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Series GSE41502 Query DataSets for GSE41502
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
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.
Contributor(s) Ballare C, Beato M
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Submission date Oct 11, 2012
Last update date Feb 22, 2018
Contact name Miguel Beato
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
This SubSeries is part of SuperSeries:
GSE41617 Nucleosome driven transcription factor binding and gene regulati
BioProject PRJNA177704

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41502_RAW.tar 70.4 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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