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GROWTH, DIFFERENTIATION, AND APOPTOSIS
Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
Submitted 22 December 2004 ; accepted in final form 15 August 2005
| ABSTRACT |
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cell cycle; transcriptional control
The biological activity of E2F6 is not fully understood, although current studies support a unique role for E2F6 as a transcriptional repressor. Recent studies have defined the structure of the human and mouse E2F6 gene, which is composed of eight exons and is subject to alternative splicing that may give rise to as many as three distinct E2F6 gene products (3, 10, 11, 21, 22). The unique structural feature of E2F6 compared with the other E2Fs is that it lacks the carboxy-terminal domains for pocket protein binding and transactivation (6, 26). E2F6 has instead a repression domain shown to associate with members of the mammalian polycomb complex, and it is believed that via this interaction, it binds to promoter regions to repress E2F-responsive genes (27). It has been shown that E2F6 overexpression can exert an inhibitory effect on S phase entry and can induce subsequent proliferative arrest (S phase accumulation) in NIH 3T3 cells (1, 6). To elaborate further on the biological role of E2F6, we have followed up the cloning of the human and mouse E2F6 promoters (11, 12, 21, 22) with an investigation of the endogenous expression profile of the gene, as well as its transcriptional regulation during the cell cycle. The data reported here show that the human E2F6 gene is regulated in a cell cycle-specific manner and that its transcriptional control may be mediated to a significant extent by E2F1.
| EXPERIMENTAL PROCEDURES |
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-galactosidase (
-gal) activity] of whole cell extracts. 5'-Rapid amplification of cDNA ends (5'-RACE) was carried out using GeneRacer (Invitrogen) with mRNA isolated from cells. mRNA was decapped and ligated to the kit oligo. mRNA was reverse transcribed to provide cDNA for the 5'-RACE. Amplification was then performed with a gene-specific primer and a primer complementary to the kit oligo. Purification, cloning, and sequencing revealed the location of the transcription start site. Cell lines and cell culture. HEK-293 cells were grown in DMEM (GIBCO) at pH 7.28 with 10% fetal bovine serum and 0.1% gentamicin reagent solution (GIBCO). MCF-7 cells were grown in DMEM at pH 7.28 with 5% fetal bovine serum, 0.1% gentamicin reagent (GIBCO), and 1% MEM nonessential amino acid solution (GIBCO). Cells were maintained at 37°C and 5% CO2.
Transient transfection. Cells were seeded to a density of 1.0 x 106 in 100-mm plates or to 3.0 x 105 in 60-mm plates. During the exponential growth phase 24 h after seeding, cells were transfected with plasmid DNA using Fugene transfection reagent (Roche) according to the manufacturer's recommendations.
Generation of stable clones.
The cytomegalovirus (CMV) promoter was excised from pcDNA3 (5.4 kb) with NruI and EcoRV (Invitrogen). An E2F6 promoter-luciferase fusion was removed from an existing pGL3-Basic vector with ClaI and XbaI (Invitrogen) and blunted with Klenow fragment (Invitrogen). Ligation between the pcDNA3-CMV and the luciferase-promoter fragment yielded the desired fusion construct containing resistance to G418 (neomycin). DH5
cells were transformed with the ligation and plated on agar plates with ampicillin at 37°C. Plasmids were isolated from selected colonies and checked for correct insertion orientation. Cells were transiently transfected with the luciferase fusion construct in a 100-mm plate as described above. Twenty-four hours after transfection, cells growing at near confluence were treated with 100 mg/ml G418 to a final concentration of 2.5 µg/ml for 810 days. Visible colonies were selected and grown in media containing G418 at 2.5 µg/ml. Cell samples from each plate were tested for luciferase expression (17).
Plated cell synchronization for time course. Adherent cells were treated with 1 mg/ml nocodazole (Sigma) to a final concentration of 250 ng/ml (6) to impose a cell cycle block at G2/M. Cells were incubated for 1620 h at 37°C and then released with fresh medium.
Reporter gene assays.
Luciferase assays were performed with a luciferase reporter gene assay kit (Roche no. 1897667), and
-gal assays (16) were performed with a
-gal kit (Stratagene no. 200383).
Western and Northern blots. Whole cell extract was prepared with 1x cell lysis buffer (Roche no. 1897667) in sterile double-distilled water. Buffer was treated with the protease inhibitor Complete Mini (Roche) at one tablet per 10 ml of buffer. The protein concentration of the whole cell lysate obtained from each time course sample was measured by the bicinchoninate protein assay method (Pierce) according to the manufacturer's recommendations. Twenty micrograms of each protein-containing sample were subjected to SDS-PAGE. The gel was transferred to a positively charged nitrocellulose membrane and probed with an appropriate primary antibody [anti-E2F1 to anti-E2F6 (Santa Cruz) and anti-GAPDH (Advanced ImmunoChemical)] followed by the corresponding horseradish peroxidase-conjugated secondary antibody.
