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Copyright © 2004 Oxford University Press The high-affinity Sp1 binding site in the HTLV-1 promoter contributes to Tax-independent basal expression 1Department of Biochemistry and Molecular Biology and 2Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1870, USA *To whom correspondence should be addressed. Tel: +1 970 491 0420; Fax: +1 970 491 0494; Email: jnyborg/at/lamar.colostate.edu Received February 22, 2004; Revised March 23, 2004; Accepted April 15, 2004. Abstract Transcriptional activation of human T-cell leukemia virus type 1 (HTLV-1) requires many cellular proteins and the virally encoded transcription factor Tax. Tax binds the three viral cAMP-response elements (CREs) with ATF/CREB (activating transcription factor/cAMP-response element-binding protein) and recruits the cellular coactivators CBP/p300. HTLV-1 also utilizes other cellular transcription factors that bind to the promoter to regulate transcription. One of these factors, Sp1, has been shown to bind to the viral promoter at two elements; one located within the third viral CRE, and the second located between the second and third viral CREs. The functional significance of Sp1 binding at each of these regions of the viral promoter is not completely understood. We set out to characterize Sp1 binding and to evaluate the functional significance of Sp1, both in the absence and presence of Tax. We found that Sp1 binds preferentially to the element located between the second and third viral CREs, and modestly activates transcription in vitro and in vivo. Sp1 was detected at the integrated HTLV-1 promoter in vivo. Surprisingly, point mutagenesis of the strong Sp1 binding site rendered the HTLV-1 reporter plasmid insensitive to Sp1 activation, and dramatically reduced basal transcription in vivo. These data indicate a role for Sp1 in basal level transcription of HTLV-1. INTRODUCTION Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of an aggressive form of cancer called adult T-cell leukemia/lymphoma (1,2). The virus is also the causative agent of other diseases, including tropical spastic paraparesis (TSP/HAM), a neurodegenerative disorder similar to multiple sclerosis (reviewed in 3–5). After infection, HTLV-1 integrates randomly into the host cell genome, and is generally expressed at very low levels. High-level expression of the virus requires strong transcriptional activation mediated by the virally encoded transactivator Tax. Many cellular proteins have also been implicated in transcriptional regulation of the virus. The best characterized promoter elements of the virus are the three imperfectly conserved 21-bp repeats, called viral cAMP-response elements (CREs). These elements carry an octanucleotide CRE core immediately flanked upstream and downstream by GC-rich sequences. The viral cAMP-responsive elements (CREs) serve as binding sites for Tax in complex with the cellular transcription factor CREB (cAMP-responsive element-binding protein) [or other members of the activating transcription factor (ATF)/CREB family of transcription factors] (6–9). Tax binds to the viral CREs through protein–DNA interactions with the GC-rich sequences (10–13) and protein–protein interactions with CREB (6,8). The formation of this promoter-bound Tax–CREB complex is critical for the recruitment of the cellular coactivators CBP and p300 (6,7,9,14–19). It has also been reported that the cellular transcription factor Sp1 binds to the promoter proximal viral CRE, and competes with CREB for binding to this sequence (20,21). In addition, the region between the second and third viral CRE (–117 to –163) binds several cellular proteins, including Sp1 and Ets (22–27). Specifically, Sp1 has been shown to bind a GC-rich sequence within this region (22,24). Studies have also suggested that this region may be responsive to Tax (26,28). Although Sp1 has been shown to bind these two distinct regions within the HTLV-1 transcriptional control region, the significance of each site remains to be fully elucidated. Sp1 is a cellular transcription factor involved in a wide variety of processes, and has been shown to bind to >1000 different promoters to regulate transcription (29,30). It was originally identified as the protein that binds GC elements in the SV40 promoter (31). Sp1 is