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Volume 271, Number 23,
Issue of June 7, 1996
pp. 13542-13548
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
Regulatory Function of Delta/YY-1 on the Locus Control
Region-like Sequence of Mouse Glycophorin Gene in Erythroleukemia
Cells*
(Received for publication, October 20, 1995, and in revised form, February 27, 1996)
Yasuhisa
Nemoto
,
Masanori
Terajima
,
Wataru
Shoji
and
Masuo
Obinata
From the Department of Cell Biology, Institute of Development,
Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aoba-ku,
Sendai 980-77, Japan
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
Acknowledgments
REFERENCES
ABSTRACT
The far upstream region ( 1.2-0.9 kilobase
pairs) of the mouse glycophorin gene contains the locus control region
(LCR)-like region, which acts as an erythroid-specific enhancer
dependent on chromosomal integration in murine erythroleukemia (MEL)
cells. In the present study, we demonstrated that this region binds six
nuclear factors. The binding of GATA-1 to corresponding sites did not
show any change before or after induction with dimethyl sulfoxide, but
the binding of Spi-1/PU.l and an unidentified factor called glycophorin
regulatory element binding factor (GRBF) showed a change during
induction. While binding activity of Spi-l/PU.l dropped soon after
induction, the GRBF activity increased after induction when expression
of the glycophorin gene began. After identification of the consensus
binding site of GRBF, we cloned cDNA for that factor by
Southwestern method, and it was identified as a previously reported
transcription factor, delta, a murine form of YY-l which is a versatile
transcription factor. Mutation analysis in the delta/YY-1 binding site
within the LCR-like region indicated that delta/YY-1 acts as a
regulatory protein in combination with the E-box-binding protein that
binds to the neighboring sequence.
INTRODUCTION
Mouse glycophorin is a red blood cell membrane protein and a good
erythroid-specific marker protein such as hemoglobin. To understand the
mechanisms underlying the stage- and tissue-specific expression of
erythroid-specific genes, we cloned a mouse glycophorin gene which is
homologous to human glycophorin A or B (1) and examined its expression
in murine erythroleukemia (MEL)1 cell
differentiation. Upon treatment with dimethyl sulfoxide
(Me2SO), MEL cells undergo terminal differentiation into
red blood cells and induce a number of different erythroid-specific
genes (2). Glycophorin gene expression precedes that of globin gene in
MEL cell differentiation (3). By nucleotide sequence analysis of the 5
upstream region of the mouse glycophorin gene (4) and its transient
transcription assay (5), we have shown that the erythroid-specific
promoter element consisted of the basal promoter containing GGTGGG and
GATA motifs, and the distal elements containing binding motifs for two
erythroid-specific nuclear factors GATA-1 and NF-E2. In addition, we
found a locus control region (LCR)-like region that was reported in the
human -globin gene cluster. The LCR-like region located far upstream
of the mouse glycophorin gene seemed to act as an enhancer of the
erythroid-specific promoter in the stable transfection assay, but not
in the transient transfection assay (5). The role of LCR of the human
-globin gene cluster located far upstream of -globin gene in the
regulation of developmental switching and erythroid-specific expression
of -like globin genes was demonstrated by analysis using transgenic
mice and MEL cells (6, 7, 8, 9, 10). The major regulatory element upstream of
the human -globin gene cluster has similar LCR activity (11). The
LCR of the human -globin genes includes two tandemly arranged
NF-E2/AP-1-binding motifs and GATA-1-binding motif. The LCR-like region
in the mouse glycophorin gene has a structure similar to globin LCR. In
this study we made a detailed analysis of the nuclear factors that
bound to the mouse glycophorin LCR-like region in MEL cells before and
after Me2SO induction.
MATERIALS AND METHODS
Cell Culture and Preparation of Nuclear Extracts
Culture
and induction of MEL cells were performed as described previously (12).
For preparation of the nuclear extracts (13), the cells were cultivated
for 2 days with or without 1.4% Me2SO. Cells were washed
twice in phosphate-buffered saline and lysed in 10 mM
HEPES, pH 7.9, 10 mM EDTA-0.5 mM
dithiothreitol, 0.5% Nonidet P-40, 0.5 mM
phenylmethylsulfonyl fluoride for 10 min on ice. After centrifugation
at 2,000 rpm for 5 min, the nuclear pellet was washed twice with the
same buffer and resuspended in the nuclear buffer, 0.5 mM
dithiothreitol, 0.5 mM phenylmethylsulfonyl fluoride, 400 mM NaCl. The elution of proteins was performed on ice for
30 min, and the nuclear extract was recovered by centrifugation at
10,000 rpm for 10 min.
