An Ideal PPAR Response Element Bound to and Activated by PPAR[alpha]

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.