- Email: [email protected]
Regulation of virus-induced interferon-A genes
Biochimie 84 (2002) 643–654
Regulation of virus-induced interferon-A genes Ahmet Civas *, Marie-Laure Island, Pierre Génin, Pierre Morin, Sébastien Navarro UPR 2228, CNRS, Laboratoire de régulation transcriptionnelle et maladies génétiques, UFR biomédicale des Saints-Pères, Université Paris V, 45, rue des Saints-Pères, 75270 Paris cedex 6, France Received 26 February 2002; accepted 31 May 2002
Abstract Different members of the interferon regulatory factor (IRF) family are early activated by viral infection of eukaryotic cells. The IRFs participate in the virus-induced transcriptional regulation of different genes, including the multigenic interferon-A (IFN-A) family, members of which are involved in the establishment of an antiviral state, cell growth inhibition or apoptosis. This study presents the recent progress in the field of virus-induced transactivation and repression of IFN-A gene promoters. Data presented on the modular organization of IFN-A gene promoters and their transactivation dependent on IRF-3 and IRF-7 provide a new insight on the cooperativity mechanisms among the different IRF family members. Data on the transcriptional repression of virus-induced interferon-A promoters by the homeodomain protein Pitx1 contribute to our understanding of the complex differential transcriptional activation, repression and antirepression of the IFN-A genes. © 2002 Société française de biochimie et biologie moléculaire / Éditions scientifiques et médicales Elsevier SAS. All rights reserved. Keywords: Interferon A; Interferon regulatory factor; Transactivation/activation; Pitx1; Repression
1. Introduction Viral infection of eukaryotic cells causes the early activation of different transcription factors including different members of the Rel, Jun, ATF, and IRF families. Among these factors, the interferon regulatory factors (IRF-1 to IRF-10) play an important role in the stimulation of cellular antiviral defence mechanisms in different cell types. The activation of constitutively expressed IRFs in the course of virus infection by phosphorylation or other posttranslational modifications such as acetylation, as well as the virus-induced or interferon-stimulated expression of other IRFs constitute crucial steps in the transactivation of target genes [1]. For instance, the IRFs participate in the virus-induced transcriptional regulation of type I IFN genes encoding different interferon-α and interferon-β [2–5]. They also regulate the expression of other cytokines or chemokines (IL-18, RANTES, IP-10, MCP-1) and a group of IFN-stimulated genes (ISG) activated either by virus or IFN (Mx, PKR, OAS, iNOS, ISG-15). The products of these
genes participate in the formation of innate or adaptive immune responses against virus infections. The IRFs also mediate cell growth inhibition or apoptosis in virus-infected cells [6,7]. The individual role of IRFs in the immune antiviral response is enlightened by gene targeting studies that also revealed their complementary rather than redundant functions in the regulation of target gene expression and host defence [8,9]. This feature is well documented in the case of IRF-3 and IRF-7 which are described as potent activators of virus-induced type I IFN and ISG transcription. This study presents the recent progress in the field of virus-induced transactivation and repression of IFN-A gene promoters and on the distinctive roles of IRF-3 and IRF-7 in virus-induced regulation of transcription. We will focus on the interactions of IRF-3 and IRF-7 with the IFN-A promoters that account for their differential expression in different cell types. We also present data on the transcriptional repression of the virus-induced interferon-A promoters by the homeodomain protein Pitx1.
* Corresponding author. Tel.: +33-1-42-86-22-84; fax: +33-1-42-86-2042. E-mail address: [email protected] (A. Civas). © 2002 Société française de biochimie et biologie moléculaire / Éditions scientifiques et médicales Elsevier SAS. All rights reserved. PII: S 0 3 0 0 - 9 0 8 4 ( 0 2 ) 0 1 4 3 1 - 1
644
A. Civas et al. / Biochimie 84 (2002) 643–654
2. Common features in the protein structure of IRFs and their DNA-binding IRFs regulate transcription by interacting with gene promoter sequences, termed IRF elements (IRF-E), and formed by direct repeats of GAAANN motifs. IRFs also bind to closely related DNA sequences, denoted as interferon-stimulated response elements (ISRE), found in the promoter of a group of virus-inducible genes transcriptionally amplified by interferon-α/β [10–14]. The highly conserved DNA-binding domain (DBD) of IRFs characterized by a unique helix-turn-helix motif containing conserved tryptophan residues is located in their N-terminal region (a.a. 1–130) [1,15]. In some IRFs, the sequence homology extends to the interaction domain (IAD) that mediates the formation of IRF homo- or heterodimers or the association of IRFs with other factors [16]. The less conserved C-terminal part includes the transactivation domain (TAD), a proline-rich domain, the nuclear export and localization signals (NES and NLS) and the serine/threonine phosphorylation domain (also referred as regulatory or signal response domain) [1]. TAD defines the specificity of each IRF to interact, directly or in association with other factors, with different components of the transcription preinitiation complex and coactivators of transcription such as CBP/p300 or PCAF/GCN5 [11,12,17,18]. Although the role of various domains contained in the C-terminal region is not yet understood, they regulate, at least in some cases, the subcellular localization of IRFs in response to virus infection [19,20] DNA-binding site selection studies have revealed that IRF-1 and IRF-2 bind to promoters carrying the consensus sequence G(A)AAASYGAAASY (S = G/C, Y = T/C). The crystal structure of IRF-1 DBD with a 13 bp IRF-E site provided a basis for GAAA sequences occurring within almost all the IRF response elements [21]. This study showed that the helix-turn-helix motif of DBD latches onto DNA through three of the five conserved tryptophans and interacts with the GAAA core sequence by base contacts with amino acids R82, C83, N86 and S87 in the major groove. Some IRFs have a very weak binding affinity for the sequences formed by GAAANN repeats, and recognize them only when associated with other transcription factors. For instance, IRF-9 recognizes the ISRE-related sequences with high affinity, when associated with Stat1 and Stat2 [22,23]. IRF-4 and IRF-8 form ternary complexes together with PU.1 to recognize composite DNA sequences containing GAAANN repeats associated with Ets binding sites [24,25].
3. Distinctive properties of IRF-3 and IRF-7 in virusinduced gene transcription Extensive studies on subcellular localization of IRF-3 and IRF-7 have revealed their distinctive activation mecha-
nisms in comparison to other IRF family members. In uninfected cells, IRF-3 normally shuttles between the nucleus and the cytoplasm. The cytoplasmic localization is predominant prior to virus infection and depends on NES and NLS sequences interacting with the exportin 1 and a subset of importin-α shuttling receptors, respectively [20]. IRF-3 has also been shown to contain an autoinhibitory domain (AID) located at the C-terminal end (spanning a.a. 380–427). Deletion of AID leads to a constitutively active form of IRF-3 capable to stimulate transcription in the absence of virus infection. Intramolecular interactions occurring between AID and the region spanning a.a. 98–240 maintain IRF-3 in a closed conformation, masking both DBD and IAD, in the cytoplasm of uninfected cells [19]. Virus-induced phosphorylation of a serine/threonine cluster located in the AID leads to a conformational change of IRF-3 that relieves the intramolecular autoinhibition and permits translocation to the nucleus. The NLS mediates the nuclear accumulation of phosphorylated IRF-3 that can bind to the CBP/p300 protein resident in the nucleus, this association preventing IRF-3 export to cytoplasm. Nuclear sequestered IRF-3 can thus form DNA-binding complexes such as VIF, the virus-induced factor which is essentially formed by IRF-3 homodimers, and the dsRNA activated factor (DRAF1) or virus-activated IRF (VA-IRF) formed by IRF-3 and CBP or p300 [12,18,26]. It has also been shown that IRF-3 associates with IRF-7 to form together with CBP and p300 the higher-order DNA-binding complex VAF (virus-activated factor). This complex recognizes with high affinity the ISRE of the ISG-15 gene promoter that is responsive either to IFN or virus [3,11,27]. Serine phosphorylation in the C-terminal regulatory domain is also required for IRF-7 activation by virus infection, even if the IRF-7A or 7B isoforms are constitutively active when overexpressed in human HEK 293 cells. The IRF-7 regulatory domain has also been shown to control the retention of the phosphorylated protein in the nucleus and the ability of IRF-7 to form homodimers or heterodimers with IRF-3 [28,29]. The IAD mapped to the C-terminal part of IRF-7 (a.a. 240–503) has not yet been precisely determined. Transcriptional activation by IRF-7 has been mapped to two distinct regions, both of which were required for full activity, while all the functions were masked in latent IRF-7 by an AID mapping to an internal region. The effect of the potential NLS/NES sequences and the role of the AID located downstream the DBD remain also to be elucidated.
4. Interferon regulatory factors 3 and 7 and the differential IFN-A gene regulation IFN-A genes are represented by a multigenic family of intronless genes clustered in a 400 kb region, containing also the IFN-B gene, on the human chromosome 9 and on chromosome 4 in the mouse [30]. They have been shown to be coordinately induced in human and mouse cells infected
A. Civas et al. / Biochimie 84 (2002) 643–654
by virus and exhibit differences in the expression of their individual mRNAs. Differential expression is shown to be dependent on the transcriptional activity of the corresponding IFN-A gene promoter in a particular cell type. Thus, human IFN-A1, IFN-A2 and IFN-A4 genes are highly expressed in Sendai virus-infected PBMC and lymphoblastoid Namalwa cells, whereas the expression of IFN-A5, IFN-A7, IFN-A8 and IFN-A14 mRNA levels is 5- to 20-fold lower in the same cells [31]. Similarly, in NDVinduced L929 cells, the murine IFN-A4 expression is predominant in comparison to IFN-A2, IFN-A5 and IFNA6, whereas IFN-A1 and IFN-A11 are very weakly expressed [32–34]. Among the multiple IFN-A genes, only human IFN-A1 and murine IFN-A4 genes are expressed without the requirement for ongoing protein synthesis, as in the case of IFN-B gene (Fig. 1). In mouse cells, virus-induced phosphorylation of IRF-3 is considered a key event in the primary activation of IFN-A4 and IFN-B [5,14,35]. Secreted IFN-α4 and IFN-β proteins acting through their common receptor on neighbouring cells activate the Jak-STAT pathway. This activation leads to the transcriptional stimulation of the IRF-7 gene by a positive feedback loop, mediated by the Interferon-Stimulated Gene Factor 3 (ISGF-3) complex [36–39]. According to this multistep induction model (Fig. 1), subsequent activation of IRF-7 protein by C-terminal serine phosphorylation following virus infection results in the induction of a set of delayed IFN-A genes which includes IFN-A2, -A5, -A6, and -A8 genes [5]. IRF-3 knock-out studies have recently confirmed this model, and further indicate that in the late phase of induction, IRF-3 and IRF-7 cooperate with each other to provide the mRNA induction profile of the IFN-A gene family depending on the cell line [8]. The molecular mechanisms that would account for the early transcription of murine IFN-A4 and human IFN-A1 genes among the multiple IFN-A genes and their differential expression after amplification by ISGF3 and IRF-7 have recently been defined better. We have shown that the differential virus-induced expression between the murine IFN-A4 and IFN-A11 genes is in part due to two substitutions in the Virus-Responsive Element of the IFN-A11 promoter which affect two binding sites for the IRF family members [40]. Similarly, two substitutions, at positions –98 and –81 of human IFNA1 and A2 promoter, have been found to be pivotal to the differential expression of these genes [41]. It has also been suggested that the ratio between the relative levels of IRF-3 and IRF-7 could be a critical determinant for the induction of the individual IFN-A subtypes in infected cells [42]. Gene disruption/introduction studies have shown that IRF-3 was critical for both immediate-early and late phases of the IFN-A/B gene induction by virus (Fig. 1). In the late phase, this factor cooperates with IRF-7 to potentiate the overall IFN-A/B mRNA induction and provide the normal mRNA induction profile for IFN-A subspecies [5,8,13,43]. These results
645
indicated that these factors have complementary rather than redundant roles in the activation of IFN-A/B genes. In fact, the biphasic induction mechanism regulated by IRF-3 and IRF-7 ensures the transcriptional activity of IFN-A/B genes and the diversity of the IFN-A genes for efficient antiviral response [5,10,13]. Recently, IRF-5 has been shown to participate in the induction of IFN-A and B genes and suggested to replace the requirement for IRF-7 in the induction of IFN-A genes, at least in lymphoid tissue [44]. This finding and the fact that other IRF family members, such as IRF-1 and IRF-2, also participate in IFN-A/B gene transcription suggest that more complex regulatory mechanisms may be involved in the pattern of the IFN-A gene expression. The individual IFN-A transcript level may depend on the identity of the IRFs as well as on the amount of the activated IRF pool expressed in a specific cell type.
5. Molecular basis of IRF-3 and IRF-7 binding on different IFN-A promoters The maximal NDV-induced transcription of the murine IFN-A4 gene requires the presence of four cooperating IRF-E (modules A to D) that form the virus-responsive element of IFN-A4 (VRE-A4) (Fig. 2): module A, represented by the GTAAAGAAAGT sequence; and B, C and D modules corresponding, respectively, to the GAAAGTGAAAAG, GAATTGGAAAGC, and GAAAGGAGAAACT sequences [40,45]. We have shown that the weak expression of IFN-A11 gene in comparison to IFN-A4 is due to the absence of C and D modules that are disrupted by the –78A/G and –57G/C substitutions (Fig. 2). We have further demonstrated that the transactivation of the murine IFN-A4 gene promoter by IRF-3 or IRF-7 is mediated through different virus-responsive modules. Thus, we have shown that the C module corresponds to a preferential binding site for IRF-3, whereas IRF-7 interacts preferentially with the distal region of VRE-A4 containing the A and B modules [26,46]. Site selection experiments have previously suggested that IRF-3 exhibits a restricted GAAANNGAAANN specificity (GAAASSGAAANY) in comparison to IRF-7 consensus recognition sequence determined as GAAWNYGAAANY [47]. The authors have shown that human IFN-B and IFN-A1 gene promoters were stimulated by IRF-3 coexpression, whereas IFN-A4, A7, and A14 promoters were preferentially induced by IRF-7. The broader DNA-binding specificity of IRF-7 was suggested to contribute to its capacity to stimulate delayed expression of human IFN-A4, A7, and A14 genes. The differential expression of IFN-A genes was then attributed to the broader sequence specificity of IRF-7 in comparison to IRF-3. We have recently shown that the GAAANN motifs contained in different modules of murine IFN-A4 gene promoter also respond differentially to IRF-3 or IRF-7 overexpression. These core sequences can be classified into
646
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 1. Virus-induced activation of mouse IFN-A genes by IRFs. Viral infection of eukaryotic cells causes early and transient expression of various cytokine genes, including type I IFN genes (IFN-A multigenic family and IFN-B gene) and type II IFN (IFN-G). Expression of these IFN genes by different cell types constitutes a crucial step in the stimulation of cellular antiviral defence mechanisms, in the inhibition of cell growth and in the induction of the apoptotic process. Virus-induced phosphorylation (P) and acetylation (Ac) of IRF-3 is considered a key event in the primary activation of IFN-A4 and IFN-B genes. Production of IFN-γ following virus infection can also lead to activation of type I IFN genes through IRF-1 expression. Secreted IFN-α4 and IFN-β proteins acting through type I IFN receptor on neighbouring cells activate the Jak-STAT pathway, resulting in the transcriptional stimulation of the IRF-7 gene by a positive feedback loop, mediated by the Interferon-Stimulated Gene Factor 3 (ISGF-3) complex. According to this multistep induction model, subsequent virus-induced activation of IRF-7 and IRF-1 proteins in cooperation with activated IRF-3 results in the amplification of IFN-A4 and IFN-B gene transcription and in the induction of a set of delayed IFN-A genes which includes mouse IFN-A2, -A5, and -A6 genes.
