, and J. Milbrandt. 1990. The zinc finger protein NGFI-A exists in both nuclear and cytoplasmic forms in nerve growth factor-stimulated PC12 cells. J. Biol. Chem. 265:15253–15260.
   PubMedGoogle Scholar
• Desjarlais, J. R., and J. M. Berg. 1992. Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl. Acad. Sci. USA 89:7345–7349.
   PubMed Web of Science ®Google Scholar
• Desjarlais, J. R., and J. M. Berg. 1993. Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. Proc. Natl. Acad. Sci. USA 90:2256–2260.
   PubMed Web of Science ®Google Scholar
• Dong, Q., E. E. Blatter, Y. W. Ebright, K. Bister, and R. H. Ebright. 1994. Identification of amino acid-base contacts in the Myc-DNA complex by site-specific bromouracil mediated photocrosslinking. EMBO J. 13:200–204.
   PubMedGoogle Scholar
• Drummond, I. A., S. L. Madden, P. Rohwer-Nutter, G. I. Bell, V. P. Sukhatme, and F. J. Rauscher. 1992. Repression of the insulin-like growth factor II gene by the Wilms tumor suppressor WT1. Science 257:674–678.
   PubMed Web of Science ®Google Scholar
• Ekker, S. C., K. E. Young, D. P. von Kessler, and P. A. Beachy. 1991. Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosoph-ila. EMBO J. 10:1179–1186.
   PubMedGoogle Scholar
• Fahrner, T. J., S. L. Carroll, and J. Milbrandt. 1990. The NGFI-B protein, an inducible member of the thyroid/steroid receptor family, is rapidly modified posttranslationally. Mol. Cell. Biol. 10:6454–6459.
   PubMed Web of Science ®Google Scholar
• Fairall, L., S. D. Harrison, A. A. Travers, and D. Rhodes. 1992. Sequence-specific DNA binding by a two zinc-finger peptide from the Drosophila melanogaster Tramtrack protein. J. Mol. Biol. 226:349–366.
   PubMedGoogle Scholar
• Fairall, L., J. W. R. Schwabe, L. Chapman, J. T. Finch, and D. Rhodes. 1993. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature (London) 366:483–487.
   PubMed Web of Science ®Google Scholar
• Gehring, W. J., Y. Q. Qian, M. Billeter, K. Furukubo-Tokunaga, A. F. Schier, D. Resendez-Perez, M. Affolter, G. Otting, and K. Wuthrich. 1994. Home-odomain-DNA recognition. Cell 78:211–223.
   PubMed Web of Science ®Google Scholar
• Gessler, M., A. Poustka, W. Cavenee, R. L. Neve, S. H. Orkin, and G. A. P. Bruns. 1990. Homozygous deletion in Wilms tumours of a zinc-finger gene identified by chromosome jumping. Nature (London) 343:774–778.
   PubMed Web of Science ®Google Scholar
• Hegde, R. S., S. R. Grossman, L. A. Laimins, and P. B. Sigler. 1992. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature (London) 359:505–512.
   PubMed Web of Science ®Google Scholar
• Hirata, Y., K. Kiuchi, H. C. Chen, J. Milbrandt, and G. Guroff. 1993. The phosphorylation and DNA binding of the DNA-binding domain of the or phan nuclear receptor NGFI-B. J. Biol. Chem. 268:24808–24812.
   PubMed Web of Science ®Google Scholar
• Hunter, T., and M. Karin. 1992. The regulation of transcription by phos-phorylation. Cell 70:375–387.
   PubMed Web of Science ®Google Scholar
• Jacobs, S., K. Chang, and P. Cuatrecasas. 1975. Estimation of hormone receptor affinity by competitive displacement of labeled ligand: effect of concentration of receptor and of labeled ligand. Biochem. Biophys. Res. Commun. 66:687–692.
   PubMed Web of Science ®Google Scholar
• Joachimiak, A., T. E. Haran, and P. B. Sigler. 1994. Mutagenesis supports water mediated recognition in the trp repressor-operator system. EMBO J. 13:367–372.
   PubMed Web of Science ®Google Scholar
• Kadonaga, J. T., K. R. Carner, F. R. Masiarz, and R. Tjian. 1987. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell 51:1079–1090.
   PubMed Web of Science ®Google Scholar
• Keller, A. D., and T. Maniatis. 1991. Selection of sequences recognized by a DNA binding protein using a preparative Southwestern blot. Nucleic Acids Res. 19:4675–4680.
   PubMedGoogle Scholar
• Kuwahara, J., A. Yonezawa, M. Futamura, and Y. Sugiura. 1993. Binding of transcription factor Sp1 to GC box DNA revealed by footprinting analysis: different contact of three zinc fingers and sequence recognition mode. Biochemistry 32:5994–6001.
