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| Status |
Public on Feb 23, 2011 |
| Title |
Cross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We used chromatin immunoprecipitation combined with deep sequencing to map all binding sites of C/EBPα and PPARγ in human SGBS adipocytes and compared these with the genome-wide profiles from mouse 3T3-L1 adipocytes to systematically investigate what biological features correlate with retention of sites in orthologous regions between mouse and human. Despite a limited interspecies retention of binding sites, several biological features make sites more likely to be retained. First, co-binding of PPARγ and C/EBPα in mouse is the most powerful predictor of retention of the corresponding binding sites in human. Second, vicinity to genes highly upregulated during adipogenesis significantly increases retention. Third, the presence of C/EBPα consensus sites correlate with retention of both factors, indicating that C/EBPα facilitates recruitment of PPARγ. Fourth, retention correlates with overall sequence conservation within the binding regions independent of C/EBPα and PPARγ sequence patterns, indicating that other transcription factors work cooperatively with these two key transcription factors.
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| |
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| Overall design |
C/EBPα and PPARγ ChIP-seq in mouse 3T3-L1 and human SGBS adipocytes.
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| |
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| Contributor(s) |
Schmidt SF, Jørgensen M, Chen Y, Nielsen R, Sandelin A, Mandrup S |
| Citation(s) |
21410980 |
| Submission date |
Feb 22, 2011 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
|
| Phone |
+45 6550 2340
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
|
| Samples (8)
|
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| Relations |
| BioProject |
PRJNA137049 |
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