| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Braman Family Breast Cancer Institute (J.S., Z.N., J.M.S.), University of Miami Sylvester Comprehensive Cancer Center, and Department of Biochemistry and Molecular Biology (Z.N., J.M.S.), University of Miami Miller School of Medicine, Miami, Florida 33136
Address correspondence to: Jun Sun or Joyce Slingerland, Braman Family Breast Cancer Institute, 1580 NW 10 Avenue (M-877), University of Miami, Miami, Florida 33136. E-mail: jsun{at}med.miami.edu or jslingerland{at}med.miami.edu.
| ABSTRACT |
|---|
|
|
|---|
| INTRODUCTION |
|---|
|
|
|---|
(3, 4) and ERß (5, 6, 7). They share similar domain organization and have overlapping but nonidentical tissue distributions (8, 9). Here we focus on ER
and refer hereafter to ER
as ER. The ligand-binding domain (LBD), located at the C terminus of the ER, binds to estrogen and is the target of selective ER modulators such as tamoxifen (10). The DNA-binding domain, located in the central region of the receptor, binds to the estrogen response elements (EREs) in ER target genes (11, 12). Upon ligand binding, the LBD of ER undergoes a structural change to provide a binding surface for cofactors (13). The p160 coactivator family includes three homologous steroid receptor coactivator (SRC) molecules, SRC-1, SRC-2, and SRC-3. They are recruited to a hydrophobic groove formed on the surface of the agonist-bound LBD through direct contact of their LXXLL motifs. ER binding to antagonists prevents this interaction (14). Although p160 coactivators have been shown to possess intrinsic histone acetyltransferase (HAT) activity, they also recruit other chromatin-modifying proteins including cAMP response element-binding protein-binding protein (CBP)/p300, p300/CBP-associated factor (pCAF), coactivator-associated arginine methyltransferase-1 (CARM1), and protein arginine N-methyltransferase (PRMT) (15). The combinatorial modification of histones dictates the modulation of gene expression (16). Histone acetylation occurs in response to hormone and serves to open the chromatin structure, facilitating receptor-coactivator complex assembly at hormone response elements. Recent evidence suggests that ER and its cofactors cycle on and off the promoter of target genes (17, 18). However, the mechanisms whereby the ER interacts with the basic transcriptional machinery to activate gene transcription are not completely understood.
One mechanism whereby ER activates gene transcription is through direct ER binding to EREs in target gene promoters (19). The ERE consensus sequence, first identified in the Xenopus A2 gene promoter, is a 5-bp inverted repeat separated by any three base pairs, GGTCAnnnTGACC, to which ER binds as a symmetrical dimer (20). Most of the well studied EREs from estrogen-responsive genes are located at the proximal promoter regions, deviate from the consensus sequence by one to three base pairs, and have reduced binding affinity for ER (19).
Microarray experiments have been used to identify ER target genes on a global scale (21). However, this type of assay does not distinguish genes that are regulated by direct ER binding to EREs from those activated by indirect tethering of ER to target promoters via other transcription factors. With the completion of the human genome project, in silico genome-wide screening has been used to identify EREs in the ER target genes with focus on the regions close to the transcriptional start sites (22, 23). Enhancers, however, can be located much farther way from transcriptional start sites, from tens of kilobases up to a megabase (24).
GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an estrogen-regulated gene expressed in breast cancer in a subtractive hybridization screen in MCF-7 cells. The three cDNAs of GREB1 (GREB1a, GREB1b, and GREB1c) have distinct 5'-untranslated regions but share extensive coding sequences, indicating different promoter usage (25). In our search for EREs, we found three consensus ERE motifs that are located within a 20-kb region on human chromosome 2, upstream of the GREB1 gene. In this study, we analyzed GREB1 gene expression and employed chromatin immunoprecipitation (ChIP) assays to monitor the binding of ER, SRC-3, and RNA polymerase II (Pol II) and the level of histone H3 acetylation at the GREB1 locus in response to 17ß-estradiol (E2) or 4-hydroxyl tamoxifen (OHT) in MCF-7 breast cancer cells. We found that E2 stimulates ER, SRC-3, and Pol II binding to all three EREs within the distal GREB1 promoter region. Our data suggest that coordinated ER binding to all three distal EREs may contribute to the regulation of estrogen-induced GREB1 gene expression. These data support a model in which the coordinated binding of ER to distal sites interacts with Pol II to activate gene transcription from core promoters located at a considerable distance.
