Establishment of Distinct MyoD, E2A, and Twist DNA Binding Specificities by Different Basic Region-DNA Conformations

REFERENCES

• Aksan, I., and Goding, C. R.. 1998. Targeting the microphthalmia basic helix-loop-helix-leucine zipper transcription factor to a subset of E-box elements in vitro and in vivo. Mol. Cell. Biol. 18:6930–6938
   PubMed Web of Science ®Google Scholar
• Anthony-Cahill, S. J., Benfield, P. A., Fairman, R., Wasserman, Z. R., Brenner, S. L., Stafford, W. F., Altenbach, C., Hubbell, W. L., and DeGrado, W. F.. 1992. Molecular characterization of helix-loop-helix peptides. Science 255:979–983
   PubMed Web of Science ®Google Scholar
• Bengal, E., Flores, O., Rangarajan, P. N., Chen, A., Weintraub, H., and Verma, I. M.. 1994. Positive control mutations in the MyoD basic region fail to show cooperative DNA binding and transcriptional activation in vitro. Proc. Natl. Acad. Sci. USA 91:6221–6225
   PubMed Web of Science ®Google Scholar
• Biesiada, E., Hamamori, Y., Kedes, L., and Sartorelli, V.. 1999. Myogenic basic helix-loop-helix proteins and Sp1 interact as components of a multiprotein transcriptional complex required for activity of the human cardiac alpha-actin promoter. Mol. Cell. Biol. 19:2577–2584
   PubMedGoogle Scholar
• Black, B. L., Molkentin, J. D., and Olson, E. N.. 1998. Multiple roles for the MyoD basic region in transmission of transcriptional activation signals and interaction with MEF2. Mol. Cell. Biol. 18:69–77
   PubMedGoogle Scholar
• Blackwell, T. K.. 1995. Selection of protein binding sites from random nucleic acid sequences. Methods Enzymol. 254:604–618
   PubMedGoogle Scholar
• Blackwell, T. K., Huang, J., Ma, A., Kretzner, L., Alt, F. W., Eisenman, R. N., and Weintraub, H.. 1993. Binding of Myc proteins to canonical and noncanonical DNA sequences. Mol. Cell. Biol. 13:5216–5224
   PubMed Web of Science ®Google Scholar
• Blackwell, T. K., Kretzner, L., Blackwood, E. M., Eisenman, R. N., and Weintraub, H.. 1990. Sequence-specific DNA binding by the c-Myc protein. Science 250:1149–1151
   PubMed Web of Science ®Google Scholar
• Blackwell, T. K., and Weintraub, H.. 1990. Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science 250:1104–1110
   PubMed Web of Science ®Google Scholar
• Bodis, S., Hemesath, T., and Fisher, D. E.. 1997. Highly conserved asparagine in the basic domain of Myc is dispensable for DNA binding, transformation, and apoptosis. Biochem. Mol. Med. 60:102–107
   PubMedGoogle Scholar
• Brennan, T. J., Chakraborty, T., and Olson, E. N.. 1991. Mutagenesis of the myogenin basic region identifies an ancient protein motif critical for activation of myogenesis. Proc. Natl. Acad. Sci. USA 88:5675–5679
   PubMedGoogle Scholar
• Brownlie, P., Ceska, T., Lamers, M., Romier, C., Stier, G., Teo, H., and Suck, D.. 1997. The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control. Structure 5:509–520
   PubMedGoogle Scholar
• Carey, J.. 1991. Gel retardation. Methods Enzymol. 208:103–117
   PubMedGoogle Scholar
• Chakraborty, T., Brennan, T. J., Li, L., Edmondson, D., and Olson, E. N.. 1991. Inefficient homooligomerization contributes to the dependence of myogenin on E2A products for efficient DNA binding. Mol. Cell. Biol. 11:3633–3641
   PubMed Web of Science ®Google Scholar
• Cripps, R. M., Black, B. L., Zhao, B., Lien, C. L., Schulz, R. A., and Olson, E. N.. 1998. The myogenic regulatory gene Mef2 is a direct target for transcriptional activation by Twist during Drosophila myogenesis. Genes Dev. 12:422–434
   PubMedGoogle Scholar
• Dang, C. V., Dolde, C., Gillison, M. L., and Kato, G. J.. 1992. Discrimination between related DNA sites by a single amino acid residue of Myc-related basic-helix-loop-helix proteins. Proc. Natl. Acad. Sci. USA 89:599–602
   PubMedGoogle Scholar
• Davis, R. L., Cheng, P. F., Lassar, A. B., and Weintraub, H.. 1990. The MyoD DNA binding domain contains a recognition code for muscle-specific gene activation. Cell 60:733–746
   PubMedGoogle Scholar
• Davis, R. L., and Weintraub, H.. 1992. Acquisition of myogenic specificity by replacement of three amino acid residues from MyoD into E12. Science 256:1027–1030
   PubMed Web of Science ®Google Scholar
