Differential chromatine state and ER binding potentially induced by NR2F2 depletion.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE132432 | GEO | 2019/10/15
REPOSITORIES: GEO
Similar Datasets
Project description:We show that most binding events of NR2F2 occur together with the ERα binding sites.To address the functional relationship between NR2F2 and ERα, we assessed the role of NR2F2 in oestrogen-induced growth in ER positive cell line MCF-7. The MTT experiment showed that inhibition of NR2F2 prevented the oestrogen-induced proliferation of MCF-7 cells.To further explore the effect of NR2F2 on estrogen response, We expanded our knockdown studies by performing RNA-seq analysis for MCF-7 cells transfected with control or NR2F2 shRNAs with or without E2.
2019-10-15 | GSE132433 | GEO
Project description:FOXA1 and GATA3 can remodel chromatin accessibility, we further explored what effect of NR2F2 would have on chromatin properties. ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) is widely used to map chromatin accessibility genome-wide. Thus, We perform ATAC-seq without oestrogen stimulation before and after NR2F2 depletion.Covalent modifications are a main chromatin property.To test whether NR2F2 favoured histone modification deposition on chromatin, we profiled ChIP-Seq of H3K4me1, H3K4me3, and H3K27ac following NR2F2 depletion in oestrogen-starved MCF-7 cells to gain comprehensive histone medication landscape.
2019-10-15 | GSE132434 | GEO
Project description:NF1 loss-of-function mutations are enriched in hormone receptor positive (HR+) metastatic breast cancer (MBC) and mediate endocrine therapy resistance. To identify therapeutic vulnerabilities in this context, we performed CRISPR/Cas9 screens in wildtype and NF1 knockout isogenic HR+ models and identified NR2F2, an orphan nuclear receptor, to be essential specifically in NF1 loss cells. The NR2F2 dependence was induced as a consequence of NR2F2 upregulation via the activation of the MAPK pathway in these cells. Enforced overexpression of NR2F2 was sufficient to confer endocrine therapy resistance in the absence of NF1 loss, while of NR2F2 knockout or knockdown could enhance the efficacy of endocrine therapies in NF1 WT and NF1 loss models. Mechanistically, our comprehensive multi-omics approaches revealed that NR2F2 modulates chromatin accessibility and regulates ER-dependent transcription through its interaction with ER, transcriptional coregulators and chromatin remodelers at chromatin. Specifically, increased NR2F2 in NF1 loss cells dramatically enhanced the association with transcriptional corepressors, which resulted in attenuation of chromatin accessibility and ER occupancy, and impaired ER transcriptional program. Our findings identify the nuclear receptor NR2F2 as a downstream effector of NF1 loss, and it is essential and potentially druggable mediator of endocrine therapy resistance. We performed ER chromatin binding profiling analysis using data obtained from ChIP-seq of MCF7 sgNT, sgNF1, sgNR2F2 and double knockout (DKO) cells under the conditions of full media, estrogen starvation and estrogen stimulation. We also performed NR2F chromatin binding profiling analysis using data obtained from ChIP-seq of MCF7 sgNT and sgNF1 cells under full media culture condition
2022-11-10 | GSE217416 | GEO
Project description:Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. MCF-7-Y537S cells encode a wild-type (tyrosine 537) and a mutant (serine 537) allele. Growth of the line is estrogen-independent and expression of ERα target genes is elevated in the absence of estrogen. ER ChIP-seq was carried out to map global ERα binding sites in the presence and absence of estrogen. RNA-seq following estrogen treatment was used for gene expression analysis. We show that expression of ER target genes and ER recruitment to ER binding regions is similar in MCF-7 and MCF-7-Y537S cells, except that ER recruitment to DNA and expression of ER target genes is frequently elevated in the absence of estrogen
2016-10-25 | GSE78284 | GEO
Project description:Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. MCF-7-Y537S cells encode a wild-type (tyrosine 537) and a mutant (serine 537) allele. Growth of the line is estrogen-independent and expression of ERα target genes is elevated in the absence of estrogen. ER ChIP-seq was carried out to map global ERα binding sites in the presence and absence of estrogen. RNA-seq following estrogen treatment was used for gene expression analysis. We show that expression of ER target genes and ER recruitment to ER binding regions is similar in MCF-7 and MCF-7-Y537S cells, except that ER recruitment to DNA and expression of ER target genes is frequently elevated in the absence of estrogen.
2016-10-25 | GSE78285 | GEO
Project description:Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.
