DNA bending and the curious case of Fos/Jun

Chemistry and Biology

Volumn 5, Issue 2, 1998, Pages

  McGill, Gaël ^a   Fisher, David E ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0032008081     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(98)90139-9     Document Type: Review

References (73)

1. Harrington, R.E. (1993). Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis 14, 732-746.
2. Trifonov, E.N. & Sussman, J.L (1980). The pitch of the chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816-3820.
3. Koo, H.S. &Crothers, D.M. (1986). DNA bending at adenine.thymine tracts. Nature 320, 501-506.
4. Nelson, H.C.M., Finch, J.T., Bonaventura, F.L. & Klug, A. (1987). The structure of an oligo(dA0.oligo(dT0 tract and its biological implications. Nature 330, 221-226.
5. Suzuki, M. & Yagi, N. (1995). Stereochemical basis of DNA bending by transcription factors. Nucleic Acids Res. 23, 2083-2091.
6. Young, M.A., Ravishanker, G., Beveridge, D.L. & Berman, H.M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophysical J. 68, 2454-2468.
7. Werner, M.H., Gronenborn, A.M. & Clore, M. (1996). Intercalation, DNA kinking, and the control of transcription. Science 271, 778-784.
8. Love, J.J., Li, X., Case, D.A., Giese, K., Grosschedl, R. & Wright, P.E. (1995). Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376, 791-795.
9. Werner, M.H., Huth, J.R., Gronenborn, A.M. & Clore, G.M. (1995). Molecular basis of the human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell 81, 705-714.
10. Schumacher, M.A., Choi, K.Y., Zalkin, H. & Brennan, R.G. (1994). Crystal structure of Lacl member, PurR, bound to DNA: minor groove binding by alpha helices. Science 266, 763-770.
11. Rice, P.A., Yang, S.-W., Mizuuchi, K. & Nash, H.A. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA u-turn. Cell 87, 1295-1306.
12. Travers, A. (1997). DNA-protein interactions: IHF - the master bender. Curr. Biol. 7, R252-R254.
13. Strauss, J.K. & Maher III, L.J. (1994). DNA bending by asymmetric phosphate neutralization. Science 266, 1829-1834.
14. Strauss-Soukup, J.K. & Maher III, L.J. (1997). DNA bending by GCN4 mutants bearing cationic residues. Biochemistry 36, 10026-10032.
15. Grove, A., Galeone, A., Mayol, L. & Geiduschek, E.P. (1996). Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 260, 120-125.
16. Kahn, J.D. & Crothers, D.M. (1992). Protein-induced bending and DNA cyclization. Proc. Natl Acad. Sci. USA 89, 6343-6347.
17. Parvin, J.D., McCormick, R.J., Sharp, P.A. & Fisher, D.E. (1995). Prebending of a promoter sequence enhances affinity for the TATA-binding factor. Nature 373, 724-727.
18. McCormick, R.J., Badalian, T. & Fisher, D.E. (1996). The leucine zipper may induce electrophoretic mobility anomalies without DNA bending. Proc. Natl Acad. Sci. USA 93, 14434-14439.
19. Grosschedl, R. (1995). Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr. Opin. Cell Biol. 7, 362-370.
20. Werner, M.H. & Burley, S.K. (1997). Architectural transcription factors: proteins that remodel DNA. Cell 88, 733-736.
21. Perez-Martin, J., Rojo, F. & de Lorenzo, V. (1994). Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev. 58, 268-290.
22. Wu, H.M. & Crothers, D.M. (1984). The locus of sequence-directed and protein-induced bending. Nature 308, 509-513.
23. Bracco, L., Kotlarz, D., Kolb, A., Diekmann, S. & Buc, H. (1989). Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J 8, 4289-4296.
24. Gartenburg, M.R. & Crothers, D.M. (1991). Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J. Mol. Biol. 219, 217-230.
25. Perez-Martin, J. & Espinosa, M. (1993). Protein-induced bending as a transcriptional switch. Science 260, 805-807.
26. Goosen, N. & van de Putte, P. (1995). The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16, 1-7.
