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(Received for publication, June 26, 1995; and in revised form, September 20, 1995)
From the
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
YY1 is a multifunctional transcription factor capable of either activation or repression of transcription. Using a series of mutant proteins, we have characterized domains responsible for activation or repression. We found that the YY1 transcriptional activation domain lies near the amino terminus and requires amino acids 16-29 and 80-100 for maximal activity. The region between residues 16 and 29 has the potential to form an acidic amphipathic helix, whereas residues between 80 and 100 are rich in proline and glutamine. The YY1 repression domain lies near the carboxyl terminus and is embedded within the YY1 zinc finger region necessary for binding to DNA. Deletion of YY1 amino acids, which include zinc fingers 3 and 4, abolishes repression. However, site-directed mutagenesis, progressive deletion, and internal deletion mutant analyses indicate that the normal structures of zinc fingers 3 and 4 are not required for repression.
YY1 (variously called NF-E1, , or UCRBP; (1, 2, 3, 4) ), is a multifunctional
transcription factor that can either activate or repress transcription.
Repression has been observed in the context of the immunoglobulin
3` enhancer, the Moloney murine leukemia virus long terminal repeat,
the adeno-associated virus P5 promoter, the skeletal 
-actin
promoter, the 
-casein promoter, - and
-globin genes, the
serum amyloid A1 promoter, the human immunodeficiency virus promoter,
and the human papilloma virus type 18 promoter (1, 4-13; reviewed
in ref. 14). In contrast YY1 can activate the c-Myc promoter, the
ribosomal protein L30 and L32 promoters, and the intracisternal
A-particle upstream promoter
element(15, 16, 17, 18) .
Interestingly, YY1 can either activate or repress some promoters
depending upon either promoter architecture or intracellular milieu.
For instance, YY1 typically represses the adeno-associated virus P5
promoter, but can be converted into a potent transcriptional activator
in the presence of adenovirus E1A protein(1) . YY1 can also
either activate or repress the c-Fos promoter based on the orientation
or the position of a YY1 binding site within the promoter(19) .
Finally, YY1 can either repress or activate the human papilloma virus
type 18 promoter depending upon the presence of an adjacent DNA
sequence that binds to a distinct nuclear factor(6) .
The
mechanism of YY1 function is presently unclear. In some cases, YY1
binding appears to preclude the binding of activator proteins. For
instance, YY1 binding competes with the binding of NF-B to an
overlapping -sequence in the serum amyloid A1 promoter(13) .
Similarly, YY1 competes with serum response factor binding in the
-actin promoter, GATA-1 binding in the -globin promoter, and
with binding of a lactation-associated factor in the
-casein
promoter(7, 9, 10, 11) . YY1
function may also relate to its ability to bend DNA(19) . In
other cases, the function of YY1 appears to be controlled by
interaction with other proteins such as adenoviral E1A, c-Myc, or
switch binding protein(1, 6, 20) .
Interestingly, loss of YY1 binding sites in the human papillomavirus
type 16 silencer region is implicated in the overexpression of viral
oncogenes and in tumor progression(21, 22) .
YY1
may also contribute to transcriptional regulation by serving as an
initiator binding protein during the formation of the basal
transcription complex. YY1 can activate transcription in vitro in the context of the adeno-associated virus P5 initiator or the
cytochrome c oxidase subunit Vb initiator
elements(23, 24) . YY1 can also support basal
transcription from supercoiled plasmid templates in vitro in
the presence of only TFIIB (
)and RNA polymerase II (25) . The multiple functions of YY1 suggest that it can
interact with many proteins and that it contains multiple functional
domains. Given its diverse functional properties and its implication in
oncogenesis, it would be interesting to more precisely characterize the
functional domains of the YY1 protein.
We show here that deletion of only 43 amino acids from the carboxyl terminus of YY1 can convert the protein into a strong transcriptional activator. Through progressive deletion and internal deletion analyses, we show that the transcriptional activation domain of YY1 is composed of two regions requiring amino acids 16-29 and 80-100 for maximal activity. The transcriptional repression domain lies within the zinc finger region near the carboxyl terminus. We show that YY1 sequences between 333 and 397 are included in the repression domain. These sequences include zinc fingers 3 and 4. However, point mutation and deletion studies show that normal zinc finger structure of fingers 3 and 4 is not necessary for repression.
