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The Journal of Immunology, 2000, 164: 5352-5361.
Copyright © 2000 by The American Association of Immunologists

Regulation of RANTES Chemokine Gene Expression Requires Cooperativity Between NF-{kappa}B and IFN-Regulatory Factor Transcription Factors1

Pierre Génin, Michèle Algarté, Philippe Roof, Rongtuan Lin and John Hiscott2

Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, and Departments of Microbiology and Immunology, Medicine and Oncology, McGill University, Montreal, Canada


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Virus infection of host cells activates a set of cellular genes, including cytokines, IFNs, and chemokines, involved in antiviral defense and immune activation. Previous studies demonstrated that virus-induced transcriptional activation of a member of the human CC-chemokine RANTES required activation of the latent transcription factors IFN-regulatory factor (IRF)-3 and NF-{kappa}B via posttranslational phosphorylation. In the present study, we further characterized the regulatory control of RANTES transcription during virus infection using in vivo genomic footprinting analyses. IRF-3, the related IRF-7, and NF-{kappa}B are identified as important in vivo binding factors required for the cooperative induction of RANTES transcription after virus infection. Using fibroblastic or myeloid cells, we demonstrate that the kinetics and strength of RANTES virus-induced transcription are highly dependent on the preexistence of IRFs and NF-{kappa}B. Use of dominant negative mutants of either I{kappa}B-{alpha} or IRF-3 demonstrate that disruption of either pathway dramatically abolishes the ability of the other to bind and activate RANTES expression. Furthermore, coexpression of IRF-3, IRF-7, and p65/p50 leads to synergistic activation of RANTES promoter transcription. These studies reveal a model of virus-mediated RANTES promoter activation that involves cooperative synergism between IRF-3/IRF-7 and NF-{kappa}B factors.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Localized and systemic pro- and anti-inflammatory cytokine production, including IFN and chemokine genes, plays an important role in the outcome of viral infection and pathogenicity. The functions of immunoregulatory cytokines include attraction of peripheral blood leukocytes to sites of inflammation, the induction of immune regulatory gene expression, the regulation of leukocyte maturation, and a role in the development of lymphoid tissue (1, 2). The CC-chemokine RANTES attracts monocytes, eosinophils, basophils, NK cells, and T cells, including memory T cells, during inflammation and immune response, arguing for a role of this chemokine in virus-related or unrelated diseases (3). RANTES expression in microglia correlates with the clinical onset of experimental autoimmune encephalitis and severity of demyelination (4, 5). RANTES secretion has also been demonstrated in T cells surrounding multiple sclerosis lesions of the human brain (6). The importance of RANTES in virus-induced pathogenesis was emphasized by the finding that infection of CD4+ T cells by M-tropic strains of HIV-1 is antagonized by the chemokines RANTES, macrophage-inflammatory protein-1{alpha}, and macrophage-inflammatory protein-1ß, the natural ligands of HIV fusion cofactor CCR5 chemokine receptor (7, 8, 9). Interestingly, RANTES is also targeted by another unrelated virus, human CMV, which encodes a homologue of a CC chemokine receptor gene (US28) that is capable of binding RANTES (10, 11).

RANTES expression is increased following cellular activation of fibroblasts, T cells, monocytes, and endothelial and epithelial cells (12). Many cell types, including fibroblasts, epithelial cells, and monocytes/macrophages, express RANTES within hours of stimulation by proinflammatory stimuli, such as TNF-{alpha} and IL-1ß (13). Unlike other members of the chemokine family, which are expressed early, RANTES mRNA is induced late (3–5 days) after T cell activation (14). Recently, Song et al. (15) reported the cloning and characterization of a late transcription factor, designated RFLAT-1 (RANTES factor of late activated T lymphocytes-1), that belongs to the TFIIIA-like zinc finger protein superfamily, and that specifically binds to the RANTES promoter. This protein is induced 3 days after T cell activation, is a strong activator of RANTES promoter in T cells, and is suggested to synergize with HMG(I/Y) and Rel family members to form an enhanceosome that activates RANTES gene transcription (15).

The RANTES promoter has been subdivided into five regions (A–E) based upon deletion studies and reporter gene assays (see Fig. 1GoA) (13, 16, 17). In this promoter, four binding sites (Fig. 1GoA) for NF-{kappa}B proteins are critical for induction by proinflammatory cytokines TNF-{alpha} or IL-1ß, or through the CD28 costimulatory pathway (18). The two proximal elements (-54 to -45 and -40 to -31) are typical NF-{kappa}B binding sites and bind p65/p50 heterodimer, the third element called NF-AT (-230 to -209) binds both NF-AT and NF-{kappa}B, and the most distal CD28 response element (-594 to -575) represents a binding site for p65/p50 or p65/c-Rel heterodimers. Recently, a polymorphism in RANTES promoter (a -28C to G mutation downstream of the first NF-{kappa}B site) was associated with reduced CD4+ lymphocyte depletion rate in HIV-1-infected individuals (19). In contrast, NF-{kappa}B sites in the murine RANTES promoter failed to play a major role in virus-mediated activation of this gene (12, 20).



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FIGURE 1. Schematic structure of the human RANTES promoter. A, Sequence of the proximal (-630 to +57) region of the human RANTES promoter. The five regions (AE) determined by deletion studies and reporter gene assays (16 ), the NF-AT domain (-230 to -209), and the most distal CD28 response element (-594 to -575) are indicated in shadowed boxes. The ISRE and the NF-{kappa}B elements shown to play the major roles in virus induction of human RANTES promoter are indicated by black bars. The mRNA start site is shown, and the TATA sequence is boxed. Arrows correspond to primers 1, 2, and 3 used in genomic footprinting to characterize the noncoding strand of RANTES promoter. B, Sequences of the wild-type and mutated RANTES promoters used in this study. Arrows indicated the localization and the orientation of consensus sequences of either the ISRE motif in the -124 to -97 region or the NF-{kappa}B site in the -46 to -30 region of the human RANTES promoter. Nucleotide substitutions introduced either in the ISRE or in the NF-{kappa}B element are underlined.

