Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE25547 | GEO | 2010/11/23
SECONDARY ACCESSION(S): PRJNA134025
REPOSITORIES: GEO
Similar Datasets
Project description:The transcription factor Peroxisome Proliferator-Activated Receptor M-NM-1 (PPARM-NM-1) is an important regulator of hepatic lipid metabolism. While PPARM-NM-1 is known to activate transcription of numerous genes, no comprehensive picture of PPARM-NM-1 binding to endogenous genes has yet been reported. To fill this gap, we performed ChIP-chip in combination with transcriptional profiling on HepG2 human hepatoma cells treated with the PPARM-NM-1 agonist GW7647. We found that GW7647 increased PPARM-NM-1 binding to 4220 binding regions. GW7647-induced binding regions showed a bias around the transcription start site and most contained a predicted PPAR binding motif. Several genes known to be regulated by PPARM-NM-1, such as ACOX1, SULT2A1, ACADL, CD36, IGFBP1 and G0S2, showed GW7647-induced PPARM-NM-1 binding to their promoter. A GW7647-induced PPARM-NM-1-binding region was also assigned to SREBP-targets HMGCS1, HMGCR, FDFT1, SC4MOL, and LPIN1, expression of which was induced by GW7647, suggesting cross-talk between PPARM-NM-1 and SREBP signaling. Our data furthermore demonstrate interaction between PPARM-NM-1 and STAT transcription factors in PPARM-NM-1-mediated transcriptional repression, and suggest interaction between PPARM-NM-1 and TBP and C/EBPM-NM-1 in PPARM-NM-1-mediated transcriptional activation. Overall, our analysis leads to important new insights into the mechanisms and impact of transcriptional regulation by PPARM-NM-1 in human liver and highlight the importance of cross-talk with other transcription factors. HepG2 cells were grown in phenol red-free DulbeccoM-bM-^@M-^Ys modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 M-BM-0C and 5% CO2. The following day, cells were treated with either 100 nM of the PPARM-NM-1 agonist GW7647 or control vehicle (DMSO). Cells used for gene expression analysis were harvested after 6 h or 24 h of GW7647 treatment. This submission represents the gene expression component of the study.
2010-11-23 | E-GEOD-25547 | biostudies-arrayexpress
Project description:Nuclear receptor activation in liver leads to coordinated alteration of the expression of multiple gene products with attendant phenotypic changes of hepatocytes. Peroxisome proliferators including endogenous fatty acids, environmental chemicals, and drugs induce a multi-enzyme metabolic response that affects lipid and fatty acid processing. We studied the signaling network for the peroxisome proliferator-associated receptor alpha (PPARα) in primary human hepatocytes using the selective PPARα ligand, GW7647. We measured gene expression over multiple concentrations and times and conducted ChIP-seq studies at 2 and 24 hours to assess genomic binding of PPARα. Over all treatments there were 192 genes differentially expressed. Of these only 51% showed evidence of PPARα binding – either directly at PPARα response elements or via alternative mechanisms. Almost half of regulated genes had no PPARα binding. We then developed two novel bioinformatics methods to visualize the dose-dependent activation of both the transcription factor circuitry for PPARα and the downstream metabolic network in relation to functional annotation categories. Available databases identified several key transcription factors involved with the non-genomic targets after GW7647 treatment, including SP1, STAT1, ETS1, ERα, and HNF4α. The linkage from PPARα binding through gene expression likely requires intermediate protein kinases to activate these transcription factors. We found enrichment of functional annotation categories for organic acid metabolism and cell lipid metabolism among the differentially expressed genes. Lipid transport processes showed enrichment at the highest concentration of GW7647 (10μM). While our strategy for mapping transcriptional networks is evolving, these approaches are necessary in moving from toxicogenomic methods that derive signatures of activity to methods that establish pathway structure, showing the coordination of the activated nuclear receptor with other signaling pathways. Primary hepatocytes from four donors were exposed to 0, 0.001, 0.01, 0.1, 1.0, or 10.0μM GW7647 for 2, 6, 12, 24, or 72 hours.
