Biopolym. Cell. 1998; 14(3):223-230.
http://dx.doi.org/10.7124/bc.0004D1
Genome and Its Regulation
Regulation of the type I interferon genes and interferon-inducible genes. 1. Organization of the promoter regulatory sequences
1Karpov A. V.
  1. D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
    154, Academika Zabolotnogo Str., Kyiv, Ukraine, 03680

Abstract

A review of information concerning the regulatory motifs in the genes coding the 1 type interferons (α- and β-lFNs) and IFN-inducibie genes is presented. The structural properties of the domains realizing both positive and negative expression regulation of these genes as well as the functional peculiarity of such sequences in heterologous promoter structures have been described. Taking into account the novel data the significance of regulatory sequences conformation above and in transcriptional complexes for the effectivity of the interferon genes expression is emphasized
Full text: (PDF, in Ukrainian)

References

[1] De Maeyer E, De Maeyer-Guignard J. Interferons and other regulatory cytokines. New York: John Wiley and Sons, 1988: 24-28.
[2] Staeheli P. Interferon-induced proteins and the antiviral state. Adv Virus Res. 1990;38:147-200.
[3] Hauptmann R, Swetly P. A novel class of human type I interferons. Nucleic Acids Res. 1985;13(13):4739-49.
[4] Roberts RM, Leaman DW, Cross JC. Role of interferons in maternal recognition of pregnancy in ruminants. Proc Soc Exp Biol Med. 1992;200(1):7-18.
[5] Maniatis T, Goodbourn S, Fischer JA. Regulation of inducible and tissue-specific gene expression. Science. 1987;236(4806):1237-45.
[6] Taniguchi T. Regulation of cytokine gene expression. Annu Rev Immunol. 1988;6:439-64.
[7] Wingender E. Gene expression in eukaryotes. Weinheim: VCH, 1993. 430 p.
[8] Kel OV, Romaschenko AG, Kel AE, Wingender E, Kolchanov NA. A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res. 1995;23(20):4097-103.
[9] Hernandez-Munain C, Krangel MS. c-Myb and core-binding factor/PEBP2 display functional synergy but bind independently to adjacent sites in the T-cell receptor delta enhancer. Mol Cell Biol. 1995;15(6):3090-9.
[10] Pongubala JM, Nagulapalli S, Klemsz MJ, McKercher SR, Maki RA, Atchison ML. PU.1 recruits a second nuclear factor to a site important for immunoglobulin kappa 3' enhancer activity. Mol Cell Biol. 1992;12(1):368-78.
[11] Goodbourn S, Zinn K, Maniatis T. Human beta-interferon gene expression is regulated by an inducible enhancer element. Cell. 1985;41(2):509-20.
[12] Whittemore LA, Maniatis T. Postinduction turnoff of beta-interferon gene expression. Mol Cell Biol. 1990;10(4):1329-37.
[13] Fujita T, Ohno S, Yasumitsu H, Taniguchi T. Delimitation and properties of DNA sequences required for the regulated expression of human interferon-beta gene. Cell. 1985;41(2):489-96.
[14] Goodbourn S, Burstein H, Maniatis T. The human beta-interferon gene enhancer is under negative control. Cell. 1986;45(4):601-10.
[15] Clark AR, Docherty K. Negative regulation of transcription in eukaryotes. Biochem J. 1993;296 ( Pt 3):521-41.
[16] Nourbakhsh M, Hoffmann K, Hauser H. Interferon-beta promoters contain a DNA element that acts as a position-independent silencer on the NF-kappa B site. EMBO J. 1993;12(2):451-9.
[17] Maniatis T, Wkittemore LA, Du W, Fan CM. et al. Transcriptional regulation. Ed. S. McKnight, K. Yamamoto. New York: Cold Spring Harbor Lab. press, 1992: 1193-220.
[18] Fujita T, Shibuya H, Hotta H, Yamanishi K, Taniguchi T. Interferon-beta gene regulation: tandemly repeated sequences of a synthetic 6 bp oligomer function as a virus-inducible enhancer. Cell. 1987;49(3):357-67.
