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Division of Cell Biology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132
| Abstract |
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| Introduction |
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Two distinct domains of the murine CD21 gene have been defined to be important for cell- and tissue-specific expression. Analysis of the 5' promoter sequence of murine CD21 has identified multiple transcription factor binding sites, including octamer, AP-1,2, and an IgE enhancer sequence (6). In addition, a sequence within the promoter, homologous to the human CD21 gene, has been identified. While these promoter sequences do drive transcription, they do not confer tissue specificity. Fusion of either the murine or human CD21 promoter sequences 5' of reporter constructs provides for virtually equivalent expression of the reporter in T and B cells (7, 8, 9).
Analyses of the expression of the murine and human CD4 genes demonstrated a similar expression pattern. In that case, the genes promoter and enhancer sequences were shown to be critical for transcription, but did not confer cell specificity (10). Expression constructs possessing CD4 5' sequences were equally effective at promoting transcriptional activity in both CD4+ T cells and CD8+ (CD4-) T cells. Only when constructs that contained intronic sequences (a putative transcriptional silencer) were analyzed was the correct tissue-specific expression pattern observed (11, 12, 13)
Based upon the CD4 model system, we utilized the intronic sequences of the murine CD21 gene within reporter constructs and found specific regions in the first intron that conferred tissue specificity (8). This effect was localized to a small region of the intron, and apparently consisted of both enhancer as well as suppressor elements. Similar data was also generated for the human CD21 gene, suggesting that the mechanism of expression control has been conserved during mammalian evolution (9). These data have raised the mechanistic question of how can two or more distinct genetic elements separated in the gene by >1000 bp be brought together to coordinately control transcriptional activation. Presumably, such an interaction would require an alteration in the structure of the chromatin.
Recent work has focused on the effect of chromatin structure on gene transcription. Chromatin remodeling has long been suggested as a mechanism by which transcription can be regulated (reviewed in Refs. 14, 15). Strict nucleosomal positioning regulates chromatin structure. Acetylation states of core histones H3 and H4 directly influence nucleosomal positioning. Acetylating lysine residues on the N termini of core histones negatively charges the lysine residues, neutralizing positive charges, thus weakening interactions with the phosphate backbone of DNA. This diminishes chromatin associations and presumably facilitates access of transcription factors to the "open" DNA. The best-characterized examples of the relationship between chromatin structure and transcriptional regulation is found in telomeric and mating type loci silencing in yeast (16, 17). A direct mechanistic correlation between histone acetylation and gene expression was established when the gene for p55, the catalytic subunit of a tetrahymena histone acetyltransferase, was cloned and identified as a homologue of Gcn5p, a yeast adapter protein that is required for full activity of a group of transcription factors (18).
If an alteration in chromatin structure is required for the appropriate expression of CD21 in developing B cells and FDCs, this may be facilitated by the state of histone acetylation. To determine the effect of acetylation on CD21 transcription, we used the deacetylase inhibitors sodium butyrate (19, 20) and trichostatin A (TSA) (21), a Streptomyces-derived fungal antibiotic with very potent and specific deacetylase inhibitor activity, to create a hyperacetylation state in murine T cells. CD21 expression in such treated cells was then analyzed via FACS and RT-PCR. Murine T cells with hyperacetylated histones expressed the CD21 gene in a time- and dose-dependent manner. This induction was specific for CD21 in T cells and was not observed in nonlymphocyte cell lines. These data suggest that intronic elements may play a role in regulating gene expression by a generalized function involving nucleosomal positioning.