| RESULTS |
|---|
|
|
|---|
|
|
The GREB1 EREs Synergistically Mediate E2-Induced Transcription in Vitro
Although GREB1 is a known ER target gene, the relative abilities of its different ERE motifs to drive estrogen-induced transcription have not been demonstrated. The ERE1 motif is 1.6 kb upstream of the transcription start site for GREB1a. To demonstrate ERE1-mediated estrogen-responsive transcription via the GREB1a promoter, a 1.7-kb fragment that included ERE1 and the GREB1a promoter region was cloned into the pGL3-basic reporter plasmid. Because ERE2 and ERE3 are too far apart to clone as a single fragment, we synthesized 50-bp oligos centered on each of the ERE2 and ERE3 motifs and including their surrounding sequences, respectively, to prepare reporter constructs. Constructs containing ERE1 alone, ERE1 and ERE2, and all three EREs were used in reported assays. As controls, reporter constructs containing mutant ERE motifs were also prepared (see Fig. 3A
for schematics of these reporter constructs). These reporter constructs were transfected into MCF-7 cells, which were then treated with either E2 or OHT for 24 h. Luciferase activity was measured, and values were corrected for transfection efficiency using renilla luciferase activity from a cotransfected reference plasmid. For the construct bearing the ERE1 motif alone, a 2.2-fold increase in luciferase activity was observed when treated with E2 over the basal level, whereas OHT did not increase luciferase activity. Mutation of the ERE1 motif in the reporter construct abolished E2-induced luciferase activity. Thus, ERE1 is capable of mediating estrogen-responsive GREB1a promoter activity in vitro. When ERE2 was inserted upstream of ERE1, E2 treatment increased luciferase activity by approximately 36-fold over its basal level. For the reporter with all three ERE motifs, E2-induced luciferase activity went up to about 170-fold over its basal level. These data indicate that all three of the EREs are functional and can act synergistically to module E2-dependent ER activity in these assays. There was no E2-induced luciferase activity from reporters with mutant ERE motifs (Fig. 3B
).
|
|
Coactivator SRC-3 Associates with Three ERE Motifs
To test further E2 regulation of the GREB1 promoters, we tested the association of the p160 coactivator, SRC-3, using quantitative ChIP assays, with regions at the GREB1 locus after E2 treatment. E2, but not OHT, induced SRC-3 binding to all three ERE motifs but not to the GREB1b or GREB1c core promoters (Fig. 5A
). There was also a low level of SRC-3 association with all three ERE motifs in the absence of E2. As was the case for ER binding, both ligand-dependent and ligand-independent SRC-3 binding to ERE1 was greater than to either ERE2 or ERE3. The estrogen-induced binding of SRC-3 to ERE2 was less than that to ERE3. This might reflect a conformational constraint at ERE2, because SRC-3 association at ERE2 was also lower in the unliganded state.
|
Of the three GREB1 core promoters, the greatest E2-induced histone H3 acetylation was seen at GREB1b and GREB1c promoters. The reduced GREB1a promoter acetylation may reflect its weaker promoter activity. The histone H3 acetylation of a coding region assayed was much lower than at the promoters (Fig. 5C
). In contrast, OHT did not increase the histone H3 acetylation at any region assayed within the GREB1 gene locus.
Pol II Binds to GREB1 Transcription Start Sites and to All Three ERE Motifs
The core promoter is classically defined as the region around the transcription start site where RNA polymerase II (Pol II) initiates transcription. ChIP assay was used to monitor Pol II binding at ERE-containing regions and at the regions containing GREB1 transcription start sites (Fig. 6A
). As expected, E2 induced strong Pol II binding to the GREB1b and GREB1c core promoters and very weak binding to the GREB1a promoter, consistent with the observed strength of each promoter based on the extent of E2 induction of their respective transcripts. ChIP failed to capture the transient Pol II interaction with a GREB1 coding region that would occur during active gene transcription.
|
In contrast to our observation with ER, which bound only ERE sites, Pol II bound to both the EREs and the core promoters. To confirm that the Pol II complex bound to the core promoters differed from the Pol II complex at the ERE sites, we used ChIP and re-ChIP assay to test Pol II association with ER. In the ER/Pol II ChIP assay where the antibody to ER was used in the first ChIP and the antibody to Pol II was used in the re-ChIP, we detected E2-induced Pol II association with ER only at the EREs but not at the GREB1b and GREB1c core promoters (data shown for ER-Pol II binding to the EREs in Fig. 6B
). Because there was no positive amplification from ChIP assays with the GREB1b and -c core promoters, they were not plotted (Fig. 6B
). Similarly, in the Pol II/ER ChIP assay where the antibody to Pol II was used in the first ChIP and the antibody to ER was used in the re-ChIP, E2-induced ER/Pol II complex was detected only at the EREs (Fig. 6C
) but not at the GREB1b and GREB1c core promoters. The latter were not plotted due to the negative real-time PCR. Thus, Pol II bound to the EREs was in a different complex from that at the core promoters.