Oligonucleotides
The DNA sequences of synthetic
oligonucleotides used for probes and competitors in the gel shift
assays and UV cross-linking analysis (both strands were shown from 5
to 3 ) were: GA,
5 -CCCTTCCCCACACTATCTCAATGCAAATATCTGTCTGAAACGGTC
C/GGACCGTTTCAGACAGATATTTGCATTGAGATAGTGTGGGGAAGGG-3 ;
TA,
5 -ATCTTTTATTTAACAGACACTAAATAATGTTGCATCATTTAAATGCT/AGCATTTAAATGATGCAACATTATTTAGTGTCTGTTAAATA
AAAGAT-3 ; PU,
5 -GATCCGTCCCAAGTGAGGAACCAATAGCATTG/CAATGCTATTGGTTCCTCACTTGGGACGGATC-3 ;
V,
5 -AGCCACTAGAGGTCGGCACGTGTCTCCATTTCCACA/TGTGGAA
ATGGAGACACGTGCCGACCTCTAGTGGCT-3 ; Hm,
5 -ACTTCAGACCACGTGGTCGGTGTTCCTGA/TCAGGAACACCGACCACGTGGTCTGAAGT-3 ;
Vm,
5 -AGCCACTAGAGGTCGGCAGGTGTCTCCATTTCACA/TGTGAAATGGAGACACCTGCCGACCTCTAGTGGCT-3 ;
Pds,
5 -ACGAAGAGAAGGGAAAGACTTGATGTTTTCTCC/GGAGAAAACATCAAGTCTTTCCCTTCTCTTCGT-3 ;
a, 5 -AGCCACTAGAGGTCG/CGACCTCTAGTGGCT-3 ; b,
5 -CTAGAGGTCGGCACG/CGTGCCGACCTCTAG-3 ; c
5 -GGTCGGCACGTGTCT/AGACACGTGCCGACC-3 ; d,
5 -GCACGTGTCTCCATT/AATGGAGACACGTGC-3 ; e,
5 -TGTCTCCATTTCCAC/GTGGAAATGGAGACA-3 ; Ma,
5 -TGTCTCCATTTGAC/GTCAAATGGAGACA-3 ; Mb
5 -TGTCTCCAGGTCCAC/GTGGACCTGGAGACA-3 ; Mc,
5 -TGTCTGGATTTCCAC/GTGGAAATCCAGACA-3 ; Md,
5 -TTGCTCCATTTCCGC/GCGGAAATGGAGCAA-3 ; Me,
5 -TGTAGCCATTTCCGC/GCGGAAATGGCTACA-3 ; Mf,
5 -TGTCGGCATTTCCGC/GCGGAAATGCCGACA-3 , HS,
5 -TCCCCACCCTTTGTCCT/AGGACAAAGGGTGGGGA-3 ; GP,
5 -GTGTCTCCATTTCCACA/TGTGGAAATGGAGACAC-3 ;
LG, 5 -GTCATAGATACGACC-3 /5 -GGTCGTATCTATGAC-3 ;
GA, 5 -ATAAAGATAACTAG-3 /5 -CTAGTTATCTTTAT-3 ;
LN, 5 -CTTGCCTGACACATT-3 /5 -AATGTGTCAGGCAAG-3 ;
LP, 5 -ACGAAGAGGAAGGGAAA-3 /5 -TTTCCCTTCCTCTTCGT-3 .
DNase I Footprinting and Electrophoretic Mobility Shift Assay
(EMSA)
For DNase I footprinting assay, a 284-bp DNA fragment from
1185 to 901 bp of the glycophorin gene containing the LCR-like
region was 32P-labeled according to standard procedures.
DNase I footprinting reaction mixtures (50 µl) contained 36 mM HEPES-KOH, pH 7.9, 57 mM KCl, 9 mM MgCl2, 0.1% Nonidet P-40, 10% glycerol, 1 mM dithiothreitol, 10,000 cpm of the DNA fragment, 50 ng of
poly(dI-dC)·poly(dI-dC) and nuclear extracts (4 µg) (14). After
incubation on ice for 15 min, various concentrations of DNase I were
added. Following incubation on ice, 6 volumes of solution containing 20 mM EDTA, 185 µM NaCl, 1% SDS, 0.8 µg of
proteinase K were added to stop the reaction. After incubation at
42 °C for 30 min, DNAs were extracted by phenol-chloroform and
ethanol-precipitated. The samples were heated to 95 °C for 3 min in
a sequencing dye solution and separated in an 8% sequencing gel. Gels
were fixed and dried prior to autoradiography. EMSA was performed as
described by Sigh et al. (15) with minor modifications. For
probe preparation, oligonucleotides synthesized by a DNA synthesizer
were annealed and 5 -end labeled with [32P]ATP (Amersham
Corp.) and T4 polynucleotide kinase (Toyobo Co., Ltd., Japan) according
to standard procedures. The labeled DNA fragment (10,000 cpm) was
incubated in a final volume containing 10 mM Tris-HCl (pH
7.5), 50 mM NaCl, 1 mM EDTA, 1 mM
dithiothreitol, 5% glycerol, 3 µg of poly(dI-dC)·poly(dI-dC), and
4 µg of nuclear extract proteins. Following 15 min of incubation on
ice, electrophoresis was performed on a 5% polyacrylamide gel in 1 × Tris borate-EDTA. Gels were dried prior to autoradiography.
