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Molecular and Cellular Biology, December 1999, p. 8272-8280, Vol. 19, No. 12
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Paired-Homeodomain Transcription Factor PAX4
Acts as a Transcriptional Repressor in Early Pancreatic
Development
Stuart B.
Smith,1
Hooi C.
Ee,1,
Jennifer R.
Conners,1 and
Michael S.
German1,2,*
Hormone Research
Institute1 and Department of
Medicine,2 University of California, San
Francisco, San Francisco, California 94143-0534
Received 25 March 1999/Returned for modification 20 May
1999/Accepted 16 August 1999
 |
ABSTRACT |
The paired-homeodomain transcription factor PAX4 is expressed in
the developing pancreas and along with PAX6 is required for normal
development of the endocrine cells. In the absence of PAX4, the numbers
of insulin-producing
cells and somatostatin-producing
cells are
drastically reduced, while the numbers of glucagon-producing
cells
are increased. To gain insight into PAX4 function, we cloned a
full-length Pax4 cDNA from a
-cell cDNA library and identified a
bipartite consensus DNA binding sequence consisting of a homeodomain
binding site separated from a paired domain binding site by 15 nucleotides. The paired half of this consensus sequence has
similarities to the PAX6 paired domain consensus binding site, and the
two proteins bind to common sequences in several islet genes, although
with different relative affinities. When expressed in an
-cell line,
PAX4 represses transcription through the glucagon or insulin promoters
or through an isolated PAX4 binding site. This repression is not simply
due to competition with the PAX6 transcriptional activator for the same
binding site, since PAX4 fused to the unrelated yeast GAL4 DNA binding
domain also represses transcription through the GAL4 binding site in
the
-cell line and to a lesser degree in
-cell lines and NIH 3T3
cells. Repressor activity maps to more than one domain within the
molecule, although the homeodomain and carboxyl terminus give the
strongest repression. PAX4 transcriptional regulation apparently plays
a role only early in islet development, since Pax4 mRNA as
determined by reverse transcriptase PCR peaks at embryonic day 13.5 in
the fetal mouse pancreas and is undetectable in adult islets. In
summary, PAX4 can function as a transcriptional repressor and is
expressed early in pancreatic development, which may allow it to
suppress
-cell differentiation and permit
-cell differentiation.
 |
INTRODUCTION |
During development, the mammalian
pancreas arises from the epithelial cells of the embryonic gut at the
foregut-midgut junction and differentiates into two distinct
compartments: the exocrine tissue, which produces digestive enzymes,
and the endocrine islets of Langerhans, which produce specific
hormones. The islets are arranged into a core of insulin-producing
cells surrounded by a mantle of glucagon-producing
cells, and
smaller numbers of somatostatin- and pancreatic polypeptide-producing
cells (
and PP cells, respectively) (34).
The coordinated regulation of gene expression required for normal
pancreatic development is not completely understood but clearly
requires the orderly activation of nuclear transcription factors by
both intracellular and extracellular signals. Several transcription
factors (PDX1, ISL1, PAX6, PAX4, BETA2/NeuroD, and NKX2.2) are required
for normal pancreatic endocrine development, and many of these factors
also regulate gene expression in mature islet cells (1, 2, 19, 24,
26, 32, 35-37). However, one of these factors, PAX4, has been
identified only as a regulator of endocrine development, and its target
genes are unknown (35).
PAX4 belongs to the PAX family of transcription factors and contains
both a paired domain and a homeodomain (18, 42) which are
potential DNA binding domains (DBDs). In the normal murine embryo, its
mRNA is detected at embryonic day 9.5 (e9.5) in ventral spinal cord and
pancreas (35). Indirect evidence from mice containing the
-galactosidase coding sequence inserted into the Pax4
gene suggests that at birth PAX4 expression is restricted to the
cells within the pancreas (35). Its critical role in
pancreatic endocrine development is demonstrated by the fact that mice
homozygous for a null mutation in the Pax4 gene have a
marked decrease in
and
cells and an increase in
cells,
although the mechanism for these changes is undefined (35).
Importantly, insulin-expressing cells are detected in the null mutants
at e10.5, suggesting that insulin transcription can occur in the
absence of PAX4. Ultimately however, the null mutants die within a few
days of birth, apparently as a consequence of insulin deficiency.
Heterozygotes containing a single mutated Pax4 allele are
normal. It is interesting that PAX6, which is highly related to PAX4,
is also required for normal endocrine pancreatic development
(36), although its absence reduces all four endocrine
lineages (32). Furthermore, double null mutants for both
Pax4 and Pax6 fail to produce any mature pancreatic endocrine cells (36), suggesting that these two
factors together are required for endocrine cell differentiation.
To gain insight into the mechanisms of PAX4 function in the endocrine
pancreas, we determined where it binds and how it regulates transcription. We identified a consensus DNA binding site for PAX4 and
showed that PAX4 can bind to various sequences in the rat insulin I,
somatostatin, and glucagon promoters, all of which have previously been
shown to bind PAX6 (32). We found that PAX4 can act as a
transcriptional repressor and showed that the homeodomain and carboxyl
portion of the molecule confers the greatest repressive activity.
