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(Received for publication, October 19, 1995; and in revised form, January 22, 1996) From the
The mouse mammary tumor virus env gene contains a
transcriptional activator (META) that can control transcription of the
adjacent long terminal repeat region. Transcriptional control by META
parallels that of several lymphokine genes, being specific to T cells,
dependent on their activation, and inhibited by the immunosuppressive
drug cyclosporine (CsA). DNase I footprinting indicated that nuclear
factors from activated T lymphocytes bound a promoter-proximal site,
META(P), and a promoter-distal site, META(D+), within the 400-base
pair META region. Nuclear factors from unstimulated, but not from
activated cells, bound a site, META(D-), adjacent to
META(D+). META(D+) directed transcription of a linked
luciferase gene, and gel shift analysis revealed binding of inducible,
CsA-sensitive T cell factors, in parallel with transfection results.
Authentic NFAT and NF-
Mouse mammary tumor virus (MMTV) ( The LTR of MMTV resembles that of other retroviruses in that it
contains the transcriptional control elements and start site for viral
RNA synthesis. We have described a second, novel promoter located in
the env gene of MMTV, which is activated in certain T lymphoma
cell lines (8, 9) (Fig. 1). This promoter
generates transcripts of the LTR found in the mouse EL4.E1 cell
line(8, 14) , in which the amplified genomic copies of
MMTV provirus contain a large deletion typical of these lymphomas. The
starting point of the transcript lies at position 7247 in the MMTV map,
within the env gene (8, 9) (Fig. 1a). The relevant
promoter is apparently controlled by the sequence immediately upstream
of it in the env gene. The transcriptional activity of a
411-bp env gene segment (Fig. 1b), which we
term META (for MMTV env transcriptional activator) was
established by transient transfection experiments(9) , and it
was further shown that this activity resembled closely the activity of
the interleukin 2 (IL2) promoter in the same cells. It was restricted
to T helper lymphocytes, it was dependent on cellular activation
through antigen receptors or their mimics, and its induction was
inhibited by the drug cyclosporine (CsA). META was active in mouse and
human T lymphocyte cell lines that resemble T helper cells by being
inducible for lymphokine synthesis, including mouse EL4.E1 cells, a
mouse T hybridoma cell line, and the human Jurkat cell line. It was not
active in HeLa cells, or, under the conditions studied, in a mouse B
cell line or a cytotoxic T lymphocyte cell line. The env gene
was shown to contain both a transcriptional activator and a start site
for mRNA synthesis. In this paper, we have examined META for
interactions with activation-induced DNA-binding factors and have
identified an element that can account for the transcriptional control
properties of the env gene itself.
Figure 1:
Structure of META.
The 9.9-kb MMTV genome is represented in a, with the META
segment located in the env gene. The LTRs (1328 bp) contain
the conventional MMTV promoter, responsible for the synthesis of MMTV
RNA, which originates near the 3` end of the 5` LTR. The MMTV provirus
from which META was first isolated, derived from EL4.E1 T lymphoma
cells, carried a 494-bp deletion within the LTR, indicated by the shaded box in the figure. META is responsible for the
activation-dependent, CsA-suppressible transcription described
earlier(8, 9) , which originates within the env gene and copies the 3` LTR. b, pBLCAT2-C30 is a plasmid
in which a META sequence lacking the transcriptional start site was
cloned as a BamHI insert upstream of the herpes simplex virus
tk promoter and the CAT coding region(9) . It represents
segment 6814-7212 of MMTV. c, the nucleotide sequence of
the META-BamHI fragment in pBLCAT2-C30, and derived plasmids
used in this study. Sequence numbering here is with respect to the
transcription initiation site within META, which occurs at position
7246 of the milk-borne virus sequence(10) . Nucleotide
positions at the ends of the fragment that were altered to generate
restriction enzyme sites are shown in lowercase. The
underlined segments represent restriction enzyme sites (thin
line) and sequence motifs that are candidates for transcription
factor binding sites (heavy underline). The potential binding
sequences, labeled ``M-'' (for motif), were
identified based on their similarity to the consensus binding sequences
for the transcription factors indicated(11) : AP2 and AP3 (activating proteins 2 and 3, respectively); MAF,
mammary cell activating factor(12) ; TCEp, proximal T
cell element of the IL2 gene(13) ; Pu box, proximal
purine box of mouse or human IL2 enhancer. Regions identified by DNase
I footprinting are delineated by boxes (META D segments, META
P; see Fig. 2and text). The sequence shown here is derived from
the MMTV provirus (clone C30) used in this and previous
work(8, 9) , and differs slightly from that of the
milk-borne virus(10) .
Figure 2:
DNase I footprinting analysis of META. The
lower (A) or the upper (B) strand of META was
end-labeled and subjected to DNase I digestion in the presence of
nuclear extracts from uninduced Jurkat cells(-), or cells
stimulated (+) with PMA plus ionomycin (A) or PMA plus
A23187 (B). The positions of segments differentially protected
in induced and uninduced extracts are indicated as
``D'' (distal) or ``P''
(proximal) on the line representation of the sequence on the left, which also shows the location of the label (*).
Protected regions META(D-) and META(D+) were observed with
the uninduced and induced nuclear extracts, respectively, and region P
was found to be weakly protected with induced extracts. N, no
nuclear extract; G, G/A, and T/C indicate
Maxam-Gilbert chemical sequencing
reactions.
The induction of
transcription from the META promoter resembles the activation of IL2
transcription in the same cells. Expression of the IL2 gene in T helper
lymphocytes is controlled primarily by the sequence lying within 300 bp
upstream of the transcriptional start site (15, 16) .
