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Series GSE48096 Query DataSets for GSE48096
Status Public on Jun 21, 2013
Title Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The C4-12/Flag.ERβ cell line which stably expressed Flag.ERβ is used to study ERβ genomic functions without ERα interference. Mapping ERβ binding sites in these cells reveals ERβ unique distribution and motif enrichment patterns. Accompanying our mapping results, nascent RNA profiling is performed on cells at the same treatment time. The combined results allow the identification of ERβ target genes. Gene ontology analysis reveals that ERβ targets are enriched in differentiation, development and apoptosis. Concurrently, E2 treatment suppresses proliferation in these cells. Within ERβ binding sites, while the most prevalent binding motif is the canonical ERE, motifs of known ER interactors are also enriched in ERβ binding sites. Moreover, among enriched binding motifs are those of GFI, REST and EBF1, which are unique to ERβ binding sites in these cells. Further characterization confirms the association between EBF1 and the estrogen receptors, which favors the N-terminal region of the receptor. Furthermore, EBF1 negatively regulates ERs at the protein level. In summary, by studying ERβ genomic functions in our cell model, we confirm the anti-proliferative role of ERβ and discover the novel cross talk of ERβ with EBF1 which has various implications in normal physiology.
Overall design C4-12/Flag.ERβ cells were treated with 10nM E2 for 1 hour then crosslinked with 1% formaldehyde; EtOH treatment was used as control. Crosslinked samples were processed for ChIP-seq and sequenced with Illumina Genome Analyzer II and aligned to hg18. QuEST was used as the peak-calling software, using default parameters recommended to analyze transcription factor ChIP-seq data. The entire ChIP-seq process was performed once on each sample (Vehicle or E2-treated).
Contributor(s) Le TP, Sun M, Luo X, Kraus WL, Greene GL
Citation(s) 23951143
Submission date Jun 19, 2013
Last update date May 15, 2019
Contact name Thien Le
Organization name University of Chicago
Lab Geoffrey Greene
Street address 929 E 57th St W325D
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (4)
GSM1168432 E2_ChIP
GSM1168433 Veh_ChIP
GSM1168434 Input1
This SubSeries is part of SuperSeries:
GSE48161 Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor
BioProject PRJNA209061
SRA SRP026205

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Supplementary file Size Download File type/resource
GSE48096_RAW.tar 110.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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