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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 07, 2008 |
| Title |
Timecourse of estradiol (10nM) exposure in MCF7 breast cancer cells. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor alpha (ERalpha) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERalpha binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5' and 3' ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERalpha binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERalpha-positive from ERalpha-negative breast tumors. The expression dynamics of the genes adjacent to ERalpha binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERalpha appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERalpha target genes. Unexpectedly, we found that only 22%-24% of the bona fide human ERalpha binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene regulation.
Keywords: time course
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| Overall design |
We used oligonucleotide expression microarrays (Affymetrix GeneChip U133 Plus 2.0) to identify estradiol (E2)-responsive genes in the estrogen-receptor positive breast cancer cell line, MCF7. MCF7 cells were grown to 30-50% confluency and exposed to 10 nM E2 (or vehicle only) at 12, 24, and 48 hours. Each timepoint was performed in triplicate (ie, biological replicates). Total RNA was isolated from cells using the Qiagen RNeasy kit, and 5 micrograms of total RNA was amplified, labeled and hybridized to the array according to the manufacturer’s protocols.
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| Contributor(s) |
Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET |
| Citation(s) |
17542648 |
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| Submission date |
May 06, 2008 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Lance David Miller |
| E-mail(s) |
millerl@gis.a-star.edu.sg
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| Phone |
65 6478 8100
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| Fax |
65 6478 9060
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| URL |
http://www.gis.a-star.edu.sg/internet/site/investigators.php?f=cv&user_id=7
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| Organization name |
Genome Institute of Singapore
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| Department |
Microarray and Expression Genomics
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| Street address |
60 Bioplois Street, #02-01 Genome
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (18)
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| GSM286756 |
12hr timepoint - Untreated control - biological rep1 |
| GSM286757 |
12hr timepoint - Untreated control - biological rep2 |
| GSM286758 |
12hr timepoint - Untreated control - biological rep3 |
| GSM286759 |
12hr timepoint - E2 treated - biological rep1 |
| GSM286760 |
12hr timepoint - E2 treated - biological rep2 |
| GSM286761 |
12hr timepoint - E2 treated - biological rep3 |
| GSM286762 |
24hr timepoint - Untreated control - biological rep1 |
| GSM286763 |
24hr timepoint - Untreated control - biological rep2 |
| GSM286764 |
24hr timepoint - Untreated control - biological rep3 |
| GSM286765 |
24hr timepoint - E2 treated - biological rep1 |
| GSM286766 |
24hr timepoint - E2 treated - biological rep2 |
| GSM286767 |
24hr timepoint - E2 treated - biological rep3 |
| GSM286768 |
48hr timepoint - Untreated control - biological rep1 |
| GSM286769 |
48hr timepoint - Untreated control - biological rep2 |
| GSM286770 |
48hr timepoint - Untreated control - biological rep3 |
| GSM286771 |
48hr timepoint - E2 treated - biological rep1 |
| GSM286772 |
48hr timepoint - E2 treated - biological rep2 |
| GSM286773 |
48hr timepoint - E2 treated - biological rep3 |
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| Relations |
| BioProject |
PRJNA106571 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE11352_RAW.tar |
80.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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