16-29, 43-53, 70-80, and
70-99 were generated by triple ligation of PCR fragments
coding 5` and 3` YY1 regions with the CMVGAL-DBD vector. The 5`
fragment was generated as indicated above and digested with EcoRI and BglII. The 3` fragment was generated using
the CMV reverse primer and the appropriate forward primer. Amplified
products were digested with BglII and XbaI and the 5`
and 3` fragments were ligated with EcoRI- and XbaI-digested CMVGAL-DBD. To generate carboxyl-terminal
truncations of the internal deletions, the mutant plasmids were
digested with EcoRI and XbaI, the resulting fragment
was purified by gel electrophoresis, and subsequently digested with SmaI. The 5` fragments containing the YY1 sequence 1-200
with the appropriate deletion mutation were purified and subcloned into
the EcoRI and XbaI/blunted sites of CMVGAL-DBD. To
prepare CMVGAL-YY1#2, an EcoRI fragment containing the
full-length YY1 sequence except the initial starting methionine was
subcloned into the EcoRI site of CMVGAL-DBD producing an
in-frame chimeric fusion protein. This plasmid differs from CMVGAL-YY1
in that it lacks the pCB6+ polylinker sites upstream of the GAL4
coding sequence. CMVGALYY1-C360S and CMVGALYY1371-380 were
generated using the Muta-Gene (Bio-Rad) oligonucleotide-mediated in
vitro mutagenesis kit. The HindIII-XbaI fragment
of CMVGAL-YY1#2 containing sequences encoding the last 83 amino acids
of YY1 was subcloned into the phagemid vector pBluescript II/KS+
(Stratagene). Preparation of uracil containing single-stranded DNA,
annealing of the appropriate mutagenic primer, and subsequent in
vitro second strand synthesis in the presence of dNTPs was
performed according to the manufacturer's specifications. The
resulting double-stranded plasmid DNAs were transformed into Escherichia coli HB101. The HindIII-XbaI
mutagenized fragment was subcloned into the corresponding sites of
plasmid CMVGAL-YY1#2, replacing the original wild-type sequences. The
identities of all constructs were confirmed by dideoxynucleotide
sequence analysis.
16-29 forward primer,
5`-GCGAGATCTACCATCCCGGTGGAGAC-3`; 43-53 forward primer,
5`-GCGAGATCTTGGCGGCGGTGGCGACCA-3`; 70-80 forward primer,
5`-GCGAGATCTCCGCCCATGATCGCTCT-3`; 70-100 forward primer,
5`-GCGAGATCTCAGGAGGTGATCCTGGT-3`; 3` CMV reverse primer,
5`-CTTCCAAGGCCAGGAGAG-3`; C360S, 5`-TGAAAGCGTTTCCCAGAGCCTTCGAACGTGC-3`;
or 371-380, 5`-GGGGCACACATAGGGCCTCAAATTGAAGTCCAGTGA-3`.
10
log phase
cells were transfected with 2.5 µg of reporter plasmid, 2.5 µg
of effector plasmid, and 1 µg of a pCB6+-based
-galactosidase expression plasmid. 3T3 cells were grown in
Dulbecco's modified Eagle's high glucose medium (Life
Technologies, Inc.) supplemented with 10% heat inactivated fetal bovine
serum (HyClone), 2 mML-glutamine (Life Technologies,
Inc.), 100 units/ml penicillin, and 0.1 mg/ml streptomycin (Life
Technologies, Inc.). Cells were transfected using the calcium phosphate
coprecipitation method(28) . Unless specified, cells were
transfected with 5 µg of reporter plasmid, 5 µg of effector
plasmid, and 1 µg of -galactosidase expression plasmid. After
48 h cellular extracts were prepared by three freeze-thaw cycles. CAT
assays of these extracts were performed as described by Gorman et
al.(29) , using -galactosidase activity to
standardize for transfection efficiency.
10 cells) were transferred to a separate tube and used to prepare
nuclear extracts. The remaining third was processed for CAT assays.
