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Molecular and Cellular Biology, April 1999, p. 2681-2689, Vol. 19, No. 4
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Interleukin-2 (IL-2) Regulates the Accessibility of the
IL-2-Responsive Enhancer in the IL-2 Receptor
Gene to
Transcription Factors
Corinne
Rusterholz,
Patricia
Corthésy
Henrioud, and
Markus
Nabholz*
Swiss Institute for Experimental Cancer
Research (ISREC), CH-1066 Epalinges, Switzerland
Received 19 November 1998/Accepted 20 January 1999
 |
ABSTRACT |
Interleukin-2 (IL-2) responsiveness of T lymphocytes is controlled
through transcription of the IL-2 receptor (IL-2R)
subunit by
antigen and by IL-2 itself. IL-2 induces IL-2R
transcription via an
IL-2-responsive enhancer (IL-2rE), whose activity depends on the
cooperative binding of IL-2-induced STAT5 to two sites and of
constitutively active Elf-1 to a third one. Here we describe the
changes in IL-2rE chromatin that occur in normal T lymphocytes upon
activation of IL-2R
expression. In cells induced to transiently express IL-2R
with concanavalin A (which mimics antigen), none of
the IL-2rE sites is occupied despite the presence of Elf-1 and STAT1,
which bind to the IL-2rE in vitro. The two STAT binding sites are
occupied rapidly upon IL-2 stimulation, concomitantly with STAT5
activation. Occupation of the Elf-1 binding site is delayed, although
Elf-1 concentration and binding activity are not modified by IL-2.
Digestion of T-cell chromatin with DNase I and micrococcal nuclease
shows that IL-2 induces the appearance of nuclease-hypersensitive sites
flanking the IL-2rE. Thus IL-2, in addition to activating STAT5,
appears to regulate IL-2R
transcription by making IL-2R
chromatin
accessible to transcription factors.
 |
INTRODUCTION |
Interleukin-2 (IL-2) is the
principal growth factor for antigen-activated T lymphocytes. It
promotes T-cell proliferation by binding to a high-affinity receptor
composed of three transmembrane proteins, the
,
, and
c chains (43). The
c chain is
shared with the receptors for IL-2, -4, -7, -9, and -15 (22, 33, 50, 54, 55) and is constitutively expressed in mature T cells and
their thymic precursors (8, 32, 48). IL-2 receptor
(IL-2R
) is present on a subpopulation of resting T cells (51, 62).
and
c chains combine to form an
intermediate-affinity IL-2R that can transmit signals (47,
49), but cannot stimulate the proliferation of normal T
lymphocytes (7, 38, 59). The
chain is undetectable on
resting T cells. Its expression is triggered by antigen
(53), a stimulus that can be mimicked by lectins such as
concanavalin A (ConA) (31) or by antibodies against the
T-cell receptor (TCR) (20). These signals also result in
secretion of IL-2, which increases and prolongs IL-2R
expression (4, 15, 39), thus acting as a positive feedback regulator of
its own high-affinity receptor.
IL-2R
gene expression is regulated mostly through changes in its
rate of transcription (13, 34, 52). In transgenic mice
bearing a reporter gene under the control of 2.6 kb of 5' flanking
region of the murine IL-2R
gene, transgene expression is restricted
to lymphoid organs (60). In T cells, the transgene can be
induced by ConA and IL-2 with kinetics very similar to those of the
endogenous gene. The responses of both the human and mouse genes to
signals from the TCR depend on cis-acting elements in the
promoter-proximal region (1, 5, 10, 28, 61). By transient
transfection of IL-2R
mutant promoter constructs into a rodent
T-cell line, PC60, we identified a 51-nucleotide (nt) enhancer
necessary and sufficient for the response of the IL-2R
gene to IL-2
1.3 kb upstream of the transcription start site (61).
Subsequently the homologue of this IL-2-responsive enhancer (IL-2rE)
was found at around
4 kb in the human IL-2R
gene (6, 29,
36). The mouse enhancer consists of three separate elements: two
binding sites for signal transducers and activators of transcription
(STAT) and a consensus motif for Ets family members. In PC60 cells, the
STAT motifs (sites I and II) and the Ets binding site (site III) are
all required for the response of the enhancer to IL-2. Recently, we
have shown that IL-2 stimulation of IL-2rE activity depends on the
cooperative binding of two IL-2-induced STAT5 dimers to sites I and II
(42). This is concordant with the finding that, in mice
lacking STAT5A, IL-2-induced IL-2R
expression is severely reduced
(46). Site II overlaps with a recognition sequence for GATA
proteins, but this motif does not appear to be important for IL-2rE
function (42). Elf-1, a member of the Ets family of
proteins, contributes to IL-2rE activity by binding to site III
(58). Elf-1 binding activity to site III is constitutive in
PC60 cells.
There is growing evidence that chromatin structure participates in gene
regulation, partly by modulating access of transcription factors to DNA
(3, 17, 65). Gene activation is often accompanied by
perturbation or disruption of the nucleosomes that occupy
