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Series GSE40129 Query DataSets for GSE40129
Status Public on Nov 26, 2012
Title GATA3 acts upstream of FOXA1 in mediating ER binding by shaping enhancer accessibility
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Estrogen Receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1, contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1 co-operating transcription factor mutated in breast tumors, however its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-sequencing in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of co-factors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1 binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3 mediated re-distribution of ESR1 binding. The GATA3-mediated re-distributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1 bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen- ESR1 mediated interactions between cis-regulatory elements. Together these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.
Overall design GATA and ER binding studied by chromatin immunoprecipitation in breast cancer cell lines, with and without estrogen stimulation and by knocking down GATA
Contributor(s) Theodorou V, Carroll J, Stark R
Citation(s) 23172872
Submission date Aug 14, 2012
Last update date May 15, 2019
Contact name Chandra Chilamakuri
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (34)
GSM986059 siNT_ER_E2_r1
GSM986060 siGATA_ER_E2_r1
GSM986061 siNT_ER_E2_r2
BioProject PRJNA172877
SRA SRP014854

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Supplementary file Size Download File type/resource
GSE40129_RAW.tar 23.6 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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