A. Civas et al. / Biochimie 84 (2002) 643–654
647
Fig. 2. Organization of the murine IFN-A4 and IFN-A11 gene promoters in the [–120 to –26] region. The Virus-Responsive Element (VRE-A4) located in the proximal region of the promoter and the enhancer modules (A to D) are represented according to Bragança et al. [40]. The minimal inducible element corresponds to the [–109 to –75] region defined by Raj et al. [97]. In this region, the weakly inducible IFN-A11 gene promoter differs from the highly inducible IFN-A4 by the nucleotide substitutions –78A/G, –59C/T, –58C/A, –57G/C, –43C/G, –41A/G. Among them, those affecting the virus inducibility of these promoters, thus explaining their differential regulation, are indicated by arrows. The GAAANN repeats contained in different modules are underlined. Numbering is relative to the transcription start of the promoter and the TATA box is indicated.
four groups according to the identity of the NN residues they contain: (i) the first group includes the NC (TC, AC, GC, CC), and ST (GT,CT) residues inducible by both IRF-3 and IRF-7; (ii) the NG (TG, AG, GG, CG) and CA containing motifs preferentially activated by IRF-3; (iii) the GAAAAT repeats responding only to IRF-7; and (iv) the DA (TA, AA, GA) group unresponsive to both factors. In the native IFN-A4 promoter, the second GT residues in the GTAAAGAAAGTGAAAAG sequence of the AB domain and the TG residues of the GAATTGGAAAGC sequence of the C module are critical for IRF-7 and IRF-3 responsiveness, respectively [46]. These results demonstrated that the preferential target sites for IRF-3 and IRF-7 are dictated by specific sets of GAAANN motifs forming the virusinducible modules in the IFN-A gene promoters. This observation allowed us to gain an insight into the molecular basis of IRF-3 and IRF-7 binding on different IFN-A promoter. The expression levels of the IFN-A genes in the early and/or delayed phases following virus infection appear to correlate directly to the integrity of the IRF-3 and IRF-7 binding sites (Fig. 3). For example, in mouse fibroblasts, the induced expression level of IFN-A2 gene is intermediate between the highly expressed IFN-A4 and the weakly inducible IFN-A11 gene. In the IFN-A2 promoter, the –78A/G substitution is also present, together with a –80G/A mutation. Thus, the C module is disrupted in IFN-A2,
suggesting that the delayed expression of IFN-A2 is essentially mediated by IRF-7 rather than by IRF-3. Cooperation between different modules may also be attenuated in other IFN-A gene promoters, including IFN-A5 and IFN-A6 which also belong to the set of delayed type IFN-A genes [32,33]. The promoters of these genes do not contain C and D modules (disrupted by –85G/C and –82T/G substitutions and the –52G/T and –50G/A substitutions, respectively) and thus may be regulated in the delayed phase of the IFN response by IRF-7. Similarly, comparison of the VRE sequences of human IFN-A gene promoters reveals that the GAAATG core sequence corresponding to the C module of the highly inducible Hs-IFN-A1 promoter is substituted by A/G and TG/TA mutations in Hs-IFN-A2, A4, A5, A7 and A14 (Fig. 3). These features may also explain the IRF-3 unresponsiveness of this group of poorly induced and late-expressed IFN-A genes, since we showed the deleterious effect of the substitutions previously mentioned, on IRF-3 mediated transcription. The preferential response of these promoters to IRF-7 may be due to the GAAAGC and GAAAAT motifs present in the B and D modules, respectively. This model may explain the expression profiles of human or mouse IFN-A genes following virus infection in different cell lines [5,42]. DNA pull-down and chromatin precipitation assays performed by another group have shown that the binding of IRF-3 and IRF-7 on the VRE of Hs-IFN-A1 promoter is
648
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 3. Comparison of the [–120 to –26] region of the human and murine IFN-A gene promoters. Nucleotide sequences of the [–120 to –26] region of the human IFN-A2, A4, A5, A7 and A14 [98,99] are presented in alignment with the sequence of human IFN-A1 gene numbered according to the start site of transcription [100]. Nucleotide sequences of the [–120 to –26] region of the murine IFN-A2, A11, A1, A5 and A6 [32,34,101–103] are presented in alignment with the sequence of murine IFN-A4 gene numbered according to the start site of transcription. Identical residues are indicated by dots and hyphens correspond to gaps introduced for better alignment. The consensus sequences (Cons.) present the nucleotide residues conserved among the IFN-A promoters; nucleotides distinguishing these sequences are indicated by stars. The TATA box and the potential modules found in the IFN-A promoters are boxed.
associated with the presence of acetylated histone H3, suggesting that HATs are tethered together with the virusactivated IRFs to the promoter [41]. In these experiments, IRF-7 has been shown to bind also to the Hs-IFN-A2 VRE, whereas the deletion of the guanine residue at position –98 and the –81G/A substitution in this promoter have been shown to affect the recruitment of IRF-3. The preferential binding of IRF-3 to human VRE-A1 is in agreement with the model presented in this study. Interestingly, Hs-IFN-A5 has been reported to be constitutively expressed in lymphoid cells including peripheral blood mononuclear cells from normal individuals and promonocytic U937 cells [48]. Constitutive transactivation of the Hs-IFN-A5 promoter may be due to the predominant expression of IRF-7 in cells of lymphoid origins. The –79G/A substitution in the HsIFN-A5 promoter may affect the recruitment of IRF-3 on the C module, whereas the –52G/A substitution may create a strong preferential binding site for IRF-7 in the D module (Fig. 3). Synergism between the B and D modules mediated
in this case by IRF-7 may thus explain the Hs-IFN-A5 constitutive expression.
6. The distal negative regulatory element in mouse IFN-A promoters A large number of repressors binding to the IFN-B promoter elements have been identified such as the transcriptional co-repressor dorsal switch protein DSP1 [49], the NFjB repressing factor NRF [50], IRF-2 which is able to antagonize activators such as factors of the IRF family by competing for their binding [51] and PRDI-BF1 [52]. Until now, repressors involved in negative regulation of the IFN-A genes are not well characterized. In addition to substitutions in the proximal VRE-A [40,45], we have shown that the repression of the IFN-A11 gene after virus induction is also due to the presence of a distal negative regulatory element of 20 base pairs (Fig. 4),
A. Civas et al. / Biochimie 84 (2002) 643–654
the DNRE, which is delimited upstream of the VRE-A [53,54]. DNRE exerts an inhibitory effect on VRE-A elements after virus induction, independent of its orientation or position, and is, therefore, considered as a silencer. On the other hand, the DNRE on its own has neither any effect on VRE-B promoter after virus induction nor any constitutive repressive effect on heterologous promoters. Therefore, the functional feature of the particular silencer DNRE consists in the fact that its silencing activity is strictly dependent on the presence of a functional VRE-A. DNRE specifically acts via repression of VRE-A positive activity after virus induction and does not function as a general negative regulator. Similar DNREs are present in some IFN-A promoters and the presence or the absence of DNRE may contribute to the differential expression of the IFN-A genes after virus induction. Two DNRE-binding factors have been observed before virus induction of L929 cells and HeLa cells and are still maintained even following induction (Fig. 4A). These results indicate the presence of murine and human constitutive binding proteins involved in the silencing effect. One of the complexes corresponds to a protein related or identical to high mobility group protein (HMG) I(Y) which binds to the minor groove of two AT-rich regions within DNRE. HMG I(Y) does not seem to modulate the binding of a second factor to DNRE. We suggested that this last factor may be considered as a protein which negatively regulates the transcription of IFN-A11 promoter [54].
7. The homeodomain Pitx1 (Pituitary homeobox 1) negatively regulates the transcription of IFN-A promoters The analysis of the distal silencer element DNRE responsible for the virus-induced transcriptional repression of some IFN-A promoters led us to clone by the one-hybrid system and study the homeodomain (HD) transcription factor, Pitx1 [55]. Homeotic genes encode the transcriptional factors that are involved in the positive and negative regulations of target genes during development. These genes contain a highly conserved sequence of 180 bp, the homeobox, which encodes a 60 amino acid residue polypeptide, called HD that represents the DNA-binding domain of these factors. Pitx1 was first described as a transcriptional activator binding the central element 3 (CE3) element of the pituitary proopiomelanocortin (POMC) gene promoter [56]. It activates transcription of other pituitary genes [57–59]. Pitx1 deficient mice studies indicate that hindlimb patterning and mandible and pituitary development require this gene [60,61]. Three members of the Pitx family have been described: the Pitx1 [56] and the Pitx2 [62] genes which are homologous and have an overlapping expression pattern and the Pitx3 gene [63]. Several known transcriptional
649
interaction factors act in synergy with Pitx1: bHLH NeuroD1 for corticotrophe-specific transcription of POMC [64,65], Pit1 to stimulate the expression of the prolactin gene [57,66], SF-1, an orphan nuclear receptor, and Egr-1, an immediate-early response gene which stimulate the expression of the βLH gene [57–59]. Pitx1 C-terminal region is involved in both transcriptional activation and physical interaction with Pit1, SF1 or Egr-1. Recently, a pituitary cell-restricted T box factor, Tpit, has been shown to activate POMC transcription in cooperation with Pitx homeoproteins [67]. We have shown that Pitx1 is detectable in cell types that express IFN-A genes after virus induction and that the recombinant or endogenous Ptx1 protein binds specifically to the DNRE (Fig. 4A). Upon virus induction, Pitx1 negatively regulates the transcription of DNRE-containing IFN-A11 promoter. After virus induction, the expression of the Pitx1 antisense RNA that leads to a significant increase of endogenous IFN-A gene transcription, is able to modify the pattern of differential expression of individual IFN-A genes, and derepresses IFN-A11 and IFN-A5 genes [55]. Most of the researches on eukaryotic gene expression have been focused on the transcriptional activation mechanisms [68]. Although positive control of gene expression is essential, it becomes clear now that the transcriptional repression is at least as important as activation. Indeed, as an inherent feature, those gene systems which are positively regulated may require an inhibition mechanism to account for temporal or spatial expression during development, cell or tissue specificity, modulation of gene expression depending on environmental changes, and rapid expression shutdown after induction [69–74]. In silencing and quenching cases, recent studies on their mechanisms of action suggest that these repressors may be considered as short-range or long-range repressors [75]. Short-range repressors for silencing and quenching interfere with the neighbouring factor and allow modular repression whereas long-range repressors can interfere with the function of several factors and co-factors that are bound kilobase distance away. We propose that Pitx1 can modulate IFN-A gene transcription through an alternative mechanism. Furthermore, in the context of the IFN-A gene promoters, the Pitx1 factor acts as a repressor and its effect is only observed after virus induction on the VRE-A positive activity. Therefore, Pitx1 may be considered as a short-range repressor including silencing activity dependent upon the presence of a functional VRE-A. For silencing and quenching, the repressor contains active repression domains, analogous to the activation domains used by transcription activators and IADs [76]. Pitx1 can modulate differently IFN-A gene and POMC or other pituitary gene expression. The activity of Pitx1 as a positive regulator of the transcription is synergized by cell-restricted transcription factors to confer pituitary-, lineage- and promoter-specific expression (see above). In this context, Pitx1 factor contains multiple positive trans-
650
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 4. Organization of the murine IFN-A11 and -A4 regulatory sequences and factors binding the DNRE. IFN-A11 and IFN-A4 promoter sequences are indicated, the numbering is relative to the transcription start site of the promoter, the TATA box being indicated in each case. Nucleotides distinguishing these sequences are represented by larger characters. Localization of the binding sites for potential transrepressors and transactivators, namely, DNRE, 4DNRE, VRE-A11 and VRE-A4 is indicated. 4D represents an antisilencer region.
regulatory domains and interaction regions. The opposite functions of Pitx1 in the regulation of the transcription of IFN-A promoters may be due to different negative transregulatory domains and interaction regions. Transcription factors able to activate and repress in different circumstances have been documented, and the molecular bases are
quite diverse [77]. For example, transcription factor Kruppel modifies an activator to a repressor [78]. Sp3 is a dual-function regulator. Predominant activity depends upon the number of DNA-binding sites present in the promoter [79]. The transcriptional activity of Ets-1 is modified upon DNA-binding [80].
A. Civas et al. / Biochimie 84 (2002) 643–654
Altogether, these results suggest that Pitx1 is a multifunctional regulator protein able to act as a repressor or as an activator and may be also interact with other proteins, similar to other transcription regulators such as p53, c-fos, SRF, YY1, Oct-2A and activating transcription factor 2 [81–86]. Our studies suggest that Pitx1 contributes to the transcriptional strength of the promoters of IFN-A genes.