cis-acting elements. Such an opening of chromatin is
generally reflected in a change in its sensitivity to nucleases.
Indeed, in mouse T lymphocytes, activation of IL-2R
expression
results in the appearance of a DNase I-hypersensitive site in, or close
to, the IL-2rE (60). Induction of DNase I-hypersensitive
sites by IL-2 has also been described in the B-cell-specific enhancer
of the immunoglobulin J chain gene (30).
Here we present the results of an analysis, by in vivo footprinting and
nuclease digestion, of the changes in IL-2rE chromatin during
activation of IL-2R
expression in normal mouse T lymphocytes. We
find that protein-DNA interactions on all three elements of the IL-2rE
depend on stimulation by IL-2, although Elf-1 binding activity is
present in resting T lymphocytes and is not affected by IL-2.
Stimulation with ConA, which induces activation of STAT1 but not STAT5,
does not result in the occupation of the STAT binding sites in the
IL-2rE, even though both site I and site II can bind STAT1 in vitro.
Stimulation of ConA-activated cells with IL-2 leads to the appearance
of micrococcal nuclease hypersensitive sites flanking the IL-2rE,
indicating that IL-2 induces translational positioning of nucleosomes
at the borders of the IL-2rE. Our data show that IL-2 regulates the
accessibility of the IL-2rE to the transcription factors which control
its enhancer activity and that IL-2rE chromatin configuration
participates in the regulation of IL-2R
transcription by IL-2.
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MATERIALS AND METHODS |
Cell preparation and culture.
Cells from spleens of 3- to
6-month-old DBA/2 mice (Harlan) were prepared by gentle homogenization.
To enrich for T cells, B cells and accessory cells were removed by
adherence to nylon wool (9). When high purity was required,
T cells were purified by incubating cell preparations with anti-Thy1.2
monoclonal antibody (MAb [mouse CD90]) coupled to magnetic microbeads
(MACS-r; Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany), followed by
two to three rounds of sorting with a magnet cell separation system
(MACS-r; Miltenyi Biotec GmbH). Cells were used either directly
(resting T lymphocytes) or cultured at 2 × 106
cells/ml for the indicated time with ConA (2.5 µg/ml; Sigma) and
human recombinant IL-2 (100 U/ml; kindly provided by Glaxo, Geneva,
Switzerland) or ConA with antimouse IL-2 MAb S4B6.1 (66) and
antimouse IL-2R
MAb 5A2 (44). Culture medium was
Dulbecco's modified Eagle's medium containing 10 mM HEPES, 50 µM
2-mercaptoethanol, and 5% fetal calf serum. For some experiments,
IL-2-responsive cells were obtained by stimulating lymphocytes for
24 h with ConA in the presence of the IL-2 blocking antibodies.
Cells were then washed in medium containing an excess of IL-2 and
subsequently cultured for the indicated time with 1,000 U of IL-2 per
ml. Splenic T lymphocytes from 3-month-old gamma interferon receptor
(IFN-
R)-deficient mice (eS/eV/129 background) and wild-type
eS/eV/129 mice (generously provided by Jacques Louis, Lausanne,
Switzerland) were enriched by passage through nylon wool and cultured
with ConA and IL-2 as mentioned above. Bone marrow cells were obtained
by flushing femur and tibia bones with ice-cold phosphate-buffered
saline (PBS) through a 26-gauge needle.
Flow cytometry.
For immunofluorescence analysis of IL-2R
surface expression, a biotinylated rat anti-mouse IL-2R
MAb (PC61)
(37) was used together with either fluorescein
isothiocyanate (FITC)-conjugated anti-CD4 (GK1.5) or anti-CD8 (53.6.7)
antibodies alone or with a mixture of both antibodies. PE-conjugated
streptavidin (Caltag Laboratories, San Francisco, Calif.) was used as
the second-step reagent. The purity of T cells after nylon wool or MACS
purification was assessed by staining with FITC-conjugated anti-CD4
plus anti-CD8 antibodies. Samples were analyzed with a
FACScan flow cytometer (Becton Dickinson, California) by using
the LYSIS II program.
In vivo footprinting analysis.
For dimethyl sulfate (DMS)
treatment, 1.5 × 107 cells were resuspended in 1 ml
of culture medium, and 40 µl of 0.5 M HEPES (pH 7.5) containing 2.5%
DMS (Fluka) was added. The reaction was stopped after 1 min by washing
twice with ice-cold PBS containing 2% 2-mercaptoethanol. Cells were
lysed in presence of 0.5 mg of proteinase K per ml, and the
genomic DNA was isolated. As a naked DNA control, 50 µg of
genomic DNA isolated from mouse liver were incubated with 0.5%
DMS for 30 s in 10 mM Tris-HCl (pH 7.5). Piperidine (Fluka)
cleavage was performed as described in reference 40.
Ligation-mediated PCR (LMPCR) was used to visualize DMS-dependent
cleavage sites. The procedure described in reference
19 was used, with the following changes. (i)
Annealing of the first primer to genomic DNA was performed at
61°C. (ii) PCR amplification was done through 22 cycles of 1 min at
95°C, 2 min at 64°C, and 3 min at 76°C. Five seconds was added to
the 76°C step at each cycle, with the exception of the last cycle,
