Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-5

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>DNA pUC19 (100 ng), untreated (control) or treated with 1 nM, 10 nM or 100 nM of the PPARδ specific ligand GW501516. . Co-transfection of pFABLuc reporter construct (200 ng) with constant amount of expression vector for PPARδ1 (50 ng) and increasing concentrations of the expression vector for PPARδ2 (50 to 200 ng) and treatment with 10 nM or 100 nM GW501516. Transfection of the pFABLuc vector alone was used as a control. Plasmid DNA pUC19 was added to ensure equal amount of DNA in all transfections. Plasmid pSV-β-galactosidase control vector (Promega) (260 ng) was co-transfected in all experiments for normalization of the transfection efficiency. The data presented are the mean (± SD) luciferase/β-galactosidase ratios of three independent transfections determined in quadruplicates. The activities are expressed as relative values setting the value of untreated control to 1 () or the value obtained without PPARδ2 expression plasmid to 1 (). C. Western blot analysis with nuclear extracts prepared from untransfected HeLa cells (Contr) and HeLa cells transfected with the expression vectors encoding PPARδ1 or PPARδ2, respectively, using a PPARδ antibody raised against the N-terminal region of the nuclear receptor (sc-7197, Santa Cruz Biotechnology). The sizes of standard molecule markers are given on the left side

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-2

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>and HeLa cells (bars), setting the value of the promoterless control plasmid to 1. . Luciferase assays on reporter gene constructs containing from 2.6 kb down to 48 bp of the region upstream of exon 1 in the PPARδ gene compared to empty pGL3 vector. . Luciferase assay on reporter gene constructs containing approximately 1 kb and 250 bp of the upstream regions of four identified alternative 5'-ends summarized in Table 2 and illustrated in Figure 1(), compared to empty pGL3 vector

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-9

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>entified exons (denoted in row) indicated. The genomic positions of the new exons were deduced by comparing their sequences to that of the human PPARδ gene [GenBank: ]. The sequences of splice junctions and alternative 5'-ends related to these exons are outlined in Tables 1 and 2, respectively. . A schematic representation of the PPARδ gene showing coding exons (boxes), previously reported untranslated exons or part of exons (boxes), and herein identified untranslated exons (boxes). The analysed and discussed variety of splicing among untranslated exons and alternative 5'-ends identified by Marathon 5'-RACE as described in "Methods" is shown below the gene ()

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-8

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>aque (; chr4) and chimpanzee (; chr6) orthologous genes are shown. Conserved sequences are defined as coding exons (blue), untranslated exons (yellow) and introns (pink). The locations of the novel untranslated human exons (2a-2e) in the PPARδ gene are indicated by arrows. The percent identity of the masked (unaligned) sequence harbouring exons 2b and 2c obtained by ClustalW alignment is indicated in the defined area, likewise the lack of identity over the masked region containing exon 2d is indicated by horizontal lines. A schematic view showing the locations of previously identified exons in human PPARδ gene are aligned above the conservation profile for orientation

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-7

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>ed for by the 63 kb versus 50 kb separating exon 2 and the first coding exon (4 or 3) in human and mouse genes, respectively. The relative positions of exons along the genes are given, specifying exons that are conserved between species (boxes) and species-specific exons (boxes). indicate the position of the initiation codon ATG and the stop codon TAA, respectively, with the intervening coding exons

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-3

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-6

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p>XRα or mock lysate as described in "Methods". Unlabelled ACO-PPRE was added at 100-fold molar excess for competition. Supershift experiments were carried out using a PPARδ antibody directed against the N-terminal region of human PPARδ. indicate the positions of the shifted and the supershifted bands. None of the receptors (PPARδ1, PPARδ2 or RXRα) alone could be supershifted in the presence of the PPARδ antibody (data not shown)

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability-1

<p><b>Copyright information:</b></p><p>Taken from "Alternative splicing of human peroxisome proliferator-activated receptor delta (PPARdelta):effects on translation efficiency and -activation ability"</p><p>http://www.biomedcentral.com/1471-2199/8/70</p><p>BMC Molecular Biology 2007;8():70-70.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2045109.</p><p></p

The power of the first and last test under a double dominant interaction model.

<p>The x-axis is the heritability of the model. The y-axis is the statistical power. The colored lines correspond to two different tests: the one performed in the first stage that tests the null hypothesis of no interaction, <i>H</i>₁, (red), and the one performed in the last stage that specifically tests the interaction parameters, <i>H</i>₂, (blue). The logit link function and a nominal significance level of 0.05 was used for the analysis.</p

Estimated family-wise error rate for all methods under different null models, using a significance threshold of 0.05.

<p>¹ Model from which data was generated</p><p>² Single main association</p><p>³ Double main association</p><p>⁴ Multivariate additive GLM</p><p>Estimated family-wise error rate for all methods under different null models, using a significance threshold of 0.05.</p