UV Cross-linking Analysis
The binding reaction mixtures
were UV-irradiated in the presence or absence of competitor
oligonucleotides by UV Stratalinker (Stratagene), and the cross-linked
protein-DNA complexes were separated on SDS-10% polyacrylamide
gels.
Isolation of a GRBF Clone from cDNA Library
The gtll
cDNA library was constructed from cDNA made from
poly(A)+ RNA isolated from the uninduced MEL cells by
oligo(dT) priming. We initially screened this cDNA library by the
method of Vinsion et al. (10) with three ligated copies of a
double-stranded synthetic oligonucleotide e which was the
GRBF recognition sequence site determined by the gel shift analysis.
Purified phage plaques that gave positive signals with the
oligonucleotide e and gave negative signals with the
oligonucleotide Mb were selected as positive clones. An
EcoRI fragment containing the cDNA sequence was excised
from the selected gtll phage and inserted into the EcoRI
site of transcriptional vector BSK(+).
Construction of Plasmids Containing Mutations in the LCR-like
Region of the Mouse Glycophorin Gene
The 5 -flanking sequence
(1.3 kb) containing the LCR-like region and the transcription start
site of the mouse glycophorin gene or its site-directed mutants
( delta/YY-1; -CCATTT- to -CCAGGT-) ( E-box; -CACGTG- to -CGATCG-)
and the 0.9-kb sequence deleting the LCR-like region ( LCR) were
subcloned and linked to luciferase gene.
Stable Transfection Assay
Cells were transfected by a
modification of the recommended protocol of the synthetic, cationic
lipopolyamine molecule (Transfectam reagent, Promega). MEL cells were
split 3 h before transfection and replated onto
poly-L-lysine (Sigma)-coated 60-mm
diameter dishes at 5 × 105 cells/dish (4-8 dishes for
each test plasmid) in ES-fetal bovine serum. For transfection, cells
were washed three times with ES and then were incubated with 5 µg of
supercoiled plasmid DNA and Transfectam reagent, 25 µg in opti-MEM I
(Life Technologies, Inc.) (1.5 ml) for 12 h at 37 °C. After the
opti-MEM I was removed, the cells were incubated for 24 h at 37 °C
in ES-fetal bovine serum (6 ml/plate) to express the selection marker,
aminoglycoside phosphotransferase. For the selection, G418 (Geneticin,
Sigma) was added to the culture medium at 400 µg/ml.
After 9 days of incubation, scores of G418-resistant colonies were
observed. To avoid clonal variation and positional effect, the cells
were resuspended and subcultured in G418-containing ES-fetal bovine
serum for 7 more days. Four to eight independent transfected
populations were established for each test plasmid (wild-type,
delta/YY-1, E-box, and LCR). Each population was split, and
one half was cultured in ES-fetal bovine serum while the other half was
induced to differentiate by addition of 1.4% Me2SO for 4 days. Luciferase assay (16) was performed at 4 days according to the
protocol of the luciferase assay kit (Toyo Ink Co. Tokyo). Six days
after induction of differentiation, benzidine staining was done to
estimate the extent of differentiation.
Northern Blot Hybridization
To measure levels of endogenous
glycophorin mRNA, total RNAs from MEL cells were prepared by
guanidinium-thiocyanate-phenol-chloroform procedure. Ten µg of RNA
from each sample were electrophoresed in a denatured 1% gel agarose
gel, transferred to a nylon membrane, and hybridized with a mouse
glycophorin cDNA probe (1) radiolabeled with a random primer
extension kit (DuPont) in the hybridization buffer (50% formamide, 5 × SSC, 1 × Denhardt's reagent, 20 mM NaHPO3,
pH 6.5, 100 mg/ml salmon sperm DNA, 10% dextran sulfate, 0.1% SDS).
After overnight incubation at 42 °C, the membrane was washed in 2 × SSC, 0.1% SDS for 10 min at room temperature and in 0.1 × SSC, 0.1%
SDS for 30 min at 60 °C, then autoradiographied.
RESULTS
Analysis of the Mouse Glycophorin LCR-like Region by DNase I
Footprinting
Mouse glycophorin LCR-like region spanning
nucleotide 1185 to 901 (Fig. 1) was analyzed for the
binding of nuclear factors by DNase I footprinting assay. The 284-bp
fragment labeled at either end was incubated with nuclear extracts from
the induced or uninduced MEL (B8/3 line) cells and digested with DNase
I. The regions presenting protection from DNase I digestion
(footprints) or increased sensitivity are shown in Fig.
