SOM analysis of established primary PPAR target genes, clusters III and IV

The genes were sorted by SOM analysis with respect to overall PPRE pattern similarity and their evolutionary conservation into cluster III and cluster IV. For more details, see the Figure 6 legend.<p><b>Copyright information:</b></p><p>Taken from "Meta-analysis of primary target genes of peroxisome proliferator-activated receptors"</p><p>http://genomebiology.com/2007/8/7/R147</p><p>Genome Biology 2007;8(7):R147-R147.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC2323243.</p><p></p

Association of genomic regions of PPAR target genes with PPARs and their partner proteins

Chromatin was extracted from HEK293 cells that had been treated with solvent (DMSO) or for 120 minutes with 100 nM GW7647. The association of PPARα, RXRα and pPol II was monitored by ChIP assays with respective antibodies on genomic regions of the eight PPAR target genes that are close to the TSS, upstream of the TSS and downstream of the TSS; for location see Figure 3 and Table 2. Since the gene is not expressed in HEK293 cells, the data for its four genomic regions were obtained using chromatin derived from HepG2 cells. Real-time quantitative PCR was performed on chromatin templates and the fold change of the antibody-precipitated template in relation to an IgG-precipitated specificity control template was calculated. PPARα shows specific association with 15 of the 23 tested regions and the relative association with these regions is shown. Columns represent means of at least three experiments and bars indicate standard deviations. Two-tailed Student's -tests were performed to determine the significance of association in reference to IgG controls (*< 0.05, **< 0.01, ***< 0.001).<p><b>Copyright information:</b></p><p>Taken from "Meta-analysis of primary target genes of peroxisome proliferator-activated receptors"</p><p>http://genomebiology.com/2007/8/7/R147</p><p>Genome Biology 2007;8(7):R147-R147.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC2323243.</p><p></p

Extra-genomic functionality of the PPRE-containing promoter regions of PPAR target genes

Reporter gene assays were performed with extracts from HEK293 and HepG2 cells that were transiently transfected with reporter constructs containing genomic regions of eight human PPAR target genes (please note that the gene forms a cluster with the genes and ). These were co-transfected with empty expression vector (endogenous PPAR) or the indicated expression vectors for PPARα, PPARγ and PPARβ/δ. Cells were then treated for 16 h with solvent or PPAR subtype-specific ligands. Relative luciferase activity was determined and normalized to the activity of empty cloning vector control co-transfected with empty expression vector (dashed horizontal red line). The genomic regions were subdivided according to their location into close to TSS (a, d), upstream of TSS (b, e) and downstream of TSS (c, f); for further details see Figure 3 and Table 2. Columns represent the means of at least three experiments and bars indicate standard deviations. Two-tailed Student's -tests were performed to determine the significance of the ligand induction in reference to solvent controls (*< 0.05, **< 0.01, ***< 0.001).<p><b>Copyright information:</b></p><p>Taken from "Meta-analysis of primary target genes of peroxisome proliferator-activated receptors"</p><p>http://genomebiology.com/2007/8/7/R147</p><p>Genome Biology 2007;8(7):R147-R147.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC2323243.</p><p></p