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. 1996 Jul 15;24(14):2640–2647. doi: 10.1093/nar/24.14.2640

DNA bending by the silencer protein NeP1 is modulated by TR and RXR.

R Arnold 1, M Burcin 1, B Kaiser 1, M Muller 1, R Renkawitz 1
PMCID: PMC146006  PMID: 8758989

Abstract

NeP1 binds to the F1 silencer element of the chicken lysozyme gene and, in the presence of TR, v-ERBA or RAR, synergistically represses transcriptional activity. This repression involves a silencing mechanism acting independently of the relative promoter position. Here we show that NeP1 alone can induce a significant directed bend on DNA. The chicken homologue of human NeP1, CTCF, shows identical binding and bending properties. In contrast, the isolated DNA binding domain of CTCF efficiently binds DNA, but fails to confer bending. Similarly, the TR-RXR hetero- or homodimer, binding adjacent to NeP1 at the F2 sequence, do not show significant DNA bending. The binding of the T3 ligand to TR changes neither the magnitude nor the direction of the NeP1 induced bend. However, when all factors are bound simultaneously as a quaternary complex, the TR-RXR heterodimer changes the location of the bend center, the flexure angle and the bending direction.

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Selected References

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  1. Andersson M. L., Nordström K., Demczuk S., Harbers M., Vennström B. Thyroid hormone alters the DNA binding properties of chicken thyroid hormone receptors alpha and beta. Nucleic Acids Res. 1992 Sep 25;20(18):4803–4810. doi: 10.1093/nar/20.18.4803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baniahmad A., Steiner C., Köhne A. C., Renkawitz R. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell. 1990 May 4;61(3):505–514. doi: 10.1016/0092-8674(90)90532-j. [DOI] [PubMed] [Google Scholar]
  3. Burcin M., Köhne A. C., Runge D., Steiner C., Renkawitz R. Factors influencing nuclear receptors in transcriptional repression. Semin Cancer Biol. 1994 Oct;5(5):337–346. [PubMed] [Google Scholar]
  4. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Falvo J. V., Thanos D., Maniatis T. Reversal of intrinsic DNA bends in the IFN beta gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell. 1995 Dec 29;83(7):1101–1111. doi: 10.1016/0092-8674(95)90137-x. [DOI] [PubMed] [Google Scholar]
  6. Giese K., Kingsley C., Kirshner J. R., Grosschedl R. Assembly and function of a TCR alpha enhancer complex is dependent on LEF-1-induced DNA bending and multiple protein-protein interactions. Genes Dev. 1995 Apr 15;9(8):995–1008. doi: 10.1101/gad.9.8.995. [DOI] [PubMed] [Google Scholar]
  7. Ikeda M., Rhee M., Chin W. W. Thyroid hormone receptor monomer, homodimer, and heterodimer (with retinoid-X receptor) contact different nucleotide sequences in thyroid hormone response elements. Endocrinology. 1994 Oct;135(4):1628–1638. doi: 10.1210/endo.135.4.7925126. [DOI] [PubMed] [Google Scholar]
  8. Kerppola T. K., Curran T. DNA bending by Fos and Jun: the flexible hinge model. Science. 1991 Nov 22;254(5035):1210–1214. doi: 10.1126/science.1957173. [DOI] [PubMed] [Google Scholar]
  9. Kerppola T. K., Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell. 1991 Jul 26;66(2):317–326. doi: 10.1016/0092-8674(91)90621-5. [DOI] [PubMed] [Google Scholar]
  10. Kerppola T. K., Curran T. Selective DNA bending by a variety of bZIP proteins. Mol Cell Biol. 1993 Sep;13(9):5479–5489. doi: 10.1128/mcb.13.9.5479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Klenova E. M., Nicolas R. H., Paterson H. F., Carne A. F., Heath C. M., Goodwin G. H., Neiman P. E., Lobanenkov V. V. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 1993 Dec;13(12):7612–7624. doi: 10.1128/mcb.13.12.7612. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kuddus R., Gu B., DeLuca N. A. Relationship between TATA-binding protein and herpes simplex virus type 1 ICP4 DNA-binding sites in complex formation and repression of transcription. J Virol. 1995 Sep;69(9):5568–5575. doi: 10.1128/jvi.69.9.5568-5575.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Köhne A. C., Baniahmad A., Renkawitz R. NeP1. A ubiquitous transcription factor synergizes with v-ERBA in transcriptional silencing. J Mol Biol. 1993 Aug 5;232(3):747–755. doi: 10.1006/jmbi.1993.1428. [DOI] [PubMed] [Google Scholar]