Several transcription factors interact with this region, including AP1,
AP3, Oct-1, NF-
DNA sequences were amplified by
the polymerase chain reaction (PCR) using primers described in Table 1, carrying the prefixes S (for sense orientation) and A
(for antisense). Primers and templates were heat denatured and
annealed(23) . Typical conditions for the PCR were: 10 mM Tris-HCl, pH 8.3, 50 mM KCl, 0.01% gelatin, 3.0 mM MgCl
A number of double-stranded DNAs were prepared by PCR
amplification using primers described in Table 1. META(D+)
DNA with protruding 5` AA (S21) and TT (A21) termini were first filled
in using Klenow DNA polymerase and then blunt-end ligated for 16 h at
14 °C to generate multimers. These were cloned upstream of the tk
promoter in pDS-tk13 to generate recombinant plasmids pDSD61 to pDSD65
(see Fig. 5). The head-to-tail configuration of the
META(D+) segments generated a HpaI restriction enzyme
site, which was used in conjunction with other methods to determine the
orientation and copy number of D(+) enhancer constructs
(head-to-head and tail-to-tail configurations lack the HpaI
site). Plasmid pDSM25F is a luciferase reporter plasmid derived from
pDS-tk13 harboring the META fragment extending from -29 to
-429 upstream of the tk promoter. The complete META fragment (411
bp) was liberated from pBLCAT2-C30 by SalI digestion, purified
by PAGE, and ligated into XhoI-cut pDS-tk13 to generate
pDSM25F. Human genomic IL2 sequences from -98 to -362 or
from +45 to -180 relative to the transcription start site
were amplified by PCR using primer pairs S17 and A17 (for -98 to
-362) or S16 and A16 (for +45 to -180) (Table 1). The hIL2 PCR product for -98 to -362
region was gel-purified, digested with EcoR I and HindIII, and ligated into pGEM-3Z vector cut with EcoRI and HindIII. The ligation mixture was
transformed into Escherichia coli DH5
Figure 5:
Inducible and CsA-suppressible expression
of META(D+)-luciferase constructs in Jurkat cells. The structures
of the plasmids used are schematically shown to the left of
the graph that depicts their induction by PMA plus A23187. Plasmid
pGL-2 control vector contained an SV40 promoter and enhancer. All other
plasmids were expressed under the control of the thymidine kinase
promoter (tk prm). The compositions of the plasmids were as
follows: pDSM25F, complete META region, containing a single copy of
META(D+); pDSD 63, pDSD 69, pDSD 61, pDSD 65, plasmids containing
the 39-bp META (D+) element in 3-7 copies upstream of the tk
promoter, in the orientations indicated by arrows. Rel.
fold induction represents the induced/uninduced signals for a
given construct, relative to the same ratio for the appropriate
enhancerless promoter. The actual values of the luciferase assay are
given in the table at the bottom of the figure (light units/10
µg of protein in the assay). pGL-2 and pDS-tk13 are the
enhancerless promoters of SV40 and thymidine kinase, respectively. The
luciferase expression values for the plasmids induced in the presence
of CsA are also given in the table (bottom row), with the
expression in CsA relative to the maximum in parentheses. Data are
presented from a single transfection experiment, but similar results
were observed in at least three independent
experiments.
Binding
reactions and DNase I digestions were carried out at room temperature
as described in the Life Technologies, Inc. DNase I footprinting
manual, with minor modifications. Briefly, the assay system contained
10 mM Tris-HCl, pH 7.0, 2 mM CaCl
To further delineate
the META(D) footprint, we performed DNase I digestions using the upper
strand of META (Fig. 2B). The footprint pattern in the
META(D) region showed some differences compared to the lower strand
results of Fig. 2A. Specifically, the -296 to
-323 region was protected by uninduced nuclear extracts, whereas
the -325 to -349 region was protected with induced
extracts. We have repeated these experiments three times with each of
the lower and upper strands, using either PMA/ionomycin or PMA/A23187
as inducing agents (the two calcium ionophores are similarly effective
in inducing IL2 synthesis in Jurkat cells, and showed no difference in
footprinting results). The META(D) footprint shown in Fig. 2A was the only case in which both parts of
META(D) were protected by nuclear extracts from induced cells only. All
of the experiments in which the upper strand was labeled were similar
to the result in Fig. 2B. Two out of three experiments
with the lower strand labeled also showed this protection pattern, i.e. protection of one element of META(D) in unstimulated
cells (META(D-)), and of an adjacent element in stimulated cells
(META(D+)). The single anomalous result shown in Fig. 2A, i.e. protection of the complete
META(D) region by induced extracts, did not result from either
peculiarities of the binding reaction or limited resolution at the top
of the gel; the results were reproducible with that extract and were
unchanged upon longer electrophoresis. In all experiments, however,
META(D) and META(P) always exhibited differential protection, and no
protected regions other than these were seen in the 411-bp META
sequence. To summarize, the META(D+) element was consistently
protected by extracts from induced cells, relative to uninduced
extracts. In most cases, META (D-) was protected by extracts from
uninduced cells (the exception being the result of Fig. 2A). META(P) was protected weakly by extracts of
induced cells. META(D+) protection was the most strongly
correlated with conditions of transcriptional induction of META itself (9) and of lymphokines, and it was therefore selected for
further analysis.
Figure 3:
Binding of nuclear factors to the META(D)
region. Mobility shift assays were carried out using META(D+) or
META(D-) probes at 0.5 nM. The probe for META(D+)
consisted of oligonucleotides S21 + A21, and the probe for
META(D-), of oligonucleotides S22 + A22 (Table 1). Lanes 1-4, META(D+) probe; lanes
5-8, META(D-) probe. NE, nuclear extract; FP, free probe; -, nuclear extract from uninduced Jurkat
cells; +, nuclear extract from Jurkat cells stimulated with PMA
and A23187; CsA, nuclear extract from induced plus CsA-treated cells. Arrow 3 on the left points to the complex found only
with induced extract, and almost completely suppressed by CsA. Arrow 1 identifies a constitutive complex, while arrow 2 points to a complex barely visible in unstimulated cells, and
strongly induced by PMA plus A23187. The complex observed with the
META(D-) probe (arrow 4) was seen with uninduced
extracts and with extracts induced in the presence of CsA, and was
barely visible with extracts from induced cells. A slower migrating
complex (arrow 5) was just detectable with uninduced and
CsA-treated cell extracts.