Pooled cells were washed once with PBS, and resuspended in 400 µl
of cold Buffer A (10 mM HEPES, pH 7.9, 10 mM KCl, 0.1
mM EGTA, 0.1 mM EDTA, 1 mM
phenylmethylsulfonyl fluoride, 1 mM pepstatin, 1 mM leupeptin). Following incubation on ice for 15 min, 25 µl of
10% Nonidet P-40 (Sigma) was added, and each sample was vortexed for 10
s. Each sample was centrifuged for 30 s to 1 min in a microcentrifuge
to collect the nuclear pellet, the supernatant was aspirated, and the
pellet resuspended in 100 µl of cold Buffer C (20 mM HEPES, pH 7.9, 0.4 M NaCl, 1 mM EDTA, 1 mM EGTA, 1 mM dithiothreitol, 2 mM
phenylmethylsulfonyl fluoride, 2 mM pepstatin, 2 mM leupeptin). Samples were incubated for 15 min on ice with frequent
gentle mixing. The nuclear extracts were centrifuged for 5 min at 4
°C to remove insoluble material, and the supernatant was stored at
-70 °C.
. After
incubation for 30 min at room temperature, reactions were
electrophoresed on native polyacrylamide gels (4%) prerun for 20 min
using either low ionic strength buffer (6.7 mM Tris, pH 7.5,
3.3 mM sodium acetate, 1 mM EDTA) or 0.25 TBE
buffer (22.5 mM Tris borate, 0.5 mM EDTA).
)
SO. After 30 min, the
precipitate was recovered by centrifugation (2000 g,
10 min). The pellet was dissolved in 2 ml of PBS and dialyzed against 2
liters of PBS overnight at 4 °C. The dialyzed fraction was brought
up to 10 ml with TBST (.01 M Tris-HCl, 0.15 M NaCl,
0.05% (v/v) Tween) and incubated with the affinity matrix overnight at
4 °C with rocking. The matrix was washed three times for 30 min
with 20 ml of TBST. Bound antibody was eluted with 1 ml of 100 mM glycine, pH 2.5. Buffer exchange was done over a NAP-5 column
(Pharmacia) equilibrated with 10 volumes of PBS (0.1% bovine serum
albumin, 0.02% sodium azide). Purified antibody was stored at -70
°C.
Figure 1: YY1 can activate or repress transcription. Panel A, the YY1 expression vector was cotransfected at various concentrations into 3T3 cells with a reporter plasmid containing four copies of the YY1 binding site upstream of TKCAT. The lower panel shows CAT data with the amount of YY1 expression plasmid transfected indicated above each lane (in nanograms). The upper panel is a histogram of the data obtained with -fold activation calculated relative to the activity obtained with the reporter plasmid and empty expression vector. Panel B, the GAL-YY1 expression plasmid was cotransfected at various concentrations into 3T3 cells with a reporter plasmid containing five copies of the GAL4 DNA binding sequence upstream of TKCAT. The lower panel shows CAT data with the amount of GAL-YY1 expression plasmid indicated above each lane (in nanograms). The upper panel is a histogram of the data obtained with -fold activation calculated relative to the activity obtained with the reporter plasmid and empty expression vector.
Previously, we studied the YY1 protein linked to the DNA binding domain of a heterologous protein (GAL4) in 3T3 or PYS-2 cells(2, 18) . These studies showed that GALYY1 repressed transcription of a GALTKCAT reporter plasmid in 3T3 cells, while it activated transcription in PYS-2 cells. To determine whether, like the wild-type YY1 protein, GALYY1 might activate transcription at certain doses of effector plasmid in 3T3 cells, the CMV-GALYY1 plasmid was transfected at various doses into 3T3 cells. Indeed, low doses of GALYY1 effector plasmid activated GALTKCAT activity (Fig. 1B). Maximal activity (7-fold) occurred at 100 ng of effector plasmid. The higher quantity of GALYY1 effector plasmid necessary for maximal activity as compared to wild-type YY1 may reflect the presence of endogenous YY1 protein within the cells. The fact that the GALYY1 fusion protein was capable of activating transcription in 3T3 cells afforded us an assay system for identifying functional domains of the YY1 protein.
