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. 1997 Sep 15;25(18):3621–3628. doi: 10.1093/nar/25.18.3621

The transcriptional activation and repression domains of RFX1, a context-dependent regulator, can mutually neutralize their activities.

Y Katan 1, R Agami 1, Y Shaul 1
PMCID: PMC146931  PMID: 9278482

Abstract

EP is a DNA element found in regulatory regions of viral and cellular genes. While being a key functional element in viral enhancers, EP has no intrinsic enhancer activity but can stimulate or silence transcription in a context-dependent manner. The EP element is bound by RFX1, which belongs to a novel, evolutionarily conserved protein family. In an attempt to decipher the mechanism by which EP regulates transcription, the intrinsic transcriptional activity of RFX1 was investigated. A functional dissection of RFX1, by analysis of deletion mutants and chimeric proteins, identified several regions with independent transcriptional activity. An activation domain containing a glutamine-rich region is found in the N-terminal half of RFX1, while a region with repressor activity overlaps the C-terminal dimerization domain. In RFX1 these activities were mutually neutralized, producing a nearly inactive transcription factor. This neutralization effect was reproduced by fusing RFX1 sequences to a heterologous DNA-binding domain. We propose that relief of self-neutralization may allow RFX1 to act as a dual-function regulator via its activation and repression domains, accounting for the context-dependent activity of EP.