The results of gel shift
analysis are consistent overall with the results from DNase
footprinting, in that a specific complex was found under conditions of
transcriptional activation when META(D+) was used as the probe,
whereas the reciprocal pattern was seen with META(D-) as probe.
Figure 4:
Specificity and saturability of the
META(D+) binding site. A gel shift experiment was carried out as
in Fig. 3, using META(D+) as the probe. Lanes 3-5 show that the binding of the induction-dependent nuclear factor (arrow) could be titrated away with the unlabeled
``self'' probe due to saturation. An unrelated
oligonucleotide, corresponding to positions -278 to -253 of
META (Fig. 1) did not compete (NS, lanes 6 and 7). Amount (x) indicates the molar ratio of unlabeled
competitors to labeled probe.
The 41-bp META(D+) probe contains an RsaI site between positions -334 and -333 ( Fig. 1and Table 1). When the probe was treated with RsaI, no retarded band was seen with any extracts (data not
shown). These results suggest that the central region of META(D+)
must be intact for binding of nuclear factors. This segment contains an
AP3/NF-
Figure 7:
Comparison of the META(D+) sequence
to various enhancer domains. The META(D+) region defined by DNase
I protection, from -349 to -325, is indicated, as is a
short inverted repeat sequence. The sequences shown here correspond to
the oligonucleotides (see Table 1) used in the mobility shift
experiments (Fig. 8Fig. 9). The binding motifs are
indicated. The NF-
Figure 8:
Competition by AP3 and NF-
Figure 9:
Binding of induced nuclear factors to the
AP3 probe. Labeled AP3 probe (see Fig. 8) was used with
unlabeled oligonucleotide competitors. Lanes 1-3, no
competitor; lanes 4-7, unlabeled AP3/SV40
oligonucleotide (self); lanes 8-12, unlabeled META
D+) oligonucleotide; lanes 13-18, unlabeled hIL2
NF-
The induced and constitutive complexes of META(D+) differed in
sensitivity to the addition of unlabeled homologous probe, with the
induced complex (Fig. 4, arrow) showing a greater
sensitivity, possibly reflecting a lower concentration of the factor
responsible. The results of competition show that the binding was
specific and saturable.
The tandem META(D+) arrays were not only induced
relatively more by activation than was the pGL-2 SV40 construct, under
induced conditions they were higher in absolute level as well, with the
most powerful, pDSD 65, being almost 100 times as strongly expressed as
the SV40 enhancer-promoter combination (numerical data are given in Fig. 5, bottom panel).
Figure 6:
Dual signal requirement and T lymphocyte
specificity of the META(D+) enhancer. A, Jurkat cells
were transfected with the luciferase expression plasmids pDS-tk 13 or
pDSD65 (Fig. 5) and stimulated with the agents shown. Data are
expressed as relative fold induction, as in Fig. 5. The
luciferase activities (light units/10 µg) were as follows:
uninduced (UI), 271; A23187 alone, 404; PMA alone, 5,520; PMA
+ A23187, 79,520; PMA + A23187 + CSA, 10,280. The
luciferase activities for the control enhancerless plasmid pDS-tk 13
was 1,870/334 (induced/uninduced). B, relative activities of
pDSD65 in different types of cells. S194 (B cell), HeLa (fibroblast),
EL4.E1 (mouse T lymphoma), and Jurkat (human T lymphocyte) were
transfected with the plasmid and stimulated with PMA plus A23187. Data
are expressed as relative fold induction as described above. The
luciferase activities (induced/uninduced) were: S194, 189/77; HeLa,
11,560/2,300; EL4.E1, 459,600/12,930; Jurkat, 111,070/460. The
luciferase activities for enhancerless plasmid pDS-tk 13 in
induced/uninduced conditions were: S194, 194/90; HeLa, 4,070/3,390;
EL4.E1, 26,790/14,890; Jurkat, 3,220/431. Data in A and B represent the results from different experiments. These profiles
were reproduced in two independent
experiments.
The activity of the META(D+) enhancer was dependent on
the type of cell used for transfection. The T lymphocyte cell lines
EL4.E1 and Jurkat showed high levels of inducible activity compared to
the non-T cells S194 and HeLa. It is noteworthy that both S194 and HeLa
cells contain active NF-
The competition by SV40 for the META(D+)-binding factor(s)
prompted us to examine the reciprocal situation (Fig. 9). The
SV40 probe exhibited a mobility shift with nuclear extracts from both
control and induced Jurkat cells, but the two patterns were completely
different. Nuclear factors from uninduced cells (lane 1)
yielded one very weak band of fairly high mobility, whereas induced
extracts (lane 2) yielded two different bands, much stronger
and of lower mobility. The two activation-dependent bands were not
significantly affected by CsA. META(D+) did not compete
effectively for the induced complexes, compared to the SV40 sequence
itself. The human IL2-derived NF-
We have identified an enhancer element in the MMTV env gene, META(D+), located between positions -325 to
-350 relative to the start site of the transcript of the 3` LTR
described earlier(8, 9) . Previously, the META
fragment extending from -431 to -34 was shown to confer
orientation-independent, induction-dependent, and CsA-suppressible
activity in T helper lymphocytes(9) . The existence of the
META(D+) element was suggested by DNase I footprinting analysis
and confirmed by gel retardation assays and transient transfection
studies. Multimers of the META(D+) element conferred
activation-dependent, T lymphocyte-specific, and CsA-suppressible
expression on the luciferase reporter gene in transient transfections.