2013-12-18 | E-GEOD-53399 | biostudies-arrayexpress
Project description:Objective : This work aimed at characterizing PPARα involvement in metabolism regulation and at comparing PPARα and PPARγ roles in human white adipocytes. Research Design and Methods : Profiling of gene expression alterations was assessed with microarrays and RT-qPCR. Primary cultures of human adipocytes were treated with PPARα agonist GW7647 or PPARγ agonist Rosiglitazone. Western blot were used to determine protein level modifications. Metabolic changes were evaluated with palmitate and glucose oxidation studies and with metabolite measurements. Results : GW7647 induces an upregulation of β-oxidation gene expression and increases palmitate oxidation. Unexpectedly glycolysis was strongly reduced at transcriptional and functional levels by GW7647 while the overall glucose oxidation remains unaltered, leading to a decrease in pyruvate and lactate production. Moreover lipogenesis was downregulated by GW7647 inhibiting triglyceride esterification and de novo lipogenesis. GW7647 induced alterations were abolished by a PPARα antagonist treatment and were clearly different from Rosiglitazone effects. Rosiglitazone had no major impact on glycolysis and β-oxidation but increased glucose incorporation into glycerol backbone of triglycerides. Conclusions : Altogether these results show that PPARα can upregulate β-oxidation in human white adipocytes. Its pharmacological activation may be used to oxidize fatty acids in situ when lipolysis is activated thus preventing their release into systemic circulation. We treated four adipocyte cultures, each one coming from different subjects, with GW7647, Rosiglitazone (ROSI) or DMSO. DMSO treated cells are control samples. Thus we have four paired sample groups for each treatment (GW7647 and ROSI).
2010-04-11 | E-GEOD-15862 | biostudies-arrayexpress
Project description:Nuclear receptor activation in liver leads to coordinated alteration of the expression of multiple gene products with attendant phenotypic changes of hepatocytes. Peroxisome proliferators including endogenous fatty acids, environmental chemicals, and drugs induce a multi-enzyme metabolic response that affects lipid and fatty acid processing. We studied the signaling network for the peroxisome proliferator-associated receptor alpha (PPARα) in primary human hepatocytes using the selective PPARα ligand, GW7647. We measured gene expression over multiple concentrations and times and conducted ChIP-seq studies at 2 and 24 hours to assess genomic binding of PPARα. Over all treatments there were 192 genes differentially expressed. Of these only 51% showed evidence of PPARα binding – either directly at PPARα response elements or via alternative mechanisms. Almost half of regulated genes had no PPARα binding. We then developed two novel bioinformatics methods to visualize the dose-dependent activation of both the transcription factor circuitry for PPARα and the downstream metabolic network in relation to functional annotation categories. Available databases identified several key transcription factors involved with the non-genomic targets after GW7647 treatment, including SP1, STAT1, ETS1, ERα, and HNF4α. The linkage from PPARα binding through gene expression likely requires intermediate protein kinases to activate these transcription factors. We found enrichment of functional annotation categories for organic acid metabolism and cell lipid metabolism among the differentially expressed genes. Lipid transport processes showed enrichment at the highest concentration of GW7647 (10μM). While our strategy for mapping transcriptional networks is evolving, these approaches are necessary in moving from toxicogenomic methods that derive signatures of activity to methods that establish pathway structure, showing the coordination of the activated nuclear receptor with other signaling pathways.
2013-12-18 | GSE53399 | GEO
Project description:Objective : This work aimed at characterizing PPARα involvement in metabolism regulation and at comparing PPARα and PPARγ roles in human white adipocytes. Research Design and Methods : Profiling of gene expression alterations was assessed with microarrays and RT-qPCR. Primary cultures of human adipocytes were treated with PPARα agonist GW7647 or PPARγ agonist Rosiglitazone. Western blot were used to determine protein level modifications. Metabolic changes were evaluated with palmitate and glucose oxidation studies and with metabolite measurements. Results : GW7647 induces an upregulation of β-oxidation gene expression and increases palmitate oxidation. Unexpectedly glycolysis was strongly reduced at transcriptional and functional levels by GW7647 while the overall glucose oxidation remains unaltered, leading to a decrease in pyruvate and lactate production. Moreover lipogenesis was downregulated by GW7647 inhibiting triglyceride esterification and de novo lipogenesis. GW7647 induced alterations were abolished by a PPARα antagonist treatment and were clearly different from Rosiglitazone effects. Rosiglitazone had no major impact on glycolysis and β-oxidation but increased glucose incorporation into glycerol backbone of triglycerides. Conclusions : Altogether these results show that PPARα can upregulate β-oxidation in human white adipocytes. Its pharmacological activation may be used to oxidize fatty acids in situ when lipolysis is activated thus preventing their release into systemic circulation.