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Selected References

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  1. Baniahmad A., Ha I., Reinberg D., Tsai S., Tsai M. J., O'Malley B. W. Interaction of human thyroid hormone receptor beta with transcription factor TFIIB may mediate target gene derepression and activation by thyroid hormone. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8832–8836. doi: 10.1073/pnas.90.19.8832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bauknecht T., Jundt F., Herr I., Oehler T., Delius H., Shi Y., Angel P., Zur Hausen H. A switch region determines the cell type-specific positive or negative action of YY1 on the activity of the human papillomavirus type 18 promoter. J Virol. 1995 Jan;69(1):1–12. doi: 10.1128/jvi.69.1.1-12.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ben-Levy R., Faktor O., Berger I., Shaul Y. Cellular factors that interact with the hepatitis B virus enhancer. Mol Cell Biol. 1989 Apr;9(4):1804–1809. doi: 10.1128/mcb.9.4.1804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blake M., Niklinski J., Zajac-Kaye M. Interactions of the transcription factors MIBP1 and RFX1 with the EP element of the hepatitis B virus enhancer. J Virol. 1996 Sep;70(9):6060–6066. doi: 10.1128/jvi.70.9.6060-6066.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bolwig G. M., Hearing P. Interaction of nuclear factor EF-1A with the polyomavirus enhancer region. J Virol. 1991 Apr;65(4):1884–1892. doi: 10.1128/jvi.65.4.1884-1892.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Buckwold V. E., Chen M., Ou J. H. Interaction of transcription factors RFX1 and MIBP1 with the gamma motif of the negative regulatory element of the hepatitis B virus core promoter. Virology. 1997 Jan 20;227(2):515–518. doi: 10.1006/viro.1996.8360. [DOI] [PubMed] [Google Scholar]
  7. Bushmeyer S., Park K., Atchison M. L. Characterization of functional domains within the multifunctional transcription factor, YY1. J Biol Chem. 1995 Dec 15;270(50):30213–30220. doi: 10.1074/jbc.270.50.30213. [DOI] [PubMed] [Google Scholar]
  8. Chasman D. I., Leatherwood J., Carey M., Ptashne M., Kornberg R. D. Activation of yeast polymerase II transcription by herpesvirus VP16 and GAL4 derivatives in vitro. Mol Cell Biol. 1989 Nov;9(11):4746–4749. doi: 10.1128/mcb.9.11.4746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. David E., Garcia A. D., Hearing P. Interaction of EF-C/RFX-1 with the inverted repeat of viral enhancer regions is required for transactivation. J Biol Chem. 1995 Apr 7;270(14):8353–8360. doi: 10.1074/jbc.270.14.8353. [DOI] [PubMed] [Google Scholar]
  10. Deng T., Karin M. JunB differs from c-Jun in its DNA-binding and dimerization domains, and represses c-Jun by formation of inactive heterodimers. Genes Dev. 1993 Mar;7(3):479–490. doi: 10.1101/gad.7.3.479. [DOI] [PubMed] [Google Scholar]
  11. Dikstein R., Agami R., Heffetz D., Shaul Y. p140/c-Abl that binds DNA is preferentially phosphorylated at tyrosine residues. Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2387–2391. doi: 10.1073/pnas.93.6.2387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dikstein R., Faktor O., Ben-Levy R., Shaul Y. Functional organization of the hepatitis B virus enhancer. Mol Cell Biol. 1990 Jul;10(7):3683–3689. doi: 10.1128/mcb.10.7.3683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dikstein R., Heffetz D., Ben-Neriah Y., Shaul Y. c-abl has a sequence-specific enhancer binding activity. Cell. 1992 May 29;69(5):751–757. doi: 10.1016/0092-8674(92)90287-m. [DOI] [PubMed] [Google Scholar]
  14. Du W., Thanos D., Maniatis T. Mechanisms of transcriptional synergism between distinct virus-inducible enhancer elements. Cell. 1993 Sep 10;74(5):887–898. doi: 10.1016/0092-8674(93)90468-6. [DOI] [PubMed] [Google Scholar]
  15. Emery P., Durand B., Mach B., Reith W. RFX proteins, a novel family of DNA binding proteins conserved in the eukaryotic kingdom. Nucleic Acids Res. 1996 Mar 1;24(5):803–807. doi: 10.1093/nar/24.5.803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Garcia A. D., Ostapchuk P., Hearing P. Functional interaction of nuclear factors EF-C, HNF-4, and RXR alpha with hepatitis B virus enhancer I. J Virol. 1993 Jul;67(7):3940–3950. doi: 10.1128/jvi.67.7.3940-3950.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Garcia A. D., Ostapchuk P., Hearing P. Methylation-dependent and -independent DNA binding of nuclear factor EF-C. Virology. 1991 Jun;182(2):857–860. doi: 10.1016/0042-6822(91)90629-p. [DOI] [PubMed] [Google Scholar]
  18. Haviv I., Vaizel D., Shaul Y. The X protein of hepatitis B virus coactivates potent activation domains. Mol Cell Biol. 1995 Feb;15(2):1079–1085. doi: 10.1128/mcb.15.2.1079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Honigwachs J., Faktor O., Dikstein R., Shaul Y., Laub O. Liver-specific expression of hepatitis B virus is determined by the combined action of the core gene promoter and the enhancer. J Virol. 1989 Feb;63(2):919–924. doi: 10.1128/jvi.63.2.919-924.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ip Y. T. Transcriptional regulation. Converting an activator into a repressor. Curr Biol. 1995 Jan 1;5(1):1–3. doi: 10.1016/s0960-9822(95)00001-7. [DOI] [PubMed] [Google Scholar]