 
Members of the NF-{kappa}B and IFN-regulatory factors (IRF)3 transcription factor families participate in the virus-mediated activation of cytokine gene transcription (21). Recent studies demonstrated that in response to virus infection, type I IFN gene activation required IRF-3 and IRF-7 gene products as direct transcriptional regulators, but played different roles in the induction of immediate-early vs delayed type I IFN gene (22, 23). Previously, we demonstrated that IRF-3 plays a primary role in the Sendai virus-inducible activation of the human RANTES gene (24), based on the following data: 1) Tet-inducible expression of a constitutively activated phosphomimetic form of IRF-3 increased endogenous RANTES mRNA levels, mediated through the ISRE domain located between nucleotide -126 to -92 in the RANTES promoter (Fig. 1GoB); 2) mutations of the ISRE domain blocked virus-mediated activation of RANTES promoter; and 3) a dominant negative mutant of IRF-3 repressed virus-induced transcription of endogenous RANTES mRNA. Moreover, a constitutively active form of IRF-7 transcription factor generated by our group constitutes a strong activator of RANTES promoter,4 suggesting a role for a distinct IRF family member in virus-induced RANTES transcription. In the present study, in vivo genomic footprinting analysis was utilized in human embryonic kidney 293 and human myeloid U937 cells to investigate protein-DNA contacts that mediate virus-induced RANTES activation. IRF-3, the related IRF-7, and NF-{kappa}B were identified as important in vivo binding factors required for the cooperative induction of RANTES transcription after virus infection. Our results reveal a model of RANTES promoter activation that involves cooperative synergism between IRF-3/IRF-7 and NF-{kappa}B factors.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Plasmid constructions and mutagenesis

RANTES/pGL3 luciferase reporter and the mutated form of RANTES promoter (see Fig. 1GoB) were prepared by cloning BglII-SalI fragment (-397 to +5, filled in with Klenow enzyme) from RANTES/chloramphenicol acetyltransferase reporter plasmid (25) into the NheI site (filled in with Klenow enzyme) of the pGL3-basic vector, as previously described (24). The IRF-3, IRF-7, p65/p50, and CBP expression plasmids used in cotransfection experiments have been previously described (24, 26).

Cell culture, transfections, and luciferase assays

The 293 cells stably expressing either IRF-3, IRF-3({Delta}N), IRF-7, or I{kappa}B{alpha}-2N were described previously (24, 25, 27). Transfections for luciferase assay were conducted in human embryonic kidney 293 cells grown in {alpha}MEM media (Life Technologies, Burlington, Canada) supplemented with 10% FBS, glutamine, and antibiotics. Subconfluent cells were transfected with 0.2 µg of pRL-TK reporter (Renilla luciferase for internal control) and 1 µg of pGL3 reporter (Firefly luciferase, experimental reporter) by calcium phosphate coprecipitation method, as previously described (28). For coexpression experiments, 0.5 µg of each expressing plasmid was added to the reporter plasmid. Sixteen hours after transfection, cells were stimulated with Sendai virus (80 HAU/ml) for 8 h and harvested. Reporter gene activity was measured by dual-luciferase reporter assay, following the instructions of Promega Technical Manual. The experiments were performed in triplicate, and the average fold induction was calculated.

Ribonuclease protection analysis

The 293-expressing cells were pretreated with DOX for 48 h. The 293 or U937 wild-type or expressing cells were either left untreated, or infected with Sendai virus (80 HAU/ml) for the times indicated. Total RNA was prepared from the cell pellets using the Qiagen (Chatsworth, CA) RNeasy kit. A total of 5 µg of RNA was subjected to RNase protection assay using hCK-5 chemokine template of RiboQuant multiprobe RPA kit, following the manufacturer’s instructions (PharMingen, San Diego, CA).

In vivo genomic footprinting

For in vivo methylation by dimethyl sulfate (DMS; Aldrich Chemical, Milwaukee, WI), U937 cells (108) were harvested and resuspended in 1 ml of RPMI, 10% FBS, while 293 adherent cells were exposed to DMS directly in the plate containing 4 ml of {alpha} MEM, 10% FBS. For both cell types, complete medium was supplemented with 20 mM HEPES (pH 7.3) and 10 µl/ml of concentrated DMS during 1 min, followed by two washes in cold PBS containing 2% 2-ME to stop the reaction. Cells were then lysed to extract genomic DNA, as previously described (29). For each genomic DNA sample, the cleavage of methylated G residues (or A residues) was performed using 20 µl of piperidine (Aldrich Chemical) for 200 µl of DNA for 30 min at 90°C. To provide control, DNA (naked DNA) cells were first lysed to extract genomic DNA and then submitted to DMS treatment, precipitated in ethanol, and treated to piperidine cleavage to allow methylation and cleavage to all G residues of the sequence. For each sample, 5 µg of DNA was submitted to LM-PCR using Vent DNA polymerase (New England Biolabs, Mississauga, Canada), as described (30, 31). To ensure elongation of different fragment sizes, PCR amplification step was 2 min for the first cycle and was progressively increased to 10 min in the last cycle, with a total of 18 cycles for DNA amplification. The third primer was radiolabeled by end labeling using T4 polynucleotide kinase (Pharmacia Biotech, Uppsala, Sweden) and [{gamma}-32P]ATP (ICN Pharmaceuticals, Costa Mesa, CA). Two more PCR cycles were performed to radiolabeled elongated DNA. The final labeled PCR product was analyzed on a 5% Explorer sequencing gel (Baker, Phillipsburg, NJ) in 1x TBE at 65 W, and exposed from 12 to 36 h with a BioMax sensitive film (Kodak, Rochester, NY). For the LM-PCR, several sets of oligonucleotides were used. For the noncoding strand: primer 1, 5'-CAC CAT TGG TGC TTG GTC A-3', Tm 60°C; primer 2, 5'-GAT GAG CTC ACT CTA GAT GAG AGC-3', Tm 63°C; and primer 3, 5'-TCT AGA TGA GAG AGC AGT GAG GGA GAG AC-3', Tm 66°C.