| DISCUSSION |
|---|
|
|
|---|
Through an in silico search for the consensus EREs in the whole human genome, we found a 20-kb region containing three consensus ERE motifs upstream of the human GREB1 transcription start sites. Here we investigated their potential involvement in E2-stimulated GREB1 gene expression. Estrogen stimulated ER binding to each of the three GREB1 EREs, and the ER cycled on and off in a synchronized fashion. In addition, the coactivator SRC-3 and Pol II were brought to the ERE sites with activated ER, accompanied by long-range histone acetylation centered on the ERE motifs and core promoters. Among the three previously identified GREB1 cDNA transcripts, induction of GREB1b and GREB1c transcripts by E2 was more robust than that of GREB1a in MCF-7 cells. Thus, the GREB1b and GREB1c core promoters, although more distant from the ERE sites, appear to be activated to a greater extent by E2 than the GREB1a core promoter.
Other reports that identified functional EREs based on in silico screening have mainly focused on regions proximal to transcription start sites. ER binding to both the proximal and middle EREs of the human GREB1 gene was reported by others during the course of the present study (22, 23). Lin et al. (23) characterized ER binding only to the proximal ERE using ChIP. Bourdeau et al. (22) assayed ER binding at all the three ERE sites in a simple nonquantitative PCR assay but initially observed only ER:ERE1 and ER:ERE2 interaction and failed to demonstrated ER binding to the most distal ERE3 site. However, at a recent meeting, this group reported ER binding to all three ERE motifs at the GREB1 locus (27). Our study extends previous observations by using quantitative analysis to demonstrate cyclic dynamics of E2-stimulated ER binding at all three ERE sites and by demonstrating coactivator and Pol II recruitment to these EREs. Our data suggest that all three EREs of the GREB1 promoter may contribute to E2-stimulated GREB1 expression. The notion that all three distantly spaced ERE motifs may contribute to E2-dependent ER regulation of the GREB1 gene expression is supported by their phylogenetic conservation. All three consensus ERE motifs within the GREB1 locus are conserved in chimpanzees and canines.
There is prior evidence that nuclear receptor target gene promoters contain multiple functional receptor binding sites (28). In the Xenopus vitellogenin B1 and B2 genes, two copies of adjacent nonconsensus EREs act synergistically to activate transcription induced by estrogen (29). Based on this observation, ER reporter plasmids have made use of multiple consensus EREs to achieve synergistic activation by ER (30). Earlier studies identified many ER target genes that contain functional EREs, most of which were located close to the core promoters and are nonconsensus (19). Nonconsensus ERE motifs usually deviate one to three nucleotides from the consensus and have been shown to have lower ER binding affinities in vitro compared with the consensus ERE. ER binding to EREs in vivo appears to be more complicated. Although all three GREB1 locus EREs are perfect consensus motifs, they exhibit different degrees of ER, coactivator, and Pol II binding, with ERE1 used more frequently than ERE2 and ERE3. Moreover, we have observed that not all the consensus ERE motifs in the genome are capable of binding to ER in vivo when cells are treated with E2 (Sun, J., and J. M. Slingerland, unpublished data). Thus, other factors may regulate the ER-ERE interaction and its functional importance in vivo. Interestingly, the GREB1 gene locus contains multiple FOXA1 binding motifs located close to all three ERE motifs. Thus, this forkhead factor may play a role to modulate ER-ERE interaction and estrogen-induced GREB1 gene expression (31, 32).
ER is thought to stimulate the assembly of an initiation complex and regulate the frequency at which new Pol II molecules reinitiate transcription (33). In the present study, we found that E2 induced Pol II association not only at the GREB1 core promoters but also at the distant ERE sites. In contrast, both the ER and the coactivator SRC-3 associated only with the ERE sites and not with the core promoters. The re-ChIP studies also confirmed that Pol II complexes at the core promoters and at the EREs are distinct, with the former lacking and the latter containing associated ER. This is in agreement with other studies that reported androgen-induced Pol II association with both the PSA promoter and enhancer regions. The androgen receptor and Pol II were present together at the enhancer but not at the promoter (34, 35). Similar findings were also recently reported by Carroll et al. (31) for the ER target gene XBP-1.
