Brown adipocytes and myocytes develop from a common adipomyocyte precursor. PPAR alpha is a nuclear receptor important for lipid and glucose metabolism. It has been suggested that in brown adipose tissue, PPAR alpha represses the expression of muscle-associated genes, in this way potentially acting to determine cell fate in brown adipocytes. To further understand the possible role of PPAR alpha in these processes, we measured expression of muscle-associated genes in brown adipose tissue and brown adipocytes from PPAR alpha-ablated mice, including structural genes (Mylpf, Tpm2, Myl3 and MyHC), regulatory genes (myogenin, Myf5 and MyoD) and a myomir (miR-206). However, in our hands, the expression of these genes was not influenced by the presence or absence of PPAR alpha, nor by the PPAR alpha activator Wy-14,643. Similarly, the expression of genes common for mature brown adipocyte and myocytes (Tbx15, Meox2) were not affected. However, the brown adipocyte-specific regulatory genes Zic1, Lhx8 and Prdm16 were affected by PPAR alpha. Thus, it would not seem that PPAR alpha represses muscle-associated genes, but PPAR alpha may still play a role in the regulation of the bifurcation of the adipomyocyte precursor into a brown adipocyte or myocyte phenotype. (C) 2010 Elsevier Inc. All rights reserved.