Electrophoretic mobility shift assay (EMSA)

Nuclear extracts were prepared from 293 cells after induction with Sendai virus (80 HAU/ml) for times ranging from 2 to 12 h, as previously described (32). A total of 10 µg of extracts was subjected to EMSA by using 32P-labeled probes, DNA-binding buffer (10 mM HEPES, pH 7.9, 2% glycerol (v/v), 40 mM KCl, 1 mM EDTA, pH 8, 0.2 mM MgCl2, 1 mM DTT, 0.05 mM PMSF), 0.2% Nonidet P-40, 0.5 µg of BSA, and 1 µg of poly(dI:dC). Incubation was performed for 30 min at room temperature using DNA oligonucleotide corresponding to the -50 to -26 NF-{kappa}B region of RANTES promoter: 5'-ACT CCC CTT AGG GGA TGC CCC TCA A-3'. The resulting protein-DNA complexes were resolved on 5% polyacrylamide (37.5:1) TBE 0.25x gels and exposed for 16 h. Supershift analysis was performed by preincubating 1 µl of anti-p65, anti-p50, and anti-c-Rel Abs with extracts and binding buffer for 30 min at 4°C before adding probe (Santa Cruz Biotechnology, Santa Cruz, CA).

RT-PCR analysis of IRF-7 mRNA expression

Total RNA isolated from U937, 293, and IRF-7-expressing 293 cells was treated with 1 U of RNase-free DNase (RQ1 Dnase; Promega, Madison, WI) for 30 min at 37°C and ethanol precipitated. Reverse transcriptase was performed on 5 µg of total RNA and 0.2 pmol of random hexamers using 200 U of Moloney murine leukemia virus reverse transcriptase (Life Technologies) in buffer containing 50 mM Tris-HCl, pH 8.3, 75 mM KCl, 10 mM DTT, 3 mM MgCl2, 500 nM dNTP, 0.1 mg/ml BSA, and 272.5 U/ml RNase inhibitors (Amersham Pharmacia Biotech, Piscataway, NJ). PCR assays were performed using 24 µl and 1 µl of reverse-transcriptase product for IRF-7 and GAPDH mRNA amplification, respectively, in 100 mM Tris-HCl, pH 8.4, 500 mM KCl, 15 mM MgCl2, 200 mM dNTP, 15 pmol of [{gamma}-32P]-labeled primers, and 1.25 U of Taq DNA polymerase (Amersham Pharmacia Biotech). Nucleotide sequence of primers used is as follows: F7/1, 5'-CAG CTG CGC TAC ACG GAG-3', and F7/2, 5'-GCC AGC TCT AGG TGG GCT-3'. The PCR reaction mixture was subjected to 25 cycles of denaturation for 1 min at 95°C, annealing for 2 min at 58°C, and polymerization for 2 min at 72°C. PCR products were analyzed on a 5% denaturing polyacrylamide gel. Primers for GAPDH were used as described previously (33).


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
In vivo binding activities on RANTES promoter in virus-infected U937 cells

Footprinting primers were designed to analyze in vivo protein-DNA interactions occurring in the proximal -10 to -130 region of the RANTES promoter (primers 1, 2, 3 for the noncoding strand; Fig. 1GoA). Sendai virus-infected cells were submitted to DMS (dimethyl sulfate) treatment which methylates G residues and to a lesser extent A residues; genomic DNA was then extracted and submitted to piperidine treatment to cleave methylated residues. Piperidine-cleaved DNA was then amplified by ligation-mediated PCR using specific primers for the RANTES promoter, as detailed in Fig. 1GoA. A G-specific sequence ladder was also generated as reference and analyzed by sequencing. Initial footprinting experiments in U937 cells revealed that only the ISRE (-124 to -97) and NF-{kappa}B (-46 to -30) sites were targeted by constitutive or virus-inducible binding activities (Fig. 2GoA). A weak constitutive protection was observed at the NF-{kappa}B sites, reflected by an increase in the methylation of -33 and -43 G residues and accompanied by a decrease in -44 to -45 G methylation (Fig. 2GoA, compare lanes 1 and 2). This protection correlated with constitutive RANTES mRNA production detected by RPA in uninfected U937 cells (Fig. 2GoB, lane 1). Following virus infection, protection of the NF-{kappa}B sites and hypermethylation of the -43G residue strongly increased by 2 h after induction and peaked between 6 and 10 h (Fig. 2GoA, lanes 3–7). In other experiments, protection of the NF-{kappa}B sites was detected as early as 30 min after virus infection (data not shown); the induced protection was sustained but decreased after 12 and 24 h of induction (Fig. 2GoA, lanes 8 and 9). A similar virus-inducible occupancy of the ISRE site was also detected, as indicated by increased methylation of -107, -113, and -119A residues, as well as the decrease in methylation of -105, -111, and -118 G residues (Fig. 2GoA, lanes 2–7). The kinetics of binding to the ISRE region followed the same pattern as the NF-{kappa}B sites: protein-DNA interaction appeared after 2 h of induction and peaked between 6 and 10 h of virus induction. Protection was reduced after 12 h and disappeared by 24 h, indicating a more transient in vivo binding to the ISRE site (Fig. 2GoA, lanes 8 and 9). Changes in the coding strand methylation pattern of RANTES promoter were also examined using specific primers (data not shown); modifications were not observed at either the NF-{kappa}B or ISRE site, suggesting that the protein-DNA interaction may be asymmetric, as discussed previously (29).