Finally, by reverse transcriptase PCR (RT-PCR), we demonstrate that
PAX4 expression peaks early in pancreatic development and that PAX4 is
not expressed in mature islets.
 |
MATERIALS AND METHODS |
Cloning of murine Pax4.
The Pax4 cDNA was
cloned from a
TC3 cell line plasmid library (a generous gift from D. Hanahan, University of California, San Francisco) by PCR, using a
high-fidelity system (Expand PCR; Boehringer Mannheim, Indianapolis,
Ind.), producing two overlapping clones. The 5' clone was produced by
PCR using the SP6 forward primer (located in the vector) and a reverse
primer beginning at the 3' end of the paired box
(5'-CGGAATTCCTGAAGTGCCCGAAGTACTCG-3'). This clone extends 18 bp 5' of the initiator ATG codon. The 3' clone was produced by using a
forward primer from the 5' end of the paired box
(5'-CGCGGATCCCTCAGCAGTGTGAATCAGCT-3') and the T7 reverse
primer (located in the vector). The two clones span 1.1 kb of the
Pax4 cDNA and include the entire predicted coding sequence.
In vitro protein expression.
To produce a PAX4 expression
vector, the two overlapping clones were digested and then religated at
an FseI site located between 43 to 50 bp into the paired
box. The full-length coding sequence was inserted into the pSP72 vector
(Promega, Madison, Wis.), enabling protein expression with the
bacterial SP6 promoter. A truncated coding sequence, terminating at
codon 274, was also created in the same vector because the full-length
PAX4 (349 amino acids [aa]) was not expressed with adequate
efficiency. The PAX6 expression vector (pmPAX6) was a gift from M. Busslinger, Research Institute of Molecular Pathology, Vienna, Austria
(4). PAX4 and PAX6 proteins were produced by in vitro
transcribed/translated (IVTT) reaction, using the TNT coupled
reticulocyte lysate system (Promega) according to the manufacturer's instructions.
PAX4 binding site selection.
To select for PAX4 binding
sequences by using a published technique (3), a 76-mer
sequence with 30 central random bases was used as a probe in an
electrophoretic mobility shift assay (EMSA). The sequence of the top
strand of the 76-mer was
5'-GTGACCAGATCTAATCGTGGTCCTN30ACGGTCGACGAGTACGCGTTAC-3'. Radiolabeling of the second strand with
[
-32P]dCTP was performed with Klenow polymerase,
deoxynucleoside triphosphates, and the primer
5'-GTAACGCGTACTCGTCGACCGT-3' (REV). The labeled, double-stranded random sequences were incubated with in vitro-produced truncated PAX4 and electrophoresed under nondenaturing conditions. The
specific retarded complex was cut out of the gel, and the selected
76-mers were eluted. The eluted 76-mers were then amplified and
relabeled by using 16 cycles of PCR with [
-32P]dCTP,
the REV primer, and the forward primer
5'-GTGACCAGATCTAATCGTGGTCCT-3' (FWD). This PCR product was
used as probe for the next round of EMSA selection. A total of 13 selection cycles were performed, and the selected 76-mers were
subcloned into pCR2.1 (Invitrogen) and sequenced after the 10th and
13th cycles.
EMSA.
Single-stranded oligonucleotide probes were 5' end
labeled with [
-32P]ATP by using T4 polynucleotide
kinase. Labeled oligonucleotides were column purified and annealed to
an excess of the complementary strand. EMSA buffers and electrophoresis
conditions were as previously described (13). Where in
vitro-synthesized PAX4 or PAX6 was used, 0.05 to 1 µl of the 50-µl
reaction volume was added.
The oligonucleotide probes used in EMSA, and their locations in
relation to the transcriptional start site for the gene, are as shown
(top strand): rat insulin I C2 element (rInsIC2), bp
328 to
304,
5'-CTGGGAAATGAGGTGGAAAATGCTC-3'; rat somatostatin upstream
enhancer (SMS.UE), bp
102 to
76,
5'-GCGAGGCTAATGGTGCGTAAAAGCACT-3'; rat glucagon G3 (GluG3),
bp
265 to
231, 5'-TTTTTCACGCCTGACTGAGATTGAAGGGTGTATTT-3'; and rat glucagon G1 (GluG1), bp
100 to
52,
5'-CAAAACCCCATTATTTACAGATGAGAAATTTATATTGTCAGCGTAATAT-3'.
Cell culture and transient transfections.
A PAX4 eukaryotic
expression vector was produced by subcloning the full-length
Pax4 cDNA into a vector (pBAT12) containing the human
cytomegalovirus (CMV) immediate-early gene promoter. pBAT12 is
identical to pBAT7 (14) except for a modification in the
polylinker and replacement of the early simian virus 40 polyadenylation
signal with the late simian virus 40 polyadenylation signal. The
reporter constructs were created by using either the
410 bp rat
insulin I promoter, the
482 bp rat glucagon promoter, the Rous
sarcoma virus (RSV) long terminal repeat (LTR), the CMV promoter, or
the isolated rInsIC2 fragment linked to the herpes simplex virus
thymidine kinase (HSV-TK) promoter to drive the chloramphenicol
acetyltransferase (CAT) gene in the pFOXCAT2 vector (25).
One-hybrid expression vectors encoding PAX4- or PAX6-GAL4 DBD fusion
proteins were made by amplifying the appropriate coding
fragments of
PAX4 or PAX6 by PCR and then ligating the fragment
in frame into the
EcoRI and
BamHI sites of the GAL4 DBD vector
(pM;
Clontech). The GAL4-TK reporter plasmids were created in
the pFOX2
plasmid backbone (
25) by ligating a single copy of
the GAL4
upstream activating sequence (UAS) to the HSV-TK promoter
driving the
CAT gene (plasmid pFOXCAT2.TK.1GAL) or five copies
upstream of the TK
promoter driving the fire fly luciferase gene
(plasmid
pFOXLuc2.TK.5GAL). The other GAL4 reporter plasmid, with
a much lower
basal promoter activity, consists of five GAL4 binding
sites linked to
the minimal adenovirus E1b promoter driving CAT
expression (pG5CAT;
Clontech). The CMV green fluorescent protein
plasmid (pFOXEGFP2.CMV)
was constructed with the CMV promoter
upstream of the enhanced green
fluorescent protein (EGFP) cDNA
(Clontech).
NIH 3T3,