The overall enhancer strength was related to the number of copies of
the element, but did not require that the individual copies be oriented
in the same direction (Fig. 5). Two other putative control
elements, META(P) and META(D-), were indicated by DNase I
footprinting analysis. Data in Fig. 2suggest that
META(D-) may be a negative control region, since in almost every
experiment a binding complex was found under non-transcribing
conditions only (either uninduced cells, or cells induced in the
presence of CsA). Of the several DNase I footprinting reactions carried
out, there was only one instance where the protection with induced
nuclear extracts occurred over the entire META(D) region (this
exception is shown in Fig. 2A). The mobility shift
experiments with META(D-) probe (Fig. 3) are in agreement
with its being a negative element (i.e. complexes were formed
under non-transcribing conditions only). Examination of the
META(D-) sequence indicated a potential AP1 binding site,
TGACcAA, in the -314 to -308 region(11) . Similar
to the closely spaced (D+) and D(-) elements in META, the
NF- META(D+) contains an inverted repeat overlapping the 5` end of
the central binding region (Fig. 7). Such structures can
negatively regulate expression of inducible genes(36) ,
including c-fos(37) and human
Given the similarities in the transcription regulatory
properties of META and the IL2 upstream region(13) , it was
reasonable to suppose that the META(D+) element might be
responding to the IL2-related NFAT binding factor(s). However, the
human IL2 NFAT probe did not compete for META(D+) in gel shift
analysis. A general hypothesis explaining the action of CsA has been
proposed, which involves a complex of proteins recognizing NFAT plus
one of several ancillary proteins such as AP1, NF- The lysolecithin method we used in
this paper to extract nuclear binding proteins utilizes 0.6 M KCl. The more conventional methods depend on hypotonic shock and
ammonium sulfate precipitation of nuclear
proteins(13, 22) . NFAT binding is diminished if the
salt concentration used for protein preparation or for binding
reactions exceeds 0.3 M KCl(41) . We found that
META(D+) probe also bound inducible nuclear factors obtained by
conventional methods of extraction, and this binding was also not
competed by NFAT oligonucleotide (data not shown). The human IL2
upstream region (+45 to -362) did not compete for
META(D+), nor did its constituent elements NF- The mammary cell-specific expression of MMTV in mice
is brought about by the net actions of positively acting
estrogen-dependent elements and negative elements within the LTR. The
induction of T cell lymphomas by MMTV has been attributed to the loss
of repressor elements in the control regions of the LTR due to
deletions and/or rearrangements. In particular, deletion of the
repressor elements between -430 and -360 in the LTR
promoted transcription of this viral strain in T cells(44) . It
is possible that the concerted action of the META(D+) enhancer
with known transcriptional regulatory sites in the LTR contributes to
the induction of T cell lymphomas. Enhancers of lymphotropic papova
virus, Moloney murine leukemia virus, and T lymphomagenic virus
SL3-3 also exhibit a high degree of homology to the AP3 binding
site in the SV40 enhancer(45, 46, 47) . These
enhancers are involved in the generation of hematopoietic
malignancies(47) , making META(D+) a candidate enhancer
for the observed MMTV-induced T cell lymphomas. A tantalizing
feature of META is that it regulates the expression, at least in
certain T lymphoma cell lines, of the LTR transcript, which normally
encodes the minor histocompatibility antigens of the Mls
family(4, 5) . META, given its lymphoid-specific
induction, makes an attractive candidate for the regulator of Mls
antigen expression, except for one thing; so far, we have seen
expression only in T lymphocytes which, although implicated as Mls
presenting cells in the induction of tolerance(48) , are not
conventional antigen-presenting cells. We have not observed META
activity in B lymphocytes, but this may be because we have not yet
looked at the correct B cells in the proper way.
The nucleotide
sequence(s) reported in this paper has been submitted to the
GenBank(TM)/EMBL Data Bank with accession number(s)
U41642[GenBank].
Volume 271,
Number 15,
Issue of April 12, 1996 pp. 8942-8950
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
B targets did not compete for the
META(D+) binding factor(s). The SV40 core sequence competed for
META(D+) binding factors, but META(D+) failed to compete for
the complexes obtained with the SV40 probe. Our results, taken
together, indicate that META(D+) is a novel transcriptional
enhancer element that is similar in its cell-type specificity,
activation dependence, and CsA sensitivity to the NFAT element. It may
be relevant to the role of MMTV in expression of Mls antigens or the
induction of T cell lymphomas.
)is involved in at
least three different biological processes: induction of mammary
adenocarcinoma, generation of thymic lymphoma, and expression of minor
histocompatibility superantigens of the Mls type. The relatively large
and complex long terminal repeat (LTR) is implicated in all three
responses. Enhancers in the LTR activate cellular proto-oncogenes to
induce tumorigenesis in mammary tumors(1) . On the other hand,
MMTV variants that induce T lymphomas rather than mammary
adenocarcinomas carry large deletions of LTR sequences(2) ,
whose absence or modification is necessary for T cell tumors to
develop(3) . And in the case of the minor Mls antigens, the LTR
encodes the protein antigen in one of several
forms(4, 5) . In each of these three systems, there is
a requirement for MMTV-related transcriptional activity in lymphocytes,
although the molecular mechanisms regulating transcription control may
differ between them. The requirement for expression in lymphocytes
includes the induction of tumors by the mammotropic strains of MMTV, as
part of the mechanism of transmission to the mammary epithelium. This
participation requires expression of the virally encoded Mls
antigen(6) . The LTR contains strong, corticosteroid-inducible
transcriptional activator elements(7) , but it is not clear
what their role is, if any, in transcriptional control in lymphocytes.
B, and NFAT(13, 17, 18) .