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FIGURE 2. Analyses of the proximal region of RANTES gene promoter in Sendai-infected U937 cells. A, In vivo genomic footprinting of the noncoding strand of the proximal (-125 to -25) region of RANTES gene promoter in Sendai-infected U937 cells. Naked DNA was treated in vitro by DMS (NAKED). U937 cells were either nonstimulated (-) or stimulated by Sendai virus for the time indicated above each lane (2, 4, 6, 8, 10, 12, or 24 h) and then treated with DMS. Genomic DNA was extracted and treated with piperidine. All DNA samples were amplified by LM-PCR and visualized on Long-Ranger sequencing gel. B, RPA. Total RNA extracted (5 µg) from U937 cells untreated or stimulated for the same times was subjected to RPA using the CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migration of labeled fragments protected from RNase digestion and corresponding to either RANTES chemokine mRNA or control GAPDH mRNA.

 
The kinetics of both NF-{kappa}B and ISRE binding correlated with the rapid induction of endogenous RANTES transcription; RANTES mRNA progressively increased 5- to 7-fold at 2 h after virus infection to a maximum of 30- to 40-fold between 6 and 10 h. RANTES mRNA levels were subsequently sustained at 12 and 24 h after infection (Fig. 2GoB, lanes 2–8). These results demonstrate a correlation between transcription of the RANTES gene and the in vivo occupancy of both ISRE and NF-{kappa}B sites, with an expected delay between binding of transcription factors and production of mRNA.

Differential in vivo binding on RANTES promoter in virus-infected 293 cells

Genomic footprinting analyses performed with 293 cells revealed distinct patterns of in vivo binding to NF-{kappa}B and ISRE sites (Fig. 3GoA). No constitutive protection was observed in nonstimulated cells at either site (Fig. 3GoA, comparison of lanes 1 and 2). Following virus infection, protection of the NF-{kappa}B sites and increased methylation of -33 and -43 G residues were observed (Fig. 3GoA, lane 3 compared with lane 2). In contrast to U937 cells, in which -33G is constitutively methylated and remained unchanged in virus-induced cells, methylation at both the -33 and -43G residues was modified by virus infection of 293 cells (Fig. 3GoA, comparison of lanes 3 and 5). Increased methylation of -101, -107, and -113 A residues of the ISRE region was detected initially at 4 h postinfection and was further increased after 6–10 h (Fig. 3GoA, lane 3 compared with lane 2, and data not shown). Protection was reduced at 12 h and disappeared by 24 h postinduction, indicating again a transient in vivo binding to the ISRE site (data not shown). In contrast to virus induction, TNF-{alpha} treatment led to the appearance of NF-{kappa}B-binding, but not ISRE-binding activity in U937 (Fig. 3GoA, comparison of lanes 3 and 5 with lane 6). Furthermore, in the absence of ISRE binding in TNF-{alpha}-treated U937 cells, only a 2- to 3-fold increase in RANTES gene expression was detected compared with the 40-fold increase after virus induction (Fig. 3GoB, lanes 4 and 5).



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FIGURE 3. Specificity of the in vivo binding induced by virus infection. A, In vivo genomic footprinting of noncoding strand of the proximal region of RANTES promoter. Naked DNA was treated in vitro by DMS (NAKED). The 293 or U937 cells were either nonstimulated (-), stimulated by Sendai virus for 12 h (SV), or treated for 2 h by TNF-{alpha} (10 ng/ml), and then treated with DMS. Genomic DNA was extracted and treated with piperidine. All DNA samples were amplified by LM-PCR and visualized on Long-Ranger sequencing gel. B, RPA. Total RNA extracted (5 µg) from the same cells untreated or stimulated by virus or by TNF-{alpha} was subjected to RPA using the CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migration of labeled fragments protected from RNase digestion and corresponding to either RANTES chemokine mRNA or control GAPDH mRNA.

 
Kinetic analyses performed in Sendai virus-infected 293 cells indicated that protection of the NF-{kappa}B sites appeared after 4 h, further increased at 6 h (Fig. 4GoA, lanes 4 and 5 compared with lane 2), and was sustained even after 24 h, although a slight decrease in methylation intensity of the -33 and -43 G residues was observed (Fig. 4GoA, lanes 6–9). Concomitant with modifications in protein-DNA occupancy on both ISRE and NF-{kappa}B sites, RANTES mRNA was undetectable before infection, but appeared at 8 h after infection (Fig. 4GoB, lanes 1–5); RANTES mRNA levels further increased 5-fold at 10 h, and 30-fold at 12 and 24 h of virus induction (Fig. 4GoB, lanes 6–8). Using the -50 to -26 NF-{kappa}B region of RANTES promoter in EMSA, the p50-p65 complex was identified as responsible for in vivo binding activity induced by either TNF-{alpha} or Sendai virus (34) (Fig. 4GoC). These data indicate that although the NF-{kappa}B complex was induced and participated in virus induction of the RANTES promoter, only the ISRE-binding activity was specifically targeted by virus infection.