TC1.6,

TC3, and HIT-T15 M2.2.2 cells were cultured,
transfected with calcium phosphate, and harvested as previously
described (
13). CAT assays and luciferase assays were
performed
as previously described, using 10 µg of cell protein
extract (
13,
14).
Mouse pancreatic buds were isolated from fetal mice at e12.5, and the
mesenchyme and epithelium were separated as previously
described
(
15). The epithelium from each bud was individually
transfected with 3 µg of the plasmid DNAs indicated and 9 µg of
the
cationic lipid transfection reagent Transfast (Promega). After
transfection, the epithelium was washed and recombined with the
mesenchyme on a surface of Matrigel (Collaborative Research).
After
culturing for 24 h, the buds were harvested and RT-PCR was
performed.
RT-PCR.
Total RNA was purified from the indicated tissue
source by using an RNAqueous kit (Ambion, Austin, Tex.) and quantified
by spectrophotometry. Using a modification of the method described by
Gittes and Rutter (16), 250 ng of total RNA was then used as
template to synthesize first-strand cDNA by the action of avian myeloblastosis virus reverse transcriptase primed by a poly(dT) primer.
The cDNA produced was used as a template for the indicated number of
cycles of PCR using primers that amplify fragments of the indicated
cDNA (PAX4 primers 1 [GTGTTGGCTCCAGTTCTTCC] and 2 [AACCAAACCCTCACCGTGTC];
-actin primers 1 [TGAGAGGGAAATCGTGCGTG] and 2 [TGCTTGCTGATCCACATCTGC]; mouse insulin II primers 1 [GCCCTAAGTGATCCGCTACAATC] and 2 [GCAGCACTGATCTACAATGCCAC]; luciferase and EGFP primer 1 [TGGGCAGGCTGCTGGTCTGAG]; luciferase primer 2 [TGCTCTCCAGCGGTTCCATC]; EGFP primer 2 [TCAGGGTCAGCTTGCCGTAGG]) Each set of primers was designed
to include at least one intron in order to allow the discrimination of
contaminating genomic or plasmid DNA from cDNA. The cycling program
used for all samples was 95°C for 2 min and then 25 to 40 cycles of
95°C for 20 s, 55°C for 30 s, and 72°C for 30 s.
Samples were analyzed on a 6% polyacrylamide gel and stained with
ethidium bromide. Identity of the amplified products was confirmed by
subcloning and DNA sequencing. PCR performed for luciferase and EGFP in
the transfected pancreatic buds included 100,000 cpm of
[
-32P] dCTP. PCR products were quantified with a
phosphorimager and expressed as the ratio of luciferase cDNA to EGFP cDNA.
 |
RESULTS |
Cloning of Pax4.
To study the function of PAX4, we
cloned the Pax4 cDNA from a
-cell tumor line (
TC3)
plasmid cDNA library. The predicted amino acid sequence of PAX4 is
identical to a recently published sequence derived from the MIN6
insulinoma cell line (18), except for a proline at position
277 in our sequence, which has been replaced with a serine. PAX4 is
therefore a 349-aa protein with its 128-aa paired domain beginning at
the fifth residue after the initiator methionine. A 36-aa intervening
sequence separates the paired domain from the 60-aa homeodomain, and a
further 121 aa extend from the homeodomain to the carboxyl terminus.
Compared to PAX6, the paired domains of both proteins begin 4 to 5 aa
from the start codon. PAX6 is a substantially longer
protein than PAX4
(422 versus 349 aa), due to a longer intervening
sequence between the
paired and homeodomains (77 versus 36 aa)
and a longer C-terminal tail
beyond the homeodomain (154 versus
121 aa). The two proteins are 70%
identical in their paired domains
and 65% identical in their
homeodomains (see Fig.
6A). Outside
the highly conserved paired and
homeodomains, PAX4 and PAX6 share
no obvious sequence
similarity.
PAX4 binding site selection.
To gain insight into PAX4
function, we attempted to determine PAX4 recognition sequences by using
a previously described strategy (3) and ultimately to
identify its downstream target genes. To select oligonucleotides with
high PAX4 binding affinity, we incubated a pool of radiolabeled
oligonucleotide probes containing a central core of 30 random bases
with in vitro-produced PAX4 and performed an EMSA. We used a
C-terminally truncated in vitro-produced PAX4 because the synthesis of
full-length PAX4 was less efficient (data not shown). The truncated
protein is 274 aa instead of 349 aa but contains both the paired and homeodomains.
After the first EMSA, the specific PAX4-DNA retarded complex was cut
from the gel and the bound oligonucleotides were eluted.
PCR was
performed to amplify and to radiolabel the selected oligonucleotides,
which were then used for the next round of EMSA selection.
Oligonucleotide
products were subcloned for sequencing after the 10th
and 13th
rounds of selection. All of the sequences obtained from the
13th
round of selection were subjected to an ungapped alignment using
the multiple sequence alignment function in the MacVector 6.5
software
package (Oxford Molecular Ltd.). This alignment reveals
a bipartite
consensus (Fig.
1A). The 3' sequence
generally conforms
to the consensus DNA binding sequences for other
paired domains
(
20) and shares a six-nucleotide overlap with
the PAX6 consensus
binding sequence (Fig.
1E) obtained by using the
paired domain
alone (
7). The 5' sequence contains the
overlapping TAAT sequence
found in many binding sites for homeodomain
transcription factors
(
39).

