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Cross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

ABSTRACT: 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.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE27450 | GEO | 2011/02/23

SECONDARY ACCESSION(S): PRJNA137049

REPOSITORIES: GEO

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Cross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

Project description: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. C/EBPα and PPARγ ChIP-seq in mouse 3T3-L1 and human SGBS adipocytes.

2011-02-23 | E-GEOD-27450 | biostudies-arrayexpress

Acute Genome-Wide Effects of Rosiglitazone on PPARγ Transcriptional Networks in Adipocytes

Project description:Here we report, for the first time, the acute effects of the synthetic PPARγ agonist rosiglitazone on the transcriptional network of PPARγ in adipocytes. Treatment with Rosiglitazone for 1 hour leads to acute transcriptional activation as well as repression of a number of genes as determined by genome-wide RNA polymerase II occupancy. Unlike what has been shown for many other nuclear receptors, agonist treatment does not lead to major changes in the occurrence of PPARγ binding sites. However, rosiglitazone promotes PPARγ occupancy at many preexisting sites, and this is paralleled by increased occupancy of the mediator subunit MED1. The increase in PPARγ and MED1 binding is correlated with an increase in transcription of nearby genes indicating that rosiglitazone, in addition to activating the receptor, also promotes its association with DNA, and that this is causally linked to recruitment of mediator and activation of genes. Notably, both Rosiglitazone-activated and -repressed genes are induced during adipogenesis. However, Rosiglitazone-activated genes are markedly more associated with PPARγ than repressed genes and are highly dependent on PPARγ for expression in adipocytes. By contrast, repressed genes are associated with the other key adipocyte transcription factor CCAAT-Enhancer binding protein (C/EBPα), and their expression is more dependent on C/EBPα. This suggests that the relative occupancies of PPARγ and C/EBPα are critical for whether genes will be induced or repressed by PPARγ agonist. Examination of binding of PPARγ, C/EBPα, RNAPII, CBP and MED1 in mature 3T3-L1 adipocytes treated with 1 μM Rosiglitazone and/or 0.1% DMSO for 1 hour.

2013-08-01 | E-GEOD-49423 | biostudies-arrayexpress

Cross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

Project description:Cross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

| PRJNA137049 | ENA

Acute Genome-Wide Effects of Rosiglitazone on PPARγ Transcriptional Networks in Adipocytes

2013-08-01 | GSE49423 | GEO

C/EBPα and PPARγ-specific transcriptional programs in mature adipocytes in vivo

Project description:We took a systematic approach to determine the transcriptional programs that are specifically regulated by C/EBPα in mature white adipocytes of mice on chow diet or high fat diet. The hypothesis tested in the present study was that C/EBPα, as a lipogenic transcription factor, has unique direct targets compared to PPARγ. Our inducible adipocyte specific knockout system allows us to test the direct targets of C/EBPα and PPARγ in adipocytes by short-term C/EBPα or PPARγ elimination in mature adipocytes in vivo. Results indicate that although it has been shown that C/EBPα and PPARγ cross-regulate each other, they have distinct direct responsive targets. Moreover, there are very few C/EBPα specific targets in mice on a chow diet, most of the C/EBPα targets in mature adipocytes are genes modulated by HFD feeding.

2014-11-04 | GSE62937 | GEO

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor γ in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

Project description:Here we have employed chromatin immunoprecipitation combined with deep sequencing to map and compare PPARγ binding in in vitro differentiated primary mouse adipocytes isolated from epididymal, inguinal, and brown adipose tissues. While these PPARγ binding profiles are overall similar, there are clear depot-selective binding sites. Most PPARγ binding sites previously mapped in 3T3-L1 adipocytes can also be detected in primary adipocytes, but there are a large number of PPARγ binding sites that are specific to the primary cells, and these tend to be located in closed chromatin regions in 3T3-L1 adipocytes. The depot-selective binding of PPARγ is associated with highly depot-specific gene expression. This indicates that PPARγ plays a role in the induction of genes characteristic of different adipocyte lineages and that preadipocytes from different depots are differentially preprogrammed to permit PPARγ lineage-specific recruitment even when differentiated in vitro.

2012-10-11 | GSE41481 | GEO

Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1 (expression)

Project description:Master transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARγ is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARγ without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARγ binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARγ cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator. Microarray expression profiling was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Each sample group consists of four biological replicates which are here defined as separate differentiations of mature 3T3-L1 adipocytes and adenoviral infections. Each replicate was hybridized to an individual array for a total of eight arrays.

2013-06-27 | E-GEOD-48344 | biostudies-arrayexpress

PPARg and C/EBPa response to acute cold stress in brown adipose tissue

Project description:Brown adipose tissue (BAT) has the ability to burn calories as heat. BAT thermogenesis is an attractive way to combat obesity pandemic. However, the transcriptional network resulting in lipid synthesis to oxidation shift during thermogenesis is not completely understood. Here, we report the regulation of two master regulators of adipogenesis, PPARγ and C/EBPα, during acute cold stress in BAT. We found PPARγ dissociated from DNA in a third of its binding sites and these included cebpa enhancers leading to decreased C/EBPα. This dissociation required PPARγ binding to activating ligands, thus modulated by diet. Meanwhile PPARα also detached from DNA, and co-activator PGC1α associated with ERR1 as part of transcriptional network regulating lipid metabolism. Subsequent global replacement of C/EBPα by C/EBPβ and its associated transcriptional machinery was required for upregulation of structural lipid synthesis despite general upregulation of fatty acid oxidation.

2023-05-17 | GSE218516 | GEO

PPARg and C/EBPa response to acute cold stress in brown adipose tissue [ChIP-Seq]

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PPARg and C/EBPa response to acute cold stress in brown adipose tissue [RNA-seq]

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