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Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell

ABSTRACT: Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell

PROVIDER: PRJNA588153 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10416353.fastq.gz	Fastqsanger.gz
	SRR10416354.fastq.gz	Fastqsanger.gz
	SRR10416355.fastq.gz	Fastqsanger.gz
	SRR10416356.fastq.gz	Fastqsanger.gz
	SRR10416357.fastq.gz	Fastqsanger.gz

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Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell

Project description:The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using ChIP-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2-HA protein. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 3 treatments (Veh, Dox, DoxTam) were performed in duplicates. After treatments, cells were collected for ChIP experiment with HA antibody. ChIP-seq libraries were sequenced and data analysis showed almost no binding in Veh treatment, indicating low backgroud and good quality of the data. PAX transcription factor motif were enriched in PAX2 peaks, indicating the reliability of the data. When crossing the ChIP-seq data with genes regulated by PAX2 in MCF-7, we could observe high level binding of PAX2 to prmoters of PAX2 up-regulated genes and the center of intergenic transcripts induced by PAX2, suggesting the role of PAX2 in regulating transcription activation.

2019-11-08 | GSE140060 | GEO

Genome wide analysis of transcripts regulated by PAX2 and Tamoxifen in MCF-7 cells

Project description:The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using GRO-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 4 treatments (Veh, Tam, Dox, DoxTam) were performed in duplicates. After treatments, nuclei were isolated and used for nuclear run-on and subsequent GRO-seq library preparation. Libraries were sequenced and data analysis showed that PAX2 could repress estrogen target genes and induce genes enriched in cytokine (TNF-alpha and INF-gamma) related pathways. When combined with tamoxifen, PAX2 could further repress estrogen target genes to a higher degree, and induce genes enriched in p53 related pathway. Moreover, PAX2 could induce the transcription of some intergenic transcripts (potential enhancers) to activate the transcription of nearby genes with could predict good outcome in estrogen receptor positive breast cancer. Overall our finding suggests that PAX2 could benifit ER positive breast cancer by 1) repressing estrogen target genes, and this effect is enhanced by tamoxifen 2) activating cell death/growth arrest related pathways, which is enhanced by potential enhancer transcription induced by PAX2 itself.

2019-11-06 | GSE139928 | GEO

Genome wide analysis of transcripts regulated by PAX2 and Tamoxifen in MCF-7 cells

Project description:Genome wide analysis of transcripts regulated by PAX2 and Tamoxifen in MCF-7 cells

| PRJNA587641 | ENA

Genome-wide maps of chromatin state in MCF-7 cells with six2 overexpression or not

Project description:By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA in MCF-7 cells with six2 overexpression or not, we generated genome-wide chromatin-state maps of these two cells. We identified the detailed binding sites of six2 in MCF-7 cells.

2019-03-10 | GSE117145 | GEO

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

Project description:Background: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. Results: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signalling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. Conclusions: We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer. Hi-C experiments were conducted in MCF-7 and MCF-10A parental cells. The RNA-seq data associated with this study is deposited under the GEO accession number GSE71862.

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O-GlcNAc sites identification and quantification proteomics analysis of O-GlcNAc chromatin in MCF-7 and MCF-7/ADR cells

Project description:We used a metabolic labeling (GalNAz) based O-GlcNAc sites identification and quantification proteomics method to compare the O-GlcNAc chromatin of MCF-7 and MCF-7/ADR cells. The O-GlcNAc chromatin-associated proteins can be metabolically labeled with azides, followed by reaction with a cleavable DADPS (dialkoxydiphenylsilane) alkyne-biotin linker and enrichment with streptavidin beads. After cleavage of DADPS by formic acid, O-GlcNAc modified peptides were quantitative analysis using tandem mass spectroscopy (MS).

2020-12-01 | PXD022857 |

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

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Pax2 Dependent Expression in the Intermediate Mesoderm at E11.5

Project description:Heterozygous and homozygous Pax2 E11.5 embryos were collected and the intermediate mesoderm was dissected and dispersed into single cells. The Pax2 positive cells also expressed EGFP, which was knocked into the Pax2 locus. EGFP positive cells were sorted by FACS and RNA isolated. We compared RNA expression levels in EGFP positive cells from Pax2 null and Pax2 heterozygote embryos.

2014-12-13 | E-GEOD-64129 | biostudies-arrayexpress

Genome-wide Mapping of GATA4 in Breast Cancer MCF-7 Cell Chromatin State.

Project description:Genome-wide Mapping of GATA4 in Breast Cancer MCF-7 Cell Chromatin State.

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Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (ChIPseq PAX2)

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