where extension proceeded for 10 min. (iii) End labeling was carried
out in a thermal cycler (two cycles of 1 min at 95°C, 2 min at
68°C, and 10 min at 76°C). Reaction mixtures were separated on a
6% polyacrylamide sequencing gel. The primers used for LMPCR of the
lower strand were 5'-ACCACCTTCTACTGTTAGAAAGAGC-3' (primer
1), 5'-CAAAGGCTCACCTCTACCCTAAGAGG-3' (primer 2),
5'-AAGGCTCACCTCTAACCTAAGAGGAGGC-3' (primer 3), or
5'-CATAACGTTCTCTTTGCTAAGCGTC-3' (primer 1'),
5'-TCCCGCTCTTCTTCATCATGATCACTG-3' (primer 2'), and
5'-CCGCTCTTCTTCATCATGATCACTGGGC-3' (primer 3'). The
unidirectional linker was formed by hybridization of
5'-GCAGTGACTCGAGAGTACTGAGCTC-3' (linker 1) with
5'-GAGCTCAGTAC-3' (linker 2).
Protein extracts, electrophoretic mobility shift assays, and
Western blots.
Nuclear extracts from fresh and cultured cells were
prepared essentially as described previously (56), in
the presence of protease inhibitors (1 µg of leupeptin per ml, 1 µg
of aprotinin per ml, 1 mM phenylmethylsulfonyl fluoride [PMSF]) and
phosphatase inhibitors (25 mM
-glycerol phosphate, 0.1 mM
Na3VO3). For STAT proteins, binding reactions
were performed in a final volume of 20 µl in binding buffer [10 mM
Tris-HCl (pH 7.5), 20 mM KCl, 1 mM EDTA, 10% glycerol, 1 mM
dithiothreitol (DTT), 1 mg of bovine serum albumin per ml, 0.1 µg of
poly(dI-dC) and 1 µg of sonicated salmon sperm DNA] containing 0.5 to 5 µg of nuclear extract and 2 × 104 to 3 × 104 cpm of end-labeled probe. For Elf-1, binding reactions
were performed as described previously (58). Reaction
mixtures were incubated for 15 min on ice and separated on a 5%
nondenaturing polyacrylamide gel in 0.3× Tris-borate buffer.
Oligonucleotide probes have been described previously (42,
58).
For Western blots, 5 µg of denatured nuclear extract was separated on
a sodium dodecyl sulfate-polyacrylamide (7.5%) gel electrophoresis
(SDS-PAGE) gel. Proteins were transferred to nitrocellulose membrane
(Amersham Life Science), and Elf-1 was detected with a 1/500 dilution
of anti-Elf-1 antibodies (C-20; Santa Cruz Biotechnology, Santa
Cruz,
Calif.) by the ECL (enhanced chemiluminescence) system (Amersham
Life
Science) with horseradish peroxidase-coupled goat anti-rabbit
antibodies (Jackson ImmunoResearch
Laboratories).
DNase I and MNase digestion.
DNase I treatment of cells was
performed as described previously (60). For micrococcal
nuclease (MNase) digestion, 5 × 107 to 6 × 107 cells were washed with PBS and resuspended in 15 ml of
ice-cold solution 1 (15 mM Tris-HCl [pH 7.4], 0.2 mM spermine, 0.5 mM
spermidine, 2 mM K-EDTA, 80 mM KCl, 0.5 mM EDTA, 1%
thiodiethylene glycol, 1 mM DTT, 0.05% Nonidet P-40) containing
freshly added protease inhibitors (0.4 mM PMSF, 3 µg of aprotinin per
ml, 0.5 µg of leupeptin per ml, 1 µg of pepstatin per ml). Cells
were submitted to 10 strokes of a tight-fitting pestle in a Dounce
homogenizer. Nuclei were pelleted by centrifugation for 5 min at
1,000 × g with the brake off, resuspended in 7.5 ml of
solution 1 containing the protease inhibitors and 20% glycerol,
and Dounce homogenized again (four or five strokes). After
centrifugation, the pellet was resuspended in 2 ml of ice-cold solution
2 (7.5 mM Tris-HCl [pH 7.4], 0.1 mM spermine, 0.25 mM spermidine, 40 mM KCl, 5% glycerol, 1% thiodiethylene glycol, 1 mM DTT, 5 mM
MgCl2, 1 mM CaCl2) containing the protease inhibitors. Nuclei were aliquoted to 1 × 107 to
2 × 107/tube, and samples were incubated with
MNase for 5 min at 25°C. Digestion was stopped by the addition of 3 volumes of SDS buffer (25 mM Tris-HCl, [pH 8.0], 10 mM EDTA, 200 mM
NaCl, 0.4% SDS) and 0.5 mg of proteinase K per ml.
Southern blotting.
Forty to fifty micrograms of DNA was
digested to completion with the indicated restriction enzymes and
electrophoresed in 1 to 1.5% agarose gels in Tris-borate buffer at 40 V. DNA was transferred by capillarity to nylon membranes (Appligene
Oncor, Illkirch, France) with 10× SSC (1× SSC is 0.15 M NaCl plus
0.015 M sodium citrate). Probes were prepared with the random priming kit supplied by Boehringer Mannheim, by using IL-2R
PCR fragments (probe 8 runs from nt
539 to +58 and probe 3 runs from nt
586 to
286 from the transcription start site) as templates. Membranes were
hybridized in Church's buffer at 68°C.
 |
RESULTS |
ConA-induced, IL-2-independent IL-2R
expression does
not require activation of STAT proteins.
Previously, we
showed that ConA or anti-TCR antibodies induce transient IL-2R
expression on mouse spleen T lymphocytes in the absence of IL-2
stimulation (reference 60 and our unpublished observations). Figure 1A confirms this
result and shows, in addition, that both CD4+ and
CD8+ T cells are homogeneously IL-2R
+ after
24 h of culture in ConA only (i.e., in the presence of a mixture
of antimouse IL-2 and antimouse IL-2R
antibodies that prevent auto-
or paracrine stimulation by IL-2). In both populations, IL-2R
expression drops to very low levels during the next 48 h unless
the cells are stimulated with IL-2.