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FIG. 1.
PAX4 binding site selection. In vitro-produced truncated
PAX4 protein including the paired domain and homeodomain was used in
EMSA to select sequences with high binding affinity from a random pool
of oligonucleotides containing 30 degenerate base pairs flanked by PCR
primer sites. (A) Alignment of sequences of oligonucleotide products
subcloned and sequenced after 13 rounds of selection. Sequences are
aligned by the MacVector multiple-sequence alignment function to show
the best fit. (B) Alignment of homeodomain type sequences after 13 rounds of selection. (C) Alignment of paired domain-type sequences
after 13 rounds of selection. (D) Alignment of oligonucleotide products
subcloned and sequenced after 10 rounds of selection. TAAT sequences
are underlined. (E) The consensus PAX4 recognition sequence established
from the aligned sequences compared to the PAX6 consensus recognition
sequence, based on paired domain binding alone (7). Matching
bases are in boldface; rat hormone gene regulatory elements with
possible PAX4 binding sites are underlined.
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Optimally alignment of the sequences for the paired domain site (Fig.
1C) reveals a 6-bp consensus, ANNN(C/T)CACCC, that varies
by only one
base from the core of the PAX6 consensus binding sequence
obtained by
using the paired domain alone (Fig.
1E) (
7). Similarly,
when
the sequences are optimally aligned for the homeodomain site
(Fig.
1B),
an 8-bp consensus, AA(T/A)AATTA, that conforms well
with common
homeodomain binding motifs (
20,
39,
43) is
apparent.
Given the wide space between the sites, we cannot rule out the
possibility that optimal homeodomain or paired domain sites
might
include additional bases on the 5' or 3' ends, respectively,
that we
cannot detect because our degenerate binding site was
30 bp long. The
paired domain actually includes two DBDs the PAI
and RED domains
(
4,
8,
20,
44). Our paired domain consensus
sequence lacks
some of the bases on the 3' end that are usually
associated with RED
binding. We cannot be certain if this is due
to differences in the RED
domain in PAX4, the presence of the
homeodomain, or the limitations of
our oligonucleotide design.
It should be noted that not all
paired-homeodomain proteins contact
DNA through the RED domain; the
intact
Drosophila Paired protein
(Prd) binds only with its
homeodomain and PAI domain (
20).
Comparison of the round 13 consensus with the sequences obtained in
round 10 demonstrates that most of the round 10 sequences
also contain
both the paired binding site and the homeodomain
binding site (Fig.
1D). As in round 13, the TAAT motifs are 5'
relative to the paired
site, but the exact position varies. It
should be kept in mind that the
distance between the homeodomain
and paired domain binding sites is
constrained by the size of
the degenerate oligonucleotides, leaving
open the possibility
of a longer intervening sequence as
well.
PAX4 binds to hormone gene promoters.
Comparison of the
consensus PAX4 binding sequence with the insulin promoter sequence
shows that a sequence matching five of the seven bases in the consensus
is found in rInsIC2 (Fig. 1E). As this element has been shown to bind
strongly to PAX6 (32), and as PAX4 and PAX6 recognition
sequences share some overlap, we compared the PAX4 consensus sequence
to sequences of other known PAX6 binding sites on islet hormone gene
promoters, namely, rat SMS.UE and rat GluG3 (32). In both
SMS.UE and GluG3, there are sites matching the PAX4 consensus (Fig.
1E). We also tested for PAX4 and PAX6 binding to rat GluG1, as it
shares sequence similarity to GluG3 (21, 29) and binds
similar protein complexes (29). The GluG1 sequence contains
two potential PAX4 paired binding sites, although with only four
matching bases at each site, and two TAAT sequences (Fig. 1E).
Oligonucleotides including these potential binding sites were end
labeled and used as probes in EMSA, initially to compare
the DNA
binding characteristics of the truncated and full-length
PAX4. PAX4
binds with highest affinity to rInsIC2, followed by
SMS.UE and GluG3
(Fig.
2A). Binding to
GluG1 is substantially
weaker than binding to the
other oligonucleotides (Fig.
2A). Importantly,
we show that the
truncated and full-length proteins have the same
relative affinities
for the different oligonucleotide probes.