We observed E2-induced histone hyperacetylation at the GREB1 core promoters and at distant upstream regions centered on all of the three ERE motifs. Our data indicate strong association of Pol II with these enhancers. Together with recent findings in other gene contexts (31, 36, 37), these data support a looping model in which ER binding may stimulate GREB1 gene activation by bringing combinations of either two or three enhancer regions and core promoters transiently into close proximity. This would facilitate transfer of Pol II from the enhancer complexes to the basal transcription machinery at the core promoters and increase the potential for fine tuning of promoter activity. This model of GREB1 activation by ER is supported by a recent analysis of ER binding in the human genome, in which a majority of ER binding sites were located at significant distances, with many over 100 kb from transcription start sites of ER target genes (31, 38). Moreover, multiple distal ER binding sites were present in a number of ER target genes. Thus, activation by coordinate ER binding at multiple distal enhancer regions within a single gene, as we have observed for GREB1, may be a common feature of ER-regulated genes.
| MATERIALS AND METHODS |
|---|
|
|
|---|
Cell Culture
MCF-7, T47D, ZR-75, and MDA-MB-231 cells were maintained in Improved MEM (IMEM) (Invitrogen, Carlsbad, CA) supplemented with 5% fetal bovine serum in a humidified incubator with 5% CO2. Before ligand treatment, the cells were maintained in phenol red-free IMEM supplemented with 5% charcoal dextran-treated fetal bovine serum for 3 d.
RNA Extraction and Real-Time RT-PCR
The total RNA from MCF-7 cells was isolated using TRIzol reagent (Invitrogen) according to the manufacturers protocol. cDNA was synthesized from 1 µg total RNA as template using iScript cDNA synthesis kit (Bio-Rad, Hercules, CA). Real-time PCR was performed using an icycleriQ PCR detection system (Bio-Rad) using 10 ng cDNA sample in iQ SyberGreen supermix (Bio-Rad). PCR conditions were 95 C for 30 sec, followed by 60 C for 60 sec for 40 cycles. The GREB1 cDNA was amplified with the following primers: forward 5'-ATCAGCTGCTCGGACTTGCTG-3' and reverse 5'-TGAGCTCCGGTCCTGACAGATG-3'. For amplification of GREB1 cDNA derived from each of three transcriptional start sites, we used promoter-specific forward primers (5'-TGTGGAAGGACATGGCTTTTA-3' for GREB1a, 5'-GGCTTTGTTTGGAGCAGAAAA-3' for GREB1b, and 5'-GTCTGTGGAGTGCCTGAAGTG-3' for GREB1c) and one reverse primer (5'-GTCTGTGGAGTGCCTGAAGTG-3') common for all three transcripts. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which was used as an internal control, was amplified with the following primers: forward 5'-GAAGGTGAAGGTCGGAGTC-3' and reverse 5'-GAAGATGGTGATGGGATTTC-3'. The comparative threshold cycle method was used to determine the relative expression level of GREB1 mRNA. Melt-curve analysis was performed to monitor the quality of the PCR amplification.
Luciferase Reporter Gene Assay
A 1.7-kb region from the GREB1a promoter containing the ERE1 motif was amplified from MCF-7 genomic DNA with the following primers: forward 5'-GGGGTACCagtgtggcaactgggtcatt-3' and reverse 5'-GCCCAAGCTTgcaagccttccattgaaaaa-3' (underlined sequences indicate the restriction sites added). The PCR-amplified product was sequenced and cloned into the pGL3-basic vector (Promega, Madison, WI) at KpnI/HindIII sites to generate reporter plasmid pGREB-ERE1. To generate a reporter construct containing mutated ERE1, site-directed mutagenesis was performed based on the QuikChange method (Stratagene, La Jolla, CA) using the primers 5'-GTACCAGTGTGGCAACTGGATCCTTCTGACCTAGAAGCAAC-3' and 5'-GTTGCTTCTAGGTCAGAAGGATCCAGTTGCCACACTGGTA C-3' to generate pGREB1-ERE1 mutant. To add ERE2 and ERE3 motifs or their mutant forms to the reporter plasmids, two complementary oligos covering each motif as well as its adjacent genomic sequence were synthesized. Each pair of oligos was phosphorylated by T4 polynucleotide kinase and annealed in vitro. The double-strand DNA was cloned into the parental report plasmid with according restriction enzyme sites. The oligos for ERE2 motif are 5'-CGAGCTCTTCTTCTCAAAAGGTCATCATGACCTTATTGTCTGGGAGTAC-3' and 5'-TCCCAGACAATAAGGTCATGATGACCTTTTGAGAAGAAGAGCTCGGTAC-3'; the ones for mutant ERE2 motif are 5'-CGAGCTCTTCTTCTCAAAACCTGATCACGTGGTTATTGTCTGGGAGTAC-3' and 5'-TCCCAGACAATAACCACGTGATCAGGTTTTGAGAAGAAGAGCTCGGTAC-3'. The oligos for ERE3 motif are 5'-CTTATAGACAAAGATAATCAGGTCAAAATGACCTTCTTTCAGTTGTTGTAC-3' and 5'-AACAACTGAAAGAAGGTCATTTTGACCTGATTATCTTTGTCTATAAGGTAC-3'; the ones for mutant ERE3 motif are 5'-CTTATAGACAAAGATAATCACGTGAAAAGTGAATTCTTTCAGTTGTTGTAC-3' and 5'-AACAACTGAAAGAATTCACTTTTCACGTGATTATCTTTGTCTATAAGGTAC-3'.
