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J. Biol. Chem., Vol. 277, Issue 37, 33901-33905, September 13, 2002
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From the Department of Molecular Biology and Biochemistry,
University of California, Irvine, California 92697-3900
Received for publication, March 4, 2002, and in revised form, June 24, 2002
Sterol regulatory element-binding proteins
(SREBPs) activate promoters for key genes of metabolism to keep pace
with the cellular demand for lipids. In each SREBP-regulated
promoter, at least one ubiquitous co-regulatory factor that binds to a
neighboring recognition site is also required for efficient gene
induction. Some of these putative co-regulatory proteins are
members of transcription factor families that all bind to the same DNA
sequence elements in vitro and are often expressed in the
same cells. These two observations have made it difficult to assign
specific and redundant functions to the unique members of a specific
gene family. We have used the chromatin immunoprecipitation
(ChIP) technique coupled with a transient complementation assay in
Drosophila SL2 cells to directly compare the ability of two
members of the CREB/ATF family to function as co-regulatory proteins
for SREBP-dependent activation of the HMG-CoA reductase
promoter. Results from both of these experimental systems demonstrate
that CREB is an efficient SREBP co-regulator but ATF-2 is not.
The sterol regulatory element-binding proteins
(SREBPs)1 are key
metabolically regulated transcription factors. They are translated as
large precursors, inserted into the membrane of the endoplasmic reticulum, and their amino-terminal domains are released into the
cytosol when the cellular lipid level falls. The signaling pathway that
results in SREBP release is not completely understood but requires two
sequential proteolytic events, the first of which is actively regulated
by sterols and fatty acids (1). The soluble amino-terminal fragment
contains the DNA binding and transcriptional stimulation functions, and
once it is released from the membrane it enters the nucleus to increase
expression of various genes that are important for cellular lipid
homeostasis (2, 3).
SREBPs are weak activators of transcription by themselves, and they
require co-regulatory transcription factors that bind nearby DNA
sequences to efficiently stimulate gene expression (3). The identity
and combinations of co-regulatory factors and the number and
arrangements of the SREBP sites are promoter-specific. These
differences likely provide a framework for gene-specific regulatory
responses to the different SREBP isoforms and to specific cellular
regulatory cues. For example, in the promoter for the low density
lipoprotein (LDL) receptor, there is a single SREBP site, and Sp1 is
the lone SREBP co-regulatory factor and binds to two separate sites
(4). In the promoters for 3-hydroxy-3-methylglutaryl-coenzyme A
(HMG-CoA) synthase, farnesyl diphosphate (FPP) synthase, and squalene
synthase there are multiple SREBP sites, and at least one of the
co-regulators is the CCAAT-binding factor/nuclear factor-Y (CBF/NF-Y)
(5-7). HMG-CoA synthase additionally requires a member of the CREB/ATF
family (8).
In previous studies, we have shown separate DNA sites that bind
CBF/NF-Y, and members of the CREB/ATF family are both required for
expression from the HMG-CoA reductase promoter (9). CREB sites were
originally identified as cis-acting elements that confer transcriptional regulation in response to elevated cAMP levels (10-12). In the somatostatin promoter it was shown that cAMP
responsiveness was mediated through the basic-leucine zipper containing
the transcription factor termed cAMP response element-binding protein
or CREB (13). Protein kinase A phosphorylates CREB in response to
increased cellular cAMP, which allows it to interact efficiently with
the transcriptional co-activator protein called CREB-binding protein (CBP) to stimulate transcription of cAMP target genes (14, 15). Several
related CRE-binding proteins have been identified and cloned (16), and
together they comprise the CREB/ATF family of transcription factors.
Individual members of this family bind to CREs present in numerous
eukaryotic promoters and activate transcription in response to various
cellular signals (17). Major questions concerning this and any other
related families of genes should determine how much overlap there is in
function and identify specific physiological roles for the individual proteins.