2010-04-11 | GSE15862 | GEO
Project description:The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice is dependent on LXR and correlates with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the role of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligand-regulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. Functional annotation of putative direct LXR target genes revealed a significant association with classical LXR-regulated pathways as well as PPAR signaling pathways, and subsequent ChIP-seq mapping of PPARα binding demonstrated binding of PPARα to 71-88% of the identified LXR:RXR binding sites. Sequence analysis of shared binding regions combined with sequential ChIP on selected sites indicate that LXR:RXR and PPARα:RXR bind to degenerate response elements in a mutually exclusive manner. Together our findings suggest extensive and unexpected cross-talk between hepatic LXR and PPARα at the level of binding to shared genomic sites
2012-01-31 | GSE35262 | GEO
Project description:Analyses of gene expression by RNA-Seq in mouse E14.5 fetal liver burst-forming unit erythroid (BFU-E) cells untreated or treated by dexamethasone (DEX) with or without PPARα agonist GW7647.
2015-06-08 | GSE63836 | GEO
Project description:Activation of PPARα pathways by some environmental chemicals causes hepatocyte proliferation and cancer in rodents. While these responses do not seem to occur in humans, the biological basis of these species differences remains uncertain. We systematically evaluated multiple readouts in rat and human hepatocytes and gene expression in intact rat livers using a PPARα-selective agonist, GW7467. In vitro rat hepatocytes had more genes significantly altered by GW7647 than did human (2320 versus 192). There were common pathways of fatty acid metabolism, amino acid metabolism and lipid transport, mostly represented by upregulated genes, shared between species. In rat hepatocytes, there were many downregulated genes enriched for processes including apoptosis, inflammation, response to hormones and chemical stimuli. In vivo, gene expression signatures for proliferation were present at high doses. In both species, a third of the genes with altered expression had direct binding of PPARα to a nearby peroxisome proliferator response element (PPRE). While the PPRE associated with upregulated genes in both species, was similar, the downregulated genes in the rat had altered flanking region conservation of nucleotides. Among the down regulated genes with direct PPARα binding in the rat were two key transcription factors – Hnf6 (onecut1) and Ets. Our results support a qualitative difference in biology of PPARα activation between human and rats. The secondary downregulated pathways, in the rat, appear to be reversion to an earlier lineage more responsive to proliferative signals that likely arise from interactions between the PPARα activated hepatocytes and other cell types in the intact liver.
2017-07-01 | GSE70583 | GEO
Project description:Activation of PPARα pathways by some environmental chemicals causes hepatocyte proliferation and cancer in rodents. While these responses do not seem to occur in humans, the biological basis of these species differences remains uncertain. We systematically evaluated multiple readouts in rat and human hepatocytes and gene expression in intact rat livers using a PPARα-selective agonist, GW7467. In vitro rat hepatocytes had more genes significantly altered by GW7647 than did human (2320 versus 192). There were common pathways of fatty acid metabolism, amino acid metabolism and lipid transport, mostly represented by upregulated genes, shared between species. In rat hepatocytes, there were many downregulated genes enriched for processes including apoptosis, inflammation, response to hormones and chemical stimuli. In vivo, gene expression signatures for proliferation were present at high doses. In both species, a third of the genes with altered expression had direct binding of PPARα to a nearby peroxisome proliferator response element (PPRE). While the PPRE associated with upregulated genes in both species, was similar, the downregulated genes in the rat had altered flanking region conservation of nucleotides. Among the down regulated genes with direct PPARα binding in the rat were two key transcription factors – Hnf6 (onecut1) and Ets. Our results support a qualitative difference in biology of PPARα activation between human and rats. The secondary downregulated pathways, in the rat, appear to be reversion to an earlier lineage more responsive to proliferative signals that likely arise from interactions between the PPARα activated hepatocytes and other cell types in the intact liver.
2017-07-01 | GSE70585 | GEO
Project description:DNA binding preferences of fungal SREBP transcription regulators
| PRJNA485525 | ENA