27. Segall, A.M., Goodman, S.D., Nash, H.A. (1994). Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13, 4536-4548.
28. Parekh, B.S. & Wesley Hatfield, G. (1996). Transcriptional activation by protein-induced DNA bending: Evidence for a DNA structural transmission model. Proc. Natl Acad. Sci. USA 93, 1173-1177.
29. Kuhnke, G., Fritz, H.-J. & Ehring, R. (1987). Unusual properties of promoter up mutations in the E coli galactose operon and evidence suggesting RNA polymerase-induced DNA bending. EMBO J. 6, 507-513.
30. Kuhnke, G., Theres, C., Fritz, H.-J. & Ehring, R. (1989). RNA polymerase and gal repressor bind simultaneously and with DNA bending to the control region of the Escherichia coli galactose operon. EMBO J. 8, 1247-1255.
31. Lamond, A.I. & Travers, A.A. (1983). Requirement for an upstream element for optimal transcription of a bacterial tRNA gene. Nature 305, 248-250.
32. Deuschle, U., Kammerer, W., Gentz, R. & Bujard, H. (1986). Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternative structures. EMBO J. 5, 2987-2994.
33. McAllister, C.F. & Achberger, E.C. (1989). Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J. Biol. Chem. 264, 10451-10456.
34. Newlands, J.T., Josaitis, C.A., Ross, W. & Gourse, R. (1992). Both Fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix-dependent. Nucleic Acids Res. 20, 719-726.
35. Sivolob, A.V. & Khrapunov, S.N. (1995). Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending.stiffness. J. Mol. Biol. 247, 918-931.
36. Baldi, P., Brunak, S., Chauvin, Y. & Krogh, A. (1996). Naturally occuring nucleosome positioning signals in human exons and introns. J. Mol. Biol. 263, 503-510.
37. Giese, K., Kingsley, C., Kirshner, J.R. & Grosschedl, R. (1995). Assembly and function of a TCRα enhancer complex is dependent on LEF-1-induced DNA bending and multiple protein-protein interactions. Genes Devel. 9, 995-1008.
38. Thanos, D. & Maniatis, T. (1995). Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome. Cell 83, 1091-1100.
39. Falvo, J.V., Thanos, D. & Maniatis, T. (1995). Reversal of intrinsic DNA bends in the IFNβ gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell 83, 1101-1111.
40. Giese, K., Cox, J. & Grosschedl, R. (1992). The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures. Cell 69, 185-195.
41. Mayall, T.P., Sheridan, P.L., Montminy, M.R. & Jones, K.A. (1997). Distinct roles for P-CREB and LEF-1 in TCRα enhancer assembly and activation on chromatin templates in vitro. Genes Devel. 11, 887-899.
42. Kim, J. & Shapiro, D.J. (1996). In simple synthetic promoters YY1-induced DNA bending is important in transcription activation and repression. Nucleic Acids Res. 24(21), 4341-4348.
43. Natesan, S. & Gilman, M.Z. (1993). DNA bending and orientation-dependent function of YY1 in the c-fos promoter. Genes Devel. 7, 2497-2509.
44. Yang, Y., Westcott, T.P., Pederson, S.C., Tobias, I. & Olson, W.K. (1995). Effects of localized bending on DNA supercoiling. Trends Biochem. Sci. 20, 313-319.
45. Bagga, R. & Emerson, B.M. (1997). An HMG I/Y-containing repressor complex and supercoiled DNA topology are critical for long-range enhancer-dependent transcription in vitro. Genes Devel. 11, 629-639.
46. Gohlke, C., Murchie, A.I.H., Lilley, D.M.J. & Clegg, R.M. (1994). Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA 91, 11660-11664.
47. Ozaki, H., Iwase, N., Sawai, H., Kodama, T. & Kyogoku, Y. (1997). Detection of DNA bending in a DNA-PAP1 protein complex by fluorescence resonance energy transfer. Biochem. Biophys. Res. Commun. 231, 553-556.
48. Thompson, J.F. & Landy, A. (1988). Empirical estimation of protein-induced DNA bending angles:applications to λ site-specific recombination complexes. Nucleic Acids Res. 16, 9687-9705.
49. Zinkel, S.S. & Crothers, D.M. (1987). DNA bend direction by phase-sensitive detection. Nature 328, 178-181.