expressed in all tissue types examined (32). It is an essential protein, as homozygous knockouts of Sp1 in mice result in embryonic lethality (33). The C-terminal DNA binding domain of Sp1 contains three zinc fingers that bind with high affinity to sequences with high GC content, called GC boxes (34). Sp1 has been shown to play a role in transcriptional activation, repression and maintenance of basal transcription of both cellular and viral genes (35). Sp1 has also been shown to be important for the transcription of genes with promoters that do not contain TATA boxes (36–39). In this study, we set out to characterize the role of Sp1 in HTLV-1 transcription further. We were first interested in establishing the recognition elements on the HTLV-1 promoter responsible for high-affinity Sp1 binding. Quantitative DNA binding assays demonstrated that Sp1 had the highest affinity for the region between the second and third viral CREs. Chromatin immunoprecipitation assays revealed that Sp1 was present at the chromosomally integrated HTLV-1 promoter. However, Sp1 only modestly activated HTLV-1 transcription when examined both in vivo and in vitro. Finally, a double point mutation of the site responsible for high affinity Sp1 binding dramatically reduced basal level expression of the virus in vivo, while having no effect on Tax transactivation. These results define a role for Sp1 in Tax-independent, constitutive expression of HTLV-1. MATERIALS AND METHODS Electrophoretic mobility shift assay End-labeled, double-stranded (ds) oligonucleotide probes (0.15 nM) were incubated with increasing amounts of purified Sp1 (Promega) for 30 min on ice as described previously (15). Protein–DNA complexes were resolved by electrophoresis on 5% non-denaturing polyacrylamide gels. The top strand sequences of the oligonucleotide probes used in the electrophoretic mobility shift assays (EMSAs) are as follows: consensus Sp1, 5′-ATTCGATCGGGGCGGGGCGAGC-3′; vSp1, 5′-GATCTCCACCAAGAACCACCCATTTCCTA-3′ (–149 to –127) (the Sp1 binding GC-box is underlined); vCRE-1 (–251 to –231), 5′-GATCTCTAAGGCTC TGACGTCTCCCCCCGGA-3′; vCRE-2 (–203 to –183), 5′-GATCTGCTAGGCCCTGACGTGTCCCCCTGAA-3′; and vCRE-3 (–103 to –83), 5′-GATCTCTCAGGCGT TGACGACAACCCCTCAC-3′. The octanucleotide CRE sequence is underlined in each vCRE. For the determination of relative binding affinities, we ensured that the concentration of free Sp1 approximated total concentration of Sp1 by keeping the amount of labeled DNA probe constant and at a low level. Both bound and free probe were quantitated to determine the percent of DNA in complex with Sp1. Analysis of the data was performed with ImageQuant software and Kaleidagraph. In vitro transcription templates All DNA templates have been described previously (40). The pHTLV-1/G-less cassette carries the full promoter (upstream to –306), driving expression of a 380-bp G-less cassette. The p4TxRE/G-less cassette carries four reiterated copies of the third viral CRE cloned immediately upstream of the HTLV-1 core promoter (–52), driving expression of a 380-bp G-less cassette. Chromatin assembly Nucleosomes were assembled on DNA templates as described previously (41). Following the addition of the DNA, ATP (3 mM), creatine phosphokinase (1 µg/ml) and phosphocreatine (30 mM) were added in a 70-µl reaction containing 10 mM HEPES (K+) (pH 7.6), 50 mM KCl, 5 mM MgCl2 and 5% (v/v) glycerol. Briefly, histone octamers were preassembled with Drosophila NAP-1 (8:1 dNAP-1/core histones) on ice for 30 min. The supercoiled plasmids were assembled into chromatin using dAcf1 and Xenopus histones, at a 0.6:1.0 histone to DNA ratio, overnight at 27°C (42). In vitro transcription assays Following chromatin assembly, preinitiation complexes were formed on 150 ng of the plasmid DNA, as described previously (42). All reactions contained 100 µM acetyl CoA (United States Biochemical). CEM (an HTLV-1-negative T-cell line) cell nuclear extract (70 µg) was added immediately following the addition of the activators and/or coactivator. Optimal amounts of Sp1 were empirically determined by titration over a wide concentration range of purified protein. Transcription from the pHTLV-1/G-less chromatin template was analyzed in the presence of Sp1 (16 nM), p300 (20 nM) and Tax (280 nM), as indicated. Following a 60-min preincubation reaction