RNA was isolated from cells with Tripure isolation reagent (Roche) according to the manufacturer's instructions. Ten micrograms of each RNA sample were added to 15 µl of RNA loading buffer (900 µl of deionized formamide, 180 µl each of formaldehyde and 10x MOPS buffer, 168 µl of gel loading buffer, and 20 µl of ethidium bromide). Samples were denatured at 65°C for 15 min and were loaded on a prerun 1.0% agarose gel (6% formaldehyde and 10% 10x MOPS buffer). The gel was transferred through capillary action to a nylon membrane overnight. It was probed with a 0.9-kb PCR-generated cDNA probe with incorporated digoxygenin (Dig)-labeled UTP nucleotides, using the primers 5'-TCTGGCTTGCTGGGCTAGGCT-3' and 5'-CGCTACTGAGAACGAGAGCACGCAC-3'.
Flow cytometry. Cells in 60-mm plates were trypsinized and treated with 1x PBS-EDTA. Samples were spun down, and pellets were resuspended and fixed in 1 part 1x PBS-EDTA and 3 parts 70% ethanol and then stored at 20°C. At the time of analysis, cells were washed and resuspended in PBS-EDTA. Cells were treated with RNase at a 1:50 dilution and stained with propidium iodide at 1:500 before cell cycle analysis on a flow cytometer at the Ottawa Regional Cancer Center (Ottawa, ON, Canada).
Site-directed mutagenesis. Complementary primers 5'-CCGCTGGGTGAGCACGGTTGCCTC-3' and 5'-GAGGCAACCGTGCTCACCCAGCGG-3' were designed with a mutated putative E2F1 binding site (GAGCACGG). With the use of the QuikChange mutagenesis kit (Stratagene no. 200519) according to the manufacturer's instructions, PCR amplification of the template (E2F6 promoter-luciferase construct i: 597 to +96) incorporated the mutation. Supercompetent bacterial cells were transformed with the product, and the resultant colonies were picked, cultured, and used to generate miniprep DNA for sequencing.
Site deletion by PCR amplification. PCR amplification with primers 5'-CTGCAGTGAGCCCTGACCACG-3' and 5'-TACACCGCCCCCCTCTGCGCATG-3' yielded a fragment from 335 to +13 of the transcriptional start site within the E2F6 promoter that eliminated the putative E2F1 binding site at +24. The product was cloned into PGL3-Basic upstream of the luciferase reporter gene.
EMSA and supershift. EMSAs involving chemiluminescence-based detection were carried out with the Lightshift Mobility/Shift Assay kit (Pierce no. 20148) according to the manufacturer's instructions. Nuclear extracts were taken from MCF-7 cells overexpressing E2F1, using the N-Per nuclear and cytoplasmic extraction reagents (Pierce no. 78833). Sixty-base pair sense and antisense oligonucleotides containing the putative E2F1 binding sites were 3' end labeled with a biotin 3' end labeling kit (Pierce no. 89818). The oligo upper strands used were as follows for the human putative E2F1 sites at 174 and +24, respectively: 5'-CACCGTCGAGAATTCCAGGCGACCGCTGGGTTTTCCCGGTTGCCTCTTTTCTCTCACCCC-3' and 5'-TGCGCAGAGGGGGCGGTGTACTGCGCATGCGGGAAGATGGCGGGGCGGGCGACTTGAGAT-3'.
Nuclear extracts were incubated with the probe in a 25-µl sample and loaded onto a 16 x 18 x 0.1-cm 5% native polyacrylamide gel. Protein samples were also incubated with an excess of unlabeled target DNA to compete labeled probe binding. For supershifts, nuclear extract was treated with 12 µl of E2F1 antibody (anti-E2F1sc-193X polyclonal; Santa Cruz) for 1 h at room temperature before incubation with the probe. For the chemiluminescence-based assays, the membrane was transferred electrophoretically to a Biodyne-B nylon membrane (Pierce no. 77016), and chemiluminescence detection was carried out according to the manufacturer's instructions.
EMSAs involving radiolabeled oligonucleotide probes were carried out as follows. Nuclear extracts were taken from HEK-293 cells overexpressing E2F1 with the N-Per nuclear and cytoplasmic extraction reagents (Pierce no. 78833). Twenty-four-base pair complementary DNA strands (5'-GTACTGCGCATGCGGGAAGATGGC-3') containing the putative E2F1 binding site GCGGGAAG were annealed and radiolabeled with [
-32P]ATP, using T4 polynucleotide kinase. Nuclear extracts were incubated with the probe in a 30-µl sample and loaded onto a 16 x 18 x 0.1-cm 5% native polyacrylamide gel. Protein samples were also incubated with an excess of unlabeled target DNA to compete labeled probe binding. The gel was wrapped and exposed to autoradiography film overnight.