[19] Goodbourn S, Maniatis T. Overlapping positive and negative regulatory domains of the human beta-interferon gene. Proc Natl Acad Sci U S A. 1988;85(5):1447-51.
[20] Keller AD, Maniatis T. Identification of an inducible factor that binds to a positive regulatory element of the human beta-interferon gene. Proc Natl Acad Sci U S A. 1988;85(10):3309-13.
[21] Kuhl D, de la Fuente J, Chaturvedi M, Parimoo S, Ryals J, Meyer F, Weissmann C. Reversible silencing of enhancers by sequences derived from the human IFN-alpha promoter. Cell. 1987;50(7):1057-69.
[22] Fan CM, Maniatis T. Two different virus-inducible elements are required for human beta-interferon gene regulation. EMBO J. 1989;8(1):101-10.
[23] Taniguchi T. Regulation of cytokine gene expression. Annu Rev Immunol. 1988;6:439-64.
[24] Fujita T, Kimura Y, Miyamoto M, Barsoumian EL, Taniguchi T. Induction of endogenous IFN-alpha and IFN-beta genes by a regulatory transcription factor, IRF-1. Nature. 1989;337(6204):270-2.
[25] Visvanathan KV, Goodbourn S. Double-stranded RNA activates binding of NF-kappa B to an inducible element in the human beta-interferon promoter. EMBO J. 1989;8(4):1129-38.
[26] Lenardo MJ, Baltimore D. NF-kappa B: a pleiotropic mediator of inducible and tissue-specific gene control. Cell. 1989;58(2):227-9.
[27] Leblanc JF, Cohen L, Rodrigues M, Hiscott J. Synergism between distinct enhanson domains in viral induction of the human beta interferon gene. Mol Cell Biol. 1990;10(8):3987-93.
[28] Zinn K, DiMaio D, Maniatis T. Identification of two distinct regulatory regions adjacent to the human beta-interferon gene. Cell. 1983;34(3):865-79.
[29] Du W, Maniatis T. An ATF/CREB binding site is required for virus induction of the human interferon beta gene. Proc Natl Acad Sci U S A. 1992;89(6):2150-4.
[30] Zinn K, Maniatis T. Detection of factors that interact with the human beta-interferon regulatory region in vivo by DNAase I footprinting. Cell. 1986;45(4):611-8.
[31] Brawerman G. mRNA decay: finding the right targets. Cell. 1989;57(1):9-10. Review.
[32] Ryals J, Dierks P, Ragg H, Weissmann C. A 46-nucleotide promoter segment from an IFN-alpha gene renders an unrelated promoter inducible by virus. Cell. 1985;41(2):497-507.
[33] Miyamoto M, Fujita T, Kimura Y, Maruyama M, Harada H, Sudo Y, Miyata T, Taniguchi T. Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-beta gene regulatory elements. Cell. 1988;54(6):903-13.
[34] Harada H, Willison K, Sakakibara J, Miyamoto M, Fujita T, Taniguchi T. Absence of the type I IFN system in EC cells: transcriptional activator (IRF-1) and repressor (IRF-2) genes are developmentally regulated. Cell. 1990;63(2):303-12.
[35] Reis LF, Harada H, Wolchok JD, Taniguchi T, Vilcek J. Critical role of a common transcription factor, IRF-1, in the regulation of IFN-beta and IFN-inducible genes. EMBO J. 1992;11(1):185-93.
[36] MacDonald NJ, Kuhl D, Maguire D, N?f D, Gallant P, Goswamy A, Hug H, B?eler H, Chaturvedi M, de la Fuente J, et al. Different pathways mediate virus inducibility of the human IFN-alpha 1 and IFN-beta genes. Cell. 1990;60(5):767-79.
[37] Au WC, Raj NB, Pine R, Pitha PM. Distinct activation of murine interferon-alpha promoter region by IRF-1/ISFG-2 and virus infection. Nucleic Acids Res. 1992;20(11):2877-84.