   PubMedGoogle Scholar
• Lee, M. S., G. P. Gippert, K. V. Soman, D. A. Case, and P. E. Wright. 1989. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245:635–637.
   PubMed Web of Science ®Google Scholar
• Lemaire, P., O. Revelant, R. Bravo, and P. Charnay. 1988. Two mouse genes encoding potential transcription factors with identical DNA-binding domains are activated by growth factors in cultured cells. Proc. Natl. Acad. Sci. USA 85:4691–4695.
   PubMed Web of Science ®Google Scholar
• Lemaire, P., C. Vesque, J. Schmitt, H. Stunnenberg, R. Frank, and P. Charnay. 1990. The serum-inducible mouse gene Krox-24 encodes a sequence-specific transcriptional activator. Mol. Cell. Biol. 10:3456–3467.
   PubMedGoogle Scholar
• Letovsky, J., and W. S. Dynan. 1989. Measurement of the binding of transcription factor Sp1 to a single GC box recognition sequence. Nucleic Acids Res. 17:2639–2653.
   PubMed Web of Science ®Google Scholar
• Li, Y., S. Camp, T. L. Rachinsky, C. Bongiorno, and P. Taylor. 1993. Promoter elements and transcriptional control of the mouse acetylcholinester-ase gene. J. Biol. Chem. 268:3563–3572.
   PubMed Web of Science ®Google Scholar
• Li, Z., and D. Paulin. 1993. Different factors interact with myoblast-specific and myotube-specific enhancer regions of the human desmin gene. J. Biol. Chem. 268:10403–10415.
   PubMedGoogle Scholar
• Luisi, B. F., W. X. Xu, Z. Otwinowski, L. P. Freedman, K. R. Yamamoto, and P. B. Sigler. 1991. Crystallographic analysis of the interaction of the glu-cocorticoid receptor with DNA. Nature (London) 352:497–505.
   PubMed Web of Science ®Google Scholar
• Lundin, M., J. O. Nehlin, and H. Ronne. 1994. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol. Cell. Biol. 14:1979–1985.
   PubMed Web of Science ®Google Scholar
• Mack, K. J., J. Cortner, P. Mack, and P. J. Farnham. 1992. Krox20 messenger RNA and protein expression in the adult central nervous system. Brain Res. Mol. Brain Res. 14:117–123.
   PubMedGoogle Scholar
• Milbrandt, J. 1987. A nerve growth factor-induced gene encodes a possible transcriptional regulatory factor. Science 238:797–799.
   PubMed Web of Science ®Google Scholar
• Miller, J., A. D. McLachlan, and A. Klug. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4:1609–1614.
   PubMed Web of Science ®Google Scholar
• Nardelli, J., T. Gibson, and P. Charnay. 1992. Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. Nucleic Acids Res. 200:4137–4141.
   Google Scholar
• Nardelli, J., T. J. Gibson, C. Vesque, and P. Charnay. 1991. Base sequence discrimination by zinc-finger DNA-binding domains. Nature (London) 349: 175–178.
   PubMedGoogle Scholar
• Nekludova, L., and C. O. Pabo. 1994. 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.
   PubMed Web of Science ®Google Scholar
• Nichols, M., F. Weih, W. Schmid, C. DeVack, E. Kowenz-Leutz, B. Luckow, M. Boshart, and G. Schutz. 1992. Phosphorylation of CREB affects its binding to high and low affinity sites: implications for cAMP induced gene transcription. EMBO J. 11:3337–3346.
   PubMed Web of Science ®Google Scholar
• Omichinski, J. G., G. M. Clore, O. Schaad, G. Felsenfeld, C. Trainor, E. Appella, S. J. Stahl, and A. M. Gronenborn. 1993. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261:438–446.
   PubMed Web of Science ®Google Scholar
• Patwardhan, S., A. Gashler, M. G. Siegel, L. C. Chang, L. J. Joseph, T. B. Shows, M. M. LeBeau, and V. P. Sukhatme. 1991. EGR3, a novel member of the Egr family of genes encoding immediate-early transcription factors. Oncogene 6:917–928.
   PubMed Web of Science ®Google Scholar
• Pavletich, N. P., and C. O. Pabo. 1991. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252:809–817.
   PubMed Web of Science ®Google Scholar
• Pavletich, N. P., and C. O. Pabo. 1993. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science 261:1701–1707.
   PubMed Web of Science ®Google Scholar
• Pellegrino, G. R., and J. M. Berg. 1991. Identification and characterization of ‘‘zinc-finger’’ domains by the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 88:671–675.