These reporter constructs were cotransfected, respectively, with the phRL-SV40 plasmid from Promega, which encodes renilla luciferase as an internal control, into MCF-7 cells using Lipofectin (Invitrogen). Cells were treated with 10 nM E2 or 100 nM OHT for 24 h before harvest. The luciferase activity was measure with a dual-luciferase reporter assay system (Promega) using a luminometer from Thermo Labsystems (Needham, MA).
ChIP Assay and Re-ChIP Assay
MCF-7 cells were grown in phenol red-free IMEM with 5% charcoal-dextran stripped serum for 3 d to 80–90% confluence before the treatment with 10 nM E2 or 100 nM OHT for specified times. ChIP assays were performed as described previously with minor modifications (17). To identify other protein components in protein-DNA complexes, re-ChIP assays were performed in which the cross-linked immunocomplex was eluted from the first ChIP with 10 mM dithiothreitol at 37 C for 30 min, and then the product was diluted 50-fold in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8.1). Re-ChIP assay was performed with a different antibody. The primers used for the real-time PCR detection of GREB1 locus are listed in Table 1
.
|
| ACKNOWLEDGMENTS |
|---|
| FOOTNOTES |
|---|
Disclosure Statement: The authors have nothing to disclose.
First Published Online July 31, 2007
Abbreviations: ChIP, Chromatin immunoprecipitation; E2, 17ß-estradiol; ER, estrogen receptor; ERE, estrogen response element; LBD, ligand-binding domain; OHT, 4-hydroxyl tamoxifen; Pol II, RNA polymerase II; SRC-3, steroid receptor coactivator-3.
Received for publication February 14, 2007. Accepted for publication July 24, 2007.
| REFERENCES |
|---|
|
|
|---|
in vivo and in vitro. Biochem Biophys Res Commun 243:122–126[CrossRef][Medline]
and ß. Endocrinology 138:863–870
(ER
) and estrogen receptor-ß (ERß) messenger ribonucleic acid in the wild-type and ER
-knockout mouse. Endocrinology 138:4613–4621
directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115:751–763[CrossRef][Medline]
target genes and response elements in breast tumor cells. Genome Biol 5:R66
in breast cancer cell line MCF-7. Nuclear receptors: bench to bedside. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 104
1 gene in breast cancer cells. Mol Endocrinol 19:1584–1592NURSA Molecule Pages Link:
This article has been cited by other articles:
![]() |
K. W. Jeong, Y.-H. Lee, and M. R. Stallcup Recruitment of the SWI/SNF Chromatin Remodeling Complex to Steroid Hormone-regulated Promoters by Nuclear Receptor Coactivator Flightless-I J. Biol. Chem., October 23, 2009; 284(43): 29298 - 29309. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. J. Ellison-Zelski, N. M. Solodin, and E. T. Alarid Repression of ESR1 through Actions of Estrogen Receptor Alpha and Sin3A at the Proximal Promoter Mol. Cell. Biol., September 15, 2009; 29(18): 4949 - 4958. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. H. Barnett, S. Sheng, T. Howe Charn, A. Waheed, W. S. Sly, C.-Y. Lin, E. T. Liu, and B. S. Katzenellenbogen Estrogen Receptor Regulation of Carbonic Anhydrase XII through a Distal Enhancer in Breast Cancer Cancer Res., May 1, 2008; 68(9): 3505 - 3515. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Zhu and U. Hansen HMGN1 Modulates Estrogen-Mediated Transcriptional Activation through Interactions with Specific DNA-Binding Transcription Factors Mol. Cell. Biol., December 15, 2007; 27(24): 8859 - 8873. [Abstract] [Full Text] [PDF] |
||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| Endocrinology | Endocrine Reviews | J. Clin. End. & Metab. |
| Molecular Endocrinology | Recent Prog. Horm. Res. | All Endocrine Journals |