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FIGURE 4. Kinetics of NF-{kappa}B binding on RANTES gene promoter. A, In vivo genomic footprinting of the -25 to -50 region of RANTES promoter. Naked DNA was treated in vitro by DMS (Naked). The 293 cells were either nonstimulated (-) or stimulated by Sendai virus for the time indicated above each lane (2, 4, 6, 8, 10, 12, or 24 h). DNA extracted from these cells was amplified by LM-PCR and visualized on Long-Ranger sequencing gel. B, RPA. Total RNA extracted (5 µg) from 293 cells untreated or stimulated for the same times was subjected to RPA using the CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migration of labeled fragments protected from RNase digestion and corresponding to either RANTES chemokine mRNA or control GAPDH mRNA. For RANTES mRNA, a 72-h exposure of the gel is presented, whereas a 16-h exposure of the gel is shown for GAPDH control mRNA. C, EMSA analysis was performed with the NF-{kappa}B site (-50 to -26) of the RANTES promoter. Nuclear extracts from 293 cells were either unstimulated (-) or stimulated for different times (2, 4, 6, 8, 10, or 12 h) with Sendai virus. The position of virus-induced p65-p50 complex is indicated by an arrow. Complex composition was analyzed by supershift analysis. Untreated or Sendai virus-induced nuclear extracts were incubated with anti-p65 ({alpha}p65), anti-p50 ({alpha}p50), and anti-c-Rel ({alpha}c-Rel) Abs. Ternary complex formed with anti-p65 (p65*) or anti-p50 (p50*) Abs is indicated. Position of virus-induced p65-p50 complex is indicated by an arrow.

 
Regulation of RANTES gene expression by IRF-7

Recent studies indicate that two members of the IRF family, IRF-3 and IRF-7, participate in the virus induction of type I IFN genes via an autostimulatory mechanism (22). The involvement of IRF-7 in virus-inducible transcription of RANTES was determined by RPA in 293 cells expressing a dominant negative IRF-7 mutant carrying a deletion in the N-terminal DNA binding domain (Fig. 5GoA). Expression of {Delta}N IRF-7 inhibited by more than 70% the virus-induced levels of RANTES mRNA (Fig. 5GoA, lanes 2 and 4). To assess whether IRF-7 can account for the differences in RANTES induction between U937 and 293 cells, the level of IRF-7 expression was determined by RT-PCR analysis (Fig. 5GoB). Interestingly, a low level of IRF-7 mRNA was detected in U937 in the absence of infection, whereas no IRF-7 mRNA was amplified in nonstimulated 293 cells (Fig. 5GoB, lanes 1 and 3). As expected, infection of both cell types with Sendai virus further enhanced IRF-7 gene expression, with a higher level in infected U937 cells (Fig. 5GoB, lanes 2 and 4). As a control, high levels of IRF-7 mRNA were detected in 293 cells inducibly expressing IRF-7, and were dramatically increased after virus infection (Fig. 5GoB, lanes 5 and 6). These observations indicate that differences in IRF-7 expression exist between 293 and U937 cells and may be responsible in part for the constitutive expression of RANTES observed in unstimulated U937 cells. The absence of constitutive expression of IRF-7 in 293 cells also suggests that virus-induced RANTES transcription is dependent on de novo synthesis of the IRF-7 gene product.



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FIGURE 5. Regulation of RANTES gene expression by IRF-7. A, RPA. Total RNA extracted (5 µg) from 293 or rtTA-293 cells expressing the dominant negative form of IRF-7 (IRF-7{Delta}N) cells untreated or stimulated for 12 h was subjected to RPA using the CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migration of labeled fragments protected from RNase digestion and corresponding to either RANTES or control GAPDH mRNA. B, Detection of IRF-7 mRNA by RT-PCR. Total RNA was extracted from 293 and U937 cells (lanes 1–4) and rtTA-293 cells expressing IRF-7 induced by DOX (2 µg/ml) for 48 h (lanes 5 and 6), and stimulated or not by Sendai virus for 12 h. Total RNA (5 µg) was subjected to RT-PCR amplification using standard protocols, as described in Materials and Methods.

 
IRF-3 and IRF-7 bind to ISRE site of RANTES promoter

Next, genomic footprinting was performed in 293 cells inducibly expressing either IRF-3 or IRF-7. Although IRF-3 binds to the ISRE site after infection and is required for virus induction of the RANTES promoter, overexpression did not affect the methylation pattern of the RANTES promoter after Sendai virus infection (Fig. 6GoA, lanes 4 and 5). In contrast, IRF-7 overexpression in 293 cells induced significant changes in the protection pattern of the ISRE site after virus infection (Fig. 6GoA, lanes 6 and 7). A strong decrease in the methylation of -106, -111, and -118 G residues was detected (Fig. 6GoA, lanes 3 and 7), leading to a pattern similar to that observed in Sendai-infected U937 cells (see Fig. 2GoA, lane 7). Furthermore, subtle changes were also observed in nonstimulated cells expressing IRF-7, such as hypermethylation of -113 A usually detected after virus induction of cells, as well as slight increase in -101 and -102 A methylation (Fig. 6GoA, comparison of lanes 2 and 6). This pattern suggests that IRF-7 binds to the RANTES ISRE site and activates the RANTES promoter (Fig. 6GoB, lane 5). Activation of IRF-7 by virus widened the observed protection at the ISRE site and further increased RANTES expression by 8-fold, which was a 2-fold higher level than in the absence of IRF-7 expression (Fig. 6GoB, comparison of lanes 2 and 6). These results also highlight the necessity for virus induction to mediate IRF-3 activation (26), binding, and transactivation ability, whereas expression of IRF-7 is sufficient to confer binding and transactivation activities.