The NF-
B and NFAT sites show activation-dependent binding with
their relevant factors in vivo(19) . NFAT is the most
sensitive of these sites to CsA, as its binding factor is completely
blocked by the drug. Both NF-
B and AP3 are somewhat less
sensitive(20) . The META region contains several transcription
factor binding motifs, but none with the exact NFAT sequence of the
human IL2 gene (Fig. 1c). Thus, it was of interest to
determine whether an element could be identified that accounted for the
characteristic transcriptional activating properties of META. This
paper describes in detail such an element, which we term META(D+).
Cells
Jurkat (human T cell leukemia), EL4.E1
(mouse T-lymphoma), S194 (mouse myeloma), and HeLa (endothelial
carcinoma) cell lines were maintained in RHFM medium comprising RPMI
1640, 20 mM HEPES (pH 7.4), 100 µM 2-mercaptoethanol, antibiotics, and 10% fetal bovine
serum(9) .Nuclear Extracts
Jurkat cells were stimulated for
4-6 h with 15 ng/ml 12-phorbol 13-myristate acetate (PMA) plus
1.5 µM ionomycin, or with PMA plus 0.5 µM A23187. IL2 was measured by bioassay(21) . CsA was present
at 100 ng/ml where indicated. Nuclear extracts from unstimulated and
stimulated cells were prepared by the lysolecithin lysis
method(22) . Nuclear extracts were aliquoted, frozen in liquid
nitrogen, and stored at -70 °C. Protein concentrations in
cell extracts were determined with a Coomassie protein assay kit
(Bio-Rad).DNA Methodology and Reagents
Restriction enzyme
digestions, DNA polymerase reactions, ligations, end labeling, agarose
or polyacrylamide gel electrophoresis (PAGE), gel elution of DNA
fragments, and Sephadex G-50 spin column chromatography were carried
out by standard protocols(23) . Oligonucleotides were obtained
from the DNA synthesis facilities of either the Departments of
Microbiology or Biochemistry at the University of Alberta. Molecular
biological reagents and enzymes were obtained from Life Technologies,
Inc. (Burlington, ON), the luciferase reporter vector pGL2 from Promega
(Madison, WI), Maxam-Gilbert chemical sequencing kit from DuPont NEN,
and the Maxi Plasmid DNA purification kit from Qiagen Inc.
(Charlesworth, CA). PMA, ionomycin, A23187, luciferin, acetyl coenzyme
A, and DNase I enzyme were purchased from Sigma. CsA was a gift from
Sandoz Canada Inc. (Dorval, Quebec).
, 0.2 mM dNTPs, 80 nM primers,
6.25 ng of plasmid template, and 1.25 units of Taq DNA
polymerase, in a total volume of 50 µl. The Hybaid thermal reactor
(Bio/Can Scientific, Toronto, ON) was programmed for the following
conditions: 96 °C for 5 min, then two cycles of 94 °C for 1
min, 45 °C for 1 min and 72 °C for 1 min; followed by 25 cycles
of 94 °C for 1 min, 60 °C for 1 min, 72 °C for 1 min; and
ending with an extension reaction at 72 °C for 3 min. PCR products
were separated by PAGE in 1 TBE (89 mM Tris, 89 mM boric acid, 2 mM EDTA).
Plasmids
Numbering of META segments is based on
the transcriptional start site of the META-driven promoter in
MMTV(9) . Construction of the plasmid pBLCAT2-C30 containing
META sequences from -29 to -439 (Fig. 1b)
has been described(9) . Plasmids pGL2 promoter and control
vectors are the luciferase reporter plasmids containing the SV40
promoter, and the SV40 promoter plus enhancer, respectively. Plasmid
pDS-tk13 has the thymidine kinase (tk) promoter in place of the SV40
promoter in the pGL2 promoter vector background, and was constructed as
follows. Plasmids pBLCAT2-C30 and pGL2 promoter vectors were digested
with BglII and HindIII, respectively, and the
recessed ends were filled in using the Klenow DNA polymerase enzyme.
Linearized, blunt-ended pBLCAT-C30 was cut with BamHI to yield
the 411-bp META fragment, a 168-bp tk promoter fragment, and a 4.3-kb
vector DNA fragment. Digestion of the linearized, blunt-ended pGL2
promoter vector with BglII yielded a 203-bp fragment
containing the SV40 promoter and 5.59-kb vector DNA fragment. The tk
promoter fragment generated from pBLCAT-30, and the linearized pGL2
vector segment lacking the SV40 promoter were purified on agarose gels
and ligated to yield the pDS-tk13 enhancerless luciferase reporter
vector.
, and plated on LB
agar-ampicillin indicator plates containing 5-bromo-4-chloro-3-indoyl
-D-galactoside and
isopropyl-1-thio-
-D-galactopyranoside for blue/white
colony selection. White colonies were selected, and the recombinant
plasmid pDIL2 thus generated was purified and sequenced. Recombinant
constructs were confirmed by both sequencing and/or restriction
digestion analysis.
DNase I Footprint Analysis
Plasmid pBLCAT2-C30 was
used as a source of META (-439 to -29, Fig. 1b). For upper strand labeling, the plasmid was
linearized with XbaI, dephosphorylated, and end-labeled using
[
-
P]ATP and T4 polynucleotide kinase I.
Radiolabeled DNA was separated from unincorporated label on a Sephadex
G50 spin column. PstI digestion of this DNA resulted in 528-bp
labeled META fragment with flanking vector sequences, a 9-bp labeled PstI-XbaI fragment from the multicloning site, and
the remaining 4363-bp vector DNA. The lower strand of META was labeled
at the XbaI end starting with pBLCAT2-C30 containing META
(-29 to -439) in the reverse orientation. HindIII
digestion of this DNA resulted in the release of a 406-bp labeled META
fragment along with labeled 20-bp XbaI-HindIII
fragment from the multicloning site and the 4485-bp of the vector DNA.