at 30°C, RNA synthesis was initiated by the addition of 250 µM ATP, GTP, CTP and 12 µM UTP plus 0.8 µM [32P-α]UTP (3000 Ci/mmol; New England Nuclear). Transcription reactions were processed and analyzed as described previously (12). Molecular weight markers (radiolabeled HpaII-digested pBR322) were used to estimate the size of the RNA products. Chromatin immunoprecipitation assays Chromatin immunoprecipitation (ChIP) assays were performed as described previously (43). Formaldehyde cross-linked chromatin from 106 (SLB-1) or 107 (CHOK1-Luc) cells/antibody was used for immunoprecipitation. Cross-linking reactions were quenched with 125 mM glycine, cells were lysed, and chromatin was sonicated to obtain an average DNA length of 500 bp. Following centrifugation, the chromatin was diluted 10-fold, and precleared with a protein A agarose slurry containing salmon sperm DNA and bovine serum albumin (Upstate Biotechnology). Precleared chromatin (1 ml) was incubated with 1–5 µg of antibody overnight at 4°C, followed by immunoprecipitation with protein A agarose. Protein A agarose was precoated with the appropriate secondary antibody when the Tax monoclonal antibody was used. Immunoprecipitated complexes were washed and eluted twice with 200 µl of elution buffer. The protein–DNA cross-links were reversed by heating at 65°C overnight, and 10% of the recovered DNA was used for PCR amplification (27–30 cycles). Antibodies For the ChIP assays, antibodies against Sp1 and CBP were purchased from Santa Cruz Biotechnology. Tax monoclonal antibody (Hybridoma 168B17-46-92) was obtained from the National Institutes of Health (NIH) AIDS Research and Reagent Program. ChIP primers The HTLV-1 promoter primer set for PCR amplification of chromatin from SLB-1 cells was as follows: –290, 5′-TT CCGAGAAACAGAAGTCTG-3′; –31, 5′-CTCCTGCTAG TTTATTGAGC-3′. The HTLV-1 promoter primer set for PCR amplification of chromatin from CHOK1-Luc cells was as follows: –349, 5′-GTGAGGGGTTGTCGTCA-3′; –81, 5′-AATGACCATGAGCCCCA-3′. Cell culture CEM cells, Jurkat T-cells and HTLV-1-transformed SLB-1 cells were cultured in Iscove’s modified Dulbecco’s medium supplemented with 10% fetal bovine serum (FBS), 2 mM l-glutamine and penicillin–streptomycin. Hamster CHOK1-Luc cells (44) were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS, 2 mM l-glutamine, penicillin–streptomycin and 500 µg/ml of G418 (Geneticin; Invitrogen). Mammalian expression plasmids and transient transfection assays Sp1 was expressed from the pCMV-Sp1 plasmid (courtesy of Robert Tjian). The HTLV-1 Tax expression plasmid has been described previously (45). The reporter plasmid, pHTLV-1/Luc, carries the HTLV-1 promoter driving the luciferase gene. For transient cotransfection assays, cells were grown to a density of 106 cells/ml and transfected with Lipofectamine (Life Technologies, Inc.) and a constant amount of DNA for 5 h. The cells were incubated for 19 h before harvest. Cells were lysed and luciferase activity was measured using the Dual-Luciferase reporter Assay System with a Turner Designs model TD 20-e luminometer. Luciferase activity was normalized to pRL-TK vector (Promega), which encodes the Renilla luciferase from HSV-TK promoter, as an internal control. Site-directed mutagenesis The pHTLV/ΔvSp1-Luc reporter plasmid was prepared by PCR-based site-directed mutagenesis. The top strand of the primer set was as follows: 5′-GGGAAGCCACCAA GAACCAAACATTTCCTCCCC-3′. The two underlined nucleotides in the GC box were changed from C (wild type) to A. The mutation was verified by DNA sequence analysis of the full promoter and the 5′ end of the luciferase gene. RESULTS Quantitative analysis of Sp1 binding to HTLV-1 promoter elements Previous studies have shown that Sp1 binds to two distinct sites in the HTLV-1 promoter, one located within a short GC-rich region between the second and third viral CRE (22,24), and the second located within the third (promoter proximal) viral CRE (20,21). We were interested in determining the relative binding affinities of Sp1 for each of these sites. For these studies, we used EMSA to characterize Sp1 binding. Although Sp1 binding was previously shown to occur at the third viral CRE, we tested all three viral CREs (vCRE-1, -2 and -3), since they each contain highly conserved GC-rich sequences. We also tested Sp1 binding to the GC-rich region located between the second and third viral CRE (vSp1; –149 to –127) (see Fig. Fig.1A).1