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FIG. 2.
PAX4 binding to islet gene promoters. (A) EMSA
using truncated (PAX4-T) and full-length (PAX4-FL) PAX4 to bind to
hormone gene regulatory elements. 32P-end-labeled
oligonucleotides (10,000 cpm) were incubated with 1 µl of a 50-µl
IVTT reaction in each lane and then electrophoresed. (B) EMSA using
PAX4-T to bind to 32P-end-labeled rInsIC2 probe (10,000 cpm). A 50- to 100-fold molar excess of unlabeled competitor
oligonucleotides was added to the lanes indicated; 0.05 µl of a
50-µl IVTT reaction was used in each lane. (C) EMSA comparing the
binding of PAX4-T and PAX6 to 32P-end-labeled hormone gene
regulatory elements; 0.1 µl of a 50-µl IVTT reaction was used in
each lane. The open arrowhead (>) points to a weak PAX4-T-GluG1
complex.
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To confirm the relative binding affinities of PAX4 to these elements,
EMSA was performed with rInsIC2 as the probe, as it
has the highest
affinity for PAX4, and the other elements were
used as unlabeled
competitors. The most effective competitor is
rInsIC2, followed by
SMS.UE, GluG3, and finally GluG1 (Fig.
2B).
These results confirm that
PAX4 has the following relative binding
affinities: rInsIC2 > SMS.UE > GluG3 >
GluG1.
We then compared binding of PAX4 and PAX6 to the same oligonucleotide
probes. An equal amount of each protein, assessed by
[
35S]Met incorporation (not shown), was used in each EMSA
binding
reaction. EMSA shows that PAX6 has a substantially higher
affinity
for all of the oligonucleotides than does the truncated PAX4
and
has the following relative affinities: GluG3 > rInsIC2 > GluG1
= SMS.UE (Fig.
2C and reference
32).
We also tested but could
not demonstrate PAX4 binding to several other

-cell promoter
elements, including the human insulin (hIns) C2
element, the rIns
and hIns C1 elements, rInsI A3/4 element, the hIns Z
element,
and the rat

-cell-specific glucokinase promoter Pal1 and
Pal2
sites (
11,
12,
31,
33) (data not
shown).
PAX4 represses transcription.
We used the high affinity PAX4
C2 binding site to assess the transcriptional effect of PAX4 in
cultured cells. A single copy of the isolated C2 element linked to the
HSV-TK promoter was used to drive CAT gene expression. PAX4 expression
was driven by the CMV immediate-early promoter in the eukaryotic
expression vector pBAT12-PAX4. Expression and reporter constructs were
cotransfected into
(
TC1.6),
(
TC3 and HIT-T15 M2.2.2), and
nonislet (NIH 3T3) cell lines, and CAT activity was assessed.
In the

-cell lines and NIH 3T3 cells, PAX4 has little effect on the
transcriptional activity of the isolated C2 element (Fig.
3B). In contrast, in

TC1.6 cells, PAX4
represses transcription
from the isolated C2 element approximately
threefold but has no
effect on the TK promoter in the absence of the C2
element.