The labeled META DNA along with the vector DNA fragments obtained by
these procedures was used without further fractionation.
, 0.5
mM DTT, 0.5 mM phenylmethylsulfonyl fluoride, 30
mM KCl, 2.5 µg/ml bovine serum, 0.5% glycerol, 100 µg
of Jurkat cell nuclear protein, and 2 µg of poly(dI-dC) in a
reaction volume of 50 µl. Reactions were incubated for 10 min
followed by the addition of 1 ng of DNA probe (20,000 cpm). After an
additional incubation of 20 min, 50 µl of DNase I buffer (10 mM HEPES, pH 7.8, 5 mM MgCl
, and 1 mM CaCl
) was added, and 50 ng of DNase I. Digestion was
carried out for 1 min, and the reaction was terminated by the addition
of 10 µl of stop buffer (10 mM MES, pH 7.0, 15 mM EDTA, 0.5% sodium dodecyl sulfate, 250 µg of salmon sperm DNA,
and 10 µg of proteinase K). Proteinase K digestion was continued
for 30 min at 37 °C. The reactions were extracted with
phenol:chloroform:isoamyl alcohol (25:24:1), precipitated using ethanol
and sodium acetate, dissolved in formamide loading buffer, and
subjected to 6% acrylamide, 7 M urea PAGE (0.4 mm thick gel)
in 1 TBE buffer using a Life Technologies, Inc. vertical gel
apparatus. Dried gels were exposed to Kodak X-Omat AR film at -70
°C with an intensifying screen.
Mobility Shift Assays
Single-stranded
oligonucleotides (sense strands) were end-labeled using
[
-
P]ATP and polynucleotide kinase, the
kinase was heat-denatured, and the fragments were annealed to
complementary antisense oligonucleotides. Unincorporated label was
separated on G-50 Sephadex spin columns. Binding reactions were carried
out with 0.5 nM probe (5,000-10,000 cpm) in a final
reaction volume of 20 µl at room temperature. Reaction mixtures
contained 25 mM HEPES, pH 7.8, 75 mM KCl, 1 mM EDTA, 0.5 mM DTT, 0.5 mM phenylmethylsulfonyl
fluoride, 5% glycerol, 3 µg of poly(dI-dC), and 10 µg of Jurkat
cell nuclear extracts. Probe was added to the reaction mix after 10
min, or a total of 25 min when cold competitor DNA was included.
Binding reactions were then continued for 30 min, analyzed on 4%
acrylamide (1.5-mm-thick gels) in 1 TBE at room temperature.
Dried gels were exposed to Kodak X-Omat AR film at -70 °C
with an intensifying screen.
Transfections and Measurement of Luciferase
Activity
Purified plasmid DNA that was >90% closed circular,
as judged by gel analysis and ethidium bromide fluorescence
quantitation (27) was used in the DEAE-dextran transfection
protocol(9) . A total of 15 µg of DNA was used in a volume
of 2 ml. Following transfection, cells were resuspended, divided, and
maintained in RHFM medium for 36-42 h. Cells were induced for 6 h
by adding PMA plus A23187 with or without CsA. Cells were pelleted,
washed twice with phosphate-buffered saline, and resuspended in lysis
buffer: 1% Triton X-100, 25 mM glycylglycine, pH 7.8, 15
mM MgSO
, 4 mM EGTA, and 1 mM DTT (28) . Luciferase activities in whole cell extracts were
measured as described in the Promega luciferase assay manual using a
Lumat LB 9501 luminometer. The luciferase assay contained 20 mM glycylglycine, pH 7.8, 1 mM Mg(CO
)
, 2.7 mM MgSO
,
0.1 mM EDTA, 33 mM DTT, 0.47 mM luciferin,
0.53 mM ATP, and 0.27 mM coenzyme A in a reaction
volume of 100 µl.
DNA Footprint Analysis of the Interaction of Nuclear
Factors from Jurkat Cells with the META Sequence
The complete
META segment of MMTV, comprising the 411-bp region lying between 29 and
439 bp upstream of the novel env promoter (Fig. 1), has
previously been shown to mediate inducible, CsA-suppressible, and T
lymphocyte-specific expression of reporter genes(9) . Overall,
it responds in parallel with lymphokine enhancers, such as that of IL2,
in T cell lines. We therefore carried out DNase I footprinting
experiments to look for interactions with nuclear factors from Jurkat
cells, a human T cell line that is induced to synthesize IL2 by a
combination of PMA and a calcium ionophore. Nuclear extracts from
uninduced Jurkat cells, and from cells stimulated with PMA plus
ionomycin, were examined. The footprint pattern shown in Fig. 2A revealed two regions of protection with induced
extracts, compared to extracts from unstimulated cells. These are
referred to as proximal (META(P)) and distal (META(D)). META(P) is
located around -116 to -146 relative to the META
transcriptional start site. Extracts from induced cells showed partial
or faint protection of this region, compared to uninduced cells. In
three independent experiments with end-labeled lower strand, partial
protection of META(P) was consistently observed. On the other hand,
META(D) comprised two strong and discrete footprints with extracts of
stimulated cells, one in the -296 to -323 region and the
other in the -325 to -349 region.Binding of Jurkat Nuclear Factors to the META(D)
Elements
The META(D+) and META(D-) elements are
delineated in Fig. 1C. Oligonucleotides containing
these sequences (Table 1) were used to look for binding factors
by gel shift analysis with nuclear extracts from Jurkat cells (Fig. 3). The D(+) probe (lanes 1-4)
demonstrated one very strong complex (arrow 1), and one that
was barely detectable (arrow 2) with extracts from
unstimulated cells. Under conditions of transcriptional activation, a
very strong additional band of intermediate mobility (arrow 3)
was seen, and a greatly enhanced amount of complex in the region of the
slower constitutive band (arrow 2). Formation of these
complexes was almost completely abolished by CsA, which blocks
activation of META transcription(8, 9) . The
META(D-) probe (lanes 5-8) showed a strong band
with uninduced cell extracts, which was almost completely abolished
under conditions of cellular induction, and was partially restored when
CsA was present (arrow 4).
