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| Status |
Public on Nov 15, 2010 |
| Title |
Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. We report the first genome-wide identification and characterization of TR4 in vivo binding. Using chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), we identified TR4 binding sites in 4 different human cell types and found that the majority of target genes were shared among different cells. TR4 target genes are involved in fundamental biological processes such as RNA metabolism and protein translation. In addition, we found that a subset of TR4 target genes exerts cell-type specific functions. Analysis of the TR4 binding sites revealed that less than 30% of the peaks from any of the cell types contained the DR1 motif previously derived from in vitro studies, suggesting that TR4 may be recruited to the genome via interaction with other proteins. A bioinformatics analysis of the TR4 binding sites predicted a cis regulatory module involving TR4 and ETS transcription factors. To test this prediction, we performed ChIP-seq for the ETS factor ELK4 and found that 30% of TR4 binding sites were also bound by ELK4. Motif analysis of the sites bound by both factors revealed a lack of the DR1 element, suggesting that TR4 binding at a subset of sites is facilitated through the ETS transcription factor ELK4. Further studies will be required to investigate the functional interdependence of these two factors.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
8 total ChIP-seq datasets; four TR4 and datasets done in duplicate from 4 different cell lines; ELK4 (Sap1a) duplicate dataset done from HeLa cells; 1 ELK1 replicate in HeLa cells, 2 individual replicates for histone mod datasets from K562 cells
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| Web link |
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/info/ENCODE.html
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| Contributor(s) |
O'Geen H, Farnham PJ |
| Citation(s) |
21126370 |
| BioProject |
PRJNA63447 |
| Submission date |
Oct 13, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip Cayting |
| E-mail(s) |
pcayting@stanford.edu
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| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Snyder
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| Street address |
1501 S California Ave
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (15)
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| Relations |
| SRA |
SRP003812 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE24685_RAW.tar |
5.9 Gb |
(http)(custom) |
TAR (of BAM, BED, BIGWIG, TAGALIGN) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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