E2F1 overexpression. A plasmid containing the complete cDNA of the human E2F1 gene was transiently transfected into cells that carried the E2F6 promoter-luciferase reporter with Fugene transfection reagent (Roche) according to the manufacturer's recommendations. Control cells were transfected with only the promoter-reporter gene construct.
Chromatin immunoprecipitation. In vivo detection of E2F6 promoter-associated E2Fs was performed by chromatin immunoprecipitation (ChIP) (13). Human HEK-293 cells were treated with 1% formaldehyde to fix protein-DNA complexes. Isolated chromatin was sonicated to lengths between 1.0 and 2.0 kb and was precleared with salmon sperm DNA to reduce nonspecific background. DNA was immunoprecipitated overnight with antibodies against E2F1 (sc-193x, Santa Cruz), E2F2 (sc-633x, Santa Cruz), E2F3 (sc-897x, Santa Cruz), E2F4 (sc-866x, Santa Cruz), and E2F5 (sc-999x, Santa Cruz). Controls included PCR reactions using a control template (no E2F6 promoter) and DNA immunoprecipitated with either IgG or no antibody. DNA-protein-antibody complexes were recovered on agarose beads and washed. The cross-links to each of the antibody-protein complexes were reversed on DNA eluted from the beads, which was subsequently used as a template in PCR with E2F6 promoter-specific primers (5'-GAGCTCACGAATAAATGAAG-3' and 5'-ATAACTGAAAGTTCTGAGGTG-3') or SLMAP promoter-specific primers (5'-CTGACTCGAGGTGGCCCATGTGCTGAGC-3' and 5'-GACTCGCGCAGCCAGGAAGGTC-3').
RT-PCR. Total RNA was extracted from MCF-7 cells transfected with an empty pcDNA3 vector (control) and MCF-7 cells transfected with an E2F1 expression vector. The RNA was subjected to an RT-PCR reaction with the One Step RT-PCR kit (Invitrogen) according to the manufacturer's instructions. A master mix was created for the PCR reactions involving buffer, water, and template, and the mix was divided among all the reactions before addition of primers specific to each reaction or enzyme mix. This was to ensure a consistent amount of template in each reaction. For the test reactions targeting the E2F6 mRNA, forward and reverse primers specific to the E2F6 cDNA were used as follows: 5'-GGTTGCAACGAAACTGGGAG-3' and 5'-CGCTACTGAGAACGAGAGCAC-3'. For the control reactions targeting GAPDH mRNA, the same template was used in RT-PCR with primers as follows: 5'-GCAGAATTCATGGGGAAGGTGAAGGTC-3' and 5'-CTCGGATCCTCTTGTGCTCTTGCTGG-3'.
Software. MatInspector (Genomatix Software 19982004) online software, which utilizes a library of matrix descriptions for transcription factor binding sites to locate matches in submitted sequences, was used.
| RESULTS |
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32 and
31 kDa were specifically recognized by anti-E2F6 and expressed in a cell cycle-regulated manner, as reported previously (6, 26). The results show an increased intensity in both E2F6 mRNA and protein expression at the 6 -h time point after synchronization, which coincided with the increased promoter induction during the luciferase assay at this time (G1/S). Furthermore, the Western blot (Fig. 3C) shows that the peak temporal expression of E2Fs 13, and most apparently E2F1, seems to manifest at 5 h after synchronization, whereas the expression levels of E2Fs 4 and 5 remain relatively unaltered during cell cycle progression. These data suggest that the activating E2Fs are induced before the induction of E2F6 and may serve a role in E2F6 activation.
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12-fold (determined by densitometry) in the E2F1-transfected cells at 48 h after transfection compared with empty pcDNA3 vector-transfected cells. A Western blot was performed on total cell extract from the transfected cells, using antibodies against E2F1 and E2F6 to verify overexpression of E2F1 and its effects on E2F6 protein levels. There was an
1.3-fold increase in E2F6 protein expression due to E2F1 compared with GAPDH (Fig. 4C).
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To test whether the protein-DNA complexes in the EMSAs contained E2Fs, a polyclonal antibodies against the E2Fs were used in supershift assays involving the two putative E2F sites in the human E2F6 promoter at +24 (Fig. 5B) and 174 (Fig. 5C). The data in Fig. 4, B and C, show diminished intensity at the level of the band shift with anti-E2F1 for the site at +24 and 174, with the appearance of a higher-molecular-weight complex, indicating that some of the protein-DNA complex was successfully recognized by the E2F1 antibody. On the basis of the comparable positions of the band shifts and supershifts, both putative E2F1 binding sites in the human E2F6 promoter were recognized by a nuclear protein complex that was immunologically identified as containing E2F1. None of the other anti-E2Fs resulted in the protein-DNA complexes being retarded, as seen with E2F1 (data not shown).