2. Analysis of the sequences within the footprint
regions revealed four putative erythroid-specific binding sites; two
GATA motifs and two AP-1/NF-E2-like motifs in the region assigned as
II in Fig. 2, A and C. Sequence of the
general form (T/A)GATA(A/G) binds the erythroid-specific transcription
factor GATA-1 (4, 17, 18, 19). Of two potential GATA-1 binding sites
referred to a nonconsensus site (AGATAC) and a consensus site (TGATAG),
the footprinting revealed a protection in the non consensus site, but
did with no difference between the induced and uninduced MEL cells. Two
AP-1/NF-E2-like consensus motifs were found upstream of the two GATA
elements, as reported for the erythroid-specific promoter of the human
prophobillinogen deaminase gene (20) and for the LCR of the human
-globin gene (3). These motifs are not completely fitted to the
NF-E2 consensus motif (T/C)GCTGA(G/C)TCA(C/T) which Andrews et
al. (21) recently reported. Between the two motifs, footprinting
revealed the hypersensitive site only in the 5 side of the upstream
AP-1/NF-E2-like motifs (Fig. 2C).
Fig. 1.
Nucleotide sequence of the LCR-like region of
the mouse glycophorin gene. The nucleotide sequence of the
LCR-like region of the mouse glycophorin gene (in nucleotide number
1185 to 901) and the possible consensus binding sites for nuclear
factors (NF-E2, GATA-1, PU.1 (Spi-1) and CACGTG) are illustrated. Five
regions (I-V) correspond to the protected regions revealed
by DNase I footprinting analysis shown in Fig. 2. Thin lines
show the protected regions and thick lines show those more
apparently protected. The arrowheads show the DNase I hypersensitive
sites. Boxes indicate possible nuclear factor binding
sites.
Fig. 2.
DNase I footprinting analysis of the LCR-like
region of the mouse glycophorin gene. From A to
C, the radiolabeled 275-bp fragment of the LCR-like region
of the mouse glycophorin gene ( 1185 to 901 as shown in Fig. 1) was
incubated in the absence (0) or presence of the nuclear
extracts prepared from the induced (DMSO(+)) and the
uninduced (DMSO( )) MEL cells (B8/3). Standard
Maxam-Gilbert purine (G + A) sequencing reactions of the same fragments
were run in parallel. Protected sequences are bracketed
(PU.I (Spi-1), GATA-1, AP-1/NF-E2, and CACGTG) and DNase I
hypersensitive sites are denoted by arrowheads. Regions I-V
correspond to those shown in Fig. 1.
The Spi-1/PU.1 consensus motif (PU box) (22), GAGGAA resides in the
central portion of the LCR-like region. The PU box in the noncoding
strand was protected in the uninduced extract (DMSO ( ) in
Fig. 2B), but was not in the induced extract
(DMSO (+) in Fig. 2B). In addition, footprinting
revealed that a hypersensitive site (an arrowhead in Fig.
2A, III) in the coding strand at the 3 -side of
the PU box was more apparent in the uninduced cells than in the induced
cells. The feature of the nuclear factor binding of the PU box was
similar to that observed in the PU box within the intervening sequence
of the mouse -globin gene (23). The Spi-1/PU.1 activity reduced
after induction of MEL cell differentiation.
The E-box (CACGTG) motif which is the binding site for basic
helix-loop-helix protein (24, 25) was found in the downstream of the
Spi-1/PU.1 element. While footprinting revealed the hypersensitive site
and the protection in the noncoding strand of the region containing
E-box element (see Fig. 2B), more apparent protection was
seen in the coding strand in the induced extract than the uninduced one
(Fig. 2A). This apparent difference indicated induction of
nuclear factors that bind the E-box and/or the neighboring element
after MEL cell differentiation. From these results we tentatively
concluded that the LCR-like region contains at least six binding sites,
in two of which the protein binding is changed after MEL cell
differentiation (Fig. 1).
Characterization of the Nuclear Factors by EMSA
To identify
which individual proteins interact with each of the binding sites, many
oligonucleotides were used as probes and competitors in EMSA; in
addition to the GATA-1 site, two binding sites in particular in which
protein binding is changed between the induced and uninduced MEL cells
were extensively studied. LG-oligo ( 1104 to 1090) of the
LCR-like region containing a GATA motif showed the retarded bands (one
major slow and one minor fast migrating bands) and they were competed
with excess amounts of either GA-oligo containing a
consensus GATA-1 site or LG-oligo, but not with unrelated
LP-oligo, indicating that the GATA-motif within the LCR-like
region can bind GATA-1.
LP-oligo ( 1071 to 1044) containing a PU.1 site within
the LCR-like region showed three retarded bands which could be competed
to the same extent with excess amounts of either PU-oligo
containing the Spi-1/PU.1 consensus binding site or
LP-oligo, but not with unrelated LN-oligo (Fig.