8. Relationship between Pitx1 and an antisilencer element Furthermore, we have shown that a DNRE (4DNRE), binding both Pitx1 and HMGI (Y), is also present in the highly inducible IFN-A4 promoter (Fig. 4B) but a central antisilencer region, named 4D, located between the silencer and the VRE-A4 overrides the silencer activity [54,55]. The central antisilencer region does not function as an activator but rather as an inhibitor of the Pitx1 silencer activity in IFN-A4 gene expression. Indeed, the central antisilencer region is able to overcome the Pitx1 silencer activity in the context of the native IFN-A4 promoter. On the contrary, in the absence of the central antisilencer region, the repressing effect of Pitx1 was observed. Protein–protein interactions between silencer and antisilencer as described for the carbamyl phosphate synthetase I promoter has been suggested [87]. Thus, in the context of the native IFN-A4 promoter, we suggested that Pitx1 cannot interact with the factors binding to the VRE4 but may interact with protein(s) binding to the central antisilencer region which may be considered as a molecular trap for Pitx1 maintaining the IFN-A4 gene highly inducible. If a protein is involved for the antisilencer activity, the precise functional relationship between Pitx1 and this factor binding to the antisilencer element remains to be established. The precise action of Pitx1 to block IFN-A11 and IFN-A5, but not IFN-A4 promoter activities, may contribute to our understanding of the complex differential transcriptional activation, repression and antirepression of the IFN-A genes.
9. IRF-3 and IRF-7 in IFN-B gene regulation Among the IRF family members, IRF-1, 2, 3, 5, 7 and 9 have also been implicated in the transcriptional induction of the IFN-B gene. Transcriptional activation in response to virus infection has been particularly studied in the case of the IFN-B gene [88]. The IFN-B gene, present as a single copy in the human and mouse genome, contains within its promoter several regulatory cis-elements, consisting of positive and negative domains. The positive regulatory domains (PRD-I to PRD-IV) constitute a composite virusresponsive element (VRE-B) [89]. The transcriptional activators, NF-jB and ATF-2/c-jun, interact with PRD-II and PRD-IV, respectively, whereas PRD-III and PRD-I form
651
separately or together a binding site(s) for IRF-1, 2, 3, 7 and 9. A recent model concerning the IFN-B transcription consists of the coordinated acetylation of the architectural protein HMGI(Y) interacting with PRD-II and PRD-IV domains [90,91]. The authors have shown that a virusinduced enhanceosome consisting of ATF-2/c-Jun, IRFs, NF-jB and HMGI(Y) is assembled in a nucleosome-free region of the IFN-B promoter. Transcription is then activated by sequential recruitment of chromatin modifying activities that target the nucleosome that masks the TATA box and the start site of transcription. The early core enhanceosome has been shown to recruit the histone acetyl transferase protein p300/CBP-associated factors PCAF/GCN5. The latter, in addition to modifying nucleosome by acetylating the histones, acetylates HMGI(Y) at lysine-71 residue. This is followed by the recruitment of the CBP-Pol II holoenzyme complex. At this step, the enhanceosome is enriched sequentially with IRF-3, c-Jun and IRF-7. Nucleosome acetylation, in turn, facilitates SWI/SNF recruitment by CBP, resulting in chromatin remodeling and binding of TFIID to the promoter. At the time of peak HMGI(Y) lysine-71 acetylation (5 h after virus infection), all the IFN-B activators are found on the virusresponsive enhanceosome at their highest amounts indicating stable enhanceosome assembly. Acetylation of HMGI(Y) by CBP at a distinct lysine residue (K65) is suggested to destabilize the enhanceosome leading to transient activation of the IFN-B promoter [3,27,90,92,93].
10. Concluding remarks on the IFN-A gene regulation Enhanceosome formation in different IFN-A gene promoters involving sequential binding of IRF-3 and IRF-7 homo- or heterodimers together with CBP or p300 and other factors acting as activators or repressors is not yet established. Determination of the assembly of enhancertranscription factor complexes would give an insight into the relationship between the modular structure of IFN-A promoters and the signal transduction pathways triggered by viral infection. The IRF dependent modules of IFN-A promoters may also provide a new understanding of the synergism among different IRF family members. Some viruses such as influenza A virus and human papillomavirus (HPV16) are able to prevent the activation of IRF-3 to counteract the IFN system [94–96]. The interaction of IRFs with the enhancer modules, which contributes to determine the specificity of IFN-A transactivation, may also provide clues on the IFN-A gene cascade inhibition by different viruses.
Acknowledgements This work was supported by the Centre National de la Recherche Scientifique, the Université René Descartes Paris
652
A. Civas et al. / Biochimie 84 (2002) 643–654
V, and grants from the Association pour la Recherche sur le Cancer (contracts no. 9994 and 5228) and the Ligue Regionale contre le Cancer (AC, PG and SN). M-L Island and Pierre Morin are recipients of the Association de Recherche contre le Cancer.
References [1]
[2] [3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
T. Taniguchi, K. Ogasawara, A. Takaoka, N. Tanaka, IRF family of transcription factors as regulators of host defense, Annu. Rev. Immunol. 19 (2001) 623–655. E. De Maeyer, J. De Maeyer-Guignard, Interferons, Academic Press, London, 1994, pp. 265–288. T.K. Kim, T. Maniatis, The mechanism of transcriptional synergy of an in vitro assembled interferon-ß enhanceosome, Mol. Cell 1 (1997) 119–129. S.L. Schafer, R. Lin, P.A. Moore, J. Hiscott, P.M. Pitha, Regulation of type 1 interferon gene expression by interferon regulatory factor 3, J. Biol. Chem. 273 (1998) 2714–2720. I. Marié, J.E. Durbin, D.E. Levy, Differential viral induction of distinct interferon-alpha genes by positive feedback through interferon regulatory factor-7, EMBO J. 17 (1998) 6660–6669. I. Julkunen, T. Sareneva, J. Pirhonen, T. Ronni, K. Melen, S. Matikainen, Molecular pathogenesis of influenza A virus infection and virus-induced regulation of cytokine gene expression, Cytokine Growth Factor Rev. 12 (2001) 171–180. T. Taniguchi, A. Takaoka, The interferon-alpha/beta system in antiviral responses: a multimodal machinery of gene regulation by the IRF family of transcription factors, Curr. Opin. Immunol. 14 (2002) 111–116. M. Sato, H. Suemori, N. Hata, M. Asagiri, K. Ogasawara, K. Nakao, T. Nakaya, M. Katsuki, S. Noguchi, N. Tanaka, T. Taniguchi, Distinct and essential roles of transcription factors IRF-3 and IRF-7 in response to viruses for IFN-alpha/beta gene induction, Immunity 13 (2000) 539–548. M. Sato, T. Taniguchi, N. Tanaka, The interferon system and interferon regulatory factor transcription factors: studies from gene knockout mice, Cytokine Growth Factor Rev. 12 (2001) 133–142. L. Zhang, J.S. Pagano, IRF-7, a new interferon regulatory factor associated with Epstein Barr Virus latency, Mol. Cell Biol. 17 (1997) 5748–5757. M.G. Wathelet, C.H. Lin, B.S. Parakh, L.V. Ronco, P.M. Howley, T. Maniatis, Virus infection induces the assembly of coordinately activated transcription factors on the IFN-ß enhancer in vivo, Mol. Cell 1 (1998) 507–518. B.K. Weaver, K.P. Kumar, N.C. Reich, Interferon regulatory factor 3 and CREB-binding protein/p300 are subunits of double-stranded RNA-activated transcription factor DRAF1, Mol. Cell Biol. 18 (1998) 1359–1368. W.C. Au, P.A. Moore, D.W. LaFleur, B. Tombal, P.M. Pitha, Characterization of the interferon regulatory factor-7 and its potential role in the transcription activation of interferon A genes, J. Biol. Chem. 273 (1998) 29210–29217. Y.T. Juang, W. Lowther, M. Kellum, W.C. Au, R. Lin, J. Hiscott, P.M. Pitha, Primary activation of interferon A and interferon B gene transcription by interferon regulatory factory-3, Proc. Natl. Acad. Sci. USA 95 (1998) 9837–9842. Y. Mamane, C. Heylbroeck, P. Genin, M. Algarte, M.J. Servant, C. LePage, C. DeLuca, H. Kwon, R. Lin, J. Hiscott, Interferon regulatory factors: the next generation, Gene 237 (1999) 1–14. R. Lin, Y. Mamane, J. Hiscott, Structural and functional analysis of interferon regulatory factor 3: localization of the transactivation and autoinhibitory domains, Mol. Cell Biol. 19 (1999) 2465–2474.
[17] M. Yoneyama, W. Suhara, Y. Fukuhara, T. Fujita, Direct activation of a factor complex composed of IRF-3 and CBP/p300 by virus infection, J. Interferon Cytokine Res. 17 (1997) S53. [18] M. Yoneyama, W. Suhara, Y. Fukuhara, M. Fukada, E. Nishida, T. Fujita, Direct triggering of the type I interferon system by virus infection: activation of a transcription factor complex containing IRF-3 and CBP/p300, EMBO J. 17 (1998) 1087–1095. [19] R. Lin, C. Heylbroeck, P.M. Pitha, J. Hiscott, Virus dependent phosphorylation of the IRF-3 transcription factor regulates nuclear translocation, transactivation potential and proteasome mediated degradation, Mol. Cell Biol. 18 (1998) 2986–2996. [20] K.P. Kumar, K.M. McBride, B.K. Weaver, C. Dingwall, N.C. Reich, Regulated nuclear-cytoplasmic localization of Interferon regulatory Factor 3, a subunit of Double-stranded RNA-Activated Factor 1, Mol. Cell Biol. 20 (2000) 4159–4168. [21] C.R. Escalante, J. Yie, D. Thanos, A.K. Aggarwal, Structure of IRF-1 with bound DNA reveals determinants of interferon regulation, Nature 391 (1998) 103–106. [22] J.E. Darnell Jr, I.M. Kerr, G.R. Stark, Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins, Science 264 (1994) 1415–1421. [23] H.A.R. Bluyssen, J.E. Durbin, D.E. Levy, ISGF3g p48, a specificity switch for interferon activated transcription factors, Cyt. Growth Fact. Rev. 7 (1996) 11–17. [24] F. Rosenbauer, J.F. Waring, J. Foerster, M. Wietstruk, D. Philipp, I. Horak, Interferon consensus sequence binding protein and interferon regulatory factor-4/Pip form a complex that represses the expression of the interferon-stimulated gene-15 in macrophages, Blood 94 (1999) 4274–4281. [25] C.F. Eisenbeis, H. Singh, U. Storb, Pip, a novel IRF family member, is a lymphoid-specific, PU.1-dependent transcriptional activator, Genes Dev. 9 (1995) 1377–1387. [26] P. Morin, P. Genin, J. Doly, A. Civas, The virus-induced factor VIF differentially recognizes the virus-responsive modules of the mouse IFNA4 gene promoter, J. Interferon Cytokine Res. 22 (2002) 77–86. [27] M. Merika, A.J. Williams, G. Chen, T. Collins, D. Thanos, Recruitment of CBP/p300 by the IFNß enhanceosome is required for synergistic activation of transcription, Mol. Cell 1 (1998) 277–287. [28] I. Marie, E. Smith, A. Prakash, D.E. Levy, Phosphorylation-induced dimerization of interferon regulatory factor 7 unmasks DNA binding and a bipartite transactivation domain, Mol. Cell Biol. 20 (2000) 8803–8814. [29] R. Lin, Y. Mamane, J. Hiscott, Multiple regulatory domains control IRF-7 activity in response to virus infection, J. Biol. Chem. 275 (2000) 34320–34327. [30] M.O. Diaz, The human type I interferon gene cluster, Sem. Virol. 6 (1995) 143–149. [31] J. Hiscott, K. Cantell, C. Weissmann, Differential expression of human interferon genes, Nucl. Acid Res. 12 (1984) 3727–3746. [32] K.A. Kelley, P.M. Pitha, Characterization of a mouse interferon gene locus II. Differential expression of alpha-interferon genes, Nucl. Acids Res. 13 (1985) 825–839. [33] A. Hoss-Homfeld, E.C. Zwarthoff, R. Zawatzky, Cell type specific expression and regulation of murine interferon alpha and beta genes, Virology 173 (1989) 539–550. [34] C. Coulombel, G. Vodjdani, J. Doly, Isolation and characterization of a novel interferon-α-encoding gene, IFN-α11, within a murine IFN cluster, Gene 104 (1991) 187–195. [35] M. Sato, N. Hata, M. Asagiri, T. Nakaya, T. Taniguchi, N. Tanaka, Positive feedback regulation of type I IFN genes by the IFNinducible transcription factor IRF-7, FEBS Lett. 441 (1998) 106–110.