• Ellenberger, T., Fass, D., Arnaud, M., and Harrison, S. C.. 1994. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 8:970–980
   PubMed Web of Science ®Google Scholar
• Ferre-D'Amare, A. R., Prendergast, G. C., Ziff, E. B., and Burley, S. K.. 1993. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363:38–45
   PubMed Web of Science ®Google Scholar
• Ferre-D'Amare, A. R., Pognonec, P., Roeder, R. G., and Burley, S. K.. 1994. Structure and function of the b/HLH/Z domain of USF. EMBO J. 13:180–189
   PubMedGoogle Scholar
• Fisher, D. E., Parent, L. A., and Sharp, P. A.. 1993. High affinity DNA-binding Myc analogs: recognition by an α helix. Cell 72:467–476
   PubMed Web of Science ®Google Scholar
• Fisher, F., Crouch, D. H., Jayaraman, P.-S., Clark, W., Gillespie, D. A. F., and Goding, C. R.. 1993. Transcription activation by Myc and Max: flanking sequences target activation to a subset of CACGTG motifs in vivo. EMBO J. 12:5075–5082
   PubMedGoogle Scholar
• Gould, K. A., and Bresnick, E. H.. 1998. Sequence determinants of DNA binding by the hematopoietic helix-loop-helix transcription factor TAL1: importance of sequences flanking the E-box core. Gene Expr. 7:87–101
   PubMedGoogle Scholar
• Halazonetis, T. D., and Kandil, A. N.. 1992. Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI. Science 255:464–466
   PubMedGoogle Scholar
• Hamamori, Y., Wu, H. Y., Sartorelli, V., and Kedes, L.. 1997. The basic domain of myogenic basic helix-loop-helix (bHLH) proteins is the novel target for direct inhibition by another bHLH protein, Twist. Mol. Cell. Biol. 17:6563–6573
   PubMedGoogle Scholar
• Harfe, B. D., Branda, C. S., Krause, M., Stern, M. J., and Fire, A.. 1998. MyoD and the specification of muscle and non-muscle fates during postembryonic development of the C. elegans mesoderm. Development 125:2479–2488
   PubMedGoogle Scholar
• Huang, J., Blackwell, T. K., Kedes, L., and Weintraub, H.. 1996. Differences between MyoD DNA binding and activation site requirements revealed by a functional random sequence selection. Mol. Cell. Biol. 16:3893–3900
   PubMed Web of Science ®Google Scholar
• Huang, J., Weintraub, H., and Kedes, L.. 1998. Intramolecular regulation of MyoD activation domain conformation and function. Mol. Cell. Biol. 18:5478–5484
   PubMedGoogle Scholar
• Jennings, B. H., Tyler, D. M., and Bray, S. J.. 1999. Target specificities of Drosophila enhancer of split basic helix-loop-helix proteins. Mol. Cell. Biol. 19:4600–4610
   PubMedGoogle Scholar
• Kophengnavong, T., Carroll, A. S., and Blackwell, T. K.. 1999. The SKN-1 amino-terminal arm is a DNA specificity segment. Mol. Cell. Biol. 19:3039–3050
   PubMed Web of Science ®Google Scholar
• Lassar, A. B., Davis, R. L., Wright, W. E., Kadesch, T., Murre, C., Voronova, A., Baltimore, D., and Weintraub, H.. 1991. Functional activity of myogenic HLH proteins requires hetero-oligomerization with E12/E47-like proteins in vivo. Cell 66:305–315
   PubMed Web of Science ®Google Scholar
• Lee, J. E.. 1997. Basic helix-loop-helix genes in neural development. Curr. Opin. Neurobiol. 7:13–20
   PubMed Web of Science ®Google Scholar
• Lemercier, C., To, R. Q., Carrasco, R. A., and Konieczny, S. F.. 1998. The basic helix-loop-helix transcription factor Mist1 functions as a transcriptional repressor of myoD. EMBO J. 17:1412–1422
   PubMed Web of Science ®Google Scholar
• Ma, P. C., Rould, M. A., Weintraub, H., and Pabo, C. O.. 1994. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell 77:451–459
   PubMed Web of Science ®Google Scholar
• Maleki, S. J., Royer, C. A., and Hurlburt, B. K.. 1997. MyoD-E12 heterodimers and MyoD-MyoD homodimers are equally stable. Biochemistry 36:6762–6767
   PubMedGoogle Scholar
• Michelson, A.. 1996. A new turn (or two) for Twist. Science 272:1449–1450
   PubMedGoogle Scholar
• Molkentin, J. D., Black, B. L., Martin, J. F., and Olson, E. N.. 1995. Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins. Cell 83:1125–1136
   PubMedGoogle Scholar
• Molkentin, J. D., and Olson, E. N.. 1996. Combinatorial control of muscle development by basic helix-loop-helix and MADS-box transcription factors. Proc. Natl. Acad. Sci. USA 93:9366–9373