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FIGURE 6. In vivo binding of IRF-3 and IRF-7 on the proximal (-125 to -25) region of RANTES gene promoter. A, In vivo genomic footprinting of noncoding strand of the proximal region of RANTES promoter. Naked DNA was treated in vitro by DMS (NAKED). Stable rtTA-293 cells expressing IRF-3 or IRF-7 proteins were treated with DOX for 48 h to induce IRF gene expression. rtTA-293, rtTA-IRF3, and rtTA-IRF7 cells were either nonstimulated (-) or stimulated by Sendai virus for 8 h (+) and then treated with DMS. Genomic DNA was extracted and treated with piperidine. All DNA samples were amplified by LM-PCR and visualized on Long-Ranger sequencing gel. B, RPA. Total RNA (5 µg) extracted from untreated or stimulated (12 h) cells was subjected to RPA using the CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migrations of labeled fragment protected from RNase digestion and corresponding to either RANTES chemokine mRNA or control GAPDH mRNA.

 
Cooperation between IRF and NF-{kappa}B factors is required for virus induction of the RANTES promoter

To determine the individual participation of the two virus-induced pathways, genomic footprinting was performed on 293 cells expressing dominant negative forms of IRF-3 or I{kappa}B{alpha}, i.e., IRF-3({Delta}N) or I{kappa}B-{alpha} 2N, respectively (Fig. 7GoA). Overexpression of IRF-3({Delta}N) completely abolished virus-induced protection at the ISRE site; surprisingly, protection at the NF-{kappa}B site was also completely inhibited (Fig. 7GoA, compare lanes 3 and 5). However, normal virus-induced NF-{kappa}B binding was observed in EMSA performed with 293 cells expressing the IRF-3({Delta}N) mutant, demonstrating that this dominant negative mutant does not directly affect the activation and binding of the NF-{kappa}B complex (data not shown). Reciprocally, overexpression of the I{kappa}B-{alpha} dominant negative not only blocked protection at the NF-{kappa}B site, but also blocked virus-induced ISRE-binding activity (Fig. 7GoA, compare lanes 3 and 7). Overexpression of either IRF-3({Delta}N) or I{kappa}B-{alpha} 2N reduced RANTES mRNA levels by 90% (Fig. 7GoB, lanes 4 and 6 compared with lane 2). These results demonstrate that NF-{kappa}B and IRF closely cooperate in the induction of RANTES gene transcription by virus and disruption of either pathway dramatically abolishes the ability of the other to bind and activate RANTES expression.



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FIGURE 7. Cooperation between ISRE and NF-{kappa}B sites in the regulation of RANTES gene promoter. A, In vivo genomic footprinting of noncoding strand of the proximal region of RANTES promoter. Naked DNA was treated in vitro by DMS (Naked). Stable rtTA-293 cells expressing dominant negative forms of IRF-3 (IRF-3{Delta}N) or I{kappa}B-{alpha} (I{kappa}B-{alpha} 2N) proteins were treated with DOX for 48 h. rtTA-293, rtTA-IRF3{Delta}N, and rtTA-I{kappa}B-{alpha} 2N cells were either nonstimulated (-) or stimulated by Sendai virus for 8 h (+) and then were treated with DMS. Genomic DNA was extracted and treated with piperidine. All DNA samples were amplified by LM-PCR and visualized on Long-Ranger sequencing gel. B, RPA. Total RNA (5 µg) extracted from untreated or stimulated (12 h) cells was subjected to RNase protection assay using CK5 human chemokine template of the RiboQuant MultiProbe RPA kit (PharMingen). Arrows indicate the migration of labeled fragments protected from RNase digestion and corresponding to either RANTES chemokine mRNA or control GAPDH mRNA.

 
To further assess cooperativity between NF-{kappa}B and IRF transcription factors, coexpression experiments were performed using the RANTES promoter (-397 to +5) linked to the luciferase reporter gene (Fig. 8Go). In the absence of virus induction, coexpression of IRF3, IRF-7, and p65/p50 increased RANTES promoter transcription by 160-fold, whereas transfection of IRF-3, IRF-7, or p65/p50 alone led only to a 5- to 30-fold induction, respectively (Fig. 8GoA, open bars). Interestingly, in unstimulated cells, coexpression of both IRF-7 and p65/p50 resulted in a similar induction of RANTES promoter transcription (130-fold), while cotransfection of p65/p50 and IRF-3 or IRF-3 and IRF-7 caused a 25- to 30-fold increase (Fig. 8GoA, open bars). These results indicate that in the absence of virus induction, cooperation between NF-{kappa}B and IRF-7 produced a synergistic activation of RANTES promoter, whereas expression of IRF-3 alone or together with other activators resulted in a relatively modest effect on RANTES transcription. Synergism between IRFs and NF-{kappa}B was also observed in virus-induced cells: RANTES promoter activity was increased by more than 300-fold when NF-{kappa}B, IRF-3, and IRF-7 were coexpressed together compared with the 30- to 150-fold increase observed when combinations such as IRF3 + p65/p50 or IRF-7 + p65/p50 were coexpressed (Fig. 8GoA, black bars). Although the requirement for coactivator recruitment for this transcriptional synergism is not excluded, no effect of CBP expression was observed on the synergistic activation of RANTES promoter when NF-{kappa}B, IRF-3, and/or IRF-7 were coexpressed (Fig. 8GoA).



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FIGURE 8. Synergism between NF-{kappa}B and IRF-3/IRF-7 in the activation of RANTES promoter transcription. The 293 cells were transfected with a luciferase reporter plasmid containing wild-type (RANTES-Luc) (A), NF-{kappa}B mutant (RANTES m{kappa}B-Luc) (B), or mutant ISRE (RANTES mISRE-Luc) (C) RANTES promoter in the absence or presence of IRF-3, IRF-7, p65/p50, and CBP expression plasmids either alone or in the different combinations indicated below the bar graphs. At 16 h after transfection, cells were stimulated with Sendai virus (80 HAU/ml) for 8 h and harvested. Reporter gene activity was measured by dual-luciferase reporter assay. Transfection efficiency was normalized by Renilla luciferase (see Materials and Methods). The experiments were performed in triplicate, and the average fold induction was calculated.

