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Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes in breast cells

ABSTRACT: Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes in breast cells

PROVIDER: PRJNA144939 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR330986.fastq.gz	Fastqsanger.gz
	SRR330987.fastq.gz	Fastqsanger.gz
	SRR330988.fastq.gz	Fastqsanger.gz
	SRR330989.fastq.gz	Fastqsanger.gz
	SRR330990.fastq.gz	Fastqsanger.gz

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Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes in breast cells

Project description:This SuperSeries is composed of the following subset Series: GSE31127: Impact of FOXA1 over-expression on progestin signalling in transformed normal breast cells GSE31128: Progestin regulation of gene expression in breast cancer and minimally transformed breast cell lines GSE31129: Genome-wide mapping of ligand-dependent progesterone receptor chromatin interactions in human breast cell lines using PR ChIP-seq Refer to individual Series

2012-04-25 | E-GEOD-31130 | biostudies-arrayexpress

Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes.

Project description:The transcriptional effects of the ovarian hormone progesterone are pleiotropic, and binding to DNA of the nuclear progesterone receptor (PR), a ligand-activated transcription factor, results in diverse outcomes in a range of target tissues. To determine whether distinct patterns of genomic interaction of PR contribute to the cell specificity of the PR transcriptome, we have compared the genomic binding sites for PR in breast cancer cells and immortalized normal breast cells. PR binding was correlated with transcriptional outcome in both cell lines, with 60% of progestin-regulated genes associated with one or more PR binding regions. There was a remarkably low overlap between the PR cistromes of the two cell lines, and a similarly low overlap in transcriptional targets. A conserved PR binding element was identified in PR binding regions from both cell lines, but there were distinct patterns of enrichment of known cofactor binding motifs, with FOXA1 sites over-represented in breast cancer cell binding regions and NF1 and AP-1 motifs uniquely enriched in the immortalized normal line. Downstream analyses suggested that differential cofactor availability may generate these distinct PR cistromes, indicating that cofactor levels may modulate PR specificity. Taken together these data suggest that cell-specificity of PR binding is determined by the coordinated effects of key binding cofactors.

| S-EPMC3335806 | biostudies-literature

Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes in breast cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-04-26 | GSE31130 | GEO

The estrogen receptor α cistrome of human endometrium and epithelial organoids and progesterone receptor cistrome in epithelial organoids

Project description:The ESR1 Cistrome in human endometrial biopsies was characterized and compared to gene regulations between the proliferative and mid-secretory pahses to infer estrogen target genes. ESR1 and PGR cistromes and 3D-cjromatin structures in cultured endometrial biopsies were characterized and compared to gene regulations induced by estrogen or progesterone in comparison to the whole endometrium.

2022-05-26 | GSE200802 | GEO

Transcriptomic Profile of Breast Tissue of Premenopausal Women Following Treatment with Progesterone Receptor Modulator: Secondary Outcomes of a Randomized Controlled Trial

Project description:Progesterone receptor antagonism is gaining attention due to progesterone's recognized role as a major mitogen in breast tissue. Limited but promising data suggest the potential efficacy of antiprogestins in breast cancer prevention. The present study presents secondary outcomes from a randomized controlled trial examining changes in breast mRNA expression following mifepristone treatment in healthy women. We analyzed 32 paired breast biopsies from 16 healthy premenopausal women at baseline and after two months of mifepristone treatment. In total, twenty-seven differentially expressed genes were identified, with enriched biological functions related to extracellular matrix remodeling. Notably, the altered gene signature induced by mifepristone in vivo was rather similar to the in vitro signature. Furthermore, this expression gene signature was associated with breast carcinogenesis and significantly correlated with progesterone receptor expression status in breast cancer, as validated in The Cancer Genome Atlas dataset using the R2 platform. The present study is the first to explore the breast transciptome following mifepristone treatment in healthy breast tissue in vivo, enhancing the understanding of progesterone receptor modulator and its potential protective effects against breast cancer by investigating its action in healthy breast tissue.

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Genome-wide mapping of ligand-dependent progesterone receptor chromatin interactions in human breast cell lines using PR ChIP-seq

2012-04-26 | GSE31129 | GEO

Genome-wide mapping of ligand-dependent progesterone receptor chromatin interactions in human breast cell lines using PR ChIP-seq

Project description:The effects of progesterone are pleiotropic, resulting in diverse outcomes in a range of target tissues. Progesterone signalling is mediated through the nuclear progesterone receptor (PR) and to identify whether the cell specificity of the PR transcriptome arises from distinct patterns of genomic interaction of PR, we have mapped the genomic binding sites for PR in breast cancer cells and minimally transformed breast cells. PR binding was correlated with transcriptional outcome in both cell lines. Three replicate PR ChIP samples and two replicate input DNA control samples from T-47D breast cancer cells and two replicate PR ChIP samples and two replicate input DNA control samples from AB32 transformed normal breast cells.

2012-04-25 | E-GEOD-31129 | biostudies-arrayexpress

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Project description:We examined the global gene expression pattern of T cells regulated by progesterone to gain further insights into the regulatory mechanisms of progesterone. We found 325-347 cord blood T cell genes up or down-regulated by P4 in the presence or absence of exogenous TGFb1. Peripheral blood T cells were relatively unresponsive with only 30-70 genes regulated by P4. IL-6 receptor (IL-6R) expression was greatly down-regulated by progesterone in cord blood, but not PB, T cells. Overall, these differences in gene expression are consistent with the differential responses of cord blood and peripheral blood T cells to progesterone. To gain insights into the differences of progesterone and control dendritic cells, we performed a microarray study and found ~180 genes regulated by progesterone in dendritic cells. The gene expression information suggests that progesterone has the potential to alter dendritic cell responses to cytokines, chemokine production, and migration which in combination would control T cell differentiation.

2012-03-02 | GSE22025 | GEO

Bcl6 and NFkB cistromes mediate opposing reulation of the innate immune response

Project description:Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling. In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and that 90% of the Bcl-6 cistrome is collapsed following Tlr4 activation. Bcl-6 deficient macrophages are acutely hypersensitive to lipopolysaccharide (LPS) and, using comparative ChIP-seq analyses, we find that the Bcl-6 and NF-κB cistromes intersect, within nucleosomal distance, at nearly half of Bcl-6 binding sites in stimulated macrophages to promote opposing epigenetic modifications of the local chromatin. These results reveal a genomic strategy for controlling the innate immune response in which repressive and inductive cistromes establish a dynamic balance between macrophage quiescence and activation via epigenetically marked cis-regulatory elements. keywords: Genome-wide location analysis Identification of BCL6 and NFkB binding sites in unstimulated and LPS-stimulated primary bone-marrow derived macrophages.

2010-11-24 | E-GEOD-16723 | biostudies-arrayexpress

Maternal Circulating miRNAs Contribute to Negative Pregnancy Outcomes by Altering Placental Transcriptome and Fetal Vascular Dynamics

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