  21. Kouskoff V., Mantovani R. M., Candéias S. M., Dorn A., Staub A., Lisowska-Grospierre B., Griscelli C., Benoist C. O., Mathis D. J. NF-X, a transcription factor implicated in MHC class II gene regulation. J Immunol. 1991 May 1;146(9):3197–3204. [PubMed] [Google Scholar]
  22. Kurokawa R., Söderström M., Hörlein A., Halachmi S., Brown M., Rosenfeld M. G., Glass C. K. Polarity-specific activities of retinoic acid receptors determined by a co-repressor. Nature. 1995 Oct 5;377(6548):451–454. doi: 10.1038/377451a0. [DOI] [PubMed] [Google Scholar]
  23. Labrie C., Lee B. H., Mathews M. B. Transcription factors RFX1/EF-C and ATF-1 associate with the adenovirus E1A-responsive element of the human proliferating cell nuclear antigen promoter. Nucleic Acids Res. 1995 Sep 25;23(18):3732–3741. doi: 10.1093/nar/23.18.3732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lehming N., Thanos D., Brickman J. M., Ma J., Maniatis T., Ptashne M. An HMG-like protein that can switch a transcriptional activator to a repressor. Nature. 1994 Sep 8;371(6493):175–179. doi: 10.1038/371175a0. [DOI] [PubMed] [Google Scholar]
  25. Licht J. D., Grossel M. J., Figge J., Hansen U. M. Drosophila Krüppel protein is a transcriptional repressor. Nature. 1990 Jul 5;346(6279):76–79. doi: 10.1038/346076a0. [DOI] [PubMed] [Google Scholar]
  26. Maheswaran S., Park S., Bernard A., Morris J. F., Rauscher F. J., 3rd, Hill D. E., Haber D. A. Physical and functional interaction between WT1 and p53 proteins. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5100–5104. doi: 10.1073/pnas.90.11.5100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Ostapchuk P., Diffley J. F., Bruder J. T., Stillman B., Levine A. J., Hearing P. Interaction of a nuclear factor with the polyomavirus enhancer region. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8550–8554. doi: 10.1073/pnas.83.22.8550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ostapchuk P., Scheirle G., Hearing P. Binding of nuclear factor EF-C to a functional domain of the hepatitis B virus enhancer region. Mol Cell Biol. 1989 Jul;9(7):2787–2797. doi: 10.1128/mcb.9.7.2787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ptashne M. How eukaryotic transcriptional activators work. Nature. 1988 Oct 20;335(6192):683–689. doi: 10.1038/335683a0. [DOI] [PubMed] [Google Scholar]
  30. Reinhold W., Emens L., Itkes A., Blake M., Ichinose I., Zajac-Kaye M. The myc intron-binding polypeptide associates with RFX1 in vivo and binds to the major histocompatibility complex class II promoter region, to the hepatitis B virus enhancer, and to regulatory regions of several distinct viral genes. Mol Cell Biol. 1995 Jun;15(6):3041–3048. doi: 10.1128/mcb.15.6.3041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Reith W., Barras E., Satola S., Kobr M., Reinhart D., Sanchez C. H., Mach B. Cloning of the major histocompatibility complex class II promoter binding protein affected in a hereditary defect in class II gene regulation. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4200–4204. doi: 10.1073/pnas.86.11.4200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Reith W., Herrero-Sanchez C., Kobr M., Silacci P., Berte C., Barras E., Fey S., Mach B. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. Genes Dev. 1990 Sep;4(9):1528–1540. doi: 10.1101/gad.4.9.1528. [DOI] [PubMed] [Google Scholar]
  33. Reith W., Kobr M., Emery P., Durand B., Siegrist C. A., Mach B. Cooperative binding between factors RFX and X2bp to the X and X2 boxes of MHC class II promoters. J Biol Chem. 1994 Aug 5;269(31):20020–20025. [PubMed] [Google Scholar]
  34. Reith W., Siegrist C. A., Durand B., Barras E., Mach B. Function of major histocompatibility complex class II promoters requires cooperative binding between factors RFX and NF-Y. Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):554–558. doi: 10.1073/pnas.91.2.554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Reith W., Ucla C., Barras E., Gaud A., Durand B., Herrero-Sanchez C., Kobr M., Mach B. RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol. 1994 Feb;14(2):1230–1244. doi: 10.1128/mcb.14.2.1230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Riley J. L., Boss J. M. Class II MHC transcriptional mutants are defective in higher order complex formation. J Immunol. 1993 Dec 15;151(12):6942–6953. [PubMed] [Google Scholar]
  37. Sauer F., Fondell J. D., Ohkuma Y., Roeder R. G., Jäckle H. Control of transcription by Krüppel through interactions with TFIIB and TFIIE beta. Nature. 1995 May 11;375(6527):162–164. doi: 10.1038/375162a0. [DOI] [PubMed] [Google Scholar]
  38. Sauer F., Jäckle H. Concentration-dependent transcriptional activation or repression by Krüppel from a single binding site. Nature. 1991 Oct 10;353(6344):563–566. doi: 10.1038/353563a0. [DOI] [PubMed] [Google Scholar]