 
To confirm that synergistic activation required both the NF-{kappa}B and ISRE sites of the RANTES promoter, similar coexpression experiments were performed using NF-{kappa}B- or ISRE-mutated RANTES promoters (Fig. 8Go, B and C). As expected, no activation or no further increase of NF-{kappa}B-mutated RANTES promoter transcription was observed when p65/p50 were transfected either alone or in combination with IRF-3 and/or IRF-7, indicating that disruption of the NF-{kappa}B binding abolished the synergistic activation observed with the wild-type promoter (Fig. 8GoB). Interestingly, coexpression of both IRF-7 and NF-{kappa}B resulted in a 70–80% inhibition of the NF-{kappa}B-mutated RANTES transcription levels observed when IRF-7 was transfected alone, in both unstimulated and virus-induced cells (Fig. 8GoB). This observation indicates that in the absence of binding to its site, NF-{kappa}B is able to interfere with IRF-7-mediated transcription of NF-{kappa}B-mutated RANTES promoter. Coexpression of IRF-3 together with IRF-7 abolished the inhibition by NF-{kappa}B. Surprisingly, CBP expression increased by more than 2-fold transcription of NF-{kappa}B-mutated RANTES by IRF-3 and IRF-7 in virus-induced cells (Fig. 8GoB, black bars). Moreover, this synergy between CBP and IRF-3/IRF-7 was not observed when p65/p50 was coexpressed, indicating again an interference of IRF-mediated activation by NF-{kappa}B when not bound to its NF-{kappa}B site in RANTES promoter. Finally, transcriptional activation of the ISRE-mutated RANTES promoter was observed only when p65/p50 was expressed alone or in combination with IRFs (Fig. 8GoC). Again, interference between NF-{kappa}B and IRF activation pathways was observed because IRF-7 coexpression with p65/p50 inhibited by 70% the NF-{kappa}B-mediated activation of the ISRE-mutated RANTES promoter in unstimulated cells (Fig. 8GoC, open bars). Altogether, these results demonstrate that synergistic cooperation among IRF-3, IRF-7, and NF-{kappa}B is required for the activation of RANTES promoter transcription.


    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
This study characterizes the regulatory control of RANTES transcription during virus infection and presents an in vivo genomic footprinting analysis of the human RANTES promoter. Studies from our group (24) and others (12) previously demonstrated the involvement of NF-{kappa}B factors and IRF-3 in the regulation of RANTES promoter. The present study identified IRF-3, IRF-7, and NF-{kappa}B as important in vivo binding factors required for the cooperative induction of RANTES transcription after virus infection. Genomic footprinting data suggest a correlation between the transcription of RANTES gene and the in vivo occupancy of both ISRE and NF-{kappa}B sites. Moreover, the transient inducibility of RANTES transcription appears to correlate with ISRE-binding activities, whereas sustained transcription is due to the in vivo occupancy of the NF-{kappa}B sites only. Using fibroblastic or myeloid cells, we showed that the kinetics and the strength of RANTES virus-induced transcription are highly dependent on the preexistence of IRFs and NF-{kappa}B, highlighting cell type specificity in the role of RANTES production following virus infection. The constitutive level and rapid induction of RANTES expression observed in myeloid U937 cells are most likely due to presence of both IRF-7 expression and NF-{kappa}B-binding activity in unstimulated cells. In contrast, virus-induced RANTES transcription in 293 cells is dependent on virus induction of NF-{kappa}B activity and on de novo synthesis of IRF-7 gene product. Genomic footprinting and EMSA further demonstrated that although NF-{kappa}B complex is induced and participates in virus induction and TNF stimulation of the RANTES promoter, only the ISRE-binding activity is specifically targeted by virus infection. This ISRE-mediated activity was further shown to be due to both IRF-3 and IRF-7 binding and transcriptional activities, the former being strictly virus inducible, whereas the latter was both constitutive and virus inducible.

Synergistic activation of RANTES transcription by NF-{kappa}B and IRF pathways

Use of the dominant negative mutant of either I{kappa}B-{alpha} or IRF-3 demonstrated that disruption of either pathway dramatically abolishes the ability of the other to bind and activate RANTES expression. This cooperation was further confirmed by transfection experiments showing that coexpression of IRF-3, IRF-7, and p65/p50 leads to maximal induction of RANTES promoter transcription even in the absence of viral infection. Use of NF-{kappa}B- or ISRE-mutated RANTES promoters demonstrated that this synergism is dependent on binding of these factors to their respective sites. As expected, cooperation between NF-{kappa}B and IRF-7 was observed in the absence of virus induction, whereas cooperation between IRF-3 and NF-{kappa}B was only observed after virus induction, highlighting again the requirement of virus-inducible activation of IRF-3 for its transcriptional activity. The ability of IRF-7 to induce RANTES transcription in the absence of viral infection was confirmed by both coexpression and RNase protection assays performed in IRF-7-expressing 293 cells. Although our results are slightly different from the modest effect of ectopic expression of IRF-7 on IFN-ß gene expression (22), they most likely reflect the fact that these experiments were performed in stably transfected 293 cells and not in transiently transfected cells. These results indicate that IRF-7 gene expression has to be tightly controlled before induction, and that an abundant accumulation of the IRF-7 protein is required for full induction of RANTES. However, an induction of IRF-7 gene transcription by the IFN-regulatory loop seems to be unlikely, because RANTES gene expression is not inducible by type I IFN either in transient transfection experiments (data not shown), or by RPA (24). The intriguing possibility that IRF-3 or NF-{kappa}B transcription factors can directly induce transcription of IRF-7 gene expression is under current investigation.

