PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale

Peroxisome proliferator-activated receptor gamma(PPAR gamma), a nuclear receptor and the target of anti-diabetic thiazolinedione drugs, is known as the master regulator of adipocyte biology. Although it regulates hundreds of adipocyte genes, PPAR gamma binding to endogenous genes has rarely been demonstrated. Here, utilizing chromatin immunoprecipitation (ChIP) coupled with whole genome tiling arrays, we identified 5299 genomic regions of PPAR gamma binding in mouse 3T3-L1 adipocytes. The consensus PPAR gamma/RXR gamma "DR-1"-binding motif was found at most of the sites, and ChIP for RXR alpha showed colocalization at nearly all locations tested. Bioinformatics analysis also revealed CCAAT/enhancer-binding protein (C/EBP)-binding motifs in the vicinity of most PPAR gamma-binding sites, and genome-wide analysis of C/EBP alpha binding demonstrated that it localized to 3350 of the locations bound by PPAR gamma. Importantly, most genes induced in adipogenesis were bound by both PPAR gamma and C/EBP alpha, while very few were PPAR gamma-specific. C/EBP beta also plays a role at many of these genes, such that both C/EBP alpha and beta are required along with PPAR gamma for robust adipocyte-specific gene expression. Thus, PPAR gamma and C/EBP factors cooperatively orchestrate adipocyte biology by adjacent binding on an unanticipated scale.