3B), indicating that the PU.1 site within the
LCR-like region can bind PU.1. PU.1 binding activities were titrated
with PU-oligo (Fig. 3C). Two major retarded bands
(shown by arrowheads) were detected in the MEL cell extract
as well as in the NS-1 cell extract, in which PU.1 activity was
reported (22). MEL cell extracts contained more abundant PU.1 activity
than NS-1 cell extracts. Binding with the induced MEL cell extract
showed a five times weaker band than with the uninduced one at the same
position. This result is consistent with that observed in DNase I
footprinting assay.
Fig. 3.
EMSA analysis of the oligonucleotide probes
with the MEL cell nuclear extracts. A, identification and
specification of GATA factors. The radiolabeled probe contains GATA
sequence (LG) in the glycophorin gene LCR-like region.
GA includes GATA factor binding motif (TAGATAA) for specific
competitor and LP is the negative control. B,
identification and specification of PU.1 (Spi-1) binding to PU.1
binding motif in LCR-like region (LP). Specific competitor
(PU) and negative control oligonucleotides (LN)
were incubated with radiolabeled probe. C, the binding
activity of PU.1 decreases after MEL cell differentiation. The
radiolabeled oligonucleotide (PU) that is the consensus PU.1
binding site was incubated with the induced (+) and uninduced ( ) MEL
cell nuclear extracts. For a positive control for the PU.1 signal,
nuclear extracts of NS-1 cells were used. D, for
identification of the E-box binding activity, probe V was
incubated with the induced (+) and uninduced ( ) MEL cell nuclear
extracts. E, competition of the nuclear factors that bind to
oligonucleotide V in the MEL cell nuclear extracts with
mutated oligonucleotides competitors. Hm is an E-box binding
element and Vm is mutated only in the E-box element of
V. Pds is the negative control. F,
sequences of competitor oligonucleotides. The sequences show only one
strand. Numbers correspond to sequence numbers in Fig. 1 and each
consensus sequence is marked as boldface letters. In the
Vm-oligo, mutations within the E-box are
underlined.
Oligonucleotide V ( 982 to 947) which contains the E-box
gave rise to three retarded bands in the MEL extract (Fig.
3D). The top band competed with Hm which includes the E-box
consensus site (CACGTG) (Fig. 3E). The second band
(arrowhead in the figure) was competed with Vm
which possesses a mutation in the E-box consensus site and thus cannot
bind E-box binding proteins. The third band did not competed with E,
thus this complex may be nonspecific binding. Interestingly, the
proportion of the second band increased after induction (approximately
3-fold) and was highest 2 days after induction when glycophorin gene
expression began (26) (Fig. 3D). Thus, the second band may
contain a key factor for glycophorin gene expression and we called this
factor GRBF.
Determination of the Consensus Binding Sequence of GRBF
In
order to determine the consensus binding sequence of GRBF, we performed
competitor scanning experiments by adding five different
oligonucleotides (Fig. 4A). Under these
conditions, efficient competition of the second band was only achieved
with oligonucleotide e, while the top band competed with
c and d, both of which contain the E-box
consensus sequence (Fig. 4A). The competition experiments
using mutated e oligonucleotides (Ma,
Mb, and Mc) indicated that consensus binding
sequence of this factor requires the TTT sequence since Mb
and Mc did not bind (Fig. 4B). The EMSA with
mutated e oligonucleotides (Md, Me,
and Mf) indicated that CCA is required for the binding (Fig.
4C). In the gel shift assay, oligonucleotide e
showed a single band that was inducible in the
Me2SO-treated cells, and Me oligonucleotide may
be an up-mutant because the band in the same migration was stronger
than that of e oligonucleotide, while Md was a
weak mutant (Fig. 4C). Mutated Mf oligonucleotide
showed a strong band whose migration was different from that of
oligonulceotide e and did not change during induction of MEL
cells, thus Mf might bind a different factor. Combining
these results, we concluded that this inducible DNA-binding factor
called GRBF could bind to CCATTT as the most probable consensus
sequence. EMSA with e oligonucleotide in the MEL cell
extracts showed that GRBF was induced by the addition of
Me2SO and was maximum on day 2 (Fig. 4D).
Fig. 4.
Specificity of the nuclear factors that bind
to the oligonucleotide V. A, competition of specific binding
of the nuclear factors to the oligonucleotide V with
100-fold excess of the overlapping oligonucleotides a,
b, c, d, and e.
B, Ma, Mb, Mc,
Md, and Me. C, induction of the
nuclear factor by Me2SO. The nuclear extracts from the
induced MEL cells (DMSO+) and uninduced cells
(DMSO ) were incubated with the radiolabeled
oligonucleotides Md, Me, Mf, and
e. The binding activities are denoted by arrowheads.