  14. Lee S., Hahn S. Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature. 1995 Aug 17;376(6541):609–612. doi: 10.1038/376609a0. [DOI] [PubMed] [Google Scholar]
  15. Love J. J., Li X., Case D. A., Giese K., Grosschedl R., Wright P. E. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature. 1995 Aug 31;376(6543):791–795. doi: 10.1038/376791a0. [DOI] [PubMed] [Google Scholar]
  16. Lu X. P., Eberhardt N. L., Pfahl M. DNA bending by retinoid X receptor-containing retinoid and thyroid hormone receptor complexes. Mol Cell Biol. 1993 Oct;13(10):6509–6519. doi: 10.1128/mcb.13.10.6509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mangelsdorf D. J., Umesono K., Kliewer S. A., Borgmeyer U., Ong E. S., Evans R. M. A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR. Cell. 1991 Aug 9;66(3):555–561. doi: 10.1016/0092-8674(81)90018-0. [DOI] [PubMed] [Google Scholar]
  18. McBroom L. D., Flock G., Giguère V. The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions. Mol Cell Biol. 1995 Feb;15(2):796–808. doi: 10.1128/mcb.15.2.796. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Meacock S., Pescini-Gobert R., DeLamarter J. F., Hooft van Huijsduijnen R. Transcription factor-induced, phased bending of the E-selectin promoter. J Biol Chem. 1994 Dec 16;269(50):31756–31762. [PubMed] [Google Scholar]
  20. Nardulli A. M., Grobner C., Cotter D. Estrogen receptor-induced DNA bending: orientation of the bend and replacement of an estrogen response element with an intrinsic DNA bending sequence. Mol Endocrinol. 1995 Aug;9(8):1064–1076. doi: 10.1210/mend.9.8.7476980. [DOI] [PubMed] [Google Scholar]
  21. Niedenthal R. K., Sen-Gupta M., Wilmen A., Hegemann J. H. Cpf1 protein induced bending of yeast centromere DNA element I. Nucleic Acids Res. 1993 Oct 11;21(20):4726–4733. doi: 10.1093/nar/21.20.4726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ribeiro R. C., Kushner P. J., Apriletti J. W., West B. L., Baxter J. D. Thyroid hormone alters in vitro DNA binding of monomers and dimers of thyroid hormone receptors. Mol Endocrinol. 1992 Jul;6(7):1142–1152. doi: 10.1210/mend.6.7.1508227. [DOI] [PubMed] [Google Scholar]
  23. Shapiro D. J., Sharp P. A., Wahli W. W., Keller M. J. A high-efficiency HeLa cell nuclear transcription extract. DNA. 1988 Jan-Feb;7(1):47–55. doi: 10.1089/dna.1988.7.47. [DOI] [PubMed] [Google Scholar]
  24. Sharrocks A. D., Shore P. DNA bending in the ternary nucleoprotein complex at the c-fos promoter. Nucleic Acids Res. 1995 Jul 11;23(13):2442–2449. doi: 10.1093/nar/23.13.2442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sheridan P. L., Sheline C. T., Cannon K., Voz M. L., Pazin M. J., Kadonaga J. T., Jones K. A. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. Genes Dev. 1995 Sep 1;9(17):2090–2104. doi: 10.1101/gad.9.17.2090. [DOI] [PubMed] [Google Scholar]
  26. Shulemovich K., Dimaculangan D. D., Katz D., Lazar M. A. DNA bending by thyroid hormone receptor: influence of half-site spacing and RXR. Nucleic Acids Res. 1995 Mar 11;23(5):811–818. doi: 10.1093/nar/23.5.811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Smith D. L., Desai A. B., Johnson A. D. DNA bending by the a1 and alpha 2 homeodomain proteins from yeast. Nucleic Acids Res. 1995 Apr 11;23(7):1239–1243. doi: 10.1093/nar/23.7.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  29. Thanos D., Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell. 1995 Dec 29;83(7):1091–1100. doi: 10.1016/0092-8674(95)90136-1. [DOI] [PubMed] [Google Scholar]
  30. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. doi: 10.1093/nar/16.20.9687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wahlström G. M., Sjöberg M., Andersson M., Nordström K., Vennström B. Binding characteristics of the thyroid hormone receptor homo- and heterodimers to consensus AGGTCA repeat motifs. Mol Endocrinol. 1992 Jul;6(7):1013–1022. doi: 10.1210/mend.6.7.1324417. [DOI] [PubMed] [Google Scholar]
  32. Yen P. M., Brubaker J. H., Apriletti J. W., Baxter J. D., Chin W. W. Roles of 3,5,3'-triiodothyronine and deoxyribonucleic acid binding on thyroid hormone receptor complex formation. Endocrinology. 1994 Mar;134(3):1075–1081. doi: 10.1210/endo.134.3.8119145. [DOI] [PubMed] [Google Scholar]

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