| Materials and Methods |
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Mouse 2PK3 and A20 cells, CD21-expressing B lymphomas, were obtained from the American Type Culture Collection (ATCC; Manassas, VA) and maintained at 37°C, 5%CO2 in DMEM (Life Technologies, Bethesda Research Laboratories, Gaithersburg, MD) with 10% FCS (HyClone Laboratories, Logan, UT) and Pen-Strep (Life Technologies). Mouse EL4 and TK.1 cells, CD21-nonexpressing lymphomas (ATCC), were grown in RPMI 1640 (Life Technologies) with 10% FCS and Pen-Strep. Mouse L cell, a fibroblast, was grown in RPMI 1640 with 10% FCS and Pen-Strep. Splenocytes and thymocytes were isolated from adult NIH outbred mice and maintained in single cell suspensions with DMEM with 10% FCS and Pen-Strep. Where indicated, cells were treated with 10, 50, 100, and 500 nM concentrations of TSA (Sigma, St. Louis, MO) and 200 µg/ml cyclohexamide in media; or with 0.01, 0.1, 1, 10, or 100 mM concentrations of sodium butyrate (Sigma) in media for 0.5, 1, 1.5, 2, 4, 8, 10, 12, 16, or 20 h.
FACS analysis
The following mAbs were prepared at the University of Utah core facility: FITC-conjugated rat anti-mouse B220, PE-conjugated rat anti-mouse CD3, FITC-conjugated rat anti-mouse CD4, and FITC-conjugated rat anti-mouse IgG2b. FITC-conjugated CD21 7G6, a rat anti-mouse CD21 mAb, was purchased from PharMingen (San Diego, CA). Abs were incubated with cells at 4°C for 1 h in the presence of 1/50 dilution of mouse serum. Incubations were followed by two washes in the staining buffer (0.1% BSA in 10% PBS). Samples were analyzed with a FACScan flow cytometer, and data were analyzed using CellQuest software (Becton Dickinson, Mountain View, CA).
RNA preparation and cDNA synthesis
Total RNA from cells was isolated using the CsCl guanidine method (22). Briefly, cells were resuspended in 4 M guanidinium solution and disrupted in a tissuemizer homogenizer. RNA was isolated by ultracentrifugation at 30,000 rpm over a 5.7 M cesium chloride gradient overnight. RNA was resuspended in water and quantified by measuring A260 absorbance. cDNA was synthesized by mixing 5 µg of RNA, 10 µl of 5x first strand buffer, 5 µl of 5 mM dNTP, 5 µl of 0.1 M DTT, 2 µl of 1.25 mM random primers (Life Technologies), 2 µl of Maloney murine leukemia virus reverse transcriptase and water to final volume of 50 µl. The reaction mixture was incubated at 37°C for 1 h. A total of 2 µl of DNase-free RNase (1 mg/ml) was then added, and the reaction mixture was incubated for an additional 5 min followed by cDNA isolation using the Qiaquick PCR purification kit (Qiagen, Chatsworth, CA)
PCR
PCR using radioactive detection was performed with 10 µl reactions containing 200 ng cDNA, 70 pM of each primer, 0.72 U Amplitaq DNA polymerase (Life Technologies), 0.8 mM dNTP, 1x Taq buffer (50 mM Tris (pH 8.3), 3 mM MgCl2, 20 mM KCl, and 500 mg/ml BSA), and 2.5 mCi [32P]dCTP. Samples were loaded into capillary tubes and incubated in an air thermocycler (Idaho Technology, Idaho Falls, ID) for denaturing at 94°C for 1 s, for annealing at 59°C for 1 s, and for extension at 72°C for 3 s (23). This cycle was repeated 18 times for amplification of ß-actin transcripts and 22 times for amplification of CD21 transcripts. After amplification, 5 µl of stop solution (United States Biochemical, Cleveland, OH) was added to the reactions, and 5 µl was resolved in a 6% acrylamide sequencing gel, which was then dried and exposed to BXR medical x-ray film (Western X-Ray, Salt Lake City, UT) overnight.
PCR using fluorescence detection was performed with 10 µl reactions containing 20 ng cDNA, 5 µM of each primer, 0.5 U Amplitaq DNA polymerase, 110 ng TaqStart Ab (Clontech Laboratories, Palo Alto, CA), 0.8 mM dNTP, 1x light cycler buffer (3 mM MgCl2, 50 mM Tris-HCl (pH 8.3), 500 mg/ml BSA), and 1:30,000 dilution of SYBR Green I (Molecular Probes, Eugene, OR). Samples were loaded into capillary tubes and incubated in a fluorescence thermocycler (LightCycler LC24; Idaho Technology) for denaturing at 94°C for 0 s, for annealing at 62°C for 0 s, and for extension and fluorescence detection at 72°C for 3 s. This cycle was repeated 40 times, preceded by an initial incubation at 94°C for 60 s and followed by a melting curve acquired by cooling to 60°C and slowly heating at 0.2°C/s to 94°C, with fluorescence data collected at 0.2°C intervals (24).