2011-01-04 | E-GEOD-23701 | biostudies-arrayexpress
Project description:Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.
2011-01-25 | E-GEOD-26831 | biostudies-arrayexpress
Project description:Estrogen receptor α (ERα) is key player in the progression of breast cancer. ERα binds to DNA and mediates long-range chromatin interactions throughout the genome, but the underlying mechanism in this process is unclear. Here, we show that AP-2 motifs are highly enriched in the ERα binding sites (ERBS) identified from the recent ChIA-PET of ERα. More importantly, we demonstrate that AP-2γ (also known as TFAP2C), a member of the AP-2 family which has been implicated in breast cancer oncogenesis, is recruited to chromatin in a ligand-independent manner and co-localized with ERα binding events. Furthermore, pertubation of AP-2γ expression disrupts ERα DNA binding, long-range chromatin interactions, and gene transcription. Using ChIP-seq, we show that AP-2γ and ERα binding occurs in close proximity on a genome-wide scale. The majority of these shared genomic regions are also occupied by the pioneer factor, FoxA1. AP-2γ is required for efficient FoxA1 binding and vice versa. Finally, we show that most ERBS associated with long-range chromatin interactions are co-localized with both AP-2γ and FoxA1. Together, our results suggest AP-2γ is an essential factor in ERα-mediated transcription, primarily working together with FoxA1 to facilitate ERα binding and long-range chromatin interactions.
2011-06-02 | GSE26740 | GEO
Project description:Estrogen receptor α (ERα) is key player in the progression of breast cancer. ERα binds to DNA and mediates long-range chromatin interactions throughout the genome, but the underlying mechanism in this process is unclear. Here, we show that AP-2 motifs are highly enriched in the ERα binding sites (ERBS) identified from the recent ChIA-PET of ERα. More importantly, we demonstrate that AP-2γ (also known as TFAP2C), a member of the AP-2 family which has been implicated in breast cancer oncogenesis, is recruited to chromatin in a ligand-independent manner and co-localized with ERα binding events. Furthermore, pertubation of AP-2γ expression disrupts ERα DNA binding, long-range chromatin interactions, and gene transcription. Using ChIP-seq, we show that AP-2γ and ERα binding occurs in close proximity on a genome-wide scale. The majority of these shared genomic regions are also occupied by the pioneer factor, FoxA1. AP-2γ is required for efficient FoxA1 binding and vice versa. Finally, we show that most ERBS associated with long-range chromatin interactions are co-localized with both AP-2γ and FoxA1. Together, our results suggest AP-2γ is an essential factor in ERα-mediated transcription, primarily working together with FoxA1 to facilitate ERα binding and long-range chromatin interactions.
2011-06-03 | GSE23852 | GEO
Project description:The interplay between mitogenic and proinflammatory signaling pathways play key roles in determining the phenotypes and clinical outcomes of breast cancers. We have used global nuclear run-on coupled with deep sequencing to characterize the immediate transcriptional responses of MCF-7 breast cancer cells treated with estradiol, TNFα, or both. In addition, we have integrated these data with chromatin immunoprecipitation coupled with deep sequencing for estrogen receptor alpha (ERα), the pioneer factor FoxA1 and the p65 subunit of the NF-κB transcription factor. Our results indicate extensive transcriptional interplay between these two signaling pathways, which is observed for a number of classical mitogenic and proinflammatory protein-coding genes. In addition, GRO-seq has allowed us to capture the transcriptional crosstalk at the genomic locations encoding for long non-coding RNAs, a poorly characterized class of RNAs which have been shown to play important roles in cancer outcomes. The synergistic and antagonistic interplay between estrogen and TNFα signaling at the gene level is also evident in the patterns of ERα and NF-κB binding, which relocalize to new binding sites that are not occupied by either treatment alone. Interestingly, the chromatin accessibility of classical ERα binding sites is predetermined prior to estrogen treatment, whereas ERα binding sites gained upon co-treatment with TNFα require NF-κB and FoxA1 to promote chromatin accessibility de novo. Our data suggest that TNFα signaling recruits FoxA1 and NF-κB to latent ERα enhancer locations and directly impact ERα enhancer accessibility. Binding of ERα to latent enhancers upon co-treatment, results in increased enhancer transcription, target gene expression and altered cellular response. This provides a mechanistic framework for understanding the molecular basis for integration of mitogenic and proinflammatory signaling in breast cancer.
2015-03-05 | GSE59531 | GEO