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FIG. 1.
IL-2 stimulates IL-2R expression on CD4+
and CD8+ T lymphocytes. Nylon wool-purified T lymphocytes
(>70% CD4+ or CD8+) from mouse spleens were
used fresh or after culture for the indicated times either with ConA in
the presence of MAbs against mouse IL-2 (S4B6.1) and the IL-2R (5A2)
that block auto- or paracrine IL-2 stimulation or with ConA and human
IL-2. (A) IL-2R expression on CD4+ or CD8+
cells was monitored by FACS analysis. (B) Nuclear extracts from 2 × 105 cells were incubated for 15 min with a probe
containing the STAT motif of the Fc RI gene and separated on a
nondenaturing polyacrylamide gel. The identity of the proteins forming
specific retarded complexes was determined by supershift experiments
with the appropriate antibodies (not shown).
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ConA triggers strong activation of STAT1, whereas STAT5 DNA binding is
induced by IL-2 (Fig.
1B). Since autocrine activation
of STAT1 by
IFN-

following T-cell activation has been reported
(
21),
it seemed likely that ConA stimulated STAT1 via IFN-

.
In order to
confirm the origin of STAT1 induction and to assess
its role in
IL-2R

expression, we monitored ConA-induced IL-2R
expression and
STAT1 activation in T lymphocytes from IFN-

R-deficient
mice
(
26). Figure
2A shows that, in
these cells, IL-2R

expression
after 1 day of stimulation with ConA
is completely normal despite
the absence of STAT1 and STAT5 (Fig.
2B).
These experiments demonstrate
that the ConA-induced wave of IL-2R

expression is independent
of STAT1 or STAT5 activation. These
observations confirm the biphasic
model of the regulation of IL-2R

transcription based on transient
transfection experiments, according to
which antigen (or ConA)
triggers IL-2R

expression through
cis-acting elements in the
promoter-proximal region while
IL-2 enhances transcription through
the distal IL-2rE (
45,
61).