CD21 transcript were amplified using primers 43 (5'-ATG GGA TCC TTG GGT TCG CTC-3') and 45 (5'-GCT AGG TGA ACA AGT GTA CCT-3'). CD19 transcripts were amplified using primers 945 (5'-GCT ACC ATG CCA TCT CCT CTC C-3') and 947 (5'-ATC CTC CAC GTT CAC TGT CCA G-3'). CD3 transcripts were amplified using primers 949 (5'-GGG TTT GAC GTC TCC TTT GCT C-3') and 950 (5'-GGC CTC TTC CTG GTG ATC TCT C-3'. ß-actin transcripts were amplified using primers 62 (5'-ATT GAA CAT GGC ATT GTT AC-3') and 339 (5'-CTC TAT CGT GGG CCG CTC TAG-3').
Relative transcript level calculation
Light cycler PCR data were analyzed using LightCycler Data
software (Idaho Technology). The software first normalizes each sample
by background subtraction of initial cycles. A fluorescence threshold
is then set at 5% full scale, and the software determines the cycle
number at which each sample reached this threshold. The fluorescence
threshold cycle number correlates inversely with the log of initial
template concentration. ß-actin transcript levels were used to
normalize the amount of cDNA in each sample, and CD21 transcript levels
were reported relative to levels found in 2PK3 B cells. Since
amplification occurs logarithmically, a difference in cycle threshold
of one correlates to an
2-fold difference in relative transcript
level. Melting curve profiles were used to confirm amplification of
specific transcripts.
| Results |
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It has previously been shown that expression of a small proportion of cellular genes can be influenced by acetylation states of core histones (25). We therefore investigated whether the expression of the murine CD21 gene could be influenced (i.e., up-regulated) in nonexpressing T cells by altering the acetylation state of histones. Treatment of various cell lines with as little as 33 nM of the deacetylase inhibitor TSA has been shown to significantly hyperacetylate all core histones (21). This concentration is five orders of magnitude lower than the similarly effective dose reported for the deacetylase inhibitor sodium butyrate (21). Toxicity of both inhibitors relates to G1 and G2 cell cycle arrest at concentrations starting at 70100 nM for TSA and 10 mM for sodium butyrate.
We treated the murine T cell line EL4 with 100 nM TSA and 10 mM Sodium
Butyrate and stained for CD21 expression on the cell surface (Fig. 1
A). The murine B cell line
2PK3 expresses CD21 on its surface without treatment, while the EL4
cell line does not. Upon treatment with Sodium Butyrate and TSA, EL4
cells express CD21. Therefore, hyperacetylation of histones resulted in
the cell surface expression of CD21 in T cells.
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Detection of CD21 transcript using continuous monitoring PCR
CD21 transcript was detected in the previous experiments by RT-PCR using radiolabeled nucleotide and autoradiography (23). In the following experiments, we used a variation of this technique in which a fluorescent dye that binds dsDNA is used instead of the radiolabeled nucleotide (24). This method continually analyzes the product during the cycle set and provides more sensitive detection of low levels of product than the radioactive protocol.
EL4 cells were treated with TSA, and total cellular RNA was isolated
and reverse transcribed as in previous experiments. PCR products were
detected and quantified by continuous monitoring PCR using detection
threshold as an indication of relative starting transcript numbers. As
shown (Fig. 2
A), fluorescence
increases as the cDNA is amplified. The cycle number at which
fluorescence can be detected was used to determine the amount of
transcript present in each sample relative to that found in 2PK3 cells.