In addition to mutagenesis studies that showed there is a CRE-like
element in the HMG-CoA reductase promoter, we have used the chromatin
immunoprecipitation technique (ChIP) to demonstrate that both CREB and
CBF/NF-Y are both recruited to the HMG-CoA reductase promoter by SREBP
when cells are deprived of exogenous cholesterol (18). Taken together,
our previous studies (9, 18) indicate that both CBF/NF-Y and
CREB are important SREBP co-regulators for HMG-CoA reductase (9, 18).
However, because CREB is a member of the CREB/ATF family, it was
important to determine whether individual members of this family can
substitute for CREB in the sterol regulatory response mediated by
SREBP. In the current report we utilize the ChIP method to provide
evidence that although CREB is recruited to the HMG-CoA reductase
promoter efficiently by SREBP activation, binding of another member of
the family, ATF-2, is not altered. We also provide evidence from direct
promoter activation studies in Drosophila SL2 cells that
CREB is an efficient SREBP co-regulator and efficiently stimulates the
HMG-CoA reductase promoter along with SREBP NF-Y. In contrast, ATF-2 is
unable to substitute for CREB in this independent assay system as well.
Cells and Media--
The CHO-7 and SL2 cell lines were cultured
as described previously (4, 18). Lipoprotein-deficient serum was
prepared by ultracentrifugation of newborn bovine serum as described
previously (19). Cholesterol and 25-OH cholesterol were obtained from
Steraloids Inc., and stock solutions were dissolved in absolute ethanol.
Cell Culture--
Stock flasks of CHO-7 cells (20) were grown in
a 50/50 mixture of Hams F12 and Dulbecco's modified essential medium
(DMEM) (Irvine Scientific) containing 10% (v/v) fetal bovine serum at 37 °C and 5% CO2. Tissue culture dishes (15 cm) were
plated at 500,000 cells/dish on day 0 in the above medium. On day 1, the dishes were rinsed twice with 1× phosphate buffered saline, and half of the dishes were fed with either induced media (HamsF12/DMEM containing lipoprotein-depleted serum instead of FBS) or suppressed media (Hams F12/DMEM containing lipoprotein-depleted serum with 10 µg/ml cholesterol and 1 µg/ml of 25-OH cholesterol). Cells were
processed for the ChIP procedure after an additional 24 h incubation.
Chromatin Immunoprecipitation Assay--
We used a modification
of the procedure of Farnham and colleagues (21) as described previously
(18). Dishes of CHO-7 cells were placed in a fume hood and treated with
formaldehyde (final concentration of 1% v/v) followed by a room
temperature incubation for 8 min. The reaction was quenched by the
addition of glycine (final concentration of 125 mM), and
the dishes were incubated for an additional 5 min at room temperature.
Medium was removed followed by 3 rinses with cold 1× PBS. Samples were
then subjected to the protocol described in our previous report (18).
The CREB and ATF-2 antibodies were from Santa Cruz Biotechnology
(sc-186 and sc-187, respectively). After immunoprecipitation, DNA was extracted, and samples were ultimately resuspended in 50 µl of sterile H2O and 2-4 µl were used in each polymerase
chain reaction (PCR).
Standard PCR reactions for hamster HMG-CoA reductase promoter were
performed with 32P-kinased oligonucleotides and AmpliTaq
Gold (PerkinElmer Life Sciences). The primers for HMG-CoA reductase
were designed to hybridize and amplify a ~230-bp product encompassing
the region displayed in Fig.
1A. To provide reactions that
were in the linear dose response for the individual samples, we
performed test PCR reactions and varied the number of cycles to obtain
conditions where the signal intensity was linear with respect to amount
of input as described previously (18).
Transient Transfection Assay in Drosophila SL2
Cells--
Drosophila SL2 cells were cultured in Shields
and Sang insect medium (Sigma) containing 10% heat inactivated fetal
bovine serum and were seeded at 480,000 cells/well in six-well dishes on day 0. On day 1, cells were transfected by the calcium phosphate co-precipitation method with each dish receiving 2
On day 3, cells were harvested and luciferase and SDS-PAGE and Immunoblot Analysis--
SL-2 nuclear extracts,
CHO-7 total chromatin extracts (equivalent amounts normalized for
A260), or equivalent amounts of material precipitated by the ATF-2 antibody were analyzed by SDS-PAGE and immunoblotting with the antibodies indicated in the figure legends. The
HSV antibody (from Novagen, catalogue no. 69171) and the IgG 7D4
monoclonal antibody directed against hamster SREBP-2 (obtained from
ATCC) were used. The blots were developed with the ECL kit from Pierce.