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FIG. 2.
ConA induces IL-2R expression in absence of active
STAT factors. T lymphocytes from IFN- R-deficient ( / ) or
wild-type (WT) mice were stimulated for 24 h with ConA in the
presence of the IL-2-blocking MAbs. (A) Flow cytometric analysis of
IL-2R expression on T cells. (B) Bandshift assay with 3 µg of
nuclear extracts incubated with the Fc RI probe for 15 min.
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|
STAT1 does not play a role in the IL-2-dependent phase of IL-2R
expression.
Figure 3A shows that
IL-2R
expression during 72 h of stimulation with ConA and IL-2
in cells from IFN-
R-deficient mice is indistinguishable from that in
wild-type cells of the same genetic background. At no time during this
period did IFN-
R-deficient cells contain detectable STAT1 activity
(Fig. 3B). This indicates that STAT1 is not necessary for IL-2-induced
IL-2R
expression, nor does it act as a negative regulator. This is
consistent with the finding that IFN-
stimulation of the rodent
T-cell line which we used to map the IL-2rE does not induce IL-2R
expression (results not shown). Thus the antiproliferative effect of
IFN-
on T cells (11) is not a consequence of reduced
IL-2R
expression.

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FIG. 3.
IL-2-induced expression of IL-2R is normal in
IFN- R-deficient mice. T lymphocytes from IFN- R-deficient ( / )
or wild-type (WT) mice were stimulated for 24 h with ConA in the
presence of the IL-2-blocking MAbs (ConA primed), and IL-2 was then
added for the indicated times. (A) FACS analysis of IL-2R expression
on T cells. (B) Bandshift assay with 3 µg of nuclear extracts
incubated with the Fc RI probe for 15 min.
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In vivo footprinting experiments confirm the role of the IL-2rE in
IL-2-induced IL-2R
expression.
Changes in protein-chromatin
interactions taking place in the IL-2rE were analyzed by DMS
footprinting. DMS specifically methylates guanine and, to a lesser
extent, adenine residues of DNA (40). The binding of a
protein to its target site modulates the accessibility of DMS to DNA by
either protecting nucleotides in the binding site from or by rendering
neighboring residues more sensitive to methylation. We compared the
methylation pattern on IL-2rE chromatin from resting T cells and cells
activated with ConA and IL-2 with that of the IL-2R
-negative bone
marrow cells (Fig. 4). Bone marrow
chromatin does not show any significant protection of nucleotides in
the IL-2rE compared to naked DNA. The enhanced methylation of adenine
bases in living cells compared to naked DNA has also been observed by
others (23) and might be due to the differences existing
between the composition of cell nuclei and the buffer in which naked
DNA is resuspended for the DMS reaction. In the chromatin of resting T
cells, we reproducibly observed increased methylation of guanine
residue
1327 located at the 5' boundary of site III. This is unlikely
to be due to Elf-1, the factor that mediates the contribution of site
III to IL-2rE activity, since in vitro binding analysis indicates that
Elf-1 protects the G doublet in the core of the Ets motif
(27). Upon activation with ConA and IL-2, G
1364, which is
part of the STAT5 consensus motif
(3'-AAGN3CTT-5') (25, 57) in site I, and G
1327 and the doublet
1320/
1321 in site III are partially protected from methylation, corroborating the previous mapping of the
IL-2-responsive elements in the IL-2rE. In vivo footprinting of the
human IL-2rE has also shown IL-2-dependent protection of site I
(36). In some experiments, IL-2 also induces a weak
reduction in methylation of G
1344 in site II (see Fig. 6). That this
protection is not always seen may reflect the low affinity of STAT5 for
site II (42). We also detected partial protection of G
1293 in activated T cells. This suggests that an additional protein
may bind to this site. However, since this residue lies outside the
IL-2rE, in a region which is not required for IL-2rE activity
(61), the protein is unlikely to play an important role in
IL-2R
regulation.

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FIG. 4.
T-lymphocyte activation results in genomic
footprints in the IL-2rE. LMPCR was performed with in vitro-methylated
liver DNA or in vivo-methylated DNA from bone marrow cells, resting T
lymphocytes, and T cells stimulated with ConA and IL-2 for 72 h.
(A) Guanine sequence of the lower strand. The positions of the three
sites that constitute the IL-2rE are shown to the left. The positions
of the guanine residues, the methylation of which varies, are indicated
on the right. The autoradiogram is representative of four independent
experiments. (B) Histogram representation of the sequences shown in the
gel presented in panel A. The gel was scanned with a phosphorimager,
and histograms of the different lanes were overlaid. Each peak in the
histogram corresponds to a band in the gel. Solid arrowheads indicate
guanine bases which are partially protected in activated T cells. The
open arrowhead points to a guanine residue at the border of site III
with increased sensitivity to DMS in resting T cells.
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No major changes in the sensitivity to DMS were detected in the upper
strand of the IL-2rE (data not shown). The G

1360 residue
that is
part of the palindromic STAT motif in site I is very poorly
methylated
on naked DNA and is insensitive to methylation in vivo.
Intriguingly, a
similar insensitivity has been observed for the
homologous G residue (G

