Peroxisome proliferator-activated receptor ␥ (PPAR␥) is a master regulator of adipocyte differentiation and function. We and others have previously mapped PPAR␥ binding at a genome-wide level in murine and human adipocyte cell lines and in primary human adipocytes. However, little is known about how binding patterns of PPAR␥ differ between brown and white adipocytes and among different types of white adipocytes. Here we have employed chromatin immunoprecipitation combined with deep sequencing to map and compare PPAR␥ binding in in vitro differentiated primary mouse adipocytes isolated from epididymal, inguinal, and brown adipose tissues. While these PPAR␥ binding profiles are overall similar, there are clear depot-selective binding sites. Most PPAR␥ binding sites previously mapped in 3T3-L1 adipocytes can also be detected in primary adipocytes, but there are a large number of PPAR␥ binding sites that are specific to the primary cells, and these tend to be located in closed chromatin regions in 3T3-L1 adipocytes. The depot-selective binding of PPAR␥ is associated with highly depot-specific gene expression. This indicates that PPAR␥ plays a role in the induction of genes characteristic of different adipocyte lineages and that preadipocytes from different depots are differentially preprogrammed to permit PPAR␥ lineage-specific recruitment even when differentiated in vitro.M ammals have fat depots at various locations in the body. Classically, these tissues have been characterized as either white adipose tissue (WAT) or brown adipose tissue (BAT). Both tissues store energy in the form of triglycerides; however, whereas WAT releases the energy as fatty acids that can be converted to metabolic energy in other tissues, BAT metabolizes the fatty acids in the adipocytes and releases the energy as heat. This unique energy-dispersing function of BAT relies on the high number of mitochondria in the adipocytes and the expression and activation of uncoupling protein 1 (UCP1), residing in the inner mitochondrial membrane (9). Previously, BAT was thought to be present only in newborn and hibernating mammals; however, recently it was demonstrated that also human adults have discrete BAT depots (13,38,46,58,61). It has been suggested that activation of these BAT depots could increase energy expenditure and lead to weight loss. Consistent with this, there seems to be a negative correlation between body mass index and the presence of BAT (13,68,69) Notably, it has also been indicated that different WAT depots are not identical but have different properties (57,62). It is currently unclear to what extent differences between the distinct WAT depots reflect differences at the cellular level between adipocytes in the depots or reflect context-dependent differences (e.g., microenvironment); however, recent evidence indicates that different subtypes of white adipocytes do exist. Thus, several studies have demonstrated different gene expression profiles between visceral and subcutaneous WAT and preadipocytes and adipocytes from these tiss...