Protein-Protein Interaction Assays--
The coding regions for
CREB or ATF-2 were inserted into pGEX2 (Amersham Biosciences) and
expressed in and purified from E. coli as described (8).
Recombinant SREBP-1a (amino acids 1-490) was incubated with purified
GST-CREB or GST-ATF-2, and the mixtures were bound to glutathione
agarose beads that were subsequently washed and analyzed for
specifically bound material by an immunoblotting protocol as described
(8).
CREB is a member of a transcription factor family where individual
proteins are all highly similar in their basic and leucine zipper DNA
binding/dimerization domains. Even though they all bind the same
cis-acting consensus sequence, the affinities of the different homo-
and heterodimeric combinations vary for different CRE elements (23,
24). Additionally, they do not all respond identically to cellular
signaling pathways. For example, ATF-2 activates transcription along
with the adenovirus E1a protein (25), whereas both ATF-1 and CREB
stimulate genes in response to changes in cAMP levels (14, 26). As more
is understood about the functions of the various CREB/ATF proteins, the
reasons for these differences will be better understood.
Using the ChIP technique we previously demonstrated (18)
that CREB was recruited to the HMG-CoA reductase CRE site when SREBP
nuclear localization was induced by sterol depletion. We wanted to
determine whether other members of the family could participate in this
key nutritional response. In the current studies we used an antibody to
the ATF-2 protein to evaluate its binding to the HMG-CoA reductase CRE
site in response to sterol deprivation and SREBP activation. Chromatin
extracts were prepared from two sets of dishes of CHO-7 cells. One set
was cultured in medium containing lipoprotein depleted serum to
stimulate SREBP nuclear localization, and the other set received LPDS
with cholesterol and 25-OH cholesterol added back to keep SREBPs
tethered to the endoplasmic reticulum membrane and sequestered away
from their target genes.
The chromatin was then processed by our standard ChIP protocol followed
by a PCR reaction with primers that amplify the HMG-CoA reductase
promoter region encompassing the CRE site (Fig. 1A). As a
control, we showed there were equivalent levels of HMG-CoA reductase
promoter DNA in the starting chromatin samples (Fig. 1B,
lanes 1 and 2). When equal amounts of chromatin
from the two sets of dishes were incubated with an antibody against
ATF-2 prior to the immunoprecipitation and PCR reaction, there were
also equal levels of HMG-CoA reductase promoter DNA present in both
samples (lanes 3 and 4). However, when the CREB
antibody was used there was a significantly higher level of HMG-CoA
reductase promoter DNA present in the sample prepared from cells
cultured under sterol depleted conditions versus the sterol
treated set (lanes 7 and 8).
An immunoblotting analysis demonstrated that the mature SREBP-2
transcription factor was properly regulated by the sterol depletion
protocol (Fig. 2A). Additional
immunoblotting experiments presented in Fig. 2, B and
C, demonstrated that equal amounts of protein for both CREB
and ATF-2 were present in the starting chromatin preparations
(lanes 1 and 2 of Fig. 2, B and
C). Also, the ATF-2 protein was quantitatively removed, and
equal amounts were recovered by the immunoprecipitation protocol (Fig.
2C, compare lanes 3-6). We could not perform an
immunoblot to determine whether CREB was quantitatively precipitated
because the CREB protein migrates too close to an immunoglobulin
protein subunit from the immunoprecipitation reaction, which reacts
with the secondary antibody and obscures the CREB band on the resulting
gel.
