Fatty acids bind to and regulate the activity of peroxisome proliferator-activated (PPAR) and liver X receptors (LXR). However, the role lipid metabolism plays in the control of intracellular fatty acid ligands is poorly understood. We have identified two strains of HEK293 cells that display differences in fatty acid regulation of nuclear receptors. Using full-length and Ga14-LBD chimeric receptors in functional assays, 20:4,n6 induced PPARalpha activity -2.2-fold and suppressed LXRalpha activity by 80% (ED50 similar to25-50 mum) in HEK293-E (early passage) cells but had no effect on PPARalpha or LXRalpha receptor activity in HEK293-L (late passage) cells. LXRbeta was insensitive to fatty acid regulation in both HEK293 strains. Metabolic labeling studies using [C-14]20:4,n6 (at 100 mum) indicated that the uptake of 20:4,n6 and its assimilation into triacylglycerol, diacylglycerol, and polar lipids revealed no difference between the two strains. Such treatment increased total cellular 20:4,n6 (similar to11-fold) and its elongation product, 22:4,n6 (similar to3.6-fold), within 6 h. Non-esterified 20:4,n6 and 22:4,n6 represented less than or equal to3% of the total cellular 20:4,n6 and 22:4,n6. In HEK293-E cells, non-esterified 20:4,n6 and 22:4,n6 increased 8- and 18-fold, respectively, by 6 h and was sustained at that level for 24 h. In HEK293-L cells, non-esterified 20:4,n6 also increased (5-fold) at 6 h but fell by 70% within 24 h. In contrast to HEK293-E cells, non-esterified 22:4,n6 did not accumulate in HEK293-L cells. Functional assays showed that 22:4,n6 was similar to2-fold more effective than 20: 4,n6 at inhibiting oxysterol-induced LXRa activity in HEK293-E cells, but had no effect on LXRa activity in HEK293-L cells. Taken together, these findings demonstrate that the rate of assimilation of exogenously added fatty acids and their metabolites into complex lipids plays an important role in regulating PPARa and LXRa activity.