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| Status |
Public on Feb 01, 2012 |
| Title |
Genome-wide mapping of HIF-2 binding in 786-O clear cell renal carcinoma cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Kidney cancer accounts for more than 100,000 deaths per year world-wide. More than 80% are clear cell tumors (ccRCCs) and the majority are associated with loss of function of the von Hippel Lindau (pVHL) tumor suppressor resulting in upregulation of HIF-{alpha} subunits, and activation of HIF-dependent transcriptional pathways. Recent GWAS studies have discovered RCC-susceptibility loci both within EPAS1 (HIF-2{alpha}) and in an intergenic region of unknown function on 11q13.3. As part of an ongoing study to define the direct transcriptional targets of HIF-2 in renal cancer, we undertook a genome-wide analysis of HIF-2-binding sites in pVHL-defective 786-O cells (that lack functional HIF-1{alpha} due to a truncated transcript) using chromatin immunoprecipitation with antibodies directed against HIF-2{alpha} and its dimerization partner HIF-1{beta}, coupled to high-throughput sequencing (ChIP-seq). Amongst approximately 600 pangenomic HIF-2{beta} ChIP signals, we observed strong binding (ranked 12th by peak height) almost precisely coinciding with the RCC predisposition SNP rs7105934 on 11q13.3.
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| Overall design |
We report binding of HIF-2{alpha} and HIF-1{beta} in 786-O clear cell renal carcinoma cells.
3 samples examined, HIF-2{alpha}, HIF-1{beta} and pre-immune control ChIP.
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| Contributor(s) |
Mole DR, Schoedel J |
| Citation(s) |
22406644 |
| Submission date |
Jan 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Robert Mole |
| E-mail(s) |
david.mole@ndm.ox.ac.uk
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| Phone |
0044 (0)1865 613956
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| Organization name |
University of Oxford
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| Department |
Nuffield Department of Medicine
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| Lab |
NDM Research Building
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| Street address |
Roosevelt Drive, Headington
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| City |
Oxford |
| ZIP/Postal code |
OX3 7FZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (3) |
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| Relations |
| SRA |
SRP010128 |
| BioProject |
PRJNA150099 |