These ChIP results along with the experiments from our previous study
strongly suggest that CREB is an efficient co-regulatory factor for
SREBP in the HMG-CoA reductase promoter and that the ATF-2 protein does
not participate in this response. To evaluate whether there is a
difference in the ability of CREB and ATF-2 to directly stimulate
transcription from the HMG-CoA reductase promoter, we used the
transfection-complementation system in Drosophila SL2 cells
that we have used extensively in previous reports. These cells do not
express functional equivalents of several mammalian transcriptional
regulatory proteins, including Sp1 (27). However, expression from
mammalian promoters can be evaluated when expression plasmids for a
critical missing regulatory protein(s) are included in the transfection
protocol. Therefore, the SL2 transfection assay provides a background
for evaluating mammalian promoters and their missing trans-acting
regulatory proteins in an intact cell system (27). In fact, we have
used SL2 cells to demonstrate that SREBP activation of the HMG-CoA
synthase promoter requires both NF-Y and CREB (8).
When we transfected SL2 cells with the HMG-CoA reductase promoter
reporter construct alone or with an SREBP expression construct, a low
level of promoter activity was observed (Fig.
3, filled triangle at
abscissa origin). This is consistent with previous studies (4), indicating that SREBP is a very weak activator by
itself. When increasing amounts of either ATF or CREB expression vectors were included in addition to SREBP, a similar low level of
activation was still observed (Fig. 3, open symbols). When expression constructs for the three subunits of NF-Y were included along with the SREBP expression construct the promoter was activated about 7-fold. When the CREB or ATF-2 constructs were included on top of
the NF-Y plasmids, a robust activation was observed for CREB (Fig. 3,
filled squares) but ATF-2 failed to induce expression above
the level achieved by SREBP and NF-Y alone (Fig. 3, filled circles). When SREBP was omitted from the transfection experiment, there was no activation by NF-Y and CREB
alone.2
A Role for Cyclic AMP Response Element-binding Protein (CREB) but
Not the Highly Similar ATF-2 Protein in Sterol Regulation of the
Promoter for 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase*
§,
,
![]()
ABSTRACT
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
![]()
INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
![]()
MATERIALS AND METHODS
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES

View larger version (51K):
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Fig. 1.
Chromatin immunoprecipitation analysis of
CREB and ATF-2 binding to HMG-CoA reductase promoter in CHO cells
cultured in the absence and presence of regulatory sterols.
A, a schematic representation of the native HMG-CoA
reductase promoter with the heterogeneous transcription initiation
sites, TATA element, and binding sites for SREBPs and NF-Y and CREB/ATF
is shown. B, an autoradiogram of a polyacrylamide
gel that displays the results of the PCR for the HMG-CoA reductase
promoter is shown. The primers were designed to hybridize just upstream
of the NF-Y site and just downstream of the ATF/CREB site as shown in
A. The input chromatin was analyzed in lanes 1 and 2 (1 µl of a 1:300 dilution), and 3 µl of each
resultant immunoprecipitation with the indicated antibodies were also
analyzed as indicated. No primary antibody was used for the reactions
in lanes 5-6.
g of each test
plasmid, 10.75
g of salmon sperm DNA, and 1
g of the control plasmid pPAC
-galactosidase containing the coding region of the Escherichia coli
-galactosidase gene driven by the
Drosophila actin 5C promoter. The pPAC SREBP-1a constructs
used for activation studies in SL2 cells contain the coding regions of
the Sp1 or SREBP-1a (amino acids 1-490) gene under the control of the
Drosophila actin 5C promoter and was described before (4).
The pPAC NF-Y constructs containing the coding regions for the 3 individual CBF/NF-Y subunits (A, B, and C) were described previously
(22). The coding sequence for an epitope
(Gln-Pro-Glu-Leu-Ala-Pro-Glu-Asp-Pro-Glu-Asp) from the herpes virus
type I glycoprotein D protein was inserted at the amino terminus of
pPAC vectors that encode the full coding sequence of human ATF-2 or
CREB.
-galactosidase
activity were measured in cell extracts as described previously (22).
The expression levels for CREB and ATF-2 proteins were normalized using
the common HSV epitope for comparison. Briefly, transfection
experiments were performed as above with differing amounts of the
HSV-CREB and HSV-ATF-2 vectors and a constant amount of the pPAC
-galactosidase control plasmid. Protein extracts from the
transfected cells were first normalized for transfection efficiency by
measuring the
-galactosidase activity of individual extracts, and
normalized amounts were analyzed by immunoblotting as described below.