D, change in the levels of the nuclear factors that bind to the
oligonucleotide e during induction of MEL cells with
Me2SO. The nuclear extracts were prepared from cultures for
1-4 days in the presence (+) of or in absence ( ) of
Me2SO. The binding activities are denoted by
arrowheads. E, sequences of competitor oligonucleotides. The
sequences show only one strand. Sequence numbers are corresponded to
those in Fig. 1. Mutations are underlined.
Estimation of the Molecular Weight of GRBF
To determine the
molecular weight of GRBF, we performed UV cross-linking analysis (Fig.
5). A mixture of 32P-labeled probe
e and MEL cell nuclear extracts was irradiated with short
wavelength UV light for 5 min. Then the mixture was resolved by
SDS-polyacrylamide gel electrophoresis and analyzed by autoradiography.
To demonstrate the sequence-specific nature of the protein, we added a
500-fold excess of cold competitors to the binding reaction mixture. We
observed four bands without competitor, although two of them with
higher molecular weight were not diminished by competitor F. Moreover,
the band in the lowest molecular weight (arrowhead) was
diminished by competitor e but not by b which
cannot bind GRBF. This indicates that the lowest band is the complex
formed with GRBF. As the size of this band was 70 kDa, the molecular
mass of this protein is expected to be about 60 kDa.
Fig. 5.
UV cross-linking analysis of GRBF. The
nuclear extracts from the induced (DMSO+) and uninduced
(DMSO ) MEL (B8/3) cells and mouse myeloma NS-1 cells
(NS-1) were incubated with the radiolabeled oligonucleotide
e in the absence ( ) or presence of 500-fold excess of the
oligonucleotides (e, Mb) and cross-linked by UV.
The proteins were analyzed by 10% polyacrylamide gel electrophoresis
in SDS-buffer and autoradiographed. Arrowhead shows the
specific band and asterisks show nonspecific bands.
Isolation of cDNA for GRBF by Southwestern
Cloning
Identification of the consensus binding sequence of GRBF
made it possible to isolate its cDNA clone by Southwestern cloning
method using the expression library constructed in gt11 vector from
the mRNA of MEL cells. By screening with the labeled
oligonucleotides containing the CCATTT consensus sequence for GRBF we
obtained clones, and the specificity of binding of these clones was
confirmed with mutant oligonucleotides including the up mutant,
Me and the weak mutant Md (data not shown).
The nucleotide sequence determination of the longest cDNA clone
indicated that the longest open reading frame completely matched with
the known DNA binding factor, delta (27), a murine form of YY-1 (28),
also called NF-E1 (29) or UCRBP (30). The molecular size of delta is
about 65 kDa by SDS-polyacrylamide gel electrophoresis and resembles
that of GRBF, which our UV cross-linking analysis identified as about
60 kDa (Fig. 5).
Functional Analysis of Delta/YY-1 Binding on LCR-like
Activity
To confirm the binding of delta/YY-1 to the CCATTT
within the LCR-like region of the mouse glycophorin gene, the antibody
was made against bacterially produced delta/YY-1 protein in rabbits and
added to the gel shift assay (Fig. 6). The gel shift
band corresponding to delta/YY-1 binding of the MEL cell extract
disappeared by addition of the anti-delta/YY-1 antibody, while
anti-c-Myc antibody showed no effect. The result indicated that
delta/YY-1 is really bound to the LCR-like region.
Fig. 6.
Effect of anti-delta/YY-1 antibody on the
nuclear factor binding. A, MEL cell nuclear extracts were
incubated with 32P-labeled oligonucleotide F
(TGTCT CCACA) containing the delta/YY-1 binding motif
( ) and competed by increasing amounts (+, 50-fold excess; ++,
500-fold excess) of either F oligonucleotide or the related
oligonucleotide GT (GACT T). Arrowhead shows the
specific band. B, rabbit antisera were obtained by injecting
the MBP-delta/YY-1 fusion protein produced in Escherichia
coli and IgG was purified by affinity matrices. Rabbit anti-c-Myc
antibody was obtained from Santa-Cruz Biotechnology Inc. Increasing
amounts of anti-delta/YY-1 (+, 1 µg; ++, 10 µg) or anti-c-Myc (+, 1 µg; ++, 10 µg) were added to the reaction mixtures of the MEL cell
nuclear extracts and the radiolabeled oligonucleotide F.
Then we examined the functional involvement of delta/YY-1 on the
LCR-like activity of the mouse glycophorin gene by stably transfecting
the mutants in the delta/YY-1 binding site and the neighboring E-box
binding site into MEL cells (Fig. 7). The 5 -flanking
sequence (1.3 kb) containing the LCR-like region and the transcription
start site of the mouse glycophorin gene and the 0.9-kb sequence
deleting the LCR-like region ( LCR) were subcloned and linked to the
luciferase gene. For introducing a mutation in the delta/YY-1 binding
site, CCATTT was changed to CCA T which could not bind to
delta/YY-1 as shown in Fig. 4 (Mb mutant) and for
introducing a mutation in the E-box binding site, CACGTG was completely
changed to C G. The plasmid DNAs were introduced into
MEL cells by a lipopolyamine method to obtain the stable transformants.