Specificity of the META(D+) Inducible
Complex
The binding of nuclear factor(s) to the META(D+)
probe was investigated by using unlabeled homologous and heterologous
competing oligonucleotides (Fig. 4). The signal due to binding
of both constitutive and induction-dependent factors to META(D+)
was titrated out by unlabeled META(D+) probe, but not by a
nonspecific oligonucleotide derived from a nearby, but unrelated, META
sequence of similar length. (The nonspecific competitor contains an
element similar to the AP3/TCEp motif of the upstream control region of
IL2(13) ).
B motif (see Fig. 7and ``Discussion'').
B motif in META(D+) is on the opposite
strand (dashed underline). Numbers in parentheses indicate the number of matches to the reported consensus binding
sequence(11) : AP2 CCC(A/C)N(G/C)(G/C)(G/C); AP3,
TGTGG(A/T)(A/T)(A/T)GT; NF-
B, GGGA(A/C)TN(T/C)CC. Mismatches of
the SV40, NF-
B, and NFAT motifs with META(D+) are shown in lowercase. The GGAAA motif characteristic of the NFAT family
of proteins is underlined.
B binding
sequences for the META(D+)-binding proteins. Gel mobility shift
experiments were carried out using labeled META(D+) probe and
unlabeled competitor oligonucleotides, either an SV40-derived AP3 site
(sequences SAP3 and AAP3, Table 1) or hIL2-derived NF-
B (S09
and A10, Table 1). Lanes 1 and 2, no
competitor; lanes 3-6, AP3/SV40 competitor; lanes
7-11, hIL2 NF-
B competitor; lanes 12-14,
nonspecific oligonucleotide competitor, corresponding to positions
-125 to -96 of META (sequences S20 plus A20, Table 1). Other symbols and conditions are as in Fig. 3and Fig. 4. The region of free probe is not shown
in this autoradiogram.
B oligonucleotide; lanes 18 and 19, a
nonspecific oligonucleotide corresponding to sequence from -125
to -96 of META (sequences S20 plus A20, Table 1). Other
symbols and conditions are as in Fig. 3and Fig. 4. Free
probe not shown.
The META(D+) Sequence Confers Inducible,
CSA-suppressible, Transcriptional Activation
To determine the
enhancer function of META(D+) in intact cells, we transfected
Jurkat cells with plasmids containing various META(D+)-related
constructs, driving the expression of a luciferase reporter gene (Fig. 5). The activities of the enhancer constructs were
compared to the relevant promoter constructs lacking enhancers. The
pGL-2 plasmid containing an SV40 promoter/enhancer sequence, included
as a control, showed increased luciferase gene expression on
stimulation with PMA plus A23187, as has been observed by
others(13, 24, 29) . The activity observed
with the full-length 411-bp META region (pDSM25F) linked to the
thymidine kinase promoter was also stimulated by activation with PMA
and calcium ionophore, and this activity was CsA-sensitive. This is
parallel to the effect of META on the expression of the CAT gene
reporter(9) . When individual META(D+) enhancer elements
were linked to the tk promoter, luciferase expression was also induced
by PMA plus A23187, with the strength of induction being related to the
number of elements placed in series. Activation did not require the
elements to be oriented in one direction, and in every case was
strongly sensitive to CsA. A 7-mer of META(D+) generated more than
a 100-fold induction upon activation, compared to the enhancerless
promoter construct, with 93% of the induced activity being inhibited by
CsA.Full Activation of the META(D+) Enhancer Requires
Both PMA and Calcium Ionophore and Is T Cell-specific
In an
earlier study we showed that the 411-bp META fragment mediates T
cell-specific, induction-dependent expression of the CAT reporter gene (9) . In that study, META was activated in both mouse (EL4.E1)
and human (Jurkat) T helper cell lines, and in a mouse T helper
hybridoma cell line. The dual signal requirement and T cell specificity
of the META(D+) enhancer element was therefore investigated using
several cell lines, including Jurkat transfected with plasmid pDSD 65 (Fig. 6). Exposure of the transfected cells to calcium ionophore
alone had no significant effect on the reporter construct. Stimulation
with PMA alone increased the activity to about 37% of the maximum
activity generated with both PMA and A23187. CsA inhibited 87% of the
fully induced activity, whereas PMA-induced activity was only inhibited
by 33%.
