Extensive mapping of PPAR binding to genomic DNA

The peroxisome proliferator-activated receptor (PPAR) transcription factors a, d and g are members of the nuclear hormone receptor super family. The PPARs bind regulatory DNA elements (PPREs) as heterodimers with the retinoid X receptor (RXR) and thereby induce transcription in response to ligand activation.

The PPARs are important regulators of transcription in response to metabolic signalling, but have diverse metabolic functions. Thus, PPARg is a lipogenic transcription factor, whereas PPARa and -d induce lipid oxidation. In vivo, the PPARs are required for regulation of diverse metabolic processes such as adaptation to fasting and cold, muscle isotype switching and adipogenesis, underscoring the metabolic importance of these transcription factors. Although the PPARs have been subject to intensive studies for almost two decades, far from all PPAR target genes are known. In addition, only few of the known target genes have well defined PPREs. In order to understand the different outcome of distinct PPAR subtype activation in diverse tissues a more thorough investigation of PPAR binding to chromatin and subsequent target gene activation is essential.

We have used ectopic expression of PPARg2 and RXR combined with ChIP-on-chip and expression array analysis to map PPAR target sites in a murine hepatoma cell line. Our analysis reveals several novel putative PPAR target genes and provides information about PPAR binding in the vicinity of known targets. These results provide the basis for an extensive analysis of the regulatory networks controlled by PPAR transcription factors, thereby allowing for a better understanding of PPAR biology.

- Adenoviral expression PPARg2 and RXR induce transcription from a wide range of hepatocyte as well as non-hepatocyte PPAR target genes in the murine AML-12 hepatoma cell line. Only very few PPAR target genes are not induced by PPARg2/RXR.

- ChIP-on-chip analysis shows ~1200 peaks on chr. 7 & 8 by peak detection software. 80% of selected peaks were positive in single ChIP experiments.

 

- PPARg2/RXR are recruited to DNA elements near several genes on chr. 7 & 8 which are significantly induced. Examples of novel target sites and putative target genes include DGAT2, ATE1, Apq11 and Eps8l2.

 - We show that PPARg2/RXR are recruited to DGAT2, ATE1, Apq11 and Eps8l2 genes during 3T3-L1 adipogenesis, thereby confirming the biological relevance of the target sites identified by ectopic expression of PPARg2/RXR in hepatoma cells.