[38] Au WC, Su Y, Raj NB, Pitha PM. Virus-mediated induction of interferon A gene requires cooperation between multiple binding factors in the interferon alpha promoter region. J Biol Chem. 1993;268(32):24032-40.
[39] Kelley KA, Pitha PM. Characterization of a mouse interferon gene locus II. Differential expression of alpha-interferon genes. Nucleic Acids Res. 1985;13(3):825-39.
[40] Megyeri K, Au WC, Rosztoczy I, Raj NB, Miller RL, Tomai MA, Pitha PM. Stimulation of interferon and cytokine gene expression by imiquimod and stimulation by Sendai virus utilize similar signal transduction pathways. Mol Cell Biol. 1995;15(4):2207-18.
[41] Bisat F, Raj NB, Pitha PM. Differential and cell type specific expression of murine alpha-interferon genes is regulated on the transcriptional level. Nucleic Acids Res. 1988;16(13):6067-83.
[42] Raj NB, Israeli R, Kellum M, Pitha PM. Upstream regulatory elements of murine alpha 4-interferon gene confer inducibility and cell type-restricted expression. J Biol Chem. 1989;264(19):11149-57.
[43] Nabel G, Baltimore D. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature. 1987 Apr 16-22;326(6114):711-3.
[44] Schirm S, Jiricny J, Schaffner W. The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity. Genes Dev. 1987;1(1):65-74.
[45] Raj NB, Au WC, Pitha PM. Identification of a novel virus-responsive sequence in the promoter of murine interferon-alpha genes. J Biol Chem. 1991;266(17):11360-5.
[46] Coulombel C, Vodjdani G, Doly J. Isolation and characterization of a novel interferon-alpha-encoding gene, IFN-alpha 11, within a murine IFN cluster. Gene. 1991;104(2):187-95.
[47] Dion M, Vodjdani G, Doly J. Sequence and expression of a novel murine interferon alpha gene--homology with enhancer elements in the regulatory region of the gene. Biochem Biophys Res Commun. 1986;138(2):826-34.
[48] Navarro S, Dion M, Vodjdani G, Berlot-Picard F, Doly J. Isolation and characterization of a functional murine interferon alpha gene which is not expressed in fibroblasts upon virus induction. J Gen Virol. 1989;70 ( Pt 6):1381-9.
[49] Harada H, Takahashi E, Itoh S, Harada K, Hori TA, Taniguchi T. Structure and regulation of the human interferon regulatory factor 1 (IRF-1) and IRF-2 genes: implications for a gene network in the interferon system. Mol Cell Biol. 1994;14(2):1500-9.
[50] Wathelet MG, Berr PM, Huez GA. Regulation of gene expression by cytokines and virus in human cells lacking the type-I interferon locus. Eur J Biochem. 1992;206(3):901-10.
[51] Reich N, Evans B, Levy D, Fahey D, Knight E Jr, Darnell JE Jr. Interferon-induced transcription of a gene encoding a 15-kDa protein depends on an upstream enhancer element. Proc Natl Acad Sci U S A. 1987;84(18):6394-8.
[52] Reid LE, Brasnett AH, Gilbert CS, Porter AC, Gewert DR, Stark GR, Kerr IM. A single DNA response element can confer inducibility by both alpha- and gamma-interferons. Proc Natl Acad Sci U S A. 1989;86(3):840-4.
[53] Raj NB, Engelhardt J, Au WC, Levy DE, Pitha PM. Virus infection and interferon can activate gene expression through a single synthetic element, but endogenous genes show distinct regulation. J Biol Chem. 1989;264(28):16658-66.
[54] Ponomarenko MP, Ponomarenko IuV, Kel' AE, Kolchanov NA, Karas H, Wingender E, Sklenar H. Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors. Mol Biol (Mosk). 1997;31(4):733-40.
[55] Thanos D, Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell. 1995;83(7):1091-100.
[56] Nissen MS, Reeves R. Changes in superhelicity are introduced into closed circular DNA by binding of high mobility group protein I/Y. J Biol Chem. 1995;270(9):4355-60.
[57] Falvo JV, 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;83(7):1101-11.