  39. Sauer F., Jäckle H. Dimerization and the control of transcription by Krüppel. Nature. 1993 Jul 29;364(6436):454–457. doi: 10.1038/364454a0. [DOI] [PubMed] [Google Scholar]
  40. Shi Y., Seto E., Chang L. S., Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18;67(2):377–388. doi: 10.1016/0092-8674(91)90189-6. [DOI] [PubMed] [Google Scholar]
  41. Siegrist C. A., Durand B., Emery P., David E., Hearing P., Mach B., Reith W. RFX1 is identical to enhancer factor C and functions as a transactivator of the hepatitis B virus enhancer. Mol Cell Biol. 1993 Oct;13(10):6375–6384. doi: 10.1128/mcb.13.10.6375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Siegrist C. A., Mach B. Antisense oligonucleotides specific for regulatory factor RFX-1 inhibit inducible but not constitutive expression of all major histocompatibility complex class II genes. Eur J Immunol. 1993 Nov;23(11):2903–2908. doi: 10.1002/eji.1830231126. [DOI] [PubMed] [Google Scholar]
  43. Steimle V., Durand B., Barras E., Zufferey M., Hadam M. R., Mach B., Reith W. A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome). Genes Dev. 1995 May 1;9(9):1021–1032. doi: 10.1101/gad.9.9.1021. [DOI] [PubMed] [Google Scholar]
  44. Sáfrány G., Perry R. P. The relative contributions of various transcription factors to the overall promoter strength of the mouse ribosomal protein L30 gene. Eur J Biochem. 1995 Jun 15;230(3):1066–1072. doi: 10.1111/j.1432-1033.1995.tb20657.x. [DOI] [PubMed] [Google Scholar]
  45. Sáfrány G., Perry R. P. Transcription factor RFX1 helps control the promoter of the mouse ribosomal protein-encoding gene rpL30 by binding to its alpha element. Gene. 1993 Oct 15;132(2):279–283. doi: 10.1016/0378-1119(93)90208-k. [DOI] [PubMed] [Google Scholar]
  46. Tjian R., Maniatis T. Transcriptional activation: a complex puzzle with few easy pieces. Cell. 1994 Apr 8;77(1):5–8. doi: 10.1016/0092-8674(94)90227-5. [DOI] [PubMed] [Google Scholar]
  47. Treitel M. A., Carlson M. Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3132–3136. doi: 10.1073/pnas.92.8.3132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Tsang S. Y., Nakanishi M., Peterlin B. M. B-cell-specific and interferon-gamma-inducible regulation of the HLA-DR alpha gene. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8598–8602. doi: 10.1073/pnas.85.22.8598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Tsang S. Y., Nakanishi M., Peterlin B. M. Mutational analysis of the DRA promoter: cis-acting sequences and trans-acting factors. Mol Cell Biol. 1990 Feb;10(2):711–719. doi: 10.1128/mcb.10.2.711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Wang Z. Y., Qiu Q. Q., Deuel T. F. The Wilms' tumor gene product WT1 activates or suppresses transcription through separate functional domains. J Biol Chem. 1993 May 5;268(13):9172–9175. [PubMed] [Google Scholar]
  51. Wang Z. Y., Qiu Q. Q., Gurrieri M., Huang J., Deuel T. F. WT1, the Wilms' tumor suppressor gene product, represses transcription through an interactive nuclear protein. Oncogene. 1995 Mar 16;10(6):1243–1247. [PubMed] [Google Scholar]
  52. Weisinger G., Remmers E. F., Hearing P., Marcu K. B. Multiple negative elements upstream of the murine c-myc gene share nuclear factor binding sites with SV40 and polyoma enhancers. Oncogene. 1988 Dec;3(6):635–646. [PubMed] [Google Scholar]
  53. Wolffe A. P. Transcription: in tune with the histones. Cell. 1994 Apr 8;77(1):13–16. doi: 10.1016/0092-8674(94)90229-1. [DOI] [PubMed] [Google Scholar]
  54. Wu S. Y., McLeod M. The sak1+ gene of Schizosaccharomyces pombe encodes an RFX family DNA-binding protein that positively regulates cyclic AMP-dependent protein kinase-mediated exit from the mitotic cell cycle. Mol Cell Biol. 1995 Mar;15(3):1479–1488. doi: 10.1128/mcb.15.3.1479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Yu B. W., Ichinose I., Bonham M. A., Zajac-Kaye M. Somatic mutations in c-myc intron I cluster in discrete domains that define protein binding sequences. J Biol Chem. 1993 Sep 15;268(26):19586–19592. [PubMed] [Google Scholar]
  56. Zajac-Kaye M., Gelmann E. P., Levens D. A point mutation in the c-myc locus of a Burkitt lymphoma abolishes binding of a nuclear protein. Science. 1988 Jun 24;240(4860):1776–1780. doi: 10.1126/science.2454510. [DOI] [PubMed] [Google Scholar]
  57. Zhang X. Y., Asiedu C. K., Supakar P. C., Khan R., Ehrlich K. C., Ehrlich M. Binding sites in mammalian genes and viral gene regulatory regions recognized by methylated DNA-binding protein. Nucleic Acids Res. 1990 Nov 11;18(21):6253–6260. doi: 10.1093/nar/18.21.6253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zhang X. Y., Jabrane-Ferrat N., Asiedu C. K., Samac S., Peterlin B. M., Ehrlich M. The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein. Mol Cell Biol. 1993 Nov;13(11):6810–6818. doi: 10.1128/mcb.13.11.6810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Zhang X. Y., Supakar P. C., Wu K. Z., Ehrlich K. C., Ehrlich M. An MDBP site in the first intron of the human c-myc gene. Cancer Res. 1990 Nov 1;50(21):6865–6869. [PubMed] [Google Scholar]

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