![]()
RESULTS
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES

View larger version (34K):
[in a new window]
Fig. 2.
Immunoblot characterization of chromatin
extracts. Equivalent amounts (A260) of
chromatin extracts from CHO-7 cells cultured in the absence
(I) or presence (S) of cholesterol and 25-OH
cholesterol were processed for immunoblotting using the indicated
antibodies. The chromatin samples before immunoprecipitation
(input) were analyzed for SREBP-2, CREB, and ATF-2
(lanes 1-2 of each panel). The chromatin was
subjected to immunoprecipitation with an antibody to ATF-2, and the
material remaining in the supernatant (panel C, Sup.,
lanes 3-4) and equal aliquots of the total immunoprecipitation
pellets from both samples (panel C, IP,
lanes 5-6) were analyzed. The migration positions for the
precursor (P) and mature (M) forms of SREBP-2 are
indicated in A. The migration positions for CREB and ATF-2
are indicated by arrows at the right in
panels B and C, respectively. The dark
staining band lower in the gel in C, lanes 5 and 6, corresponds to immunoreaction with a subunit of the
antibody used for the immunoprecipitation reaction.

View larger version (20K):
[in a new window]
Fig. 3.
Activation of the HMG-CoA reductase promoter
in Drosophila SL2 cells. SL2 cells were
transfected with the wild-type HMG-CoA reductase reporter construct
along with the pPAC
-galactosidase construct as an internal control
for specificity and transfection efficiency. A pPAC vector expressing
amino acids 1-490 of SREBP-1a was included at 1 ng, and it resulted in
a basal level of activation that was set at 1.0. The pPAC HSV-ATF-2
(circles) or pPAC HSV-CREB (squares) plasmids
were included at increasing concentrations as indicated on the
abscissa. Where indicated (closed symbols), 3 ng
of pPAC constructs encoding each of the three NF-Y/CBF subunits; A, B,
and C were also added to the transfection precipitate. DNA
transfections, luciferase, and
-galactosidase assays were performed
as described previously (22) and under "Materials and Methods."
Data represent average values from a typical experiment performed in
duplicate for each sample.
To evaluate whether the low activation mediated by ATF-2 could be
explained by a lower level of protein accumulation relative to CREB, we
evaluated expression of the two proteins after transfection into SL2
cells. We had inserted the coding sequence for an HSV glycoprotein D
epitope at the extreme amino terminus of the two expression vectors so
that we could compare protein expression levels using the same
antibody. When protein extracts from the transfected SL2 cells were
analyzed, both CREB and ATF-2 were expressed at similar levels (Fig.
4).
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Taken together with the results from the ChIP experiments of Fig. 1, these transfection results provide strong support for the conclusion that CREB is recruited to the native HMG-CoA reductase promoter and efficiently activates the isolated promoter in SL2 cells, and both are dependent on SREBP. However, ATF-2 is neither recruited to the native HMG-CoA reductase promoter by SREP nor is it an efficient co-regulator for SREBP activation of the cloned promoter in the SL2 cell system.
In previous studies (8), we showed that CREB interacts with
SREBP in solution and this interaction is likely part of the mechanism
for the synergistic activation of transcription of the HMG-CoA synthase
promoter by these two proteins (8). To evaluate whether ATF-2 was also
capable of interacting with SREBP we compared the ability of GST fusion
proteins of CREB and ATF-2 to bind to SREBP in solution (Fig.
5). The results demonstrate that under conditions where CREB binds SREBP efficiently, ATF-2 binding was minimal (compare lanes 3 and 4). Thus, the lack
of efficient interaction between SREBP and ATF-2 is likely part of the
reason why it is not recruited to the HMG-CoA reductase promoter by
SREBP activation.