   PubMedGoogle Scholar
• Pu, W. T., and K. Struhl. 1992. Uracil interference, a rapid and general method for defining protein-DNA interactions involving the 5-methyl group of thymines: the GCN4-DNA complex. Nucleic Acids Res. 20:771–775.
   PubMedGoogle Scholar
• Rauscher, F. J., J. F. Morris, O. E. Tournay, D. M. Cook, and T. Curran. 1990. Binding of the Wilms’ tumor locus zinc finger protein to the EGR-1 consensus sequence. Science 250:1259–1262.
   PubMed Web of Science ®Google Scholar
• Rivera, V. M., C. K. Miranti, R. P. Misra, D. D. Ginty, R. H. Chen, J. Blenis, and M. E. Greenberg. 1993. A growth factor-induced kinase phosphorylates the serum response factor at a site that regulates its DNA-binding activity. Mol. Cell. Biol. 13:6260–6273.
   PubMed Web of Science ®Google Scholar
• Rould, M. A., J. J. Perona, and T. A. Steitz. 1991. Structural basis of antic-odon loop recognition by glutaminyl-tRNA synthetase. Nature (London) 352:213–218.
   PubMed Web of Science ®Google Scholar
• Schwabe, J. W. R., L. Chapman, J. T. Finch, and D. Rhodes. 1993. The crystal structure of the estrogen receptor DNA binding domain bound to DNA: how receptors discriminate between their response elements. Cell 75:567–578.
   PubMed Web of Science ®Google Scholar
• Sham, M. H., C. Vesque, S. Nonchev, H. Marshall, M. Frain, R. D. Gupta, J. Whiting, D. Wilkinson, P. Charnay, and R. Krumlauf. 1993. The zinc finger gene Krox20 regulates HoxB2 (Hox2.8) during hindbrain segmentation. Cell 72:183–196.
   PubMedGoogle Scholar
• Spindler, K. R., D. S. E. Rosser, and A. J. Berk. 1984. Analysis of adenovirus transforming proteins from early regions 1A and 1B with antisera to inducible fusion antigens produced in Escherichia coli. J. Virol. 49:132–141.
   PubMedGoogle Scholar
• Steitz, T. A. 1993. Structural studies of protein-nucleic acid interaction. Cambridge University Press, Cambridge.
   Google Scholar
• Sukhatme, V. P., X. Cao, L. C. Chang, C. Tsai-Morris, D. Stamenkovich, P. C. P. Ferreira, D. R. Cohen, S. A. Edwards, T. B. Shows, T. Curran, M. M. Le Beau, and E. D. Adamson. 1988. A zinc finger-encoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization. Cell 53:37–43.
   PubMed Web of Science ®Google Scholar
• Thukral, S. K., M. L. Morrison, and E. T. Young. 1991. Alanine scanning site-directed mutagenesis of the zinc fingers of transcription factor ADR1: residues that contact DNA and that transactivate. Proc. Natl. Acad. Sci. USA 88:9188–9192.
   PubMedGoogle Scholar
• Thukral, S. K., M. L. Morrison, and E. T. Young. 1992. Mutations in the zinc fingers of ADR1 that change the specificity of DNA binding and transacti-vation. Mol. Cell. Biol. 12:2784–2792.
   PubMed Web of Science ®Google Scholar
• von Hippel, P. H., and O. G. Berg. 1994. Protein-nucleic acid interaction. CRC Press, Inc., Boca Raton, Fla.
   Google Scholar
• Watson, M. A., and J. Milbrandt. 1990. Expression of the nerve growth factor-regulated NGFI-A and NGFI-B genes in the developing rat. Development 110:173–183.
   PubMedGoogle Scholar
• Weaver, C. A., R. E. Paulsen, T. J. Fahrner, and J. Milbrandt. Phosphory-lation of the orphan receptor NGFI-B affects DNA binding and subcellular localization. Submitted for publication.
   Google Scholar
• Wilson, T. E., M. L. Day, T. Pexton, K. A. Padgett, M. Johnston, and J. Milbrandt. 1992. In vivo mutational analysis of the NGFI-A zinc fingers. J. Biol. Chem. 267:3718–3724.
   PubMedGoogle Scholar
• Wilson, T. E., T. J. Fahrner, and J. Milbrandt. 1993. The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction. Mol. Cell. Biol. 13:5794–5804.
   PubMedGoogle Scholar
• Wuthrich, K. 1993. Hydration of biological macromolecules in solution: surface structure and molecular recognition. Cold Spring Harbor Symp. Quan. Biol. LVIII:149–157.
   Google Scholar