This article is available online at http://www.jlr.org targeted to treat lipid disorders, diabetes, and obesity, is highly expressed in the liver. Its induction by fasting promotes lipid uptake, fatty acid  -oxidation, ketogenesis, and gluconeogenesis ( 1, 2 ). Ligand binding to PPAR ␣ causes it to heterodimerize with retinoid X receptor (RXR) ␣ , allowing activation of gene transcription at peroxisome proliferator response elements (PPRE) ( 3, 4 ). Synthetic PPAR ␣ ligands, such as fi brates, used for human lipid disorders ( 5 ) have been known for decades, but potential endogenous ligands were identifi ed only recently ( 6, 7 ). Mice with liver-specifi c deletion of the lipogenic enzyme fatty acid synthase (FAS) have impaired PPAR ␣ activity ( 8 ), and FAS activates PPAR ␣ by producing an endogenous phospholipid ligand ( 6 ). FAS also activates PPAR ␣ in brain and macrophages ( 9, 10 ).Mammalian FAS synthesizes long-chain fatty acids, primarily palmitate, through the activities of seven functional domains: acyl carrier, acyl transferase,  -ketoacyl synthase,  -ketoacyl reductase,  -hydroxyacyl dehydratase, enoyl reductase, and thioesterase ( 11 ). Like PPAR ␣ , FAS is highly expressed in liver ( 12 ). In times of nutrient excess, hepatic FAS converts carbohydrate to lipid that is stored in lipid droplets or secreted in the form of VLDL ( 13 ). Nutrient excess is associated with elevated levels of insulin, known to induce FAS expression.These accepted physiological roles for PPAR ␣ and FAS appear to confl ict with the observation that inactivation of FAS impairs PPAR ␣ activation. How might FAS activate a process stimulated by feeding such as insulin-responsive lipogenesis and also activate a process stimulated by fasting such as the induction of PPAR ␣ -dependent gene expression?We hypothesized that distinct subcellular pools of FAS mediate these disparate effects. Compartmentalization would permit regulation of an FAS pool generating lipids for signaling that would be distinct from an FAS pool generating lipids for energy storage. In support of this hypothesis, Abstract Peroxisome proliferator-activated receptor (PPAR) ␣ is a nuclear receptor that coordinates liver metabolism during fasting. Fatty acid synthase (FAS) is an enzyme that stores excess calories as fat during feeding, but it also activates hepatic PPAR ␣ by promoting synthesis of an endogenous ligand. Here we show that the mechanism underlying this paradoxical relationship involves the differential regulation of FAS in at least two distinct subcellular pools: cytoplasmic and membrane-associated. In mouse liver and cultured hepatoma cells, the ratio of cytoplasmic to membrane FAS-specifi c activity was increased with fasting, indicating higher cytoplasmic FAS activity under conditions associated with PPAR ␣ activation. This effect was due to a nutrient-dependent and compartment-selective covalent modifi cation of FAS. Cytoplasmic FAS was preferentially phosphorylated during feeding or insulin treatment at Thr-1029 and Thr-1033, which fl ank a d...