50. Ulanovsky, L, Bodner, M., Trifonov, E.N. & Choder, M. (1986). Curved DNA: design, synthesis, and circularization. Proc. Natl Acad. Sci. USA 83, 862-866.
51. Lyubchenko, Y. Shlyahtenko, L, Chemov, B. & Harrington, R.E. (1991). DNA Bending induced by Cro protein binding as demonstrated by gel electrophoresis. Proc Natl. Acad. Sci. USA 88, 5331-5334.
52. Bohmann, D., Bos, T.J., Admon, A., Nishmura, T., Vogt, P.K. & Tjian, R. (1987). Human proto-oncogene c-jun encodes a DNA binding protein with structural and functional properties of transcription factor AP-1. Science 238, 1386-1392.
53. Rauscher, F.J., Cohen, D.R., Curran, T., Bos, T.J., Vogt, P.K., Bohmann, D., Tjian, R. & Franza, B.R. (1988). Fos-associated protein p39 is the product of the jun proto-oncogene. Science 240, 1010-1016.
54. Franza, B.R., Rauscher, F.J.I., Josephs, S.F. & Curran, T. (1988). The Fos complex and Fos-related antigens recognize sequence elements that contain AP-1 binding sites. Science 239, 1150-1153.
55. Hai, T. & Curran, T. (1991). Fos/Jun and ATF/CREB cross-family dimerization alters DNA binding specificity. Proc. Natl Acad. Sci. USA 88, 3720-3724.
56. Patel, L, Abate, C. & Curran, T. (1990). DNA binding by Fos and Jun results in altered protein conformation. Nature 347, 572-574.
57. Weiss, M.A., et al. (1990). Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature 347, 575-578.
58. Kerppola, T.K. & Curran, T. (1991). Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell 66, 317-326.
59. Kerppola, T.K. & Curran, T. (1991). DNA bending by Fos and Jun: the flexible hinge model. Science 254, 1210-1214.
60. Diamond, M.I., Miner, J.N., Yoshinaga, S.K. & Yamamoto, K.R. (1990). c-Jun and c-Fos levels specify positive or negative glucocorticoid regulation from a composite GRE. Science 249, 1266-1272.
61. Kerppola, T.K. & Curran, T. (1993). Selective DNA bending by a variety of bZIP proteins. Mol. Cell. Biol. 13(9), 5479-5489.
62. Gartenburg, M.R., Ampe, C., Steitz, T.A. & Crothers, D.M. (1990). Molecular characterization of the GCN4-DNA complex. Proc. Natl Acad. Sci. USA 87, 6034-6038.
63. Ellenberger, T.E., Brandl, C.J., Struhl, K. & Harrison, S.C. (1992). The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell 71, 1223-1237.
64. Glover, M.J.N. & Harrison, S.C. (1995). Crystal structure of the heterodimeric bZip transcription factor c-Fos-c-Jun bound to DNA. Nature 373, 257-261.
65. Kerppola, T. & Curran, T. (1995). Zen and the art of Fos and Jun. Nature 373, 199-200.
66. Sitlani, A. & Crothers ,D.M. (1996). Fos and Jun do not bend the AP-1 recognition site. Proc. Natl Acad. Sci. USA 93, 3248-3252.
67. Kerppola, T.K. (1996). Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending. Proc. Natl Acad. Sci. USA 93, 10117-10122.
68. Sitlani, A. & Crothers, D.M. (1997). Fos-Jun does not induce DNA curvature: an investigation using solution- and gel-based methods. Proc. Natl Acad. Sci. USA in press.
69. Fisher, D.E., Parent, L.A. & Sharp, P.A. (1992). Myc/Max and other helix-loop-helix/leucine zipper proteins bend DNA toward the minor groove. Proc. Natl. Acad. Sci. USA 89, 11779-11783.
70. Wechsler, D.S. & Dang, C.V. (1992). Opposite orientations of DNA bending by c-Myc and Max. Proc. Natl. Acad. Sci. USA 89, 7635-7639.
71. O'Shea, E.K., Rutkowski, R., Stafford, W.F. & Kim, P.S. (1989). Preferential heterodimer formation by isolated leucine zippers from fos and jun. Science 245, 646-648.
72. Ferre-D'Amare, A.R., Prendergast, G.C., Ziff, E.B. & Burley, S.K. (1993). Recognition by Max of its cognate DNA through a dimeric b/HLH/Zip domain. Nature 363, 38-45.
73. Kerppola, T.K. & Curran, T. (1997). The transcription activation domains of Fos and Jun induce DNA bending through electrostatic interactions. EMBO J. 16, 2907-2916.