Adipose tissue is increasingly recognized as a dynamic, endocrine organ responsible for regulating metabolic homeostasis via the collective action of its two principal subtypes: white adipose tissue (WAT) and brown adipose tissue (BAT). Recently, the discovery of metabolically active brown fat reserves and brown in white fat (also known as "brite" or "beige" fat) in adult humans has prompted fundamental research to understand the development and function of brown adipocytes. The functional property of brown adipocytes is executed by the mitochondrial protein, Un- coupling Protein 1 (UCP1). UCP1 is responsible for uncoupling oxidative phosphorylation from ATP production thereby dissipating heat. The gene expression of Ucp1 is orchestrated by a multitude of transcriptional regulators and co-regulators that are distinct from those governing white adipocyte differentiation and function. However, in contrast to its counter- part, the white adipocyte, the gene regulatory mechanisms and transcriptional drivers of the brown adipocyte differentiation program remain elusive. Thus the focus of this thesis is to elucidate the gene regulatory network underlying brown fat cell differentiation and to decou- ple differentiation from the thermogenesis program using an integrative genomics approach. The main contributions of this work are as follows (1) construction of a comprehensive map integrating signaling, transcriptional and metabolic modules necessary for the activation of a brown adipocyte, (2) systematic, comprehensive analysis of transcriptional and chromatin state dynamics during brown fat cell differentiation leading to the identification of novel transcriptional regulators, (3) genomic characterization of the TF BCL6 during brown fat cell differentiation and (4) phenotypic characterization of a novel conditional BCL6 knockout mouse model.