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DISCUSSION |
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All CREB/ATF family proteins are highly similar in their basic and leucine zipper regions, and they bind the same cis-acting consensus sequence. Therefore, it is possible that individual members can have both overlapping and unique roles in specific and diverse biological processes. In the current studies, we tested the ability of ATF-2 to substitute for CREB in activation of the HMG-CoA reductase promoter by SREBPs. Using antibodies to each protein in chromatin immunoprecipitation studies, we showed that SREBP activation by sterol depletion resulted in efficient recruitment of CREB to the HMG-CoA reductase promoter, but ATF-2 binding was unaltered by this nutritional challenge. We did detect the HMG-CoA reductase promoter DNA in the chromatin samples that were precipitated with the ATF-2 antibody; however, the level was unaltered by the sterol manipulation protocol. These results indicate that ATF-2 may bind and activate the HMG-CoA reductase promoter at basal levels, but it is not recruited to the promoter by SREBP, and thus it cannot substitute for CREB as an important SREBP co-regulatory protein.
The result of our co-transfection studies in Drosophila SL2 cells supports and significantly extends this conclusion as well. The data in Fig. 3 shows that SREBP activates the HMG-CoA reductase promoter in cooperation with NF-Y and CREB, but when expressed at similar levels, ATF-2 cannot substitute for CREB.
Because CREB and ATF-2 bind to the same DNA sequence in vitro, it was important to investigate the mechanism for the differential recruitment of CREB to the HMG-CoA reductase promoter measured in the chromatin immunoprecipitation analysis. In Fig. 5, we show that CREB but not ATF-2 was capable of interacting with SREBP in solution in the absence of DNA. Thus, consistent results from three separate experimental approaches support our conclusions and provide at least a partial mechanistic understanding for the selectivity. It was previously shown (28) that the somatostatin promoter is stimulated in a cell type-specific manner by cAMP through the action of CREB. Importantly, these authors showed that ATF-2 was also unable to substitute for CREB in this response.
Our earlier mutational studies of the HMG-CoA reductase promoter showed that both the CRE and NF-Y sites were simultaneously required for normal sterol-dependent regulation (9). The data from Fig. 3 are also consistent with this conclusion because both CREB and NF-Y were required along with SREBP for efficient activation. These observations are similar to our previous findings for the HMG-CoA synthase promoter where both CREB and CBF/NF-Y were required for efficient activation by SREBP. Thus, two early genes that control simple carbon flux into the cholesterol/isoprenoid biosynthetic pathway require a similar set of SREBP co-regulatory proteins. This provides a molecular strategy to ensure the common early steps of the multivalent cholesterol/isoprenoid pathway are tightly co-regulated (29).
The chromatin immunoprecipitation method is a useful procedure for
analyzing changes in the binding of specific regulatory proteins to
their putative target elements in native chromatin in response to
change in the intracellular environment. With the availability of
antibodies with suitable specificity, ChIP can be used to effectively
analyze the functional roles of highly similar proteins or even
differentially modified versions of the same transcriptional regulatory
protein that bind to very similar or identical DNA sites in
vitro.
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FOOTNOTES |
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* This work was supported in part by Grant HL48044 from the National Institutes of Health and Grant 0150231N from the American Heart Association.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.
Both authors contributed equally to this work.
§ Recipients of undergraduate fellowships from the Undergraduate Research Opportunities Program at the University of California, Irvine.
¶ To whom correspondence should be addressed: Dept. of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900. Tel.: 949-824-2979; Fax: 949-824-8551.
Published, JBC Papers in Press, July 10, 2002, DOI 10.1074/jbc.M202135200
2 T. Ngo and T. F. Osborne, unpublished data.
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ABBREVIATIONS |
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The abbreviations used are: SREBP, sterol regulatory element-binding protein; LDL, low density lipoprotein; HMG-CoA, 3-hydroxy-3-methylglutaryl coenzyme A; CREB, cyclic AMP response element-binding protein; ATF-2, activating transcription factor-2; CBF, CAAT-binding factor; NF-Y, nuclear factor-Y; 25-OH cholesterol, 25-hydroxycholesterol; ChIP, chromatin immunoprecipitation; HSV, herpes simplex virus.
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