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Series GSE55680 Query DataSets for GSE55680
Status Public on Dec 11, 2022
Title Analysis of the impact of FOXA1 expression on MDA::ER E2-sensitive transcriptomes and ER cistromes [Transcriptome data]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The primordial actions of the estrogen receptor alpha (ER) in controlling breast cancer cells proliferation rate are particularly documented. However, reintroducing ER into ER-negative cells does not reprogram their transcriptome towards an estrogen-sensitive growth phenotype. Member of the Forkhead (FKH) family of transcription factors, FOXA1 has been characterized to be essential for the appropriate binding of ER onto chromatin in MCF-7 cells. FOXA1 pioneering actions involve modulations of histone post-translational modifications (HPTMs) and local depletion in methylated CpGs. Using MDA-MB231 cells which are ER and FOXA1 negative, we aimed at determining whether the introduction of ER and FOXA1 would be sufficient to restore an estrogen-sensitive growth and to coincidently reprogram chromatin. We used ChIP-seq experiments to map ER and FOXA1 binding sites (BSs) and to profile H3K4me2 and H3K27ac marks, and surprisingly observed that FOXA1 had rather a global negative impact on ER actions, associated with an inhibition of growth and a reorientation of the transcriptome of the cells towards cell death. We demonstrate that the re-introduction of FOXA1 in these cells actually competes for the binding and pioneering actions of FOXA2, another FKH protein, on a number of ER BSs. As demonstrated for its alter ego FOXA1 in MCF-7 cells, abrogating FOXA2 expression drastically diminished ER binding onto its cognate sites, associated with a local loss of HPTMs for active chromatin.
Overall design A 12 chip study aiming to characterize Estradiol (E2)-sensitive genes in MDA::ER cells conditionnally expressing FOXA1 following a 4h treatment with E2. RNAs were prepared from three independent triplicate experiments. Each of the three technical replicate correspond to pooled RNAs from 1 experiment. Controls for these experiments are 6 arrays corresponding to vehicle-treated cells.

This submission represents transcriptome component of study.
Contributor(s) Quintin J, Le Péron C, Mahé E, Sérandour AA, Palierne G, Bizot M, Percevault F, Avner S, Salbert G, Métivier R
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Submission date Mar 07, 2014
Last update date Dec 12, 2022
Contact name Raphaël Métivier
Organization name CNRS UMR 6290
Street address Campus de Beaulieu
City Rennes
ZIP/Postal code 35042 Cedex
Country France
Platforms (1)
GPL15143 NimbleGen Human Expression Array [2006-08-03_HG18_60mer_expr]
Samples (12)
GSM1341604 MDA::ER::pcDNA_EtOH_1
GSM1341605 MDA::ER::pcDNA_EtOH_2
GSM1341606 MDA::ER::pcDNA_EtOH_3
This SubSeries is part of SuperSeries:
GSE55741 Analysis of the impact of FOXA1 expression on MDA::ER E2-sensitive transcriptomes and ER cistromes
BioProject PRJNA240535

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55680_RAW.tar 102.4 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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