A. Civas et al. / Biochimie 84 (2002) 643–654 [36] T. Kawakami, M. Matsumoto, M. Sato, H. Harada, T. Taniguchi, M. Kitagawa, Possible involvement of the transcription factor ISGF3g in virus-induced expression of the IFN-ß gene, FEBS Lett. 358 (1995) 225–229. [37] T. Kimura, Y. Kadokawa, H. Harada, M. Matsumoto, M. Sato, Y. Kashiwazaki, M. Tarutani, R.S.P. Tan, T. Takasugi, T. Matsuyama, T.M. Mak, S. Noguchi, T. Taniguchi, Essential and non-redundant roles of p48 (ISGF3γ) and IRF-1 in both type I and type II interferon responses, as revealed by gene targeting studies, Genes Cells 1 (1996) 115–124. [38] M. Yoneyama, W. Suhara, Y. Fukuhara, M. Sato, K. Ozato, T. Fujita, Autocrine amplification of type I interferon gene expression mediated by interferon stimulated gene factor 3 (ISGF3), J. Biochem. 120 (1996) 160–169. [39] H. Harada, M. Matsumoto, M. Sato, Y. Kashiwazaki, T. Kimura, M. Kitagawa, T. Yokochi, R.S.P. Tan, T. Takasugi, Y. Kadokawa, C. Schindler, R.D. Schreiber, S. Noguchi, T. Taniguchi, Regulation of IFN-α/ß genes: evidence for a dual function of the transcription factor complex ISGF3 in the production and action of IFN-α/ß, Genes Cells 1 (1996) 995–1005. [40] J. Bragança, P. Génin, M.T. Bandu, N. Darracq, M. Vignal, C. Cassé, J. Doly, A. Civas, Synergism between multiple virus-induced-factorbinding elements involved in the differential expression of IFN-A genes, J. Biol. Chem. 272 (1997) 22154–22162. [41] W.C. Au, P.M. Pitha, Recruitment of multiple interferon regulatory factors and histone acetyltransferase to the transcriptionally active interferon a promoters, J. Biol. Chem. 276 (2001) 41629–41637. [42] W.S. Yeow, W.C. Au, W.J. Lowther, P.M. Pitha, Downregulation of IRF-3 levels by ribozyme modulates the profile of IFNA subtypes expressed in infected human cells, J. Virol. 75 (2001) 3021–3027. [43] W.S. Yeow, W.C. Au, Y.T. Juang, C.D. Fields, C.L. Dent, D.R. Gewer, P.M. Pitha, Reconstitution of virus-mediated expression of interferon alpha genes in human fibroblast cells by ectopic Interferon Regulatory Factor-7, J. Biol. Chem. 275 (2000) 6313–6320. [44] B.J. Barnes, P.A. Moore, P.M. Pitha, Virus-specific activation of a novel interferon regulatory factor, IRF-5, results in the induction of distinct interferon alpha genes, J. Biol. Chem. 276 (2001) 23382–23390. [45] P. Genin, J. Braganca, N. Darracq, J. Doly, A. Civas, A novel PRD I and TG binding activity involved in virus-induced transcription of IFN-A genes, Nucl. Acids Res. 23 (1995) 5055–5063. [46] P. Morin, J. Bragança, M.T. Bandu, R. Lin, J. Hiscott, J. Doly, A. Civas, Preferential binding sites for interferon regulatory factors 3 and 7 involved in interferon-A gene transcription, J. Mol. Biol. 316 (2002) 1009–1022. [47] R. Lin, P. Génin, Y. Mamane, J. Hiscott, Selective DNA binding and association with the CREB binding protein coactivator contribute to differential activation of alpha/beta interferon genes by Interferon Regulatory Factors 3 and 7, Mol. Cell Biol. 20 (2000) 6342–6353. [48] C. Lallemand, P. Lebon, P. Rizza, B. Blanchard, M.G. Tovey, Constitutive expression of specific interferon isotypes in peripheral blood leukocytes from normal individuals and in promonocytic U937 cells, J. Leukoc. Biol. 60 (1996) 137–146. [49] N. Lehming, D. Thanos, J.M. Brickman, J. Ma, T. Maniatis, M. Ptashne, An HMG-like protein that can switch a transcriptional activator to a repressor, Nature 371 (1994) 175–179. [50] M. Nourbakhsh, H. Hauser, Constitutive silencing of IFN-beta promoter is mediated by NRF (NF-kappaB-repressing factor), a nuclear inhibitor of NF-kappaB, EMBO J. 18 (1999) 6415–6425. [51] H. Harada, T. Fujita, M. Miyamoto, Y. Kimura, M. Maruyama, A. Furia, T. Miyata, T. Taniguchi, Structurally similar but functionally distinct factors, IRF-1 and IRF-2, bind to the same regulatory elements of IFN and IFN-inducible genes, Cell 58 (1989) 729–739.
653
[52] B. Ren, K.J. Chee, T.H. Kim, T. Maniatis, PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins, Genes Dev. 13 (1999) 125–137. [53] P. Roffet, S. Lopez, S. Navarro, M.T. Bandu, C. Coulombel, M. Vignal, J. Doly, G. Vodjdani, Identification of distal silencing elements in the murine interferon-A11 gene promoter, Biochem. J. 317 (1996) 697–706. [54] S. Lopez, R. Reeves, M.L. Island, M.T. Bandu, N. Christeff, J. Doly, S. Navarro, Silencer activity in the interferon-A gene promoters, J. Biol. Chem. 272 (1997) 22788–22799. [55] S. Lopez, M.L. Island, J. Drouin, M.T. Bandu, N. Christeff, N. Darracq, R. Barbey, J. Doly, D. Thomas, S. Navarro, Repression of virus-induced interferon A promoters by homeodomain transcription factor Ptx1, Mol. Cell Biol. 20 (2000) 7527–7540. [56] T. Lamonerie, J.J. Tremblay, C. Lanctot, M. Therrien, Y. Gauthier, J. Drouin, Ptx1, a bicoid-related homeo box transcription factor involved in transcription of the pro-opiomelanocortin gene, Genes Dev. 10 (1996) 1284–1295. [57] J.J. Tremblay, C. Lanctot, J. Drouin, The pan-pituitary activator of transcription, Ptx1 (pituitary homeobox 1), acts in synergy with SF-1 and Pit1 and is an upstream regulator of the Lim-homeodomain gene Lim3/Lhx3, Mol. Endocrinol. 12 (1998) 428–441. [58] J.J. Tremblay, J. Drouin, Egr-1 is a downstream effector of GnRH and synergizes by direct interaction with Ptx1 and SF-1 to enhance luteinizing hormone beta gene transcription, Mol. Cell Biol. 19 (1999) 2567–2576. [59] J.J. Tremblay, A. Marcil, Y. Gauthier, J. Drouin, Ptx1 regulates SF-1 activity by an interaction that mimics the role of the ligand-binding domain, EMBO J. 18 (1999) 3431–3441. [60] C. Lanctot, A. Moreau, M. Chamberland, M.L. Tremblay, J. Drouin, Hindlimb patterning and mandible development require the Ptx1 gene, Development 126 (1999) 1805–1810. [61] D.P. Szeto, C. Rodriguez-Esteban, A.K. Ryan, S.M. O’Connell, F. Liu, C. Kioussi, A.S. Gleiberman, J.C. Izpisua-Belmonte, M.G. Rosenfeld, Role of the bicoid-related homeodomain factor Pitx1 in specifying hindlimb morphogenesis and pituitary development, Genes Dev. 13 (1999) 484–494. [62] E.V. Semina, R. Reiter, N.J. Leysens, W.L. Alward, K.W. Small, N.A. Datson, J. Siegel-Bartelt, D. Bierke-Nelson, P. Bitoun, B.U. Zabel, J.C. Carey, J.C. Murray, Cloning and characterization of a novel bicoid-related homeobox transcription factor gene, RIEG, involved in Rieger syndrome, Nat. Genet. 14 (1996) 392–399. [63] M.P. Smidt, H.S. van Schaick, C. Lanctot, J.J. Tremblay, J.J. Cox, A.A. van der Kleij, G. Wolterink, J. Drouin, J.P. Burbach, A homeodomain gene Ptx3 has highly restricted brain expression in mesencephalic dopaminergic neurons, Proc. Natl. Acad. Sci. USA 94 (1997) 13305–13310. [64] G. Poulin, M. Lebel, M. Chamberland, F.W. Paradis, J. Drouin, Specific protein–protein interaction between basic helix-loop-helix transcription factors and homeoproteins of the Pitx family, Mol. Cell Biol. 20 (2000) 4826–4837. [65] G. Poulin, B. Turgeon, J. Drouin, NeuroD1/beta2 contributes to cell-specific transcription of the proopiomelanocortin gene, Mol. Cell Biol. 17 (1997) 6673–6682. [66] D.P. Szeto, A.K. Ryan, S.M. O’Connell, M.G. Rosenfeld, P-OTX: a PIT-1-interacting homeodomain factor expressed during anterior pituitary gland development, Proc. Natl. Acad. Sci. USA 93 (1996) 7706–7710. [67] B. Lamolet, A.M. Pulichino, T. Lamonerie, Y. Gauthier, T. Brue, A. Enjalbert, J. Drouin, A pituitary cell-restricted T box factor, Tpit, activates POMC transcription in cooperation with Pitx homeoproteins, Cell 104 (2001) 849–859. [68] R. Tjian, T. Maniatis, Transcriptional activation: a complex puzzle with few easy pieces, Cell 77 (1994) 5–8. [69] M. Levine, J.L. Manley, Transcriptional repression of eukaryotic promoters, Cell 59 (1989) 405–408.
654
A. Civas et al. / Biochimie 84 (2002) 643–654
[70] R. Renkawitz, Transcriptional repression in eukaryotes, Trends Genet. 6 (1990) 192–197. [71] S. Goodbourn, Negative regulation of transcriptional initiation in eukaryotes, Biochim. Biophys. Acta 1032 (1990) 53–77. [72] A.R. Clark, K. Docherty, Negative regulation of transcription in eukaryotes, Biochem. J. 296 (1993) 521–541. [73] A.D. Johnson, The price of repression, Cell 81 (1995) 655–658. [74] S. Lopez, S. Navarro, Transcriptional repression of type I IFN genes, Biochimie 80 (1998) 689–701. [75] S. Gray, M. Levine, Transcriptional repression in development, Curr. Opin. Cell Biol. 8 (1996) 358–364. [76] W. Hanna-Rose, U. Hansen, Active repression mechanisms of eukaryotic transcription repressors, Trends Genet. 12 (1996) 229–234. [77] S.G. Roberts, M.R. Green, Transcription. Dichotomous regulators, Nature 375 (1995) 105–106. [78] F. Sauer, J.D. Fondell, Y. Ohkuma, R.G. Roeder, H. Jackle, Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta, Nature 375 (1995) 162–164. [79] B. Majello, P. De Luca, L. Lania, Sp3 is a bifunctional transcription regulator with modular independent activation and repression domains, J. Biol. Chem. 272 (1997) 4021–4026. [80] J.M. Petersen, J.J. Skalicky, L.W. Donaldson, L.P. McIntosh, T. Alber, B.J. Graves, Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix, Science 269 (1995) 1866–1869. [81] F.E. Johansen, R. Prywes, Identification of transcriptional activation and inhibitory domains in serum response factor (SRF) by using GAL4-SRF constructs, Mol. Cell Biol. 13 (1993) 4640–4647. [82] M.A. Subler, D.W. Martin, S. Deb, Overlapping domains on the p53 protein regulate its transcriptional activation and repression functions, Oncogene 9 (1994) 1351–1359. [83] H.J. Brown, J.A. Sutherland, A. Cook, A.J. Bannister, T. Kouzarides, An inhibitor domain in c-Fos regulates activation domains containing the HOB1 motif, EMBO J. 14 (1995) 124–131. [84] S. Bushmeyer, K. Park, M.L. Atchison, Characterization of functional domains within the multifunctional transcription factor, YY1, J. Biol. Chem. 270 (1995) 30213–30220. [85] E.M. Friedl, P. Matthias, Mapping of the transcriptional repression domain of the lymphoid- specific transcription factor oct-2A, J. Biol. Chem. 271 (1996) 13927–13930. [86] X.Y. Li, M.R. Green, Intramolecular inhibition of activating transcription factor-2 function by its DNA-binding domain, Genes Dev. 10 (1996) 517–527. [87] I.S. Goping, G.C. Shore, Interactions between repressor and antirepressor elements in the carbamyl phosphate synthetase I promoter, J. Biol. Chem. 269 (1994) 3891–3896. [88] T. Maniatis, L.A. Whittenmore, W. Du, C.M. Fan, A.D. Keller, V.J. Palombella, D. Thanos, Positive and negative control of human interferon β gene expression, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY, 1992, pp. 1193–1220.
[89] D. Thanos, T. Maniatis, Virus induction of human IFNß gene expression requires the assembly of an enhanceosome, Cell 83 (1995) 1091–1100. [90] T. Agalioti, S. Lomvardas, B. Parekh, J. Yie, T. Maniatis, D. Thanos, Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter, Cell 103 (2000) 667–678. [91] N. Munshi, T. Agalioti, S. Lomvardas, M. Merika, G. Chen, D. Thanos, Coordination of a transcriptional switch by HMGI(Y) acetylation, Science 293 (2001) 1133–1136. [92] J. Yie, M. Merika, N. Munshi, G. Chen, D. Thanos, The role of HMG I(Y) in the assembly and function of the IFN-beta enhanceosome, EMBO J. 18 (1999) 3074–3089. [93] J. Yie, K. Senger, D. Thanos, Mechanism by which the IFN-beta enhanceosome activates transcription, Proc. Natl. Acad. Sci. USA 96 (1999) 13108–13113. [94] L. Ronco, A. Karpova, M. Vidal, P. Howley, Human papillomavirus 16 E6 oncoprotein binds to interferon regulatory factor-3 and inhibits its transcriptional activity, Genes Dev. 12 (1998) 2061–2072. [95] D. Patel, S.M. Huang, L.A. Baglia, D.J. McCance, The E6 protein of human papillomavirus type 16 binds to and inhibits co-activation by CBP and p300, EMBO J. 18 (1999) 5061–5072. [96] J. Talon, C.M. Horvath, R. Polley, C.F. Basler, T. Muster, P. Palese, A. Garcia-Sastre, Activation of Interferon Regulatory Factor 3 is inhibited by the Influenza A virus NS1 protein, J. Virol. 74 (2000) 7989–7996. [97] N.B.K. Raj, J. Engelhardt, W.C. Au, D.E. Levy, P.M. Pitha, Virus infection and interferon can activate gene expression through a single synthetic element, but endogenous genes show distinct regulation, J. Biol. Chem. 264 (1989) 16658–16666. [98] M. Streuli, S. Nagata, C. Weissmann, At least three human type alpha interferons: structure of alpha 2, Science 209 (1980) 1343–1347. [99] K. Henco, J. Brosius, A. Fujisawa, J.I. Fujisawa, J.R. Haynes, T. Kovacic, M. Pasek, A. Schambock, J. Schmid, K. Todokoro, M. Walchli, S. Nagata, C. Weissmann, Structural relationship of human interferon-α genes and pseudogenes, J. Mol. Biol. 185 (1985) 227–260. [100] N. Mantei, M. Schwarzstein, M. Streuli, S. Panem, S. Nagata, C. Weissmann, The nucleotide sequence of a cloned human leukocyte interferon cDNA, Gene 10 (1980) 1–10. [101] G.D. Shaw, W. Boll, H. Taira, N. Mantei, P. Lengyel, C. Weissmann, Structure and expression of cloned murine IFN-alpha genes, Nucl. Acids Res. 11 (1983) 555–573. [102] E.C. Zwarthoff, A.T. Mooren, J. Trapman, Organization, structure and expression of murine interferon alpha genes, Nucl. Acids Res. 13 (1985) 791–804. [103] K.A. Kelley, P.M. Pitha, Characterization of a mouse interferon gene locus I. Isolation of a cluster of four alpha interferon genes, Nucl. Acids Res. 13 (1985) 805–823.