)Therefore, we tested function of each GALYY1 deletion
construct at high doses of effector plasmid (5 µg). The CAT
activity for each construct relative to the GAL4 basal activity is
summarized in Fig. 2. Removal of 17 amino acids from the
carboxyl terminus (construct 2; GAL-1-397) did not convert GALYY1
into a constitutive activator. However, removal of an additional 27
amino acids (construct 3; GAL-1-370) showed a 4-fold increase in
CAT activity over the GAL4YY1 full-length construct (GAL-1-414)
and a 9-fold increase over basal CAT activity. Carboxyl-terminal
truncations to amino acids 341, 256, 200, 188, 143, or 102 fused to
GAL4 (constructs 4-9) produced proteins that were potent
activators of CAT transcription, ranging from 12- to 33-fold activity
above basal CAT activity. CAT activity diminished with progressive
deletions to amino acids 69 or 42 and returned to basal level upon
deletion to amino acid 15.
Figure 2: The YY1 activation domain resides within the amino-terminal 100 amino acids. Constructs 1-12 contain the GAL 4 DNA binding domain (amino acids 1-147; solid rectangles) linked to various portions of the YY1 sequence (open rectangles). The positions of the acidic amphipathic helix, the consecutive acid stretch, the consecutive histidine stretch, and the zinc fingers are indicated. Numbers on the left indicate the YY1 sequences present in each construct. Each construct was transfected into 3T3 fibroblast and S194 plasmacytoma cells with a reporter plasmid containing five copies of the GAL4 DNA binding site upstream of TKCAT. CAT activity in transfected cell extracts is calculated relative to the reporter plasmid alone. In each case the first number represents relative CAT activity with standard errors shown in parentheses. n numbers represent the number of times each transfection was performed.
Similar results were obtained in S194 plasmacytoma cells, although there were some quantitative differences (Fig. 2). For instance, the full-length GALYY1 protein was a more potent activator in S194 cells as compared to 3T3 cells, and the various deletions did not have as dramatic of an activation over the full-length protein. This can be seen by comparing the -fold induction over wild-type YY1 for each construct in 3T3 versus S194 cells (Fig. 3). Whether this represents differences in the cellular milieu of 3T3 and S194 cells is uncertain. However, others have shown that YY1 can be a potent activator in plasmacytoma cells(31) . In any case, similar to the case in 3T3 cells, truncation to amino acids 69 and 42 reduced activity in S194 cells, and all activation was lost upon deletion to amino acid 15 (Fig. 2).
Figure 3: Deletion of YY1 carboxyl-terminal sequences converts YY1 into a strong activator in 3T3 cells. The data in Fig. 2are represented as -fold induction over the activity observed with the full-length YY1 protein. Solid bars are data from 3T3 cells, whereas open bars represent data obtained with S194 cells.
To assure that the protein products of the various deletion constructs were being made within the transfected cells, nuclear extracts were prepared from 3T3 cells transfected with each deletion construct. These nuclear extracts were evaluated by EMSA with a GAL4 DNA binding site probe. Representative EMSAs of the carboxyl-terminal deletion constructs are shown in Fig. 4A. Carboxyl-terminal deletions containing YY1 amino acids 15-256 (with the exception of the GAL-1-42 construct) showed similar amounts of probe shifted and complexes of the appropriate size based on the predicted size of the fusion proteins (Fig. 4A, lanes 1-9). Numerous attempts have failed to demonstrate a complex with nuclear extracts isolated from 3T3 cells transfected with construct GAL-1-42 (lane 2). However, this construct must be expressed within the cells because it consistently yielded modest activation of transcription (Fig. 2). Somewhat unusual EMSA complexes were observed with carboxyl-terminal deletion constructs GAL-1-341, GAL-1-370, and GAL-1-397, as well as the full-length fusion protein GAL-1-414 (lanes 10 and 12-14). To assure that these fusion proteins were synthesized in transfected cells, nuclear extracts were subjected to Western blot analysis with polyclonal YY1 antibody (Fig. 4B). This analysis showed that the GAL-1-341, GAL-1-370, GAL-1-397, and GAL-1-414 (wild-type) proteins are indeed expressed in transfected cells. The endogenous YY1 protein was also detected in these extracts and served as a loading control.
