Coativator Function Defines the Active Estrogen Receptor Alpha Cistrome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE19328 | GEO | 2009/12/09
SECONDARY ACCESSION(S): PRJNA121689
REPOSITORIES: GEO
Similar Datasets
Project description:Proper activation of transcriptional networks in complex organisms is central to the response to stimuli. We demonstrate that the selective activation of a subset of the estrogen receptor alpha (ERalpha) cistrome in MCF7 breast cancer cells provides specificity to the estradiol (E2) response. ERalpha-specific enhancers that are subject to E2-induced coactivator-associated arginine methyltransferase 1 (CARM1) action are critical to E2-stimulated gene expression. This is true for both FoxA1-dependent and independent enhancers. In contrast, a subset of E2-suppressed genes are controlled by FoxA1-independent ERalpha binding sites. Nonetheless, these are sites of E2-induced CARM1 activity. In addition, the MCF7 RNA polymerase II cistrome reveals preferential occupancy of E2-regulated promoters prior to stimulation. Interestingly, E2-suppressed genes tend to lie in otherwise silent genomic regions. Together, our results suggest that the transcriptional response to E2 in breast cancer cells is dependent on the interplay between polymerase II pre-occupied promoters and the subset of the ERalpha cistrome associated with coactivation.
| S-EPMC2698732 | biostudies-literature
Project description:We have developed a new method to study DNA-protein interaction in vivo called DamIP, which is based on fusing a protein of interest to a mutant form of DNA adenine methylatransferase (Dam) from E. coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor alpha (hERα). In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq defined hERα cistrome overlaps significantly with those determined by ChIP-chip or ChIP-seq, but identifies many new binding regions. As shown by conventional ChIP assay, many DamIP-seq unique hERα binding regions show relatively stable hERα binding, whereas DamIP-seq misses some regions with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 days. In summary, the current study provides both an alternate view of the hERα cistrome to further understand the mechanism of hERα mediated transcription, and a new tool to explore other transcriptional factors and cofactors. MCF7 cells were transfected with DamK9A or DamK9A-hERalpha. DamIP were performed from each sample and subjected to solexa sequencing
2011-11-19 | E-GEOD-33804 | biostudies-arrayexpress
Project description:Analysis of MCF7 cells transfected with ER mutants (S463P, Y537S and D538G) in phenol-red free, charcoal stripped FBS media and regular DMEM/F12 media. Results provide insight on the gene expression profiles induced by the various ER mutants. Total RNA extracted from transfected cells 48 hours after transfection
2013-10-25 | GSE51448 | GEO
Project description:The human oestrogen-positive breast cancer cell line MCF7 was cultured in phenol red-free RPMI medium supplemented with 10% fetal bovine serum, 10mg/ml insulin and 1nM estradiol (E2) and was referred to as wild-type MCF7. The wt-MCF7 cells were passaged weekly and medium was replenished every two to three days. To model acquisition of resistance to long term estrogen deprivation (LTED) on an aromatase inhibitor (AI), wt-MCF7 cells were cultured in phenol red-free RPMI medium supplemented with 10% dextran charcoal-stripped bovine serum (DCC) and 10mg/ml insulin. RNA was extracted from the LTED monolayers using RNeasy columns (Qiagen) according to manufacturerﾒs protocol. RNA amplification, labeling and hybridization on HumanWG-6 v3 Expression BeadChips were performed according to the manufacturer's instructions (http://www.illumina.com) to assess changes in gene expression during adaptation to LTED.
2012-05-03 | E-MTAB-922 | biostudies-arrayexpress
Project description:Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.
| S-EPMC6959601 | biostudies-literature
Project description:Gene expression is tightly regulated by transcription factors and cofactors that function by directly or indirectly interacting with DNA of the genome. Understanding how and where these proteins bind provides essential information to uncover genetic regulatory mechanisms. We have developed a new method to study DNA-protein interaction in vivo called DNA adenine methyltransferase (Dam)IP, which is based on fusing a protein of interest to a mutant form of Dam from Escherichia coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor (hER)α. In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq-defined hERα cistrome identifies many new binding regions and overlaps with those determined by chromatin immunoprecipitation (ChIP)-chip or ChIP-seq. Elements uniquely identified by DamIP-seq include a unique class of elements that show low, but persistent, hERα binding when reexamined by conventional ChIP. In contrast, DamIP-seq fails to detect some elements with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 d. In summary, the current study provides both an alternate view of the hERα cistrome to further understand the mechanism of hERα-mediated transcription and a new tool to explore other transcriptional factors and cofactors that is very different from conventional ChIP.
| S-EPMC3384088 | biostudies-literature
Project description:Human breast cancer cell lines were cultured in phenol red-free RPMI1640 medium supplemented with 10% fetal bovine serum and 1nM E2. All cell lines were banked in multiple aliquots to reduce the risk of phenotypic drift and identity confirmed using STR. Cells were routinely screened for mycoplasma contamination. Long-term E deprived (LTED) cells modelling resistance to an AI were derived from all parental cell lines as previously described. Two models of MCF7-LTED cells were available: one harbouring a Y537C mutation in ESR1 and the other with wt-ESR1. SUM44-LTED was shown to harbour a natural heterozygous ESR1Y537S mutation. Elacestrant resistant cell lines were generated by growing parental cells (MCF7-LTEDY537C) long-term in the presence of RPMI1640 containing 10% DCC + 0.1nM E2 + 1μM elacestrant. All cell lines were stripped of steroids for 48-72 hours prior to the start of experiments.
2023-03-10 | PXD031377 | Pride
Project description:ChIP-chip of 6 chromatin marks (FAIRE, H3K4me1, H3K4me3, H3K27me3, H3R17me2, H3AZAce) in breast cancer cell line MCF7
| PRJNA182368 | ENA
Project description:We have developed a new method to study DNA-protein interaction in vivo called DamIP, which is based on fusing a protein of interest to a mutant form of DNA adenine methylatransferase (Dam) from E. coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor alpha (hERα). In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq defined hERα cistrome overlaps significantly with those determined by ChIP-chip or ChIP-seq, but identifies many new binding regions. As shown by conventional ChIP assay, many DamIP-seq unique hERα binding regions show relatively stable hERα binding, whereas DamIP-seq misses some regions with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 days. In summary, the current study provides both an alternate view of the hERα cistrome to further understand the mechanism of hERα mediated transcription, and a new tool to explore other transcriptional factors and cofactors.
2011-11-19 | GSE33804 | GEO
Project description:Wild type (wt) MCF7 cells, modelling breast cancer at primary diagnosis, were cultured in phenol red-free RPMI supplemented with 10% FBS and 1nM estradiol (E2). Long-term oestrogen deprived (LTED) cell lines, which model resistance to endocrine therapy, were cultured in phenol red-free RPMI in the absence of exogenous E2 and supplemented with 10% dextran charcoal-stripped bovine serum (DCC). Samples were harvested at baseline and at the point of resistance (LTED). To reveal differential protein abundances between wt-MCF7 and MCF7 LTED, the peptides were labelled with chemical labelling and underwent fractionation using OFFGEL electrophoresis.
2016-06-01 | PXD004085 | Pride