To minimize the variation of each transformant, four to eight
independent neomycin-resistant transformants for each plasmid were
pooled, and the transcriptional activities in the induced and uninduced
cells were measured by luciferase assays at 4 days of culture. To
confirm that the cells selected after transfection did not change their
properties, levels of endogenous glycophorin mRNAs before and after
induction in each pool of transformants were measured by Northern
blotting (Fig. 7D). The result showed that induction of the
endogenous glycophorin gene was not altered in these transformants.
Induction of differentiation monitored by benzidine staining in each
transformant also showed that the transfection did not affect extent of
differentiation in these transformants (data not shown). When the
luciferase activities were measured at 4 days of culture, the deletion
in the LCR-like region ( LCR) reduced its transcriptional activity to
50% of that of the 1.3-kb sequence containing the LCR-like region ( )
(Fig. 7B). The mutation in the delta/YY-1 binding site
( delta/YY-1 in Fig. 7A) itself reduced to 60% that of
the original activity. On the other hand, mutation in the neighboring
E-box biding site ( E-box) resulted in complete loss of LCR-like
activity. Activity of the mutations in both sites resumed to a level
similar to that of the deletion in the delta/YY-1 binding site alone.
To confirm the change in the transcriptional activities in these
transformants, the time course of luciferase activities after induction
was measured (Fig. 7C). The result showed that luciferase
activities were dependent on induction.
Fig. 7.
Stable transfection assay of the mutants
within the LCR-like region of the mouse glycophorin gene.
Transfection of the plasmids containing the LCR-like region and its
mutants and their luciferase assay were described under ``Materials
and Methods.'' The luciferase activities in the induced
(DMSO (+)) or uninduced (DMSO ( )) MEL cells
were expressed as arbitrary units (counts/cell number). A, LCR-like activities of the MEL cells transfected
with the LCR-like region containing plasmid and site directed mutants
( : no mutation, E-box, a mutant in the E-box binding
site;  /YY-1, a mutant in the delta/YY-1 binding site.
B, the LCR-like activities of the nondeletion mutant ( )
and the mutant deleting the LCR-like region ( LCR).
C, time course of luciferase activities after induction in
each transformant. Luciferase activities were measured at 1-4 days
after induction in each transformant. D, induction of
endogenous glycophorin mRNA in each transformant. Ten µg of total
RNA from each transformant at 4 days after induction with (+) or
without ( ) Me2SO was prepared and analyzed by Northern
blot hybridization as described under ``Materials and Methods.''
Actin mRNA was used for internal control.
DISCUSSION
The LCR-like region found in the far upstream region ( 1.2 to
0.9 kb) of the mouse glycophorin gene has been shown to contain
several erythroid-specific nuclear factor binding sites as observed in
the human -globin gene. Deletion analysis of the 5 far upstream
region of this gene conferred high levels of expression in a stable
transfection assay, but, interestingly, when tested in transient
expression assays in MEL cells, it showed no stimulation of
transcriptional activity (5) as shown in the LCR of -globin gene
(31). Thus, the far upstream region of the mouse glycophorin gene was
clearly distinguished from general enhancers, which were originally
defined in transient transcription assays (16). It is likely that this
region may activate the glycophorin gene on the chromatin structure
like the LCR of the -globin gene (7, 31, 32).
To understanding the mechanism of the differentiation-specific gene
regulation by the glycophorin LCR-like region, it is important to
investigate the nuclear proteins that bind to it before and after
induction of MEL cell differentiation. Our DNase I footprinting and
EMSA consistently showed that several nuclear factors bound to the
LCR-like region (Figs. 1, 2, 3, 4). We showed the presence of binding sites
for the erythroid-specific transcription factor GATA-1, and they did
not show any change in their binding activities before or after
induction of MEL cells. Although the hypersensitive site was observed
in the 5 side of the upstream AP1/NF-E2-like motifs in the two
AP1/NF-E2-like motifs within this region (Fig. 2C),
suggesting the nuclear factor binding, we could not observed clear gel
shift bands with these DNA sequences.2 The
co-localization of these binding sites in the glycophorin LCR-like
region was very similar to the globin gene LCR (3, 6, 16, 21, 33, 34).
Of interest is the apparent difference in the binding activity of
GATA-1 to the GATA site within the LCR-like region and the promoter
region of the glycophorin gene during MEL cell differentiation. It is
likely that GATA-1 binding is affected by the neighboring sequence
(5).