Regulation of virus-induced interferon-A genes Ahmet Civas *, Marie-Laure Island, Pierre Génin, Pierre Morin, Sébastien Navarro UPR 2228, CNRS, Laboratoire de régulation transcriptionnelle et maladies génétiques, UFR biomédicale des Saints-Pères, Université Paris V, 45, rue des Saints-Pères, 75270 Paris cedex 6, France Received 26 February 2002; accepted 31 May 2002
Abstract Different members of the interferon regulatory factor (IRF) family are early activated by viral infection of eukaryotic cells. The IRFs participate in the virus-induced transcriptional regulation of different genes, including the multigenic interferon-A (IFN-A) family, members of which are involved in the establishment of an antiviral state, cell growth inhibition or apoptosis. This study presents the recent progress in the field of virus-induced transactivation and repression of IFN-A gene promoters. Data presented on the modular organization of IFN-A gene promoters and their transactivation dependent on IRF-3 and IRF-7 provide a new insight on the cooperativity mechanisms among the different IRF family members. Data on the transcriptional repression of virus-induced interferon-A promoters by the homeodomain protein Pitx1 contribute to our understanding of the complex differential transcriptional activation, repression and antirepression of the IFN-A genes. © 2002 Société française de biochimie et biologie moléculaire / Éditions scientifiques et médicales Elsevier SAS. All rights reserved. Keywords: Interferon A; Interferon regulatory factor; Transactivation/activation; Pitx1; Repression
1. Introduction Viral infection of eukaryotic cells causes the early activation of different transcription factors including different members of the Rel, Jun, ATF, and IRF families. Among these factors, the interferon regulatory factors (IRF-1 to IRF-10) play an important role in the stimulation of cellular antiviral defence mechanisms in different cell types. The activation of constitutively expressed IRFs in the course of virus infection by phosphorylation or other posttranslational modifications such as acetylation, as well as the virus-induced or interferon-stimulated expression of other IRFs constitute crucial steps in the transactivation of target genes [1]. For instance, the IRFs participate in the virus-induced transcriptional regulation of type I IFN genes encoding different interferon-α and interferon-β [2–5]. They also regulate the expression of other cytokines or chemokines (IL-18, RANTES, IP-10, MCP-1) and a group of IFN-stimulated genes (ISG) activated either by virus or IFN (Mx, PKR, OAS, iNOS, ISG-15). The products of these
genes participate in the formation of innate or adaptive immune responses against virus infections. The IRFs also mediate cell growth inhibition or apoptosis in virus-infected cells [6,7]. The individual role of IRFs in the immune antiviral response is enlightened by gene targeting studies that also revealed their complementary rather than redundant functions in the regulation of target gene expression and host defence [8,9]. This feature is well documented in the case of IRF-3 and IRF-7 which are described as potent activators of virus-induced type I IFN and ISG transcription. This study presents the recent progress in the field of virus-induced transactivation and repression of IFN-A gene promoters and on the distinctive roles of IRF-3 and IRF-7 in virus-induced regulation of transcription. We will focus on the interactions of IRF-3 and IRF-7 with the IFN-A promoters that account for their differential expression in different cell types. We also present data on the transcriptional repression of the virus-induced interferon-A promoters by the homeodomain protein Pitx1.
* Corresponding author. Tel.: +33-1-42-86-22-84; fax: +33-1-42-86-2042. E-mail address: [email protected] (A. Civas). © 2002 Société française de biochimie et biologie moléculaire / Éditions scientifiques et médicales Elsevier SAS. All rights reserved. PII: S 0 3 0 0 - 9 0 8 4 ( 0 2 ) 0 1 4 3 1 - 1
644
A. Civas et al. / Biochimie 84 (2002) 643–654
2. Common features in the protein structure of IRFs and their DNA-binding IRFs regulate transcription by interacting with gene promoter sequences, termed IRF elements (IRF-E), and formed by direct repeats of GAAANN motifs. IRFs also bind to closely related DNA sequences, denoted as interferon-stimulated response elements (ISRE), found in the promoter of a group of virus-inducible genes transcriptionally amplified by interferon-α/β [10–14]. The highly conserved DNA-binding domain (DBD) of IRFs characterized by a unique helix-turn-helix motif containing conserved tryptophan residues is located in their N-terminal region (a.a. 1–130) [1,15]. In some IRFs, the sequence homology extends to the interaction domain (IAD) that mediates the formation of IRF homo- or heterodimers or the association of IRFs with other factors [16]. The less conserved C-terminal part includes the transactivation domain (TAD), a proline-rich domain, the nuclear export and localization signals (NES and NLS) and the serine/threonine phosphorylation domain (also referred as regulatory or signal response domain) [1]. TAD defines the specificity of each IRF to interact, directly or in association with other factors, with different components of the transcription preinitiation complex and coactivators of transcription such as CBP/p300 or PCAF/GCN5 [11,12,17,18]. Although the role of various domains contained in the C-terminal region is not yet understood, they regulate, at least in some cases, the subcellular localization of IRFs in response to virus infection [19,20] DNA-binding site selection studies have revealed that IRF-1 and IRF-2 bind to promoters carrying the consensus sequence G(A)AAASYGAAASY (S = G/C, Y = T/C). The crystal structure of IRF-1 DBD with a 13 bp IRF-E site provided a basis for GAAA sequences occurring within almost all the IRF response elements [21]. This study showed that the helix-turn-helix motif of DBD latches onto DNA through three of the five conserved tryptophans and interacts with the GAAA core sequence by base contacts with amino acids R82, C83, N86 and S87 in the major groove. Some IRFs have a very weak binding affinity for the sequences formed by GAAANN repeats, and recognize them only when associated with other transcription factors. For instance, IRF-9 recognizes the ISRE-related sequences with high affinity, when associated with Stat1 and Stat2 [22,23]. IRF-4 and IRF-8 form ternary complexes together with PU.1 to recognize composite DNA sequences containing GAAANN repeats associated with Ets binding sites [24,25].
3. Distinctive properties of IRF-3 and IRF-7 in virusinduced gene transcription Extensive studies on subcellular localization of IRF-3 and IRF-7 have revealed their distinctive activation mecha-
nisms in comparison to other IRF family members. In uninfected cells, IRF-3 normally shuttles between the nucleus and the cytoplasm. The cytoplasmic localization is predominant prior to virus infection and depends on NES and NLS sequences interacting with the exportin 1 and a subset of importin-α shuttling receptors, respectively [20]. IRF-3 has also been shown to contain an autoinhibitory domain (AID) located at the C-terminal end (spanning a.a. 380–427). Deletion of AID leads to a constitutively active form of IRF-3 capable to stimulate transcription in the absence of virus infection. Intramolecular interactions occurring between AID and the region spanning a.a. 98–240 maintain IRF-3 in a closed conformation, masking both DBD and IAD, in the cytoplasm of uninfected cells [19]. Virus-induced phosphorylation of a serine/threonine cluster located in the AID leads to a conformational change of IRF-3 that relieves the intramolecular autoinhibition and permits translocation to the nucleus. The NLS mediates the nuclear accumulation of phosphorylated IRF-3 that can bind to the CBP/p300 protein resident in the nucleus, this association preventing IRF-3 export to cytoplasm. Nuclear sequestered IRF-3 can thus form DNA-binding complexes such as VIF, the virus-induced factor which is essentially formed by IRF-3 homodimers, and the dsRNA activated factor (DRAF1) or virus-activated IRF (VA-IRF) formed by IRF-3 and CBP or p300 [12,18,26]. It has also been shown that IRF-3 associates with IRF-7 to form together with CBP and p300 the higher-order DNA-binding complex VAF (virus-activated factor). This complex recognizes with high affinity the ISRE of the ISG-15 gene promoter that is responsive either to IFN or virus [3,11,27]. Serine phosphorylation in the C-terminal regulatory domain is also required for IRF-7 activation by virus infection, even if the IRF-7A or 7B isoforms are constitutively active when overexpressed in human HEK 293 cells. The IRF-7 regulatory domain has also been shown to control the retention of the phosphorylated protein in the nucleus and the ability of IRF-7 to form homodimers or heterodimers with IRF-3 [28,29]. The IAD mapped to the C-terminal part of IRF-7 (a.a. 240–503) has not yet been precisely determined. Transcriptional activation by IRF-7 has been mapped to two distinct regions, both of which were required for full activity, while all the functions were masked in latent IRF-7 by an AID mapping to an internal region. The effect of the potential NLS/NES sequences and the role of the AID located downstream the DBD remain also to be elucidated.
4. Interferon regulatory factors 3 and 7 and the differential IFN-A gene regulation IFN-A genes are represented by a multigenic family of intronless genes clustered in a 400 kb region, containing also the IFN-B gene, on the human chromosome 9 and on chromosome 4 in the mouse [30]. They have been shown to be coordinately induced in human and mouse cells infected
A. Civas et al. / Biochimie 84 (2002) 643–654
by virus and exhibit differences in the expression of their individual mRNAs. Differential expression is shown to be dependent on the transcriptional activity of the corresponding IFN-A gene promoter in a particular cell type. Thus, human IFN-A1, IFN-A2 and IFN-A4 genes are highly expressed in Sendai virus-infected PBMC and lymphoblastoid Namalwa cells, whereas the expression of IFN-A5, IFN-A7, IFN-A8 and IFN-A14 mRNA levels is 5- to 20-fold lower in the same cells [31]. Similarly, in NDVinduced L929 cells, the murine IFN-A4 expression is predominant in comparison to IFN-A2, IFN-A5 and IFNA6, whereas IFN-A1 and IFN-A11 are very weakly expressed [32–34]. Among the multiple IFN-A genes, only human IFN-A1 and murine IFN-A4 genes are expressed without the requirement for ongoing protein synthesis, as in the case of IFN-B gene (Fig. 1). In mouse cells, virus-induced phosphorylation of IRF-3 is considered a key event in the primary activation of IFN-A4 and IFN-B [5,14,35]. Secreted IFN-α4 and IFN-β proteins acting through their common receptor on neighbouring cells activate the Jak-STAT pathway. This activation leads to the transcriptional stimulation of the IRF-7 gene by a positive feedback loop, mediated by the Interferon-Stimulated Gene Factor 3 (ISGF-3) complex [36–39]. According to this multistep induction model (Fig. 1), subsequent activation of IRF-7 protein by C-terminal serine phosphorylation following virus infection results in the induction of a set of delayed IFN-A genes which includes IFN-A2, -A5, -A6, and -A8 genes [5]. IRF-3 knock-out studies have recently confirmed this model, and further indicate that in the late phase of induction, IRF-3 and IRF-7 cooperate with each other to provide the mRNA induction profile of the IFN-A gene family depending on the cell line [8]. The molecular mechanisms that would account for the early transcription of murine IFN-A4 and human IFN-A1 genes among the multiple IFN-A genes and their differential expression after amplification by ISGF3 and IRF-7 have recently been defined better. We have shown that the differential virus-induced expression between the murine IFN-A4 and IFN-A11 genes is in part due to two substitutions in the Virus-Responsive Element of the IFN-A11 promoter which affect two binding sites for the IRF family members [40]. Similarly, two substitutions, at positions –98 and –81 of human IFNA1 and A2 promoter, have been found to be pivotal to the differential expression of these genes [41]. It has also been suggested that the ratio between the relative levels of IRF-3 and IRF-7 could be a critical determinant for the induction of the individual IFN-A subtypes in infected cells [42]. Gene disruption/introduction studies have shown that IRF-3 was critical for both immediate-early and late phases of the IFN-A/B gene induction by virus (Fig. 1). In the late phase, this factor cooperates with IRF-7 to potentiate the overall IFN-A/B mRNA induction and provide the normal mRNA induction profile for IFN-A subspecies [5,8,13,43]. These results
645
indicated that these factors have complementary rather than redundant roles in the activation of IFN-A/B genes. In fact, the biphasic induction mechanism regulated by IRF-3 and IRF-7 ensures the transcriptional activity of IFN-A/B genes and the diversity of the IFN-A genes for efficient antiviral response [5,10,13]. Recently, IRF-5 has been shown to participate in the induction of IFN-A and B genes and suggested to replace the requirement for IRF-7 in the induction of IFN-A genes, at least in lymphoid tissue [44]. This finding and the fact that other IRF family members, such as IRF-1 and IRF-2, also participate in IFN-A/B gene transcription suggest that more complex regulatory mechanisms may be involved in the pattern of the IFN-A gene expression. The individual IFN-A transcript level may depend on the identity of the IRFs as well as on the amount of the activated IRF pool expressed in a specific cell type.
5. Molecular basis of IRF-3 and IRF-7 binding on different IFN-A promoters The maximal NDV-induced transcription of the murine IFN-A4 gene requires the presence of four cooperating IRF-E (modules A to D) that form the virus-responsive element of IFN-A4 (VRE-A4) (Fig. 2): module A, represented by the GTAAAGAAAGT sequence; and B, C and D modules corresponding, respectively, to the GAAAGTGAAAAG, GAATTGGAAAGC, and GAAAGGAGAAACT sequences [40,45]. We have shown that the weak expression of IFN-A11 gene in comparison to IFN-A4 is due to the absence of C and D modules that are disrupted by the –78A/G and –57G/C substitutions (Fig. 2). We have further demonstrated that the transactivation of the murine IFN-A4 gene promoter by IRF-3 or IRF-7 is mediated through different virus-responsive modules. Thus, we have shown that the C module corresponds to a preferential binding site for IRF-3, whereas IRF-7 interacts preferentially with the distal region of VRE-A4 containing the A and B modules [26,46]. Site selection experiments have previously suggested that IRF-3 exhibits a restricted GAAANNGAAANN specificity (GAAASSGAAANY) in comparison to IRF-7 consensus recognition sequence determined as GAAWNYGAAANY [47]. The authors have shown that human IFN-B and IFN-A1 gene promoters were stimulated by IRF-3 coexpression, whereas IFN-A4, A7, and A14 promoters were preferentially induced by IRF-7. The broader DNA-binding specificity of IRF-7 was suggested to contribute to its capacity to stimulate delayed expression of human IFN-A4, A7, and A14 genes. The differential expression of IFN-A genes was then attributed to the broader sequence specificity of IRF-7 in comparison to IRF-3. We have recently shown that the GAAANN motifs contained in different modules of murine IFN-A4 gene promoter also respond differentially to IRF-3 or IRF-7 overexpression. These core sequences can be classified into
646
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 1. Virus-induced activation of mouse IFN-A genes by IRFs. Viral infection of eukaryotic cells causes early and transient expression of various cytokine genes, including type I IFN genes (IFN-A multigenic family and IFN-B gene) and type II IFN (IFN-G). Expression of these IFN genes by different cell types constitutes a crucial step in the stimulation of cellular antiviral defence mechanisms, in the inhibition of cell growth and in the induction of the apoptotic process. Virus-induced phosphorylation (P) and acetylation (Ac) of IRF-3 is considered a key event in the primary activation of IFN-A4 and IFN-B genes. Production of IFN-γ following virus infection can also lead to activation of type I IFN genes through IRF-1 expression. Secreted IFN-α4 and IFN-β proteins acting through type I IFN receptor on neighbouring cells activate the Jak-STAT pathway, resulting in the transcriptional stimulation of the IRF-7 gene by a positive feedback loop, mediated by the Interferon-Stimulated Gene Factor 3 (ISGF-3) complex. According to this multistep induction model, subsequent virus-induced activation of IRF-7 and IRF-1 proteins in cooperation with activated IRF-3 results in the amplification of IFN-A4 and IFN-B gene transcription and in the induction of a set of delayed IFN-A genes which includes mouse IFN-A2, -A5, and -A6 genes.
