Genomics

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Genome-wide profiling of PPARγ:RXR and RNA polymerase II


ABSTRACT: Genome-wide profiling of PPARγ:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis. Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activated receptor gamma (PPARg) and retinoid X receptor (RXR) binding sites, and RNA polymerase II (RNAPII) occupancy at high resolution throughout adipocyte differentiation of 3T3-L1 cells. The data provides the first positional and temporal map PPARγ and RXR occupancy during adipocyte differentiation at a global scale. The number of PPARγ:RXR shared binding sites is steadily increasing from D0 to D6. At Day6 there are over 5000 high confidence shared PPARy:RXR binding sites. We show that at the early days of differentiation several of these sites bind not only PPARγ:RXR but also other RXR dimers. The data also provides a comprehensive temporal map of RNAPII occupancy at genes throughout 3T3-L1 adipogenesis thereby uncovering groups of similarly regulated genes belonging to glucose and lipid metabolic pathways. The majority of the upregulated but very few downregulated genes have assigned PPARγ:RXR target sites, thereby underscoring the importance of PPARγ:RXR in gene activation during adipogenesis and indicating that a hitherto unrecognized high number of adipocyte genes are directly activated by PPARγ:RXR Examination of PPARg and RXR bindingsites during adipocyte differentiation (day 0 to 6) and association with transcription via RNAPII occupancy.

ORGANISM(S): Mus musculus  

SUBMITTER: P Moulos   Susanne Mandrup  D Hagenbeek  H. Stunnenberg  Kees-Jan Françoijs  Michael Børgesen  Rasmus Siersbæk  Ronni Nielsen  Thomas Åskov Pedersen  Henk G Stunnenberg  Sergei Denissov  Eva Megens 

PROVIDER: E-GEOD-13511 | ArrayExpress | 2008-12-10

SECONDARY ACCESSION(S): SRP000630GSE13511PRJNA110113

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis.

Nielsen Ronni R   Pedersen Thomas Askov TA   Hagenbeek Dik D   Moulos Panagiotis P   Siersbaek Rasmus R   Megens Eva E   Denissov Sergei S   Børgesen Michael M   Francoijs Kees-Jan KJ   Mandrup Susanne S   Stunnenberg Hendrik G HG  

Genes & development 20081101 21


The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma) is a key regulator of adipocyte differentiation in vivo and ex vivo and has been shown to control the expression of several adipocyte-specific genes. In this study, we used chromatin immunoprecipitation combined with deep sequencing to generate genome-wide maps of PPARgamma and retinoid X receptor (RXR)-binding sites, and RNA polymerase II (RNAPII) occupancy at very high resolution throughout adipocyte differentiat  ...[more]

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