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| Status |
Public on Jan 04, 2011 |
| Title |
Integrative model of genomic factors for determining binding site selection by estrogen receptor alpha in MCF-7 cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction.
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| Overall design |
The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.
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| Contributor(s) |
Joseph R, Kong SL, Orlov YL, Liu ET |
| Citation(s) |
21179027, 21878914 |
| Submission date |
Aug 18, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuriy L Orlov |
| E-mail(s) |
orlovy@gis.a-star.edu.sg
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| Organization name |
Genome Institute of Singapore
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| Department |
Computational Systems Biology
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| Street address |
60 Biopolis Street
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (16)
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| GSM588562 |
FAIRE sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588563 |
FAIRE sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588564 |
H3K27me3 sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588565 |
H3K27me3 sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588566 |
H3K9me3 sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588567 |
H3K9me3 sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588568 |
H3K4me1 sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588569 |
H3K4me1 sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588570 |
H3K4me3 sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588571 |
H3K4me3 sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588572 |
H3K9ac sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588573 |
H3K9ac sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588574 |
H3K14ac sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588575 |
H3K14ac sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
| GSM588576 |
RNA Pol II sequencing in estradiol (E2) treated MCF-7 cells |
| GSM588577 |
RNA Pol II sequencing in non-treated (DMSO as vehicle) MCF-7 cells |
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| Relations |
| SRA |
SRP005377 |
| BioProject |
PRJNA130905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23701_RAW.tar |
640.6 Mb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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