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FIG. 3.
PAX4 transcriptional repression. Transient transfections
of the indicated cell lines were performed with the PAX4 expression
vector and reporter constructs consisting of the HSV-TK promoter alone
(TK) or the isolated rInsIC2 element linked to TK-HSV (C2-TK) (A) and
the 410-bp rat insulin I promoter (RIP), 482-bp rat glucagon
promoter (GLU), RSV LTR (RSV), or CMV promoter (CMV) driving CAT
expression. Transfections were performed in duplicate on at least three
separate occasions. Relative CAT activity of the TK-CAT reporter in the
absence of PAX4 expression is set arbitrarily at +1. In panel B,
relative CAT activity of each construct in the absence of PAX4
expression is set arbitrarily at +1. Graphs show mean ± standard
error of the mean.
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Confirming the results with the isolated C2 binding site, PAX4 also
represses transcription from the intact insulin and glucagon
promoters
(Fig.
3C). Repression is again seen predominantly in
the

TC1.6 cells
but does not occur with the unrelated RSV and
CMV promoters (Fig.
3C).
These results demonstrate that PAX4 represses
transcription through its
binding site and that this effect may
depend on the cellular
context.
PAX4 contains transcriptional repression domains.
Repression
by PAX4 could result from competition for binding at the rInsIC2 site
with a strong activator (such as PAX6) or could reflect an intrinsic
repressor function of the PAX4 molecule. To distinguish between these
two possibilities, we made chimeric proteins by fusing portions of PAX4
to the yeast GAL4 DBD. We also used the C-terminal region of PAX6
(codon 271 to COOH) as a known positive activating domain (17,
32). To allow direct comparison to the experiments using the C2
site, an analogous reporter construct was constructed by simply
replacing the C2 element in the C2-TK-CAT plasmid with a single GAL4
DNA-binding site (the GAL4 UAS). The fusion protein constructs and
reporter constructs were cotransfected into cultured cells. This
approach allows for DNA binding through the GAL4 DBD, independent of
the PAX4 paired and homeodomains.
In

TC1.6 cells, the region of PAX4 C terminal to the paired domain
(codon 127 to COOH) represses CAT activity to approximately
40% of
baseline (Fig.
4B), a degree of
repression similar to that
produced by intact PAX4 acting through an
isolated C2 site. The
PAX4 carboxyl terminus beyond the homeodomain
(codon 211 to COOH)
can also repress CAT activity. While there is some
weak repression
in the other cell lines, the

-cell line gives the
strongest repression,
consistent with the

-cell repression
demonstrated by the intact
PAX4 protein on the C2 element (Fig.
3B).
When a reporter construct
that contains multiple GAL4 UAS binding sites
is used, the repression
by GAL4-PAX4 fusion proteins is more pronounced
and can be detected
in NIH 3T3 and

TC3 cells as well (Fig.
4C).

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FIG. 4.
PAX4 repressor domains. (A) Comparison of PAX4 and PAX6
structure. PD, paired domain; HD, homeodomain. (B) Transient
transfections of the indicated cell lines were performed with the
chimeric PAX4-GAL4 DBD fusion protein constructs shown and a reporter
construct consisting of the GAL4 binding site linked to HSV-TK driving
CAT expression (GAL4UAS-TK-CAT). (C) Transient transfections of TC3
and NIH3T3 cells were performed with a reporter construct consisting of
five copies of the GAL4 GAL4 UAS. (D) Transient transfections of
TC1.6 cells were performed with a reporter construct consisting of
HSV-TK driving CAT expression without a GAL4 binding site (TK-CAT). (E)
Transient transfections of TC3 cells were performed with a reporter
consisting of five GAL4 binding sites linked to the minimal adenovirus
E1b promoter driving CAT expression (5XGAL4UAS-E1b-CAT). Note that the
lowermost expression construct consists of the PAX6 C-terminal domain
fused to the GAL4 DBD. Transfections were performed in duplicate on at
least three separate occasions. Relative CAT activity of the GAL4-DBD
expression construct alone is set arbitrarily at +1. Graphs show
mean ± standard error of the mean.
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To demonstrate that PAX4 repression in this assay requires specific DNA
binding between the GAL4 DBD and its cognate recognition
sequence (GAL4
UAS), we used a reporter construct consisting of
the HSV-TK promoter
driving CAT but without a GAL4 UAS. None of
the PAX4-GAL4 fusion
constructs produced a repressive effect when
cotransfected with this
reporter in

