Axial pattern formation is sustained in the mammalian gut epithelium despite rapid and continuous renewal of its four principal cell lineages. The mouse and rat liver fatty acid-binding protein (L-FABP) genes (Fabpl) represent an excellent model for understanding the mechanisms that determine differentiation-dependent, cell lineage-specific, and distinct regional patterns of expression along the crypt-to-villus and duodenal-to-ileal axes of the gut, as well as within the liver acinus. We have used transgenic mice to map cis-acting elements in rat Fabpl that control these patterns of gene expression. Seven transgenes were analyzed, representing sequential deletions of the 5'-nontranscribed domain of Fabpl linked to the human growth hormone (hGH) gene beginning at its nucleotide +3 (L-FABP/hGH+3). Several pedigrees of mice containing each one of the L-FABP/hGH+3 transgenes were examined at the end of their 8th and 20th weeks of postnatal life using immunocytochemical and RNA hybridization analyses. A remarkably compact sequence spanning nucleotides -132 to +21 of Fabpl is sufficient to establish and maintain a distribution of reporter mRNA and protein in villus-associated enterocytes located along the duodenal-to-ileal axis of the gut that resembles the pattern of expression of the endogenous Fabpl gene. L-FABP-132 to +21/hGH+3 is also expressed in surface and pit mucous cells of gastric units and in enterocytes located in the colonic homologs of small intestinal villi, the surface epithelial cuffs. This pattern of transgene expression in the stomach and colon recapitulates that of the intact endogenous donor rat Fabpl but not that of mouse Fabpl, which is silent in these proximal and distal segments of the gastrointestinal tract. Analysis of mice containing L-FABP-4000 to +21/hGH+3, L-FABP-1600 to +21/hGH+3, L-FABP-596 to +21/hGH+3, L-FABP-246 to +21/hGH+3, and L-FABP-186 to +21/hGH+3 indicate that Fabpl's cephalocaudal gradient is influenced by cis-acting suppressors of cecal and colonic expression located between nucleotides -4000 and -1600 and by cis-acting activators of cecal and colonic expression located between nucleotides -597 and -351. L-FABP-132 to +21/hGH+3 is precociously activated in proliferating and nonproliferating epithelial cells located in intestinal crypts. The suppressor(s) of L-FABP accumulation in crypt epithelial cell populations are not represented between nucleotides -4000 and +21, indicating that different cis-acting sequences regulate regional and differentiation-dependent patterns of Fabpl expression.(ABSTRACT TRUNCATED AT 400 WORDS)