EMSA of Sp1 binding at each of these sequences is shown in Figure Figure1B.1 Sp1 binds to the HTLV-1 promoter in vivo Although it has been clearly established that Sp1 binds to the HTLV-1 promoter in vitro, we were interested in investigating whether Sp1 binds to the proviral promoter under physiological conditions in the HTLV-1 productively infected human T-cell line SLB-1. ChIP was used to investigate the binding of Sp1 in these cells. Cross-linked SLB-1 chromatin was immunoprecipitated with an antibody to Sp1 and the purified genomic DNA was amplified with primers specific to the HTLV-1 promoter (–31/–290). As shown in Figure Figure2A,2
Since SLB-1 cells express large amounts of Tax protein, the previous experiment revealed Sp1 binding to the HTLV-1 promoter in the presence of Tax. However, since Sp1 has been shown to be involved in basal transcription, we were interested in comparing Sp1 binding in the absence and presence of Tax. For these experiments, we used a cell line that contained the HTLV-1 5′ promoter, driving luciferase expression, stably integrated in the genome of the cell line CHOK1 (44). In the absence of Tax, the HTLV-1 promoter in this cell line is transcriptionally repressed, exhibiting low levels of luciferase activity [data not shown and (44)]. Upon transfection of a plasmid that expresses Tax, strong activation of the HTLV-1 promoter was observed (44). Figure Figure2B2 Functional significance of Sp1 binding to the HTLV-1 long terminal repeat (LTR) To determine the functional role of Sp1 in living cells, we examined the transcriptional effects of Sp1 on the HTLV-1 promoter in transient transfection assays. In the ChIP assays shown in Figure Figure2,2
To examine further the role of Sp1 in HTLV-1 transcription, the function of purified, recombinant Sp1 in an in vitro transcription assay was measured. A DNA template carrying the natural HTLV-1 promoter driving synthesis of a 380-nucleotide guanine-less transcript was used (see Fig. Fig.4A).4
Since the vSp1 site has been identified as the high-affinity binding site for Sp1 on the HTLV-1 promoter, we were interested in testing whether this site contributes to the 2-fold Sp1 activation observed in the in vitro transcription assay described above. To perform this experiment, we used a DNA template that carries four reiterated copies of the third viral CRE, cloned upstream of the first 52 bp of the core HTLV-1 promoter (see Fig. Fig.4C).4 Sp1 plays a role in constitutive expression of HTLV-1 in vivo As shown above, functional assays with Sp1 revealed only modest activation of HTLV-1 transcription both in vitro and in vivo. We reasoned that this modest activation may be due to near saturating levels of endogenous Sp1 present in the Jurkat cells and the CEM nuclear extracts. This endogenous Sp1 may have been sufficient for HTLV-1 transcription, thereby masking the effects of exogenous Sp1. To evaluate endogenous Sp1 levels, western blot analysis was performed. Figure Figure5A5
To circumvent this problem, and to test directly the role of Sp1 in HTLV-1 transcription, site-directed mutagenesis was used to create a double point mutation in the high-affinity vSp1 site. This site was selected as Sp1 binds to this region with a 3-fold higher affinity than vCRE-3, as shown above. This mutation left the remainder of the HTLV-1 reporter plasmid fully intact. We then compared this construct, named pHTLV/ΔvSp1-Luc, with the wild-type reporter plasmid in transient transfection assays. Surprisingly, the basal level of transcription from pHTLV/ΔvSp1-Luc was significantly reduced (15-fold) compared with the wild-type HTLV-1 reporter plasmid (Fig. (Fig.5B).5 DISCUSSION Previous studies have shown that Sp1 binds to two distinct promoter elements in the HTLV-1 promoter. The first is a GC box located between the second and third viral CRE (22,24). This site was originally identified by DNase I footprinting, and purified Sp1 was shown to bind between nucleotides –149 and –127 of the HTLV-1 promoter (vSp1) (22). This sequence is functionally responsive to a transfected Sp1 expression vector in Sp1-deficient Schneider cells, and cooperates with the cellular transcription factor Ets in HTLV-1 transcriptional activation (24). The second Sp1 binding site is located within the upstream GC-rich sequence of the third viral CRE (vCRE-3) (20,21). This sequence has also been shown to bind purified Sp1, and is functionally responsive to Sp1. Unfortunately, the respective contribution of these two sites to HTLV-1 transcription by Sp1 has not been addressed. In this study, we set out to compare the relative binding affinities of Sp1 for these two regions. Quantitative EMSAs revealed that Sp1 binds with 3-fold higher affinity to the vSp1 site relative to the vCRE-3 site, a result corroborated by oligonucleotide competition assays. The affinity of Sp1 for the vSp1 site was within 2-fold of that observed for a consensus Sp1 site, indicating relatively high affinity binding. To establish the physiological relevance of Sp1 binding, we also tested whether Sp1 bound to the chromosomally integrated HTLV-1 promoter in vivo. Using ChIP, Sp1 binding on the integrated HTLV-1 promoter was detected in two cell lines. Sp1 binding was comparable in the absence and presence of Tax, suggesting that under conditions of strong HTLV-1 transcriptional activation, Sp1 binding remains unchanged. Together, these binding data suggest that Sp1 plays a physiological role in the regulation of basal HTLV-1 transcription, and that the effects of Sp1 are likely mediated primarily through the vSp1 site. The two previous studies that defined the promoter proximal viral CRE as the major Sp1 binding site did not simultaneously examine Sp1 binding at vSp1 (20,21), and therefore may have been unaware of the significance of this element. Although the affinity of Sp1 for vCRE-3 is 75 nM (compared with 23 nM for vSp1) under conditions of high Sp1 protein concentrations, it is probable that Sp1 also binds to the third viral CRE. However, since CREB displaces Sp1 from this sequence (21), and since the binding affinity of CREB for vCRE-3 is only 5 nM, it is unlikely that Sp1 occupies this site under most conditions in vivo. We also examined the transcriptional effects of Sp1 both in transient transfection assays and in in vitro transcription assays using chromatin-assembled DNA templates. We found that in all cases, Sp1 only modestly activated HTLV-1 transcription. However, we found that endogenous Sp1 was present in the cell lines and extracts used in the assays, and reasoned that this may account for the low-level activation observed upon Sp1 addition. To address this issue, we prepared a double point mutation in the GC box at the vSp1 binding site (CC –135/–136 → AA) and found that basal transcription levels in the transient transfection assay were dramatically reduced. Interestingly, this mutation had no effect on Tax transactivation. These data support a prominent role for Sp1 in basal HTLV-1 expression and raise the question of whether Sp1 participates in activated viral transcription. We have not observed a synergistic effect of Sp1 on Tax transactivation in vivo or in vitro (data not shown), however it is has been shown that Sp1 cooperates with the cellular transcription factors Ets and p53 in Tax-independent activated transcription (24,48). Perhaps the significantly higher levels (15-fold) of basal transcription observed with the wild-type HTLV-1 promoter, relative to the vSp1 mutant HTLV-1 promoter, reflect a synergy between Sp1 and other cellular factors binding within this region. Together, the data indicate that Sp1, specifically via the vSp1 site, is required for supporting physiological expression of the HTLV-1 genome in the absence of Tax. ACKNOWLEDGEMENTS We thank Isabelle Lemasson and Nick Polakowski for their significant intellectual contributions to this research. We also thank Teh Jeang for the CHOK1-Luc cells and Robert Tjian for the Sp1 expression plasmid. This work was supported by NIH grant R01 CA55035. REFERENCES 1. Poiesz B.J., Ruscetti,F.W., Gazdar,A.F., Bunn,P.A., Minna,J.D. and Gallo,R.C. (1980) Detection and isolation of type C retrovirus particle from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. Proc. Natl Acad. Sci. USA, 77, 7415–7419. [PubMed] 2. Yoshida M., Miyoshi,I. and Hinuma,Y. (1982) Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease. Proc. Natl Acad. Sci. USA, 79, 2031–2035. [PubMed] 3. Manns A., Hisada,M. and La Grenade,L. 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