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Indeed, the enhanced expression of the SIRT1 gene after PPAR��/�� ligand activation is not associated with PPAR��/�� binding to its 5�� flanking region, but is mediated instead by a canonical Sp1 binding site. Consistently, this potent trans-activating effect of PPAR��/��/""type"":""entrez-nucleotide"",""attrs"":""text"":""GW501506"",""term_id"":""289075971"",""term_text"":""GW501506""GW501506 was completely abolished in the presence of Mithramycin, an inhibitor of Sp1, suggesting that Sp1 could act as an ancillary factor for PPAR��/�� [Okazaki et al., 2010]. Finally, in HCT116 colorectal [http://www.selleckchem.com/products/MK-2206.html selleck inhibitor] carcinoma cells, VEGFA transcription is regulated by PPAR��/�� via ��-catenin-mediated chromatin loops. The authors show that chromatin loops around VEGFA are released upon PPAR��/�� activation. The model predicts that ��-catenin mediates repressive looping and that PPAR��/��-specific ligands release the loops, creating an active transcription unit [Hwang et al., 2012]. In concert, this limited number of examples (this presentation is not exhaustive) demonstrate that ChIP of PPAR��/�� can be obtained in certain contexts. Other contexts were not so successful and required, for example, the use of a V5- PPAR��/�� tagged protein [Yamamoto et al., 2011]. Recently, however, two groups have succeeded in performing genome-wide analyses of PPAR��/�� binding. Adhikary et al.,[Adhikary et al., 2011] performed genome-wide analyses of human myofibroblasts (WPMY-1 cell line), treated with or without agonist (""type"":""entrez-nucleotide"",""attrs"":""text"":""GW501516"",""term_id"":""289075981"",""term_text"":""GW501516""GW501516), [http://en.wikipedia.org/wiki/ROR1 ROR1] in control cells and in PPAR��/��-depleted cells, to identify PPAR��/��-mediated gene regulation. ChIP-Seq analyses of PPAR��/��, RNA POL II, and H3K4me3 have been performed, using for PPAR��/�� a Santa Cruz antibody. The sequencing data identified a total of 4542 enriched peaks for PPAR��/��, most of them inside transcribed genomic regions or less than 25Kb upstream. Among the 4542 enriched peaks for PPAR��/��, the high confidence peak set defined as having a false discovery rate (FDR) [http://www.selleckchem.com/products/ABT-263.html http://www.selleckchem.com/products/ABT-263.html] inducible proximal promoter. The identified enriched sites were subsequently combined with transcriptional profiling derived from both agonist ""type"":""entrez-nucleotide"",""attrs"":""text"":""GW501516"",""term_id"":""289075981"",""term_text"":""GW501516""GW501516-treated or PPAR��/��-silenced myofibroblasts. This additional analysis enabled the definition of 112 bona fide PPAR��/�� target genes classified according to three distinct types of transcriptional response: ligand-independent repression by PPAR��/��; ligand-induced activation and/or derepression by PPAR��/��; and ligand-independent activation by PPAR��/��.

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