TC1.6 cells (Fig.
4D). Thus,
the repressive effects seen
in this system can occur only when
the expressed chimeric PAX4-GAL4 DBD
proteins bind specifically
to a promoter containing the GAL4
UAS.
To ensure that the transcriptional activation potential of PAX4 was not
hidden by the high basal activity of the HSV-TK promoter,
we also
tested the same fusion constructs with a construct containing
five GAL4
UASs linked to the adenovirus E1b promoter driving CAT
expression
(pG5CAT; Clontech). Even with this minimal promoter,
the PAX4
constructs do not activate in

TC3 cells, whereas stimulatory
activity of the PAX6 carboxyl terminus is obvious (Fig.
4E).
PAX4 is not expressed in mature
cells.
Transgenic
experiments have previously suggested that PAX4 is expressed
specifically in pancreatic
cells, making its role as a
transcriptional repressor, especially of the insulin promoter, difficult to understand. Because of this inconsistency and our inability to detect PAX4 protein in mature
cells by EMSA or Western
blot analysis (data not shown), we tested for the expression of
Pax4 mRNA by RT-PCR.
Pax4 mRNA can be detected in the fetal mouse pancreas,
peaking at e13.5, but no
Pax4 mRNA can be detected in mature
mouse
islets (Fig.
5A), even when PCR is
extended to 40 cycles (data
not shown).
Pax4 mRNA can also
be detected in

TC3 cells, but
not in the NIH 3T3 fibroblast cells
(Fig.
5B).
Pax4 mRNA is expressed
at much lower level in

TC1.6 cells, and a faint band can be detected
in Fig.
5B, although
this is more obvious with additional cycles
of PCR (data not shown).

View larger version (24K):
[in this window]
[in a new window]
|
FIG. 5.
Expression of Pax4 mRNA. RT-PCR was performed
with 250 ng of total RNA from the tissues shown. PCR products were
removed and separated by polyacrylamide gel electrophoresis after 30 cycles for PAX4 and -actin, and 25 cycles for insulin II. Lanes
labeled-RT show the product of identical samples performed without
reverse transcriptase using RNA from e13.5 fetal mouse pancreas (A) and
TC3 cells (B).
|
|
Given its expression in the fetal pancreas, we tested the
transcriptional function of PAX4 in the fetal pancreas. Pancreatic
epithelium from E12.5 mouse fetuses was cotransfected with the
GAL4-PAX4 expression vector containing the region of PAX4 C-terminal
to
the paired domain (codon 127 to COOH) and a reporter plasmid
containing
five copies of the GAL4 UAS upstream of the TK promoter
driving the
firefly luciferase gene. A plasmid with the CMV promoter
driving an
EGFP cDNA was included as an internal standard. After
24 h,
transcriptional activity was gauged by measuring luciferase
mRNA levels
by RT-PCR and normalizing with EGFP mRNA levels. The
results
demonstrate that as in the cell lines, the PAX4 carboxy
terminus
represses transcription, unlike PAX6, which activates
transcription
(Fig.
6).

