The peroxisome proliferator-activated receptor (PPAR alpha) has been implicated in fatty acid regulation of gene transcription, Lipogenic gene transcription is inhibited by polyunsaturated fatty acids (PUFA), We have used the PUFA-sensitive rat liver S14 gene as a model to examine the role PPAR alpha plays in fatty acid regulation of hepatic lipogenic gene transcription, Both PPAR alpha and the potent peroxisome proliferator, WY14643, inhibit S14CAT activity in transfected primary hepatocytes. WY14643 and PPAR alpha target the S14 T-3 regulatory region (TRR, -2.8 to -2.5 kilobases), a region containing 3 T-3 response elements (TRE). Transfer of the TRR to the thymidine kinase (TK) promoter conferred negative control to the TKCAT gene following WY14643 and PPAR alpha treatment, Gel shift analysis showed that PPAR alpha, either alone or with RXR alpha, did not bind the S14TRR. However, PPAR alpha interfered with TR beta/RXR alpha binding to a TRE (DR+4). Functional studies showed that co-transfected RXR alpha, but not T-3 receptor beta(1) (TR beta 1), abrogated the inhibitory effect of PPAR alpha on S14 gene transcription. These results suggest that WY14643 and PPAR alpha functionally interfere with T-3 regulation of S14 gene transcription by inhibiting TR beta 1/RXR binding to S14 TREs. Previous studies had established that the cis-regulatory targets of PUFA control were located within the proximal promoter region of the S14 gene, i.e. between -220 and -80 bp. Finding that the cis-regulatory elements for WY14643/PPAR alpha and PUFA are functionally and spatially distinct argues against PPAR alpha as the mediator of PUFA suppression of S14 gene transcription.