In contrast to these elements, two binding sites for Spi-1/PU.1 and
GRBF showed a change. Spi-1 is an oncogene activated during
leukemogenesis induced by Friend virus (35) and is identified as PU.1,
which is a transcription factor and one of the protein products of the
ets protooncogene family (22, 36, 37). The binding activity
of PU.1 dropped after induction as shown in Figs. 2 and 3, and these
results are consistent with our previous report that levels of PU.1
mRNA dropped rapidly when these cells were treated with
Me2SO (26). We speculate that Spi-1 itself acts as a
negative factor for transcription and/or that its binding to the
element may interfere with the binding of other nuclear factors to it.
The globin gene seems not to contain the PU.1 binding site within the
LCR-like region; however, its binding site was found in the 3 -enhancer
of the mouse -globin gene (23). Thus, it is possible that PU.1 acts
as a negative factor for erythroid-specific gene expression, as it has
a regulatory function in other hematopoietic cells such as T cells
(22).
Another factor with binding activity that changes after induction is
GRBF. We concluded by gel shift competition analysis that the consensus
sequence for GRBF is CCATTT. The GRBF activity increased after
induction of MEL cells when the transcription of glycophorin began to
rise (1, 26). By screening with the CCATTT consensus sequence, we
isolated the cDNA clone for GRBF and surprisingly, found that GRBF
was identical to delta, a murine form of YY-1 (28) which is a versatile
transcription factor that has a zinc finger DNA binding domain. The
band shift with oligonucleotide e in the MEL cell extract
was retarded with the addition of rabbit anti-delta/YY-1 antibody.
Delta/YY-1 is involved in negative and positive regulation of
transcription of many genes (38). For example, two YY-1 binding sites
at 60 and at +1 of the adeno-associated virus P5 promoter mediate
repression of transcription by YY-1, an effect which is relieved by E1A
(28), and delta activates transcription of mouse ribosomal protein
genes that lack a TATA box from binding sites upstream of the
transcription start site (27). Its binding sites were found in many
genes (27, 28, 29, 30, 39, 40, 41); those found in adeno-associated virus (28), in
the upstream conserved region of MuLV (30), and in one of
c-myc upstream elements (40) are CCATTT, which is completely
matched with that of GRBF, while those found in immunoglobulin 3
gene enhancer (29) and in ribosomal protein rpL30 gene (27) are CCATCT.
By comparison with the functional core of the globin LCR-HS3, we found
that the well conserved element FP-6 (33) has CCTTT, which resembles to
a consensus core sequence for delta/YY-1. Our preliminary gel shift
assay with the FP-6 sequence probe demonstrated that delta/YY-1 can
bind to this element (data not shown). This result suggests that
delta/YY-1 may play an important role in regulating LCR-like activity
in erythroid differentiation. This possibility was examined by stable
transfection of the point mutants in the GRBF binding site and the
neighboring E-box binding site within the LCR-like region of the mouse
glycophorin gene. The stable assays showed that a point mutation in the
delta/YY-1 binding site reduced its LCR activity to 60% of original
activity. More interestingly, a mutation in the E-box binding site
completely lost the LCR-like activity. Based on these results, the
following models may be plausible. 1) YY-1 is a transcriptional
activator which inhibits transcription in the absence of E-box binding
protein. 2) E-box binding protein is a transcriptional activator which
is nonfunctional without YY-1, and YY-1 by itself acts as an inhibitor.
In either model, it is clear that delta/YY-1 regulates the LCR-like
activity in combination with the E-box binding protein.
It is interesting to learn how the activity of delta/YY-1 can be
modulated during induction of MEL cells. The nucleotide sequence
adjacent to the delta/YY-1 binding site consisted of E-box binding site
whose binding activity did not change before or after induction (Fig.
3B). It is important to identify the E-box-binding protein
in MEL cells. Since the E-box found in the LCR-like region is CACGTG
which is the consensus binding site for Max/Max and Myc/Max (42, 43),
it would be of interest to know whether c-Myc could bind to this
element, because overexpressed c-Myc interferes with induction of
differentiation of MEL cells (12), and the association of c-Myc with
YY-1 inhibits YY-1 activity (38).
FOOTNOTES
*
This work was supported by a Grant-in-Aid for Cancer
Research from the Ministry of Education, Science and Culture of the
Japanese government. The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
``advertisement'' in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed: Tel.: 81-22-717-8483 (ext. 3461); Fax: 81-22-717-8488.
1
The abbreviations used are: MEL, murine
erythroleukemia; Me2SO, dimethyl sulfoxide; LCR, locus
control region; GBRF, glycophorin regulatory element binding factor;
EMSA, electrophoretic mobility shift assay; bp, base pair(s); kb,
kilobase pair(s).
2
Y. Nemoto, unpublished observation.
Acknowledgments
We thank Drs. A. Kuroiwa, M. Yamamoto, and H. Sasaki for helpful discussions.
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