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| Status |
Public on Dec 01, 2012 |
| Title |
Nucleosome driven transcription factor binding and gene regulation [microarray] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Elucidating the global function of a transcription factor implies the identification of its target genes and genomic binding sites. The role of chromatin in this context is unclear, but the dominant view is that factors bind preferentially to nucleosome-depleted regions, identified as DNaseI-hypersensitive sites (DHS). Here we show by chromatin-IP, MNase and DNaseI assays followed by deep sequencing that the progesterone receptor (PR) requires nucleosomes for optimal binding and function. In breast cancer cells treated with progestins we identified 25,000 PR binding sites (PRbs), the majority encompassing several copies of the hexanucleotide TGTYCY, highly abundant in the genome. We found that functional PRbs accumulate around progesterone-induced genes mainly in enhancers, are enriched in DHS but exhibit high nucleosome occupancy. Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes are crucial for PR binding and hormonal gene regulation.
Keywords: time course
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| Overall design |
Whole genome expression microarrays were performed in T47D-MTVL cells stimulated 0, 1 and 6 hr with 10 nM of progestin R5020. 3 biological replicas were performed for T0 and 6 hr treatments and 4 for the one of 1hr.
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| Contributor(s) |
Ballare C, Beato M |
| Citation missing |
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| |
| Submission date |
Oct 11, 2012 |
| Last update date |
Feb 22, 2018 |
| Contact name |
Miguel Beato |
| E-mail(s) |
miguel.beato@crg.eu
|
| Organization name |
CRG
|
| Street address |
Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platforms (1) |
| GPL4133 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) |
|
| Samples (10)
|
| GSM1018351 |
R5020 T0 replicate 1 hybridized against UHRR |
| GSM1018352 |
R5020 T0 replicate 2 hybridized against UHRR |
| GSM1018353 |
R5020 T0 replicate 3 hybridized against UHRR |
| GSM1018354 |
R5020 1h replicate 1 hybridized against UHRR |
| GSM1018355 |
R5020 1h replicate 2 hybridized against UHRR |
| GSM1018356 |
R5020 1h replicate 3 hybridized against UHRR |
| GSM1018357 |
R5020 1h replicate 4 hybridized against UHRR |
| GSM1018358 |
R5020 6h replicate 1 hybridized against UHRR |
| GSM1018359 |
R5020 6h replicate 2 hybridized against UHRR |
| GSM1018360 |
R5020 6h replicate 3 hybridized against UHRR |
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| This SubSeries is part of SuperSeries: |
| GSE41617 |
Nucleosome driven transcription factor binding and gene regulati |
|
| Relations |
| BioProject |
PRJNA177704 |
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