Knockdown of GRHL2 affects active enhancers (H3K27ac sites) enriched for ER binding
ABSTRACT: Differential ChIP-Seq data monitoring changes in active enhancer marks (H3K27ac sites) after treatment with siGRHL2 in MCF7 and T47D breast cancer models. Comparing sites altered by treatment with siGRHL2 after 48hours revealed these sites to be enriched for Estrogen Receptor (ER) binding. Overall design: ChIP-seq data monitoring H3K27ac in MCF7 and T47D cells after treatment with siGRHL2 and siCTRL for 48 hours.
Project description:H3K27Ac ChIP-seq in MCF7 Y537S ER mutant cells RNAseq analysis of MCF7 Y537S ER mutant cells treated with veh and THZ1 Overall design: H3K27ac ChIP-seq in MCF7 cells with DOX-inducible expression of the Y537S ER mutant in cells without induction of the mutation in E2 stimulated conditions and cells with DOX induction of the mutation in hormone deprived conditions RNAseq of cells with DOX-induced expression of the Y537S mutation with veh treatment and THZ1 treatment for 6 hrs and 24 hrs
Project description:Expression profile of MCF7 and T47D human breast cancer cell lines upon treatment with the BET bromodomian inhibitor JQ1 Overall design: Two breast cancer cell lines (MCF7 and T47D) were treated with 1uM JQ1 or vehicle for 24 hours. Three biological replicates were obtained for each condition.
Project description:MEF2C is one of the substantially expressed transcriptional factors in endothelial cells, but its genomic localization is unknown. This time, we established a new antibody for MEF2C, and performed ChIP-seq to identify MEF2C binding site in whole genome manner. H3K27Ac binding sites were also detected in the same way. We used chromatin immunoprecipitation with deep sequencing (ChIP-seq) of HUVECs treated with or without pitavastatin for 4hours, we identified MEF2C and H3K27Ac binding regions.HUVECs were used within the first 6 passages. For MEF2C studies, HUVECs were cultivated in medium EGM2MV containing pitavastatin at a concentration of 1 μM, and same concentration of DMSO was used as a control sample. For H3K27ac, HUVECs were starved for 16 hours and harvested without statin treatment.
Project description:Gene expression levels were determined with control or PD-0332991 treatment MCF7, T47D cells were subject to DMSO/ PD-0332991 treatment . RNA was harvested at 120 hours post treatment and analyzed on Illumina microarrays
Project description:The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding to distinct regulatory regions in different tissues. To test this hypothesis, we performed ChIP-seq for TCF7L2 in 6 human cell lines. We identified 116,000 non-redundant TCF7L2 binding sites, with only 1,864 sites common to the 6 cell lines. Using ChIP-seq, we showed that many genomic regions that are marked by both H3K4me1 and H3K27Ac are also bound by TCF7L2, suggesting that TCF7L2 plays a critical role in enhancer activity. Bioinformatic analysis of the cell type-specific TCF7L2 binding sites revealed enrichment for multiple transcription factors, including HNF4alpha and FOXA2 motifs in HepG2 cells and the GATA3 motif in MCF7 cells. ChIP-seq analysis revealed that TCF7L2 co-localizes with HNF4alpha and FOXA2 in HepG2 cells and with GATA3 in MCF7 cells. Interestingly, in MCF7 cells the TCF7L2 motif is enriched in most TCF7L2 sites but is not enriched in the sites bound by both GATA3 and TCF7L2. This analysis suggested that GATA3 might tether TCF7L2 to the genome at these sites. To test this hypothesis, we depleted GATA3 in MCF7 cells and showed that TCF7L2 binding was lost at a subset of sites. RNA-seq analysis suggested that TCF7L2 represses transcription when tethered to the genome via GATA3. Our studies demonstrate a novel relationship between GATA3 and TCF7L2, and reveal important insights into TCF7L2-mediated gene regulation. RNAseq analysis of MCF7 cells transfected with siCONTROL, siTCF7L2 or siGATA3. ChIP-seq analysis of H3K27ac, H3K4me1, H3K27me3, H3K9me3 in MCF7 cells; H3K4me1 and H3K27ac in HCT116 cells.
Project description:Comparison of the basal and estrogen-induced effects on genome-wide transcription in ERα-positive breast cancer cell lines T47D and MCF7 after lentiviral transduction with ERβ. Comparison of ERβ-transduced T47D and MCF7 cells versus respective control-transduced cells, in the presence of vehicle or estrogen. Each comparison in technical and biological duplicate.
Project description:KD of Crebbp at mouse cells results in reduced H3K27ac enrichment at a subset of promoters and enhancers. Overall design: Genome-wide H3K27Ac ChIPseq binding sites in mouse cells with shCrebbp and scramble control.
Project description:KD of CREBBP at lymphoma cell line, MD901, results in reduced H3K27ac enrichment at a subset of promoters and enhancers. Overall design: Genome-wide H3K27Ac ChIPseq binding sites in human cell line MD901 (CREBBP wild type) with shCREBBP (11027 and 3752) and scramble control.