4175) in the human gene (
36). Site
II differs from the
STAT consensus motif in that it contains a
T instead of a G in position

1340.
We did not observe any protection of the G

1342 residue in the GATA
consensus motif that overlaps with site II (data not
shown).
Although more than 95% of the activated cells were expressing IL-2R

at their surface, protections were only partial. The
most plausible
explanation for this is that binding of STAT5 and
Elf-1 to the IL-2rE
is not strong enough to prevent access of
DMS completely or that the
IL-2rE sites are not occupied all the
time.
Occupation of site III depends on stimulation with IL-2.
From
the studies with PC60 cells, we had proposed that Elf-1 was
constitutively bound to the IL-2rE. The observation that occupation of
all three sites of the IL-2rE depends on stimulation of T cells
indicates that this model is too simple. One explanation for this
apparent inconsistency could be that activation of normal T cells, in
contrast to stimulation of PC60, results in an increase in nuclear
Elf-1 concentration. Figure 5 shows that
this is not the case. Although the absolute amount of Elf-1 binding
activity per cell is augmented with activation (Fig. 5A, left panel),
the relative concentration of this activity compared to total nuclear protein (Fig. 5A, right panel) remains constant, as does the
concentration of Elf-1 protein (Fig. 5B). Activation of T cells affects
neither the electrophoretic mobility of Elf-1-site III complexes or
denatured Elf-1 protein, nor does it result in an alteration of the
affinity of Elf-1 for site III as measured by in vitro assays (data not shown).

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FIG. 5.
Elf-1 DNA binding activity is not modified upon T-cell
activation. (A) Nuclear extracts from 2 × 105 cells
(left panel) or a constant amount of protein of the same extracts
(right panel) was incubated with a labeled oligonucleotide containing
site III, and the complexes formed were fractionated on a nondenaturing
gel. The amount of protein per sample is indicated on the bottom of
each lane. The identity of the Elf-1 complex was confirmed by
supershift analysis with an anti-Elf-1 antibody (not shown) and has
been fully documented (58). (B) Five micrograms of nuclear
extract was fractionated on a denaturing gel, and the Western blot was
probed with anti-Elf-1 antibodies. Molecular mass markers (in
kilodaltons) are indicated on the right.
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In order to distinguish whether the appearance of the footprint on site
III was the result of ConA activation or depended
on
stimulation by IL-2, we compared the chromatin of T lymphocytes
activated with ConA alone with that of cells stimulated with ConA
for
24 h (ConA primed), and then subsequently cultured with IL-2
for
different times (Fig.
6). Stimulation
with ConA only for 24
or 48 h does not result in any detectable
changes in the IL-2rE
methylation pattern. IL-2 stimulation of
ConA-primed cells leads,
as expected, to a rapid reduction of the
sensitivity of sites
I and II to DMS, correlating with
IL-2-induced apparition of active
STAT5 (data not shown).
Protection in site I is observed as soon
as 1 h after IL-2
addition and is maintained throughout stimulation,
as is nuclear
STAT5 activity (Fig.
1B). The persistence of active
STAT5 in
response to IL-2 was also observed in PC60 cells and
paralleled
IL-2r

expression and IL-2rE-driven reporter gene activity
(
42,
61). Continuous STAT5 activation in T cells can be explained
by
the fact that IL-2R

expression and STAT5 activation are regulated
by
a positive feedback loop. Protection of the G doublet in the
core of
site III also depends on IL-2 stimulation, but this response
is slower
than the changes in the STAT motifs. In vivo changes
in site III are
first detected 4 h after addition of IL-2, but
maximal protection
is observed only after 24 h of culture in the
presence of IL-2.