B and AP3 factors under constitutive
and/or inducing conditions, yet did not significantly activate
META(D+).Comparison of the META(D) Sequence to Various Cellular
and Viral Enhancers
Examination of the META(D) region revealed
several potential motifs for binding transcription factors AP1, AP2,
AP3, NFAT, and NF-
B (Fig. 7). The AP3 binding site in the
SV40 enhancer mediates tissue-specific, inducible enhancer functions in
a variety of cell types. Several factors interact with SV40 core
sequence, including a family of NF-
B related proteins (p50, p55,
p65, p75, p85) from stimulated Jurkat cells(30) , TCF-1, -2,
and -3 from EL4 cells(31) , NP-TCII from unstimulated Jurkat
cells(32) , AP3 from HeLa cells, and authentic NF-
B from
B-lymphocytes(25, 33) . These classes of proteins also
bind the NF-
B sequence in the human IL2
enhancer(13, 18, 31) . The META(D+)
sequence shows similarity to AP3 and NF-
B binding sites. Except
for the NF-
B element of the IL2 enhancer (tGAAA), all others shown
in Fig. 7have the conserved motif GGAAA characteristic of the
binding regions for AP3, NF-
B, NFAT, and other members of the
Dorsal/Rel family of transcription factors. The NP-TC II motif in the
SV40 enhancer resembles the NF-
B binding site, but it binds a
different factor(32) . Enhancers from META(D+), SV40, and
IL2 have 7-8 nucleotide matches to the consensus NF-
B site
(GGGA(A/C)TN(T/C)CC)(11) . The NFAT core sequence of the human
IL2 enhancer exhibits 6/10 matches to the consensus AP3 binding
sequence (TGTGG(A/T)(A/T)(A/T)GT)(11) . We therefore used IL2
enhancer DNA or specific oligonucleotides to compete for binding of the
META(D+) element to its factor(s) in nuclear extracts.The SV40 Oligonucleotide Competes for the META(D+)
Binding Factor, but NF-
We investigated the
binding of factors in activated Jurkat nuclei to the META(D+)
probe in the presence of competing SV40 promoter sequences and hIL2
NF-
B Does Not
B oligonucleotides. SV40 contains an AP3 motif(33) ,
and also an element that binds both the inducible factor NF-
B (34) and factor NF-TCII(32) , which is expressed
constitutively in T and B lymphocyte cell lines. The mobility shift
experiments shown in Fig. 8demonstrate that the 22-bp SV40
oligonucleotide (lanes 3-6) competed quite efficiently
for the factor(s) binding META(D+), comparable to the
META(D+) self-competition (cf. lane 4 of Fig. 4). On the other hand, the hIL2 NF-
B element, which
shows only a limited similarity to META(D+) (Fig. 7), was a
poor competitor; even a 200-fold molar excess produced only a modest
diminution of the signal (lanes 7-11). An
oligonucleotide containing the mammary cell activating factor-like
region of META (-126 to -96, see Fig. 1and Table 1), and which also contains the central GGAAA
pentanucleotide characteristic of the AP3 or NFAT sites, did not
compete (lanes 12-14), suggesting that sequences
flanking the pentanucleotide are essential for META(D+) binding.
B probe competed moderately well
for the lower mobility SV40 activation-dependent complex, but not for
the other one.Search for a META(D+) Competitor Sequence in the IL2
Gene
One of the interesting features of the META(D+)
complex is that its induction is abolished by the immunosuppressive
drug CsA. This is characteristic of very few transcriptional activating
elements, chief among these being the NFAT element of the IL2 and other
cytokine genes (20) . Although NFAT and META(D+) elements
both contain a central GGAAA pentanucleotide, there is no overall
similarity between them (Fig. 7). Nevertheless, because of their
functional similarity, we tested human IL2 upstream DNA probes, as well
as an oligonucleotide carrying the NFAT motif, for their ability to
compete with META(D+). DNA from the human IL2 gene representing
the regions +45 to -183, -98 to -362, as well as
the AP1 and NFAT oligonucleotides were tested as competitors
individually. The oligonucleotides corresponding to the various regions
in META, namely AP3/TCEp, polypurine element, and mammary cell
activating factor, which harbor the GG(A/T)(A/T)(A/T) motifs (Fig. 1c) were also end-labeled and tested individually
in mobility shift assays. However, the induction-dependent binding to
META(D+) was not affected by any of the IL2 enhancer elements
(data not shown). The overall conclusion is that there is a major
binding site for inducible, CsA-suppressible nuclear factors in the
META(D+) region, and that it is activated in parallel with, but
distinct from, the IL2 NFAT site.
B (-208 to -188) and AP1 (-185 to -178)
elements in the IL2 enhancer are also adjacent. Footprinting analysis
of the IL2 enhancer in vivo has revealed that the AP1 element
is protected under uninduced conditions, whereas the NF-
B element
is protected under conditions of induction(19) . A negative
role for the distal AP1 site in mouse IL2 upstream sequence has been
suggested, since it showed diminished binding of nuclear factors from
stimulated cells compared to the unstimulated ones(35) . In
contrast to the strong and reproducible footprints found for
META(D+), the proximal site at META(P) was only weakly protected,
and we do not know whether it has an enhancer function.
-interferon(38) . The dyad symmetry element encompasses an
AP2 motif (7/8), but there was no evidence that it bound an inducible
protein.
B, or
Oct(39, 40) .
B (Fig. 8), NFAT, or AP1 (data not shown). The only strong
competition for META(D+) was by the SV40 AP3 element(33) ,
which encompasses an NF-
B site (42) and a site for
NP-TCII, which is expressed constitutively in lymphocyte
nuclei(32) . However, META(D+) differs from each of these
factors in terms of its T helper lymphocyte specificity, its dependence
on activation, and its CsA sensitivity, as well as lack of competition
for binding. S194 cells (a B-cell line) and HeLa cells (fibroblast) are
known to produce NF-
B and AP3 proteins, respectively, but
META(D+) did not promote transcriptional activity in these cells,
either uninduced or exposed to PMA plus A23187 (Fig. 6). In
short, its properties cannot be explained by interaction with known
binding factors. The nature of the META(D+) binding factor remains
uncertain, but it is reasonable to speculate that an NFATp/c family
member is involved(43) , perhaps in conjunction with other
components that differentiate it from the NF-AT binding factor of the
human IL2 gene.
)
B, nuclear factor
B; NFAT, nuclear factor of activated T cells; PMA, phorbol
myristate acetate; TCEp, proximal T cell element; tk, thymidine kinase;
kb, kilobase pair(s); DTT, dithiothreitol; MES,
4-morpholineethanesulfonic acid; bp, base pair(s); CsA, cyclosporine;
PCR, polymerase chain reaction; PAGE, polyacrylamide gel
electrophoresis.
-We thank Dr. C. L. Miller for discussions and
Cliff Gibbs for technical assistance.
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
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