Formation of an enhanceosome on the RANTES promoter

Using cells derived from mice in which the IFN signaling pathway is disrupted, several groups recently proposed a two-step model of IFN gene activation (22, 23). Following virus infection, IRF-3, NF-{kappa}B, and the activating transcription factor-2/c-Jun complex are activated by posttranslational phosphorylation and cooperate to form a transcriptionally active enhanceosome complex, at the promoter of the immediate early IFN-ß gene, in association with the CBP/p300 coactivator and the chromatin-associated HMG proteins (35, 36). Secreted IFN produced as a consequence of this protein synthesis-independent mechanism acts through an autocrine or paracrine loop to activate the Jak/STAT pathway. IFN activation of ISGF3 (latent cytosolic transcription factor) induces the expression of the IRF-7 gene (22, 37). In the second step, virus-activated IRF-7 participates with IRF-3 in the transcriptional induction of delayed-type IFN-{alpha} genes (22). In the case of RANTES promoter, formation of an enhanceosome composed of NF-{kappa}B and/or IRF-3/IRF-7 and potential coactivators such as CBP/p300 is supported by the cooperativity between the NF-{kappa}B and IRF pathways. Synergism between IRF and NF-{kappa}B proteins is emphasized by the complete inhibition of both ISRE- and NF-{kappa}B-dependent in vivo activities by dominant negative forms of I{kappa}B{alpha} or IRF-3. However, the persistence of virus-induced NF-{kappa}B binding in 293 cells expressing the IRF-3({Delta}N) mutant argues against a direct effect of this dominant negative mutant on the NF-{kappa}B activation pathway. Similarly, the absence of activation of IRF-3 after induction by known activators of the NF-{kappa}B pathway such as TNF-{alpha} or IL-1 (38), as well as the inability of the I{kappa}B kinase (IKK) complex to phosphorylate IRF-3 either in vivo or in vitro (data not shown), is inconsistent with a direct inhibition of the IRF-3 activation pathway by I{kappa}B-{alpha} 2N. These data rather indicate that cooperation between NF-{kappa}B and IRF occurs at the promoter level and involves direct or indirect contacts between subunits of the NF-{kappa}B complex and at least IRF-3, but also probably IRF-7. Remarkably, both NF-{kappa}B and IRF-3 interact with the coactivators CBP/p300 (39, 40), and Wathelet et al. (36) demonstrated that virus infection leads to an unusually stable association of IRF-3 and IRF-7 with CBP/p300. Similarly, binding of IRF-3 and IRF-7 to the ISRE site may permit an indirect interaction with NF-{kappa}B via association with CBP/p300 coactivators. This interaction would result in the in vivo assembly of a highly specific multicomponent enhancer complex on the RANTES promoter, thus insuring transcriptional activation in response to virus infection. Furthermore, activation of both IRF-3 and IRF-7 as well as NF-{kappa}B has been observed in different primary cells, including mouse embryonic fibroblasts and monocytes/macrophages (22 and data not shown). Thus, a common virus-induced mechanism of RANTES regulation involving synergism among IRF-3, IRF-7, and NF-{kappa}B is also active in primary cell models. Interestingly, virus transcription of another member of the chemokine family, the IFN-{gamma}-inducible protein-10 ({gamma}-IP-10) gene, also requires cooperation of the ISRE elements with the adjacent NF-{kappa}B site (41). As in the case of RANTES, {gamma}-IP-10 mRNA is induced by virus in 293 cells and by TNF-{alpha} and virus in U937 cells, and is also strongly inhibited by both IRF-3({Delta}N) and I{kappa}B-{alpha} 2N overexpression (data not shown). Such interactions between IRF and NF-{kappa}B families represent the point of convergence between these two virus-inducible pathways and denote a recurrent theme in the coordinate regulation of virus-inducible cytokine genes.


    Acknowledgments
 
We thank Dr. Illka Julkunen for reagents used in this study. We also thank members of the Molecular Oncology Group, Lady Davis Institute, for helpful discussions.


    Footnotes
 
1 This research was supported by grants from the Medical Research Council of Canada and Canadian Foundation for AIDS Research. M.A. and P.G. were supported by Fonds de la Recherche en Santé du Québec (FRSQ) Postdoctoral Fellowships, P.R. by a FRSQ-Fonds pour la Formation de Chercheur et d’Aide à la Recherche (FCAR) Studentship, R.L. by a Fraser Monat McPherson Fellowship from McGill University, and J.H. by a Medical Research Council Senior Scientist award. Back

2 Address correspondence and reprint requests to Dr. John Hiscott, Lady Davis Institute for Medical Research, 3755 Cote Ste. Catherine, Montreal, Quebec, Canada H3T1E2. Back

3 Abbreviations used in this paper: IRF, IFN-regulatory factor; CBP, CREB-binding protein; DMS, dimethyl sulfate; DOX, doxycycline; HAU, hemagglutinating unit; I{kappa}-B-{alpha}, inhibitor of NF{kappa}-B; ISRE, IFN-stimulated response element; LM-PCR, ligation-mediated PCR; RPA, RNase protection analyses. Back

4 R. Lin, P. Giening, Y. Mamane, and J. Hiscott. Submitted for publication. Back

Received for publication December 6, 1999. Accepted for publication March 6, 2000.


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Curcumin Inhibits Activation of V{gamma}9V{delta}2 T Cells by Phosphoantigens and Induces Apoptosis Involving Apoptosis-Inducing Factor and Large Scale DNA Fragmentation
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