Plotting the log fluorescence vs cycle number more clearly defines this
cycle threshold. In this panel, 2PK3 cells, EL-4 cells, and TSA-treated
EL-4 cells had equivalent levels of ß-actin transcripts. Virtually
identical amplification profiles for CD21 transcripts were generated
for 2PK3 and TSA-treated EL-4 cells. No CD21 transcripts were detected
in the untreated EL-4 sample in the 40 cycle profile.
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2 h after treatment, compared with 8 h using the
radiolabeled nucleotide protocol (Fig. 2
To ensure that induction of the CD21 gene in murine T cells was not due
to the TSA-induced expression of a transcription factor required for
CD21 transcription, we incubated EL4 cells with 100 nM TSA and 200
µg/ml cyclohexamide, which blocks de novo protein synthesis. We also
performed a shorter time course to more clearly define the point of
CD21 gene induction by TSA. Addition of cyclohexamide had no effect on
the induction of CD21 transcription in EL4 cells, which produced
transcript in as little as 90 min after TSA treatment (Fig. 3
).
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The preceding experiment demonstrated that continuous PCR
monitoring can efficiently and effectively determine relative CD21
transcript levels. TSA was previously shown to induce CD21
transcription in EL4 cells in a time-dependent manner. As shown,
deacetylase inhibitors induced CD21 transcription in a dose-dependent
fashion (Fig. 4
). TSA induced
transcription of CD21 by EL4 cells starting at a concentration of 10
nM, with maximal induction at 500 nM (Fig. 4
A). Sodium
butyrate induction of CD21 transcription by EL4 cells was seen at 10
nM, with maximal induction at 100 mM (Fig. 4
B). These data
suggest that the extent of histone hyperacetylation influences the
degree to which the CD21 gene is transcribed in T cells.
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The induction of CD21 transcription by deacetylase inhibitors was
shown in the previous experiments to be time- and dose-dependent. We
were concerned as to the specificity of this induction. First, was this
induction specific for the CD21 gene in T cells, or were other
quiescent genes also activated? Second, could other, nonlymphocytic
cells be induced to express CD21 after histone hyperacetylation? To
address these questions, a variety of cell types were treated with TSA,
and continuous monitoring PCR was performed using primer sets for
additional genes. TSA treatment of EL4 cells did not induce the
expression of CD19, a gene expressed specifically in B cells (Fig. 5
A). Expression of CD3, a gene
specifically expressed in T cells, was also unaffected. Additionally,
TSA treatment induced CD21 transcription in TK1 cells, a T cell line,
but not in L cells, a fibroblast cell line (Fig. 5
B).
Finally, TSA treatment increased CD21 expression 4-fold in A20 cells, a
pre-B cell line. These data demonstrated that induction of CD21 gene
expression by histone hyperacetylation was highly selective for the
CD21 gene in lymphoid cell lines.
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The data presented thus far have been generated using transformed
cell lines that display characteristics of immature cells. We were
interested to observe the effects of TSA on CD21 gene expression in
splenocytes and thymocytes. Accordingly, single cell suspensions were
prepared from spleens and thymuses isolated from mice. Splenocytes and
thymocytes were treated with TSA and analyzed for protein and
transcript. No increase in CD21 cell surface expression was observed in
either splenocytes or thymocytes (Fig. 6
A). However, CD21 transcript
levels did increase significantly in thymocytes after treatment (Fig. 6
B). Paradoxically, CD21 transcript levels decreased
significantly in splenocytes after treatment. While the induction of
CD21 transcription in thymocytes would be expected from the previous
experiments, the suppression of transcription in splenocytes was not.
One difference between the spleen and thymus is that the spleen has a
large percentage of mature, end-stage cells, while the thymus does not.
It may be that maturing lymphocytes are more sensitive to the effects
of histone acetylation than mature, committed cells. The 4-fold
increase of CD21 transcription by the pre-B cell line A20 (Fig. 5
)
after TSA treatment supports this view.
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| Discussion |
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The transcriptional activation of the CD21 gene in T cells is specific for this gene in that other, transcriptionally silent genes were not similarly activated. These data do not suggest, however, that the CD21 gene is the only gene within these cells that is activated by such treatment. Previous screening analyses have found that up to 2% of cellular genes can be similarly activated via histone hyperacetylation (25). Thus, the CD21 gene must be a member of a select subset of genes whose transcriptional control is thus influenced by hyperacetylation.
