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Series GSE39277 Query DataSets for GSE39277
Status Public on Sep 05, 2012
Title Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription factors require coactivators and corepressors to modulate transcription in mammalian cells. The vitamin D receptor (VDR) utilizes coactivators and corepressors to gain tight control over the activity of a diverse set of genes that can regulate calcium transport, slow proliferation and promote immune responses. We have recently established the VDR/RXR cistrome in human colon cancer cells and have linked these binding sites to the genes that are regulated by 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). In additional studies described herein, we demonstrate that the coactivators SRC1, CBP and MED1 are recruited to upregulated genes to facilitate transcription as expected. SRC1 was the most highly correlated to VDR/RXR binding (50%). However, we also found that corepressor molecules such as NCoR and SMRT were present along with SRC1, CBP or MED1 at these 1,25(OH)2D3 activated gene enhancers. Interestingly, genome-wide NCoR binding mimicked VDR binding by increasing its association with VDR binding in response to 1,25(OH)2D3 treatment. Overall, these data indicate a complex role for corepressor and coactivator complexes in the activation or active repression of 1,25(OH)2D3 responsive genes.
Overall design 5 coregulators are analyzed by ChIP-seq. The Input from GSE31939 was used as the normalizing factor for all transcription factor IPs. If lanes had more than 1 replicate, these lanes were combined for greater read depth.
Contributor(s) Meyer MB, Pike JW
Citation(s) 22944139
Submission date Jul 11, 2012
Last update date May 15, 2019
Contact name Mark B Meyer
Phone 608-890-0857
Organization name University of Wisconsin-Madison
Department Nutritional Sciences
Lab Meyer Lab
Street address 1415 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (10)
GSM959625 LS180_SRC1_Veh
GSM959626 LS180_SRC1_125
GSM959627 LS180_CBP_Veh
BioProject PRJNA170469
SRA SRP014204

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Supplementary file Size Download File type/resource
GSE39277_RAW.tar 8.4 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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