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FIG. 6.
IL-2-induced in vivo protection of IL-2rE sites follows
a temporal pattern. (A) In vivo footprinting analysis was performed
with ConA-primed cells or primed cells cultured further with or without
IL-2 for the indicated times. (B) The phosphorimager histograms of the
footprints obtained with the different populations are compared to the
one from ConA-primed cells. The results shown are representative of
three experiments. Arrowheads indicate partial protection of guanine
bases. Nucleotide positions are marked to the right of panel A.
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Taken together, these results suggest that the accessibility of site
III to Elf-1 in vivo depends on changes in the IL-2rE
chromatin that
are induced by IL-2.
STAT1 does not occupy sites I and II in ConA-primed cells.
Nuclei of T cells activated with ConA for 24 h contain substantial
amounts of active STAT1 (Fig. 1B). Although STAT1 can specifically bind
to sites I and II, as shown by the ability of wild-type but not mutated
IL-2rE to compete for STAT1-Fc
RI complex formation (data not shown),
these sites are not protected against DMS methylation in cells
stimulated with ConA only (Fig. 6). Comparison of the affinities of
STAT1 and STAT5 for the IL-2rE shows that both proteins bind with
similar efficiency to the latter (data not shown). Thus, the lack of
occupation of the STAT motifs in the IL-2rE in chromatin of
ConA-activated cells is not due to a lower avidity of STAT1 for the
IL-2rE. Since we observe occupation of the STAT sites very early after
addition of IL-2 to primed cells, at a time when the amounts of STAT1
and STAT5 DNA binding activity are similar, it is unlikely that, in
ConA-primed cells, the IL-2rE is not occupied because the STAT1
concentration is too low. These data rather suggest that the IL-2rE in
ConA-activated cells is not accessible to STAT1.
IL-2 induces positioning of nucleosomes around the IL-2rE.
Previously we described the appearance of a DNase I-hypersensitive site
(DH2) at the IL-2rE in T cells activated with ConA and IL-2
(60). Figure 7A shows that
this site is not detectable in cells stimulated with ConA alone
but appears after stimulation with IL-2. This confirms our hypothesis
that IL-2 induces a modification of IL-2rE chromatin, making it
accessible for transcription factors.

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|
FIG. 7.
IL-2 induces the appearance of DNase I and MNase sites
flanking the IL-2rE. (A) DNase I-treated chromatin from ConA-primed
cells or primed cells induced further with or without IL-2 for 24 h was digested with TaqI and PstI and
electrophoresed in 1% agarose gels. DNase I-hypersensitive (DH) sites
were visualized by hybridization with probe 8. DH1 is a
lymphocyte-specific constitutive site that maps close to the
transcription start site (60). DH2 is located at the IL-2rE.
Size markers are indicated on the left (in kilobases). (B) MNase
cleavage of naked DNA and chromatin from resting T cells or cells
stimulated for 72 h with ConA and IL-2. DNA was digested with
TaqI and EcoNI and electrophoresed in a 1.5%
agarose gel. The DNase I-treated samples from activated cells in the
right panel were digested with the same restriction enzymes. Blots were
hybridized with probe 3. Solid arrowheads indicate chromatin-specific
cleavage sites in activated cells. Open arrowheads indicate the cutting
sites in naked DNA. (C) Summary of MNase analysis. The IL-2rE is
represented as a hatched box. Arrowheads (as in panel B) show mean
cleavage positions of the MNase cuts deduced from two experiments.
|
|
By probing IL-2rE chromatin with MNase, we observed a number of cuts in
resting T cells (Fig.
7B). Most of these were also
observed when naked
DNA was digested with MNase and can be attributed
to the sequence
preferences of this nuclease. Thus, in resting
T cells, there appears
to be little or no translational positioning
of nucleosomes over the
IL-2rE. In fully activated cells, however,
MNase cuts IL-2rE chromatin
preferentially at positions flanking
the IL-2rE core (which contains
sites I, II, and III). An additional
site appears downstream of the
IL-2rE. Most of the cuts observed
in resting cells and naked DNA are no
longer detectable. Digestion
of the same population of activated T
cells with DNase I shows
that the region between the two
MNase-hypersensitive sites, i.e.,
the IL-2rE itself, is hypersensitive
to DNase
I.
Thus, stimulation of IL-2R