View larger version (17K):
[in this window]
[in a new window]
|
FIG. 6.
PAX4 transcriptional repression in fetal pancreatic
epithelium. Transient transfections were performed in mouse e11.5
pancreatic epithelium with expression vectors containing the GAL4 DBD
coding sequence fused with the PAX4 and PAX6 cDNA fragments shown, the
pFOXLuc2.TK.5GAL reporter plasmid, and the pFOXEGFP.CMV internal
standard. Transfections were performed in triplicate on individual
fetal pancreatic buds. Luciferase mRNA levels were measured by RT-PCR
and standardized to EGFP mRNA levels. The graph shows mean ± standard error of the mean.
|
|
 |
DISCUSSION |
In these studies, we selected DNA oligonucleotides that bind to a
PAX4 protein that contains both the paired domain and the homeodomain.
Sequences of the selected oligonucleotides reveal the presence of two
linked sites: a consensus homeodomain binding site and a consensus
paired domain binding site. The relative position of these two sites
appears to be important, since in the more highly selected set of
oligonucleotides the spacing becomes fixed. Both PAX3 (28)
and Drosophila Prd (20) have also been found to
bind with high affinity to sequences that include both paired and
homeodomain binding sites. Interestingly, both on a natural site in the
even-skipped gene (9) and in sites selected by a
method similar to the one used here (20), the two binding sites for Prd are much closer than we found for PAX4, a difference of
approximately one helical turn. For both PAX4 and Prd, the paired and
homeodomain binding sites lie on opposite sides of the DNA.
The paired-like half of the bipartite DNA binding sequence for
Pax4 is similar but not identical to the consensus binding site for the PAX6 paired domain (7). The differences from
the PAX6 binding sequence could be due to the fact that we used a PAX4
protein containing both the paired and homeodomains for binding site
selection, while only the paired domain was used for determining the
PAX6 consensus sequences. The presence of both domains may alter the
specificity of each, as is the case for PAX3 (40). However,
differences in DNA binding specificity were confirmed by using a set of
paired domain binding sites from islet genes that demonstrate different
relative affinities for the full-length PAX4 and PAX6 proteins. The
presence and exact position of a linked homeodomain binding site could
potentially increase these differences. Furthermore, in the
intranuclear environment, within the context of chromatin structure and
other interacting proteins, the differences in binding affinities may
be further accentuated. Nonetheless, these studies suggest that PAX4
and PAX6 could potentially compete for some binding sites.
Our transient transfection experiments show that PAX4 can repress
transcription through a single isolated binding site linked to a
promoter or through a binding site in the context of an intact promoter. Furthermore, the experiments with GAL4 DBD fusion constructs mapped this repressor function predominantly to the region of PAX4 C
terminal to the paired domain. DNA binding is necessary for repression
but may be mediated by a heterologous DBD, such as the yeast GAL4 DBD,
in place of the paired and homeodomains. Transcriptional repression is
not unique within the PAX family, having been shown with PAX5 (5,
41) and the Drosophila paired domain family member,
Goosecoid (23). More recently, PAX6 has also been shown to
act as a transcriptional repressor, requiring both its paired domain
and homeodomain for this effect on
-crystallin genes in the lens
(6). This finding suggests that PAX6 repression may be due
to competition with transcriptional activators for DNA binding sites.
However, chimeric proteins consisting of the GAL4 DBD fused to various
regions of PAX6 show that some regions of PAX6 may also have modest
intrinsic repressor activity (38).
It is becoming increasingly recognized that some transcription factors
can act as either repressors or activators, depending on the cell type,
promoter context, and concentration of the factor (reviewed in
references 22, 27, and 30).
Indeed, within the PAX family, both PAX5 (BSAP) and PAX6 have recently
been shown to have such a dual function (6, 41). However, it
is important to note that in many studies, transcriptional effects are
assessed with DNA regulatory elements removed from their native
chromosomal locations, and using highly efficient vectors to express
the transcription factors, potentially resulting in supraphysiological
intranuclear concentrations of the factors. In addition, differential
splicing of the Pax4 mRNA within the region coding the
carboxy end of the protein has been detected and could affect the
balance of repressor/activator function. Thus, our studies do not
exclude the possibility that PAX4 can function as a transcriptional
activator in some contexts. In fact, Fujitani et al. (10)
have now shown that in certain cellular contexts, portions of PAX4 may
function as transcriptional activators.
Even if PAX4 can function as a transcriptional activator, it seems
unlikely that it is an important regulator of islet hormone gene
expression in vivo. Despite the high affinity of PAX4 for rInsIC2 and
the evidence that PAX4 may be expressed in early
cells
(35), insulin transcription persists in animals lacking PAX4
(35), and we have failed to detect activation of the insulin promoter by PAX4 in any context. PAX4 could potentially suppress insulin transcription in
cells, but PAX4 expression has not been
detected in
cells in vivo (35). Finally, its absence from adult islets rules out a role for PAX4 in maintaining the differentiated phenotype of the mature endocrine cells.
Could opposing effects on transcription by PAX4 and PAX6 modulate the
expression of target genes? While PAX4 and PAX6 could potentially
compete for some binding sites, their differences in binding
specificity suggest that the two proteins may have different target
genes. There also may be little or no overlap in the expression of the
two proteins since PAX4 is expressed in developing islet cells, and
PAX6 is expressed in the fully differentiated islet cells
(32).
On the other hand, the repressor function of PAX4 may play an essential
role during pancreatic development, by suppressing the
-cell gene
expression program and committing developing endocrine cells to the
- and
-cell lineages. The loss of PAX4 repression would explain
the marked increase in
cells and decrease in
and
cells seen
in animals homozygous for a targeted disruption of the Pax4
gene (35). Identifying the target genes for PAX4 could help
explain how the
cell phenotype is established and maintained.
 |
ACKNOWLEDGMENTS |
The first two authors contributed equally to this work.
We thank J. Wang, J. Leong, Y. Zhang, and J. Lau for technical
assistance, members of the Michael German laboratory for helpful comments and criticisms, and Gabriele Bergers for advice on PCR strategies for cloning Pax4. H.C.E. and S.B.S. are
recipients of Juvenile Diabetes Foundation International postdoctoral
fellowships. This work was supported by National Institutes of Health
grant DK41822.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Hormone Research
Institute, University of California, San Francisco, San Francisco, CA
94143-0534. Phone: (415) 476-9262. Fax: (415) 731-3612. E-mail: german{at}cgl.ucsf.edu.
Present address: Gastroenterology Department, Sir Charles Gairdner
Hospital, Nedlands, Western Australia 6009, Australia.
 |
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