   PubMed Web of Science ®Google Scholar
• Murre, C., McCaw, P. S., and Baltimore, D.. 1989. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell 56:777–783
   PubMed Web of Science ®Google Scholar
• Murre, C., McCaw, P. S., Vaessin, H., Caudy, M., Jan, L. Y., Jan, Y. N., Cabrera, C. V., Buskin, J. N., Hauschka, S. D., Lassar, A. B., Weintraub, H., and Baltimore, D.. 1989. Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence. Cell 58:537–544
   PubMed Web of Science ®Google Scholar
• Neuhold, L., and Wold, B.. 1993. HLH forced dimers: tethering MyoD to E47 generates a dominant positive myogenic factor insulated from negative regulation by Id. Cell 74:1033–1042
   PubMed Web of Science ®Google Scholar
• Olson, E. N., and Klein, W. H.. 1994. bHLH factors in muscle development: dead lines and commitments, what to leave in and what to leave out. Genes Dev. 8:1–8
   PubMed Web of Science ®Google Scholar
• Pabo, C. O., and Sauer, R. T.. 1992. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61:1053–1095
   PubMed Web of Science ®Google Scholar
• Parraga, A., Bellsolell, L., Ferre-D'Amare, A. R., and Burley, S. K.. 1998. Cocrystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure 6:661–672
   PubMedGoogle Scholar
• Postigo, A. A., and Dean, D. C.. 1999. ZEB represses transcription through interaction with the corepressor CtBP. Proc. Natl. Acad. Sci. USA 96:6683–6688
   PubMedGoogle Scholar
• Schwarz, J. J., Chakraborty, T., Martin, J., Zhou, J. M., and Olson, E. N.. 1992. The basic region of myogenin cooperates with two transcription activation domains to induce muscle-specific transcription. Mol. Cell. Biol. 12:266–275
   PubMedGoogle Scholar
• Shimizu, T. X., Toumoto, A., Ihara, K., Shimizu, M., Kyogoku, Y., Ogawa, N., Oshima, Y., and Hakoshima, T.. 1997. Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J. 16:4689–4697
   PubMedGoogle Scholar
• Spolar, R. S., Record, M. T.Jr.. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777–784
   PubMed Web of Science ®Google Scholar
• Steitz, T. A.. 1990. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23:205–280
   PubMed Web of Science ®Google Scholar
• Studier, F. W.. 1991. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219:37–44
   PubMed Web of Science ®Google Scholar
• Szymanski, P., and Levine, M.. 1995. Multiple modes of dorsal-bHLH transcriptional synergy in the Drosophila embryo. EMBO J. 14:2229–2238
   PubMedGoogle Scholar
• Thayer, M. J., and Weintraub, H.. 1993. A cellular factor stimulates the DNA-binding activity of MyoD and E47. Proc. Natl. Acad. Sci. USA 90:6483–6487
   PubMedGoogle Scholar
• Van Antwerp, M. E., Chen, D. G., Chang, C., and Prochownik, E. V.. 1992. A point mutation in the MyoD basic domain imparts c-Myc-like properties. Proc. Natl. Acad. Sci. USA 89:9010–9014
   PubMed Web of Science ®Google Scholar
• Voronova, A., and Baltimore, D.. 1990. Mutations that disrupt DNA binding and dimer formation in the E47 helix-loop-helix protein map to distinct domains. Proc. Natl. Acad. Sci. USA 87:4722–4726
   PubMed Web of Science ®Google Scholar
• Weintraub, H., Davis, R., Tapscott, S., Thayer, M., Krause, M., Benezra, R., Blackwell, T. K., Turner, D., Rupp, R., Hollenberg, S., Zhuang, Y., and Lassar, A.. 1991. The MyoD gene family: nodal point during specification of the muscle cell lineage. Science 251:761–766
   PubMed Web of Science ®Google Scholar
• Weintraub, H., Dwarki, V. J., Verma, I., Davis, R., Hollenberg, S., Snider, L., Lassar, A., and Tapscott, S. J.. 1991. Muscle-specific transcriptional activation by MyoD. Genes Dev. 5:1377–1386
   PubMed Web of Science ®Google Scholar
• Weintraub, H., Genetta, T., and Kadesch, T.. 1994. Tissue-specific gene activation by MyoD: determination of specificity by cis-acting repression elements. Genes Dev. 8:2203–2211
   PubMed Web of Science ®Google Scholar
• Wendt, H., Thomas, R. M., and Ellenberger, T.. 1998. DNA-mediated folding and assembly of MyoD-E47 heterodimers. J. Biol. Chem. 273:5735–5743
   PubMedGoogle Scholar
• Yin, Z., Xu, X. L., and Frasch, M.. 1997. Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development. Development 124:4971–4982
   PubMedGoogle Scholar