A. Civas et al. / Biochimie 84 (2002) 643–654
647
Fig. 2. Organization of the murine IFN-A4 and IFN-A11 gene promoters in the [–120 to –26] region. The Virus-Responsive Element (VRE-A4) located in the proximal region of the promoter and the enhancer modules (A to D) are represented according to Bragança et al. [40]. The minimal inducible element corresponds to the [–109 to –75] region defined by Raj et al. [97]. In this region, the weakly inducible IFN-A11 gene promoter differs from the highly inducible IFN-A4 by the nucleotide substitutions –78A/G, –59C/T, –58C/A, –57G/C, –43C/G, –41A/G. Among them, those affecting the virus inducibility of these promoters, thus explaining their differential regulation, are indicated by arrows. The GAAANN repeats contained in different modules are underlined. Numbering is relative to the transcription start of the promoter and the TATA box is indicated.
four groups according to the identity of the NN residues they contain: (i) the first group includes the NC (TC, AC, GC, CC), and ST (GT,CT) residues inducible by both IRF-3 and IRF-7; (ii) the NG (TG, AG, GG, CG) and CA containing motifs preferentially activated by IRF-3; (iii) the GAAAAT repeats responding only to IRF-7; and (iv) the DA (TA, AA, GA) group unresponsive to both factors. In the native IFN-A4 promoter, the second GT residues in the GTAAAGAAAGTGAAAAG sequence of the AB domain and the TG residues of the GAATTGGAAAGC sequence of the C module are critical for IRF-7 and IRF-3 responsiveness, respectively [46]. These results demonstrated that the preferential target sites for IRF-3 and IRF-7 are dictated by specific sets of GAAANN motifs forming the virusinducible modules in the IFN-A gene promoters. This observation allowed us to gain an insight into the molecular basis of IRF-3 and IRF-7 binding on different IFN-A promoter. The expression levels of the IFN-A genes in the early and/or delayed phases following virus infection appear to correlate directly to the integrity of the IRF-3 and IRF-7 binding sites (Fig. 3). For example, in mouse fibroblasts, the induced expression level of IFN-A2 gene is intermediate between the highly expressed IFN-A4 and the weakly inducible IFN-A11 gene. In the IFN-A2 promoter, the –78A/G substitution is also present, together with a –80G/A mutation. Thus, the C module is disrupted in IFN-A2,
suggesting that the delayed expression of IFN-A2 is essentially mediated by IRF-7 rather than by IRF-3. Cooperation between different modules may also be attenuated in other IFN-A gene promoters, including IFN-A5 and IFN-A6 which also belong to the set of delayed type IFN-A genes [32,33]. The promoters of these genes do not contain C and D modules (disrupted by –85G/C and –82T/G substitutions and the –52G/T and –50G/A substitutions, respectively) and thus may be regulated in the delayed phase of the IFN response by IRF-7. Similarly, comparison of the VRE sequences of human IFN-A gene promoters reveals that the GAAATG core sequence corresponding to the C module of the highly inducible Hs-IFN-A1 promoter is substituted by A/G and TG/TA mutations in Hs-IFN-A2, A4, A5, A7 and A14 (Fig. 3). These features may also explain the IRF-3 unresponsiveness of this group of poorly induced and late-expressed IFN-A genes, since we showed the deleterious effect of the substitutions previously mentioned, on IRF-3 mediated transcription. The preferential response of these promoters to IRF-7 may be due to the GAAAGC and GAAAAT motifs present in the B and D modules, respectively. This model may explain the expression profiles of human or mouse IFN-A genes following virus infection in different cell lines [5,42]. DNA pull-down and chromatin precipitation assays performed by another group have shown that the binding of IRF-3 and IRF-7 on the VRE of Hs-IFN-A1 promoter is
648
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 3. Comparison of the [–120 to –26] region of the human and murine IFN-A gene promoters. Nucleotide sequences of the [–120 to –26] region of the human IFN-A2, A4, A5, A7 and A14 [98,99] are presented in alignment with the sequence of human IFN-A1 gene numbered according to the start site of transcription [100]. Nucleotide sequences of the [–120 to –26] region of the murine IFN-A2, A11, A1, A5 and A6 [32,34,101–103] are presented in alignment with the sequence of murine IFN-A4 gene numbered according to the start site of transcription. Identical residues are indicated by dots and hyphens correspond to gaps introduced for better alignment. The consensus sequences (Cons.) present the nucleotide residues conserved among the IFN-A promoters; nucleotides distinguishing these sequences are indicated by stars. The TATA box and the potential modules found in the IFN-A promoters are boxed.
associated with the presence of acetylated histone H3, suggesting that HATs are tethered together with the virusactivated IRFs to the promoter [41]. In these experiments, IRF-7 has been shown to bind also to the Hs-IFN-A2 VRE, whereas the deletion of the guanine residue at position –98 and the –81G/A substitution in this promoter have been shown to affect the recruitment of IRF-3. The preferential binding of IRF-3 to human VRE-A1 is in agreement with the model presented in this study. Interestingly, Hs-IFN-A5 has been reported to be constitutively expressed in lymphoid cells including peripheral blood mononuclear cells from normal individuals and promonocytic U937 cells [48]. Constitutive transactivation of the Hs-IFN-A5 promoter may be due to the predominant expression of IRF-7 in cells of lymphoid origins. The –79G/A substitution in the HsIFN-A5 promoter may affect the recruitment of IRF-3 on the C module, whereas the –52G/A substitution may create a strong preferential binding site for IRF-7 in the D module (Fig. 3). Synergism between the B and D modules mediated
in this case by IRF-7 may thus explain the Hs-IFN-A5 constitutive expression.
6. The distal negative regulatory element in mouse IFN-A promoters A large number of repressors binding to the IFN-B promoter elements have been identified such as the transcriptional co-repressor dorsal switch protein DSP1 [49], the NFjB repressing factor NRF [50], IRF-2 which is able to antagonize activators such as factors of the IRF family by competing for their binding [51] and PRDI-BF1 [52]. Until now, repressors involved in negative regulation of the IFN-A genes are not well characterized. In addition to substitutions in the proximal VRE-A [40,45], we have shown that the repression of the IFN-A11 gene after virus induction is also due to the presence of a distal negative regulatory element of 20 base pairs (Fig. 4),
A. Civas et al. / Biochimie 84 (2002) 643–654
the DNRE, which is delimited upstream of the VRE-A [53,54]. DNRE exerts an inhibitory effect on VRE-A elements after virus induction, independent of its orientation or position, and is, therefore, considered as a silencer. On the other hand, the DNRE on its own has neither any effect on VRE-B promoter after virus induction nor any constitutive repressive effect on heterologous promoters. Therefore, the functional feature of the particular silencer DNRE consists in the fact that its silencing activity is strictly dependent on the presence of a functional VRE-A. DNRE specifically acts via repression of VRE-A positive activity after virus induction and does not function as a general negative regulator. Similar DNREs are present in some IFN-A promoters and the presence or the absence of DNRE may contribute to the differential expression of the IFN-A genes after virus induction. Two DNRE-binding factors have been observed before virus induction of L929 cells and HeLa cells and are still maintained even following induction (Fig. 4A). These results indicate the presence of murine and human constitutive binding proteins involved in the silencing effect. One of the complexes corresponds to a protein related or identical to high mobility group protein (HMG) I(Y) which binds to the minor groove of two AT-rich regions within DNRE. HMG I(Y) does not seem to modulate the binding of a second factor to DNRE. We suggested that this last factor may be considered as a protein which negatively regulates the transcription of IFN-A11 promoter [54].
7. The homeodomain Pitx1 (Pituitary homeobox 1) negatively regulates the transcription of IFN-A promoters The analysis of the distal silencer element DNRE responsible for the virus-induced transcriptional repression of some IFN-A promoters led us to clone by the one-hybrid system and study the homeodomain (HD) transcription factor, Pitx1 [55]. Homeotic genes encode the transcriptional factors that are involved in the positive and negative regulations of target genes during development. These genes contain a highly conserved sequence of 180 bp, the homeobox, which encodes a 60 amino acid residue polypeptide, called HD that represents the DNA-binding domain of these factors. Pitx1 was first described as a transcriptional activator binding the central element 3 (CE3) element of the pituitary proopiomelanocortin (POMC) gene promoter [56]. It activates transcription of other pituitary genes [57–59]. Pitx1 deficient mice studies indicate that hindlimb patterning and mandible and pituitary development require this gene [60,61]. Three members of the Pitx family have been described: the Pitx1 [56] and the Pitx2 [62] genes which are homologous and have an overlapping expression pattern and the Pitx3 gene [63]. Several known transcriptional
649
interaction factors act in synergy with Pitx1: bHLH NeuroD1 for corticotrophe-specific transcription of POMC [64,65], Pit1 to stimulate the expression of the prolactin gene [57,66], SF-1, an orphan nuclear receptor, and Egr-1, an immediate-early response gene which stimulate the expression of the βLH gene [57–59]. Pitx1 C-terminal region is involved in both transcriptional activation and physical interaction with Pit1, SF1 or Egr-1. Recently, a pituitary cell-restricted T box factor, Tpit, has been shown to activate POMC transcription in cooperation with Pitx homeoproteins [67]. We have shown that Pitx1 is detectable in cell types that express IFN-A genes after virus induction and that the recombinant or endogenous Ptx1 protein binds specifically to the DNRE (Fig. 4A). Upon virus induction, Pitx1 negatively regulates the transcription of DNRE-containing IFN-A11 promoter. After virus induction, the expression of the Pitx1 antisense RNA that leads to a significant increase of endogenous IFN-A gene transcription, is able to modify the pattern of differential expression of individual IFN-A genes, and derepresses IFN-A11 and IFN-A5 genes [55]. Most of the researches on eukaryotic gene expression have been focused on the transcriptional activation mechanisms [68]. Although positive control of gene expression is essential, it becomes clear now that the transcriptional repression is at least as important as activation. Indeed, as an inherent feature, those gene systems which are positively regulated may require an inhibition mechanism to account for temporal or spatial expression during development, cell or tissue specificity, modulation of gene expression depending on environmental changes, and rapid expression shutdown after induction [69–74]. In silencing and quenching cases, recent studies on their mechanisms of action suggest that these repressors may be considered as short-range or long-range repressors [75]. Short-range repressors for silencing and quenching interfere with the neighbouring factor and allow modular repression whereas long-range repressors can interfere with the function of several factors and co-factors that are bound kilobase distance away. We propose that Pitx1 can modulate IFN-A gene transcription through an alternative mechanism. Furthermore, in the context of the IFN-A gene promoters, the Pitx1 factor acts as a repressor and its effect is only observed after virus induction on the VRE-A positive activity. Therefore, Pitx1 may be considered as a short-range repressor including silencing activity dependent upon the presence of a functional VRE-A. For silencing and quenching, the repressor contains active repression domains, analogous to the activation domains used by transcription activators and IADs [76]. Pitx1 can modulate differently IFN-A gene and POMC or other pituitary gene expression. The activity of Pitx1 as a positive regulator of the transcription is synergized by cell-restricted transcription factors to confer pituitary-, lineage- and promoter-specific expression (see above). In this context, Pitx1 factor contains multiple positive trans-
650
A. Civas et al. / Biochimie 84 (2002) 643–654
Fig. 4. Organization of the murine IFN-A11 and -A4 regulatory sequences and factors binding the DNRE. IFN-A11 and IFN-A4 promoter sequences are indicated, the numbering is relative to the transcription start site of the promoter, the TATA box being indicated in each case. Nucleotides distinguishing these sequences are represented by larger characters. Localization of the binding sites for potential transrepressors and transactivators, namely, DNRE, 4DNRE, VRE-A11 and VRE-A4 is indicated. 4D represents an antisilencer region.
regulatory domains and interaction regions. The opposite functions of Pitx1 in the regulation of the transcription of IFN-A promoters may be due to different negative transregulatory domains and interaction regions. Transcription factors able to activate and repress in different circumstances have been documented, and the molecular bases are
quite diverse [77]. For example, transcription factor Kruppel modifies an activator to a repressor [78]. Sp3 is a dual-function regulator. Predominant activity depends upon the number of DNA-binding sites present in the promoter [79]. The transcriptional activity of Ets-1 is modified upon DNA-binding [80].
A. Civas et al. / Biochimie 84 (2002) 643–654
Altogether, these results suggest that Pitx1 is a multifunctional regulator protein able to act as a repressor or as an activator and may be also interact with other proteins, similar to other transcription regulators such as p53, c-fos, SRF, YY1, Oct-2A and activating transcription factor 2 [81–86]. Our studies suggest that Pitx1 contributes to the transcriptional strength of the promoters of IFN-A genes.