Figure 4: GAL-YY1 fusion proteins in transfected cells can be detected by EMSA or Western blot. Panel A, nuclear extracts were prepared from transfected 3T3 cells and EMSA was performed with a GAL4 DNA binding site probe. The GAL-YY1 construct used for transfection is indicated above each lane. The positions of GAL-YY1 fusion protein-DNA complexes are indicated by the bracket on the right. Panel B, some nuclear extracts were subjected to Western blot analysis with a YY1-specific antibody. Above each lane is indicated the GAL-YY1 construct used for transfection. GAL-DBD represents the GAL4 DNA binding domain (amino acids 1-147). The position of endogenous YY1 is shown by the arrow on the right, and the positions of the GAL-YY1 fusion proteins are indicated by the brackets on the left.
EMSA studies were also performed with nuclear extracts prepared from transfected S194 cells. However, no complexes were observed perhaps due to the lower transfection efficiency of plasmacytoma cells.
70-80)
or acid (43-53) stretches had no deleterious effect on
transactivation. However, deletion of the amphipathic helix region
between amino acids 16 and 29 reduced activation to 33 and 26% of
maximal CAT activity in 3T3 and S194 cells, respectively. The above
results suggest that the YY1 activation domain is bipartite. Sequences
between amino acids 16 and 29 are clearly important for activity.
Sequences between 80 and 100 contribute to maximal activity since the
16-80 construct shows higher activity than the
16-100 construct. However, this region is somewhat redundant
because deletion of residues 70-99 alone did not decrease
transcriptional activity.
Figure 5: The YY1 activation domain is bipartite. YY1 residues 1-200 were linked to the GAL DNA binding domain either intact, or with various internal deletion mutants in the context of a eukaryotic expression vector. Constructs were transfected into cells and CAT activities were determined. The lower panel shows the constructs used for transfection. Percent CAT activity relative to the GAL-1-200 construct (defined as 100%) is shown for transfections into either 3T3 or S194 cells. In each case the first number represents relative CAT activity with standard errors shown in parentheses. n numbers represent the number of times each transfection was performed. The upper panel shows a histogram for the data obtained with solid bars representing data from 3T3 cells and open bars representing data from S194 cells.
To assure that the internal deletion proteins were synthesized in vivo, nuclear extracts were made from the transfected cells and subjected to EMSA with the GAL4 DNA binding probe (Fig. 6). All constructs produced the expected complexes indicating that a loss in transcriptional activity was not simply due to a lack of efficient production of mutant proteins (lanes 1-8).
Figure 6: The amino-terminal internal deletion mutants are expressed in vivo. Nuclear extracts were prepared from transfected cells and subjected to EMSA with a GAL4 DNA binding site oligonucleotide probe. The DNA constructs used for transfection are shown above each lane and the positions of the GAL-YY1 DNA complexes are indicated by the bracket on the right.
Figure 7:
The YY1 repression domain lies near the
carboxyl terminus. Panel A, 3T3 cells were transfected with
DNA constructs containing the GAL4 DNA binding domain either alone, or
linked to various YY1 sequences, in the presence of the GAL4TKCAT
reporter plasmid. The lower panel shows the expression
plasmids used for transfection. The solid rectangle represents
GAL4 sequence 1-147, and the open rectangles represent
various YY1 sequences. CAT activity is shown with the activity of the
reporter plasmid cotransfected with the GAL-DBD expression plasmid
defined as 1.0. Numbers in parentheses represent
standard errors, and n numbers indicate the number of times
the transfections were performed. The data are shown in histogram form
in the upper panel. Panel B, nuclear extracts
isolated from transfected cells were subjected to Western blot analysis
with anti-GAL4 antisera. Arrows show the positions of the
GAL4-YY1 fusion proteins, and the asterisk indicates a
background band recognized by the GAL4 antisera. Panel C,
transfections were performed with either the full-length GAL-YY1
expression plasmid (1-414) or expression plasmids with either
cysteine 360 changed to a serine (C360S) or with the sequence
371-380 deleted (371-380). The activity of the
full-length YY1 protein is defined as 1.0, and CAT activities are
calculated relative to this value. The data are shown in histogram form
in the upper panel. Panel D, nuclear extracts
isolated from transfected cells were subjected to Western blot analysis
with YY1-specific antibodies. The source of the nuclear extract is
indicated above each lane. The position of endogenous YY1 is indicated
by the arrow on the right, and the positions of the
various GAL-YY1 fusion proteins are shown by the bracket on
the left.