gene transcription results in the
translational positioning of nucleosomes at the borders of the
IL-2rE
sequence and in the opening of the IL-2rE
chromatin.
 |
DISCUSSION |
Our results reveal that the function of the IL-2-responsive
enhancer in the IL-2R
gene depends not only on the presence of previously identified transcription factors, but also on IL-2-induced changes in IL-2rE chromatin. We show that IL-2 controls the
accessibility of the binding site for Elf-1 that is required for
enhancer activity.
We confirm the two-stage model of the regulation of IL-2R
gene
transcription during T-cell activation (45). According to this model, antigen or ConA stimulates a transient peak of IL-2R
transcription through promoter-proximal elements. In a second phase,
IL-2 increases the level of IL-2R
transcription by activating STAT5,
which binds to an IL-2-responsive enhancer conserved in mice and
humans. Here we show that ConA stimulation of IL-2R
transcription in
normal T lymphocytes is independent of STAT activation and does not
involve the IL-2rE. IL-2 induces genomic footprints in the
IL-2rE, confirming the function of the three distinct
cis-acting elements in the IL-2rE mapped by transient
transfection in lymphoid cell lines (29, 36, 61). In the
chromatin of mouse T lymphocytes stimulated to express the
high-affinity receptor chain by IL-2, all three sites within the 51-nt
IL-2rE are occupied. From transient transfection experiments, we
concluded that the two more distal sites control IL-2 responsiveness by
binding to STAT5 (42), whereas Elf-1 contributes to enhancer
activity by binding to the third site (58). The in vivo
footprints shown here are completely consistent with this
interpretation. In both site I and site II, the consensus STAT binding
motif is protected. The absence of protection of the GATA consensus
motif that overlaps with site II supports our previous results that
argued against a role of GATA proteins in IL-2rE function
(42). Protection of the G doublet and the 5' flanking G
residue in site III by Elf-1 is predicted by methylation interference
analysis of the in vitro interaction between Elf-1 and its binding site
(27, 28). The enhanced sensitivity to methylation 5' of site
III specifically observed in the chromatin of nonactivated T
lymphocytes raises the possibility that a protein may bind at or near
site III in resting T cells, although such a factor has not yet been
detected by in vitro binding experiments.
Occupation of the STAT binding sites in the IL-2rE requires stimulation
with IL-2 and is concomitant with STAT5 activation. That IL-2
stimulation is essential for prolonged IL-2R
expression is reflected
in the persistence of activated STAT5 and in vivo footprints in the
IL-2rE. Occupation of the Elf-1 binding site also depends on IL-2
stimulation. This is surprising, because Elf-1 DNA binding activity is
present in the nuclei of unstimulated T cells, and IL-2 does not
stimulate an increase in the nuclear concentration or in the in vitro
binding affinity of the protein for the IL-2rE, nor does it induce any
detectable changes in Elf-1 electrophoretic mobility in native or
denaturing gels. Binding of Elf-1 to certain sites has been shown to
depend on cooperation with other transcription factors that are
activated by stimuli which mimic antigen triggering (63).
This is clearly not the case for site III, which matches very closely
the highest-affinity sites for mouse and human Elf-1 obtained in
site-selection experiments (12, 27) and is identical in 7 of
8 nt to the Ets binding site, which regulates transcription of the
terminal deoxytransferase gene (16). Elf-1 binding to this
sequence is also independent of activation signals. We have failed to
find any evidence for interactions between Elf-1 and STAT5 in in vitro
binding assays or in transient transfection experiments (references
42 and 58 and our unpublished results).
The simplest hypothesis for the delayed occupation of site III by Elf-1
is suggested by the comparison of the accessibility of the IL-2rE to
nucleases in resting, ConA-primed and fully activated cells. IL-2, but
not ConA, induces substantial changes in IL-2rE chromatin. Our data
indicate that IL-2 triggers both an opening of IL-2rE chromatin (that
accounts for the sensitivity of the IL-2rE to DNase I) and the
translational positioning of nucleosomes at the borders of the IL-2rE
(resulting in MNase-hypersensitive sites). Thus, it appears likely that
accessibility of site III to Elf-1 depends on the IL-2-induced opening
of the IL-2rE chromatin. Elucidation of the molecular events and the
role of STAT5 in the IL-2-induced chromatin changes will require
different experimental approaches.
Finally, our data also suggest that sites I and II in IL-2rE chromatin
are accessible to STAT5 but not to STAT1. If confirmed, this finding
would add a new level at which the specificity of cytokine-induced gene
expression may be controlled and provide a possible explanation for the
conclusion from the analysis of STAT1-deficient mice that the
physiological role of STAT1 is restricted to transduction of IFN
responses (14, 41), although STAT1 is activated by many
other cytokines (18, 24, 35, 64).
In summary, while the experiments described here provide a clear-cut
confirmation of the previously formulated model of the regulation
of IL-2R
gene expression during T-cell activation, they indicate
that changes in chromatin also play an important role in
IL-2-stimulated gene transcription.
 |
ACKNOWLEDGMENTS |
We are grateful to Glaxo, Geneva, Switzerland, for the generous
gift of IL-2. Jacques Louis, WHO, IRTC, Biochemistry Institute, Lausanne, Switzerland, kindly provided IFN-
R-deficient mice. Anne-Lise Peitrequin, Ludwig Institute, Lausanne, supplied us with the
antibodies for the FACS analyses. We thank Jovan Mirkovitch, Jean
Imbert, and Michèle Algarté for helpful technical advice and Véronique Imbert, Friedrich Beermann, and Moira Cockell for valuable discussions and advice during the preparation of the manuscript.
This work was supported, in part, by grants from the Swiss National
Science Foundation, the Swiss Cancer League, and the Swiss Federal
Office of Science and Technology.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Swiss Institute
for Experimental Cancer Research (ISREC), 155 Chemin des Boveresses, CH-1066 Epalinges, Switzerland. Phone: 41 21 692-5834. Fax: 41 21 652-6933. E-mail: Markus.Nabholz{at}isrec.unil.ch.
 |
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Molecular and Cellular Biology, April 1999, p. 2681-2689, Vol. 19, No. 4
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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