8. Relationship between Pitx1 and an antisilencer element Furthermore, we have shown that a DNRE (4DNRE), binding both Pitx1 and HMGI (Y), is also present in the highly inducible IFN-A4 promoter (Fig. 4B) but a central antisilencer region, named 4D, located between the silencer and the VRE-A4 overrides the silencer activity [54,55]. The central antisilencer region does not function as an activator but rather as an inhibitor of the Pitx1 silencer activity in IFN-A4 gene expression. Indeed, the central antisilencer region is able to overcome the Pitx1 silencer activity in the context of the native IFN-A4 promoter. On the contrary, in the absence of the central antisilencer region, the repressing effect of Pitx1 was observed. Protein–protein interactions between silencer and antisilencer as described for the carbamyl phosphate synthetase I promoter has been suggested [87]. Thus, in the context of the native IFN-A4 promoter, we suggested that Pitx1 cannot interact with the factors binding to the VRE4 but may interact with protein(s) binding to the central antisilencer region which may be considered as a molecular trap for Pitx1 maintaining the IFN-A4 gene highly inducible. If a protein is involved for the antisilencer activity, the precise functional relationship between Pitx1 and this factor binding to the antisilencer element remains to be established. The precise action of Pitx1 to block IFN-A11 and IFN-A5, but not IFN-A4 promoter activities, may contribute to our understanding of the complex differential transcriptional activation, repression and antirepression of the IFN-A genes.
9. IRF-3 and IRF-7 in IFN-B gene regulation Among the IRF family members, IRF-1, 2, 3, 5, 7 and 9 have also been implicated in the transcriptional induction of the IFN-B gene. Transcriptional activation in response to virus infection has been particularly studied in the case of the IFN-B gene [88]. The IFN-B gene, present as a single copy in the human and mouse genome, contains within its promoter several regulatory cis-elements, consisting of positive and negative domains. The positive regulatory domains (PRD-I to PRD-IV) constitute a composite virusresponsive element (VRE-B) [89]. The transcriptional activators, NF-jB and ATF-2/c-jun, interact with PRD-II and PRD-IV, respectively, whereas PRD-III and PRD-I form
651
separately or together a binding site(s) for IRF-1, 2, 3, 7 and 9. A recent model concerning the IFN-B transcription consists of the coordinated acetylation of the architectural protein HMGI(Y) interacting with PRD-II and PRD-IV domains [90,91]. The authors have shown that a virusinduced enhanceosome consisting of ATF-2/c-Jun, IRFs, NF-jB and HMGI(Y) is assembled in a nucleosome-free region of the IFN-B promoter. Transcription is then activated by sequential recruitment of chromatin modifying activities that target the nucleosome that masks the TATA box and the start site of transcription. The early core enhanceosome has been shown to recruit the histone acetyl transferase protein p300/CBP-associated factors PCAF/GCN5. The latter, in addition to modifying nucleosome by acetylating the histones, acetylates HMGI(Y) at lysine-71 residue. This is followed by the recruitment of the CBP-Pol II holoenzyme complex. At this step, the enhanceosome is enriched sequentially with IRF-3, c-Jun and IRF-7. Nucleosome acetylation, in turn, facilitates SWI/SNF recruitment by CBP, resulting in chromatin remodeling and binding of TFIID to the promoter. At the time of peak HMGI(Y) lysine-71 acetylation (5 h after virus infection), all the IFN-B activators are found on the virusresponsive enhanceosome at their highest amounts indicating stable enhanceosome assembly. Acetylation of HMGI(Y) by CBP at a distinct lysine residue (K65) is suggested to destabilize the enhanceosome leading to transient activation of the IFN-B promoter [3,27,90,92,93].
10. Concluding remarks on the IFN-A gene regulation Enhanceosome formation in different IFN-A gene promoters involving sequential binding of IRF-3 and IRF-7 homo- or heterodimers together with CBP or p300 and other factors acting as activators or repressors is not yet established. Determination of the assembly of enhancertranscription factor complexes would give an insight into the relationship between the modular structure of IFN-A promoters and the signal transduction pathways triggered by viral infection. The IRF dependent modules of IFN-A promoters may also provide a new understanding of the synergism among different IRF family members. Some viruses such as influenza A virus and human papillomavirus (HPV16) are able to prevent the activation of IRF-3 to counteract the IFN system [94–96]. The interaction of IRFs with the enhancer modules, which contributes to determine the specificity of IFN-A transactivation, may also provide clues on the IFN-A gene cascade inhibition by different viruses.
Acknowledgements This work was supported by the Centre National de la Recherche Scientifique, the Université René Descartes Paris
652
A. Civas et al. / Biochimie 84 (2002) 643–654
V, and grants from the Association pour la Recherche sur le Cancer (contracts no. 9994 and 5228) and the Ligue Regionale contre le Cancer (AC, PG and SN). M-L Island and Pierre Morin are recipients of the Association de Recherche contre le Cancer.
References [1]
[2] [3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
T. Taniguchi, K. Ogasawara, A. Takaoka, N. Tanaka, IRF family of transcription factors as regulators of host defense, Annu. Rev. Immunol. 19 (2001) 623–655. E. De Maeyer, J. De Maeyer-Guignard, Interferons, Academic Press, London, 1994, pp. 265–288. T.K. Kim, T. Maniatis, The mechanism of transcriptional synergy of an in vitro assembled interferon-ß enhanceosome, Mol. Cell 1 (1997) 119–129. S.L. Schafer, R. Lin, P.A. Moore, J. Hiscott, P.M. Pitha, Regulation of type 1 interferon gene expression by interferon regulatory factor 3, J. Biol. Chem. 273 (1998) 2714–2720. I. Marié, J.E. Durbin, D.E. Levy, Differential viral induction of distinct interferon-alpha genes by positive feedback through interferon regulatory factor-7, EMBO J. 17 (1998) 6660–6669. I. Julkunen, T. Sareneva, J. Pirhonen, T. Ronni, K. Melen, S. Matikainen, Molecular pathogenesis of influenza A virus infection and virus-induced regulation of cytokine gene expression, Cytokine Growth Factor Rev. 12 (2001) 171–180. T. Taniguchi, A. Takaoka, The interferon-alpha/beta system in antiviral responses: a multimodal machinery of gene regulation by the IRF family of transcription factors, Curr. Opin. Immunol. 14 (2002) 111–116. M. Sato, H. Suemori, N. Hata, M. Asagiri, K. Ogasawara, K. Nakao, T. Nakaya, M. Katsuki, S. Noguchi, N. Tanaka, T. Taniguchi, Distinct and essential roles of transcription factors IRF-3 and IRF-7 in response to viruses for IFN-alpha/beta gene induction, Immunity 13 (2000) 539–548. M. Sato, T. Taniguchi, N. Tanaka, The interferon system and interferon regulatory factor transcription factors: studies from gene knockout mice, Cytokine Growth Factor Rev. 12 (2001) 133–142. L. Zhang, J.S. Pagano, IRF-7, a new interferon regulatory factor associated with Epstein Barr Virus latency, Mol. Cell Biol. 17 (1997) 5748–5757. M.G. Wathelet, C.H. Lin, B.S. Parakh, L.V. Ronco, P.M. Howley, T. Maniatis, Virus infection induces the assembly of coordinately activated transcription factors on the IFN-ß enhancer in vivo, Mol. Cell 1 (1998) 507–518. B.K. Weaver, K.P. Kumar, N.C. Reich, Interferon regulatory factor 3 and CREB-binding protein/p300 are subunits of double-stranded RNA-activated transcription factor DRAF1, Mol. Cell Biol. 18 (1998) 1359–1368. W.C. Au, P.A. Moore, D.W. LaFleur, B. Tombal, P.M. Pitha, Characterization of the interferon regulatory factor-7 and its potential role in the transcription activation of interferon A genes, J. Biol. Chem. 273 (1998) 29210–29217. Y.T. Juang, W. Lowther, M. Kellum, W.C. Au, R. Lin, J. Hiscott, P.M. Pitha, Primary activation of interferon A and interferon B gene transcription by interferon regulatory factory-3, Proc. Natl. Acad. Sci. USA 95 (1998) 9837–9842. Y. Mamane, C. Heylbroeck, P. Genin, M. Algarte, M.J. Servant, C. LePage, C. DeLuca, H. Kwon, R. Lin, J. Hiscott, Interferon regulatory factors: the next generation, Gene 237 (1999) 1–14. R. Lin, Y. Mamane, J. Hiscott, Structural and functional analysis of interferon regulatory factor 3: localization of the transactivation and autoinhibitory domains, Mol. Cell Biol. 19 (1999) 2465–2474.
[17] M. Yoneyama, W. Suhara, Y. Fukuhara, T. Fujita, Direct activation of a factor complex composed of IRF-3 and CBP/p300 by virus infection, J. Interferon Cytokine Res. 17 (1997) S53. [18] M. Yoneyama, W. Suhara, Y. Fukuhara, M. Fukada, E. Nishida, T. Fujita, Direct triggering of the type I interferon system by virus infection: activation of a transcription factor complex containing IRF-3 and CBP/p300, EMBO J. 17 (1998) 1087–1095. [19] R. Lin, C. Heylbroeck, P.M. Pitha, J. Hiscott, Virus dependent phosphorylation of the IRF-3 transcription factor regulates nuclear translocation, transactivation potential and proteasome mediated degradation, Mol. Cell Biol. 18 (1998) 2986–2996. [20] K.P. Kumar, K.M. McBride, B.K. Weaver, C. Dingwall, N.C. Reich, Regulated nuclear-cytoplasmic localization of Interferon regulatory Factor 3, a subunit of Double-stranded RNA-Activated Factor 1, Mol. Cell Biol. 20 (2000) 4159–4168. [21] C.R. Escalante, J. Yie, D. Thanos, A.K. Aggarwal, Structure of IRF-1 with bound DNA reveals determinants of interferon regulation, Nature 391 (1998) 103–106. [22] J.E. Darnell Jr, I.M. Kerr, G.R. Stark, Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins, Science 264 (1994) 1415–1421. [23] H.A.R. Bluyssen, J.E. Durbin, D.E. Levy, ISGF3g p48, a specificity switch for interferon activated transcription factors, Cyt. Growth Fact. Rev. 7 (1996) 11–17. [24] F. Rosenbauer, J.F. Waring, J. Foerster, M. Wietstruk, D. Philipp, I. Horak, Interferon consensus sequence binding protein and interferon regulatory factor-4/Pip form a complex that represses the expression of the interferon-stimulated gene-15 in macrophages, Blood 94 (1999) 4274–4281. [25] C.F. Eisenbeis, H. Singh, U. Storb, Pip, a novel IRF family member, is a lymphoid-specific, PU.1-dependent transcriptional activator, Genes Dev. 9 (1995) 1377–1387. [26] P. Morin, P. Genin, J. Doly, A. Civas, The virus-induced factor VIF differentially recognizes the virus-responsive modules of the mouse IFNA4 gene promoter, J. Interferon Cytokine Res. 22 (2002) 77–86. [27] M. Merika, A.J. Williams, G. Chen, T. Collins, D. Thanos, Recruitment of CBP/p300 by the IFNß enhanceosome is required for synergistic activation of transcription, Mol. Cell 1 (1998) 277–287. [28] I. Marie, E. Smith, A. Prakash, D.E. Levy, Phosphorylation-induced dimerization of interferon regulatory factor 7 unmasks DNA binding and a bipartite transactivation domain, Mol. Cell Biol. 20 (2000) 8803–8814. [29] R. Lin, Y. Mamane, J. Hiscott, Multiple regulatory domains control IRF-7 activity in response to virus infection, J. Biol. Chem. 275 (2000) 34320–34327. [30] M.O. Diaz, The human type I interferon gene cluster, Sem. Virol. 6 (1995) 143–149. [31] J. Hiscott, K. Cantell, C. Weissmann, Differential expression of human interferon genes, Nucl. Acid Res. 12 (1984) 3727–3746. [32] K.A. Kelley, P.M. Pitha, Characterization of a mouse interferon gene locus II. Differential expression of alpha-interferon genes, Nucl. Acids Res. 13 (1985) 825–839. [33] A. Hoss-Homfeld, E.C. Zwarthoff, R. Zawatzky, Cell type specific expression and regulation of murine interferon alpha and beta genes, Virology 173 (1989) 539–550. [34] C. Coulombel, G. Vodjdani, J. Doly, Isolation and characterization of a novel interferon-α-encoding gene, IFN-α11, within a murine IFN cluster, Gene 104 (1991) 187–195. [35] M. Sato, N. Hata, M. Asagiri, T. Nakaya, T. Taniguchi, N. Tanaka, Positive feedback regulation of type I IFN genes by the IFNinducible transcription factor IRF-7, FEBS Lett. 441 (1998) 106–110.
