An Ideal PPAR Response Element Bound to and Activated by PPARα

Peroxisome proliferator-activated receptor-alpha (PPAR alpha), a nuclear receptor, plays an important role in the transcription of genes involved in fatty acid metabolism through heterodimerization with the retinoid x receptor (RXR). The consensus sequence of the PPAR response element (PPRE) is composed of two AGGTCA-like sequences directionally aligned with a single nucleotide spacer. PPAR alpha and RXR bind to the 5' and 3' hexad sequences, respectively. However, the precise sequence definition of the PPRE remains obscure, and thus, the consensus sequence currently available remains AGGTCANAGGTCA with unknown redundancy. The vague PPRE sequence definition poses an obstacle to understanding how PPAR alpha regulates fatty acid metabolism. Here we show that, rather than the generally accepted 6-bp sequence, PPAR alpha actually recognized a 12-bp DNA sequence, of which the preferred binding sequence was WAWVTRGGBBAH. Additionally, the optimized RXR alpha hexad binding sequence was RGKTYA. Thus, the optimal PPAR alpha/RXR alpha heterodimer binding sequence was WAWVTRGGBBAHRGKTYA. The single nucleotide substitution, which reduces binding of RXR alpha to DNA, attenuated PPAR alpha-induced transcriptional activation, but this is not always true for PPAR alpha. Using the definition of the PPRE sequence, novel PPREs were successfully identified. Taken altogether, the provided PPRE sequence definition contributes to the understanding of PPAR alpha signaling by identifying PPAR alpha direct target genes with functional PPAR alpha response elements.