Our carboxyl-terminal
truncation experiments (Fig. 2) indicated that there was a
transition from a weak transcriptional activator to a strong
transcriptional activator when the third zinc finger was disrupted.
Thus, the GAL-1-397 mutant protein, which has a disrupted fourth
zinc finger, is relatively inactive, while the GAL-1-370 mutant
protein, which has a disrupted third zinc finger, is 4 times more
active when compared to the full-length GAL-YY1 fusion. To determine if
the third zinc finger is critical in possibly masking strong
transcriptional activity mediated by the amino-terminal activation
domain, two additional GAL4-YY1 fusion mutants were prepared. One
mutant has a 10-amino acid deletion removing amino acids 371-380
(GAL-371-380), which encompasses the second half of the
third zinc finger including the histidines. The other mutant creates a
point mutation at amino acid 360 (GAL-C360S), changing the second
cysteine of the third zinc finger to a serine. A stable third zinc
finger is not formed by either of these mutations, because these mutant
proteins are incapable of binding to DNA (data not shown). Neither
internal zinc finger mutation mimicked the strong transcriptional
activity of the carboxyl truncated third zinc finger mutant
GAL-1-370 (Fig. 7C). The latter is on average
4-fold more active as a transcriptional activator than the full-length
GAL-1-414 (Fig. 2). The serine-360 mutant was
approximately half as active as full-length YY1, while the 10-amino
acid deletion activated transcription 1.5-2-fold.
To assure
that the fusion proteins were made in vivo, we performed
Western blots on nuclear extracts prepared from the transfected cells.
The two third zinc finger mutants (GAL-C360S and
GAL-371-380) were readily detectable on Western blots with
YY1 antibody and were expressed at an abundance similar to the
GAL-1-370 truncation (Fig. 7D).
Our deletion studies showed that the YY1 repression domain includes
sequences in the region of the third and fourth zinc fingers.
Carboxyl-terminal deletion to residue 397, which does not disrupt the
repression domain, interrupts the fourth zinc finger indicating that
function of an intact fourth zinc finger is not necessary for
repression. To determine whether repressor function requires the intact
structure of the third zinc finger, we prepared mutations C360S and
371-380, which disrupt the structure of the third zinc
finger. Neither the C360S nor the 371-380 mutants mimicked
the strong transcriptional activity of the 370 deletion mutant. These
results indicate that repression does not absolutely require the normal
structure of either the third or the fourth zinc fingers.
While zinc fingers are typically considered DNA binding motifs, it is interesting to note that some zinc finger regions have been implicated in protein-protein interactions. For instance, the zinc finger of the adenovirus E1A protein has been implicated in interaction with transcription factors (36) and is necessary for physical interaction with TATA-binding protein(37) . Similarly, the zinc finger region of ATF2 can interact with the leucine zipper region of cAMP response element-binding protein, whereas the Sp1 zinc fingers can interact with RelA(38, 39) . A short region containing a zinc finger in TFIIB is necessary for efficient interaction with TFIIF(40) , and the zinc finger-containing LIM domain has been implicated in protein-protein interactions(41) . In addition, the GATA-1 zinc finger region can self-associate (42) and can interact with other proteins(43) .
The repression domain of YY1 is unlike other characterized repression domains. A number of repressor proteins have been identified and include Kruppel, eve, engrailed, SCIP, Dr1, Msx-1, Tst-1, WT1, AEF1, and Ssn6/Tup6 proteins(44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56) . Repression domains within these proteins are either alanine-rich(51, 52, 56) , alanine-, glycine-, and proline-rich(5) , or rich in glutamine and proline(53, 54) . Repressor proteins constructed from E. coli sequences are rich in basic amino acids(57) . The YY1 protein contains a region rich in alanine and glycine (residues 137-201), but this segment is dispensable for repressor function.
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