ABSTRACT: BACKGROUND: The present study coupled expression profiling with chromatin immunoprecipitation sequencing (ChIP-seq) to examine peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta)-dependent regulation of gene expression in mouse keratinocytes, a cell type that expresses PPARbeta/delta in high concentration. RESULTS: Microarray analysis elucidated eight different types of regulation that modulated PPARbeta/delta-dependent gene expression of 612 genes ranging from repression or activation without an exogenous ligand, repression or activation with an exogenous ligand, or a combination of these effects. Bioinformatic analysis of ChIP-seq data demonstrated promoter occupancy of PPARbeta/delta for some of these genes, and also identified the presence of other transcription factor binding sites in close proximity to PPARbeta/delta bound to chromatin. For some types of regulation, ATF4 is required for ligand-dependent induction of PPARbeta/delta target genes. CONCLUSIONS: PPARbeta/delta regulates constitutive expression of genes in keratinocytes, thus suggesting the presence of one or more endogenous ligands. The diversity in the types of gene regulation carried out by PPARbeta/delta is consistent with dynamic binding and interactions with chromatin and indicates the presence of complex regulatory networks in cells expressing high levels of this nuclear receptor such as keratinocytes. Results from these studies are the first to demonstrate that differences in DNA binding of other transcription factors can directly influence the transcriptional activity of PPARbeta/delta.