The induction of CD21 expression was shown to be dependent upon treatment of the correct cell type. T and B cells share many common lymphoid transcriptional control proteins, which are absent in other cell lines, such as fibroblasts. The lack of CD21 activation in fibroblasts following histone hyperacetylation suggests that both T and B cells possess the required transcriptional control apparatus proteins to transcribe CD21, but that such transcription is inhibited in T cells. Our previous mapping of specific transcriptional suppressor/silencing elements within the first intron of the CD21 gene supports this view (see below) (8).
The CD21 gene is expressed in a subset of cells (B cells and FDCs) and is under the transcriptional control of promoter and intronic sequences. We have found at least two silencer/suppressor sites within the murine CD21 intronic sequence (8), and Makar et al. (9) have proposed the presence of intronic silencer sites within the human CD21 first intron. These data, in total, suggest that the positioning of silencing elements within the first intron several hundred to thousands of base pairs from the promoter region, places them in a region of the gene in which they exert their effect via chromosomal alterations. The general question can thus be asked whether or not histone hyperacetylation similarly affects other genes that possess such intronic silencer regions.
The role that the state of histone acetylation has upon gene transcription has been an actively investigated area of study. Histone hyperacetylation itself (acetylation of lysine residues) has been proposed to lead to an increased level of transcription by opening up the chromatin for the insertion of transcription factors (reviewed in Ref. 26). How such hyperacetylation is accomplished falls into two contrasting models. The first is that promoter TFIID complexes recruit specific acetyl transferases (27, 28). Such transferases allow for an increased level of acetylation of histones holding the promoter region of the gene, allowing for the recruitment of additional control factors and eventual up-regulation of the gene. This model does not appear to fit that of the CD21 gene. The lack of expression of CD21 in T cells does not appear to be due to the lack of an effective transcriptional activation complex at the promoter region, but instead due to a repression of transcription via the intron control sequences.
The second model to explain histone hyperacetylation control of gene transcription is based upon the model of recruiting sequence-specific histone deacetylases. A number of systems have demonstrated that transcriptional inhibition can be mediated by the recruitment of a deacetylase via a sequence-specific DNA binding factor (29, 30, 31, 32, 33, 34, 35). Once in place, the deacetylase removes acetyl groups on the histones, thus inhibiting the entrance of proteins that bind to enhancer and promoter elements. These systems have described the effect of deacetylase recruitment within promoter sites, while the CD21 model would suggest analogous intron control.
The second model of deacetylase recruitment fits with the model system
of CD21, which we previously proposed (8). We demonstrated
the existence of at least one transcriptional enhancer sequence and two
silencer elements within fragment A of the first intron of the CD21
gene (Fig. 7
). Previously, we could not
predict the nature of the proteins that would bind the silencer
elements: we can now propose that they may be histone deacetylases. The
binding of such deacetylases, in a T cell-specific fashion, would
silence the activity of the enhancer element. This enhancer element is
equally active in T and B cells (our unpublished observations). The
repression gained by the deacetylase would be abrogated by the addition
of TSA or sodium butyrate into the cell. The repressive effect of
histone deacetylases has, in yeast systems, a limitation of only a few
hundred base pairs (32, 36). Thus, the presence of an
enhancer element close to the sites of suppression (i.e., deacetylase
binding) would be required. The enhancer element we have described is
within this functional range of chromatin. Thus, the key pertinent
question to address in the future is the identification of the proteins
that affect this transcriptional repression, and the determination of
whether or not they are, or are linked to, a histone deacetylase.
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| Acknowledgments |
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| Footnotes |
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2 Address correspondence and reprint requests to Dr. John H. Weis, Department of Pathology, University of Utah School of Medicine, 50 North Medical Drive, Salt Lake City, UT 84132. E-mail address: ![]()
3 Abbreviations used in this paper: FDC, follicular dendritic cell; TSA, trichostatin A. ![]()
Received for publication February 17, 1999. Accepted for publication June 21, 1999.
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