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| Status |
Public on May 13, 2010 |
| Title |
A quantitative model of transcription regulation reveals the role of non-conserved enhancers |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We identify sites of combinatorial control by performing high throughput ChIP experiments on p300, CREB-binding protein (CBP), the deacetylase SIRT1 and on multiple DNA-binding transcription factors in three different tissues. We present a quantitative model of transcriptional regulation that reveals the contribution of each binding site to tissue-specific gene expression in several mouse cell types. Binding to both evolutionarily conserved and non-conserved sequences is found to contribute significantly to transcriptional regulation. We demonstrate that binding location strongly predicts the expression level of nearby genes.
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| Overall design |
Liver hepatocytes and cerebellum tissue were harvested from male C57BL/6J mice. RNA was extracted and hybridized to Affymetrix arrays. Examination of transcriptional regulator binding in three mouse tissues by ChIP-IP using tiling arrays. Examination of CBP binding in mouse liver and cerebellum by ChIP-seq.
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| Contributor(s) |
MacIsaac K, Fraenkel E |
| Citation(s) |
20442865 |
| Submission date |
Jul 13, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenzie MacIsaac |
| E-mail(s) |
macisaac@mit.edu
|
| Phone |
617-253-2042
|
| Fax |
617-395-2661
|
| URL |
http://fraenkel.mit.edu
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| Organization name |
MIT
|
| Street address |
77 Massachusetts Ave.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (4)
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| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
| GPL8846 |
Agilent Mus musculus proximal promoter 185k array slide 1 |
| GPL8847 |
Agilent Mus musculus proximal promoter 185k array slide 2 |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (28)
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| Relations |
| SRA |
SRP002283 |
| BioProject |
PRJNA119775 |
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