A. Civas et al. / Biochimie 84 (2002) 643–654 [36] T. Kawakami, M. Matsumoto, M. Sato, H. Harada, T. Taniguchi, M. Kitagawa, Possible involvement of the transcription factor ISGF3g in virus-induced expression of the IFN-ß gene, FEBS Lett. 358 (1995) 225–229. [37] T. Kimura, Y. Kadokawa, H. Harada, M. Matsumoto, M. Sato, Y. Kashiwazaki, M. Tarutani, R.S.P. Tan, T. Takasugi, T. Matsuyama, T.M. Mak, S. Noguchi, T. Taniguchi, Essential and non-redundant roles of p48 (ISGF3γ) and IRF-1 in both type I and type II interferon responses, as revealed by gene targeting studies, Genes Cells 1 (1996) 115–124. [38] M. Yoneyama, W. Suhara, Y. Fukuhara, M. Sato, K. Ozato, T. Fujita, Autocrine amplification of type I interferon gene expression mediated by interferon stimulated gene factor 3 (ISGF3), J. Biochem. 120 (1996) 160–169. [39] H. Harada, M. Matsumoto, M. Sato, Y. Kashiwazaki, T. Kimura, M. Kitagawa, T. Yokochi, R.S.P. Tan, T. Takasugi, Y. Kadokawa, C. Schindler, R.D. Schreiber, S. Noguchi, T. Taniguchi, Regulation of IFN-α/ß genes: evidence for a dual function of the transcription factor complex ISGF3 in the production and action of IFN-α/ß, Genes Cells 1 (1996) 995–1005. [40] J. Bragança, P. Génin, M.T. Bandu, N. Darracq, M. Vignal, C. Cassé, J. Doly, A. Civas, Synergism between multiple virus-induced-factorbinding elements involved in the differential expression of IFN-A genes, J. Biol. Chem. 272 (1997) 22154–22162. [41] W.C. Au, P.M. Pitha, Recruitment of multiple interferon regulatory factors and histone acetyltransferase to the transcriptionally active interferon a promoters, J. Biol. Chem. 276 (2001) 41629–41637. [42] W.S. Yeow, W.C. Au, W.J. Lowther, P.M. Pitha, Downregulation of IRF-3 levels by ribozyme modulates the profile of IFNA subtypes expressed in infected human cells, J. Virol. 75 (2001) 3021–3027. [43] W.S. Yeow, W.C. Au, Y.T. Juang, C.D. Fields, C.L. Dent, D.R. Gewer, P.M. Pitha, Reconstitution of virus-mediated expression of interferon alpha genes in human fibroblast cells by ectopic Interferon Regulatory Factor-7, J. Biol. Chem. 275 (2000) 6313–6320. [44] B.J. Barnes, P.A. Moore, P.M. Pitha, Virus-specific activation of a novel interferon regulatory factor, IRF-5, results in the induction of distinct interferon alpha genes, J. Biol. Chem. 276 (2001) 23382–23390. [45] P. Genin, J. Braganca, N. Darracq, J. Doly, A. Civas, A novel PRD I and TG binding activity involved in virus-induced transcription of IFN-A genes, Nucl. Acids Res. 23 (1995) 5055–5063. [46] P. Morin, J. Bragança, M.T. Bandu, R. Lin, J. Hiscott, J. Doly, A. Civas, Preferential binding sites for interferon regulatory factors 3 and 7 involved in interferon-A gene transcription, J. Mol. Biol. 316 (2002) 1009–1022. [47] R. Lin, P. Génin, Y. Mamane, J. Hiscott, Selective DNA binding and association with the CREB binding protein coactivator contribute to differential activation of alpha/beta interferon genes by Interferon Regulatory Factors 3 and 7, Mol. Cell Biol. 20 (2000) 6342–6353. [48] C. Lallemand, P. Lebon, P. Rizza, B. Blanchard, M.G. Tovey, Constitutive expression of specific interferon isotypes in peripheral blood leukocytes from normal individuals and in promonocytic U937 cells, J. Leukoc. Biol. 60 (1996) 137–146. [49] N. Lehming, D. Thanos, J.M. Brickman, J. Ma, T. Maniatis, M. Ptashne, An HMG-like protein that can switch a transcriptional activator to a repressor, Nature 371 (1994) 175–179. [50] M. Nourbakhsh, H. Hauser, Constitutive silencing of IFN-beta promoter is mediated by NRF (NF-kappaB-repressing factor), a nuclear inhibitor of NF-kappaB, EMBO J. 18 (1999) 6415–6425. [51] H. Harada, T. Fujita, M. Miyamoto, Y. Kimura, M. Maruyama, A. Furia, T. Miyata, T. Taniguchi, Structurally similar but functionally distinct factors, IRF-1 and IRF-2, bind to the same regulatory elements of IFN and IFN-inducible genes, Cell 58 (1989) 729–739.
653
[52] B. Ren, K.J. Chee, T.H. Kim, T. Maniatis, PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins, Genes Dev. 13 (1999) 125–137. [53] P. Roffet, S. Lopez, S. Navarro, M.T. Bandu, C. Coulombel, M. Vignal, J. Doly, G. Vodjdani, Identification of distal silencing elements in the murine interferon-A11 gene promoter, Biochem. J. 317 (1996) 697–706. [54] S. Lopez, R. Reeves, M.L. Island, M.T. Bandu, N. Christeff, J. Doly, S. Navarro, Silencer activity in the interferon-A gene promoters, J. Biol. Chem. 272 (1997) 22788–22799. [55] S. Lopez, M.L. Island, J. Drouin, M.T. Bandu, N. Christeff, N. Darracq, R. Barbey, J. Doly, D. Thomas, S. Navarro, Repression of virus-induced interferon A promoters by homeodomain transcription factor Ptx1, Mol. Cell Biol. 20 (2000) 7527–7540. [56] T. Lamonerie, J.J. Tremblay, C. Lanctot, M. Therrien, Y. Gauthier, J. Drouin, Ptx1, a bicoid-related homeo box transcription factor involved in transcription of the pro-opiomelanocortin gene, Genes Dev. 10 (1996) 1284–1295. [57] J.J. Tremblay, C. Lanctot, J. Drouin, The pan-pituitary activator of transcription, Ptx1 (pituitary homeobox 1), acts in synergy with SF-1 and Pit1 and is an upstream regulator of the Lim-homeodomain gene Lim3/Lhx3, Mol. Endocrinol. 12 (1998) 428–441. [58] J.J. Tremblay, J. Drouin, Egr-1 is a downstream effector of GnRH and synergizes by direct interaction with Ptx1 and SF-1 to enhance luteinizing hormone beta gene transcription, Mol. Cell Biol. 19 (1999) 2567–2576. [59] J.J. Tremblay, A. Marcil, Y. Gauthier, J. Drouin, Ptx1 regulates SF-1 activity by an interaction that mimics the role of the ligand-binding domain, EMBO J. 18 (1999) 3431–3441. [60] C. Lanctot, A. Moreau, M. Chamberland, M.L. Tremblay, J. Drouin, Hindlimb patterning and mandible development require the Ptx1 gene, Development 126 (1999) 1805–1810. [61] D.P. Szeto, C. Rodriguez-Esteban, A.K. Ryan, S.M. O’Connell, F. Liu, C. Kioussi, A.S. Gleiberman, J.C. Izpisua-Belmonte, M.G. Rosenfeld, Role of the bicoid-related homeodomain factor Pitx1 in specifying hindlimb morphogenesis and pituitary development, Genes Dev. 13 (1999) 484–494. [62] E.V. Semina, R. Reiter, N.J. Leysens, W.L. Alward, K.W. Small, N.A. Datson, J. Siegel-Bartelt, D. Bierke-Nelson, P. Bitoun, B.U. Zabel, J.C. Carey, J.C. Murray, Cloning and characterization of a novel bicoid-related homeobox transcription factor gene, RIEG, involved in Rieger syndrome, Nat. Genet. 14 (1996) 392–399. [63] M.P. Smidt, H.S. van Schaick, C. Lanctot, J.J. Tremblay, J.J. Cox, A.A. van der Kleij, G. Wolterink, J. Drouin, J.P. Burbach, A homeodomain gene Ptx3 has highly restricted brain expression in mesencephalic dopaminergic neurons, Proc. Natl. Acad. Sci. USA 94 (1997) 13305–13310. [64] G. Poulin, M. Lebel, M. Chamberland, F.W. Paradis, J. Drouin, Specific protein–protein interaction between basic helix-loop-helix transcription factors and homeoproteins of the Pitx family, Mol. Cell Biol. 20 (2000) 4826–4837. [65] G. Poulin, B. Turgeon, J. Drouin, NeuroD1/beta2 contributes to cell-specific transcription of the proopiomelanocortin gene, Mol. Cell Biol. 17 (1997) 6673–6682. [66] D.P. Szeto, A.K. Ryan, S.M. O’Connell, M.G. Rosenfeld, P-OTX: a PIT-1-interacting homeodomain factor expressed during anterior pituitary gland development, Proc. Natl. Acad. Sci. USA 93 (1996) 7706–7710. [67] B. Lamolet, A.M. Pulichino, T. Lamonerie, Y. Gauthier, T. Brue, A. Enjalbert, J. Drouin, A pituitary cell-restricted T box factor, Tpit, activates POMC transcription in cooperation with Pitx homeoproteins, Cell 104 (2001) 849–859. [68] R. Tjian, T. Maniatis, Transcriptional activation: a complex puzzle with few easy pieces, Cell 77 (1994) 5–8. [69] M. Levine, J.L. Manley, Transcriptional repression of eukaryotic promoters, Cell 59 (1989) 405–408.
654
A. Civas et al. / Biochimie 84 (2002) 643–654
[70] R. Renkawitz, Transcriptional repression in eukaryotes, Trends Genet. 6 (1990) 192–197. [71] S. Goodbourn, Negative regulation of transcriptional initiation in eukaryotes, Biochim. Biophys. Acta 1032 (1990) 53–77. [72] A.R. Clark, K. Docherty, Negative regulation of transcription in eukaryotes, Biochem. J. 296 (1993) 521–541. [73] A.D. Johnson, The price of repression, Cell 81 (1995) 655–658. [74] S. Lopez, S. Navarro, Transcriptional repression of type I IFN genes, Biochimie 80 (1998) 689–701. [75] S. Gray, M. Levine, Transcriptional repression in development, Curr. Opin. Cell Biol. 8 (1996) 358–364. [76] W. Hanna-Rose, U. Hansen, Active repression mechanisms of eukaryotic transcription repressors, Trends Genet. 12 (1996) 229–234. [77] S.G. Roberts, M.R. Green, Transcription. Dichotomous regulators, Nature 375 (1995) 105–106. [78] F. Sauer, J.D. Fondell, Y. Ohkuma, R.G. Roeder, H. Jackle, Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta, Nature 375 (1995) 162–164. [79] B. Majello, P. De Luca, L. Lania, Sp3 is a bifunctional transcription regulator with modular independent activation and repression domains, J. Biol. Chem. 272 (1997) 4021–4026. [80] J.M. Petersen, J.J. Skalicky, L.W. Donaldson, L.P. McIntosh, T. Alber, B.J. Graves, Modulation of transcription factor Ets-1 DNA binding: DNA-induced unfolding of an alpha helix, Science 269 (1995) 1866–1869. [81] F.E. Johansen, R. Prywes, Identification of transcriptional activation and inhibitory domains in serum response factor (SRF) by using GAL4-SRF constructs, Mol. Cell Biol. 13 (1993) 4640–4647. [82] M.A. Subler, D.W. Martin, S. Deb, Overlapping domains on the p53 protein regulate its transcriptional activation and repression functions, Oncogene 9 (1994) 1351–1359. [83] H.J. Brown, J.A. Sutherland, A. Cook, A.J. Bannister, T. Kouzarides, An inhibitor domain in c-Fos regulates activation domains containing the HOB1 motif, EMBO J. 14 (1995) 124–131. [84] S. Bushmeyer, K. Park, M.L. Atchison, Characterization of functional domains within the multifunctional transcription factor, YY1, J. Biol. Chem. 270 (1995) 30213–30220. [85] E.M. Friedl, P. Matthias, Mapping of the transcriptional repression domain of the lymphoid- specific transcription factor oct-2A, J. Biol. Chem. 271 (1996) 13927–13930. [86] X.Y. Li, M.R. Green, Intramolecular inhibition of activating transcription factor-2 function by its DNA-binding domain, Genes Dev. 10 (1996) 517–527. [87] I.S. Goping, G.C. Shore, Interactions between repressor and antirepressor elements in the carbamyl phosphate synthetase I promoter, J. Biol. Chem. 269 (1994) 3891–3896. [88] T. Maniatis, L.A. Whittenmore, W. Du, C.M. Fan, A.D. Keller, V.J. Palombella, D. Thanos, Positive and negative control of human interferon β gene expression, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY, 1992, pp. 1193–1220.
[89] D. Thanos, T. Maniatis, Virus induction of human IFNß gene expression requires the assembly of an enhanceosome, Cell 83 (1995) 1091–1100. [90] T. Agalioti, S. Lomvardas, B. Parekh, J. Yie, T. Maniatis, D. Thanos, Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter, Cell 103 (2000) 667–678. [91] N. Munshi, T. Agalioti, S. Lomvardas, M. Merika, G. Chen, D. Thanos, Coordination of a transcriptional switch by HMGI(Y) acetylation, Science 293 (2001) 1133–1136. [92] J. Yie, M. Merika, N. Munshi, G. Chen, D. Thanos, The role of HMG I(Y) in the assembly and function of the IFN-beta enhanceosome, EMBO J. 18 (1999) 3074–3089. [93] J. Yie, K. Senger, D. Thanos, Mechanism by which the IFN-beta enhanceosome activates transcription, Proc. Natl. Acad. Sci. USA 96 (1999) 13108–13113. [94] L. Ronco, A. Karpova, M. Vidal, P. Howley, Human papillomavirus 16 E6 oncoprotein binds to interferon regulatory factor-3 and inhibits its transcriptional activity, Genes Dev. 12 (1998) 2061–2072. [95] D. Patel, S.M. Huang, L.A. Baglia, D.J. McCance, The E6 protein of human papillomavirus type 16 binds to and inhibits co-activation by CBP and p300, EMBO J. 18 (1999) 5061–5072. [96] J. Talon, C.M. Horvath, R. Polley, C.F. Basler, T. Muster, P. Palese, A. Garcia-Sastre, Activation of Interferon Regulatory Factor 3 is inhibited by the Influenza A virus NS1 protein, J. Virol. 74 (2000) 7989–7996. [97] N.B.K. Raj, J. Engelhardt, W.C. Au, D.E. Levy, P.M. Pitha, Virus infection and interferon can activate gene expression through a single synthetic element, but endogenous genes show distinct regulation, J. Biol. Chem. 264 (1989) 16658–16666. [98] M. Streuli, S. Nagata, C. Weissmann, At least three human type alpha interferons: structure of alpha 2, Science 209 (1980) 1343–1347. [99] K. Henco, J. Brosius, A. Fujisawa, J.I. Fujisawa, J.R. Haynes, T. Kovacic, M. Pasek, A. Schambock, J. Schmid, K. Todokoro, M. Walchli, S. Nagata, C. Weissmann, Structural relationship of human interferon-α genes and pseudogenes, J. Mol. Biol. 185 (1985) 227–260. [100] N. Mantei, M. Schwarzstein, M. Streuli, S. Panem, S. Nagata, C. Weissmann, The nucleotide sequence of a cloned human leukocyte interferon cDNA, Gene 10 (1980) 1–10. [101] G.D. Shaw, W. Boll, H. Taira, N. Mantei, P. Lengyel, C. Weissmann, Structure and expression of cloned murine IFN-alpha genes, Nucl. Acids Res. 11 (1983) 555–573. [102] E.C. Zwarthoff, A.T. Mooren, J. Trapman, Organization, structure and expression of murine interferon alpha genes, Nucl. Acids Res. 13 (1985) 791–804. [103] K.A. Kelley, P.M. Pitha, Characterization of a mouse interferon gene locus I. Isolation of a cluster of four alpha interferon genes, Nucl. Acids Res. 13 (1985) 805–823.