To determine whether the putative E2F binding site (+15) in the murine promoter can bind nuclear factors as shown in the studies of the human promoter above, we performed an EMSA on mouse p19 cell nuclear extract (Fig. 5D). There is retardation of the probe in lane 2 relative to the lane containing the probe alone (lane 1) (Fig. 5D). This complex is specifically competed out by the addition of an excess of unlabeled probe (Fig. 5D, lane 3); however, it is retained when a cold probe containing a mutated version of the E2F consensus binding site is used in competition (Fig. 5D, lane 4).
E2F targets E2F6 promoter in vivo. Because EMSA results suggest that the E2F6 promoter contains sequences recognized by E2F1, we sought to determine the molecular basis for this interaction in vivo. ChIP assay was used to determine whether there existed in vivo binding of E2F species to the E2F6 promoter in HEK-293 cells. Sonicated chromatin from a population of asynchronous cells was immunoprecipitated as a chromatin-protein complex by polyclonal antibodies raised against E2Fs 15. Primers specific to the E2F6 promoter (Fig. 6A) and to the control promoter SLMAP (Fig. 6B) were used in PCR amplification of a sample from each immunoprecipitation. PCR was also performed on a control template (not containing the E2F6 promoter), DNA immunoprecipitated with either IgG or no antibody, as well as the total input sample of chromatin attained before the immunoprecipitation step. PCR with the E2F6 primer set yielded a 372-bp product from the immunoprecipitations with anti-E2Fs 15, and this was sequenced and positively identified as a region of the E2F6 promoter spanning sequences 597 to 226 from the transcription start site. As expected, PCR with the SLMAP primer set yielded no product, because the SLMAP promoter has no consensus E2F binding sites (Salih M and Tuana BS, unpublished results).
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The effects of mutation and deletion of the E2F binding sites on human and murine E2F6 promoter activity were compared in an asynchronous population of cells under similar conditions. Figure 7D indicates a more than twofold increase in human promoter activity in the presence of ectopic E2F1. Deletion of the putative site at +24 resulted in a significant decrease in promoter activity, as was the case with the mutation of the site at 174. When asynchronous mouse p19 cells were subjected to similar experimental conditions (Fig. 7F), an increase in promoter activity comparable to that observed in human cells was observed in the presence of ectopic E2F1. The mutation of the E2F binding site at +15 abolished promoter activity. These results show that E2F1 is capable of enhancing the activity of both the human and the mouse E2F6 promoter, and the putative E2F binding sites at +24 and 174 for human and +15 for mouse may be viable transcription factor binding sites that are important to the regulation of the E2F6 gene.
| DISCUSSION |
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We found that the human E2F6 promoter was induced in a cell cycle-specific manner, with peak activity at G1/S. The temporal induction of E2Fs 13 that occurs just before the upregulation of E2F6, as demonstrated by their expression profiles, suggests that the transactivating E2Fs may be upstream regulators of E2F6 gene expression. Two mRNA transcripts and three proteins encoding E2F6 were consistently detected, with the upregulation noted at the G1/S phase of the cell cycle as defined previously (3, 6, 26). Thus these data collectively suggest that E2F1 may derive E2F6 gene expression at the level of the promoter in a cell cycle-dependent manner.
Our data presented herein imply the existence of a potential novel feedback mechanism through E2F1 transactivation of the repressor E2F6. Thus E2F6 would experience upregulation at G1/S transition to exert an opposing effect on the activities of E2F-responsive promoters. We propose a model in which E2F recognizes two consensus sequences on the human E2F6 promoter to play a primary role in its induction (Fig. 8). The cell cycle mediation imposed by E2F6 would be exerted by interfering in the transcriptional activation of E2F target genes. Because such genes are required for cell cycle progression and S phase entry, the repressive effects of E2F6 therefore direct the orderly progression of the cell cycle and ultimately approppriate cell cycle exit and differentiation (5, 7, 24, 28). The mechanism of repression by E2F6 is not yet clear, although recent studies have shown that E2F6 interacts with certain repressive factors that associate with the multimeric mammalian polycomb protein complex through its repression domain (26, 27). This suggests that the complex is required for the gene-silencing effect of E2F6, which is thought to occur through the recognition of consensus sequences because E2F6 does bind DP to form a functional DNA binding complex through its domains for heterodimerization and DNA binding (12, 19, 26, 27). In fact, ChIP assays have shown that E2F6 associates with and negatively regulates many loci that contain E2F1 binding sites, such as in the promoters of BRCA1 (tumor suppressor), TRFP (transcription mediator), NEK11 (DNA replication), and DHPS (amino acid synthesis) (18).
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| GRANTS |
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| FOOTNOTES |
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The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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