The activity of the apical membrane Na ؉ /H ؉ exchanger NHE3 isoform of renal or intestinal epithelial cells is chronically regulated by a wide variety of stimuli, including acidosis, cAMP, glucocorticoids, and thyroid hormone. To understand the molecular mechanisms responsible for long term regulation of this cation transporter, we have isolated and determined the structure of this gene from a rat genomic library. The Nhe3 gene spans >40 kilobases and contains 17 exons that are flanked by typical splice donor and acceptor sequences at the exon-intron boundaries. The transcription initiation site was mapped by S1 nuclease protection analyses of mRNA from rat kidney and intestine. Multiple start sites were clustered between nucleotides ؊100 and ؊96 The Na ϩ /H ϩ exchanger (NHE) 1 is an integral membrane protein present in all mammalian cells. Multiple isoforms (NHE1 to NHE5) have been identified by molecular cloning techniques (1-7). They range in size between ϳ81 and 93 kDa and appear to exist in the membrane as homodimers, at least in the cases of NHE1 and NHE3 (8). These isoforms exhibit differences in their patterns of tissue expression, biochemical and pharmacological characteristics, and physiological functions (reviewed in Refs. 9 and 10).In addition, Na ϩ /H ϩ exchanger activity is influenced by a wide variety of molecular signals (e.g. neurotransmitters, growth factors, peptide hormones, phorbol esters, cAMP, chemotactic factors, lectins, osmotic shrinkage, acidosis, glucocorticoids, and thyroid hormone) that act either rapidly (seconds to minutes) or following a considerable latent period (hours to days) before the effects on the rate of transport are manifested (reviewed in Refs. 11 and 12). Recent studies have begun to identify the stimuli and signaling pathways that acutely modulate the individual NHE isoforms (13-20). The mechanisms responsible for these alterations, although not fully resolved, appear to involve both phosphorylation-dependent and -independent processes.Considerably less is known about the molecular mechanisms involved in the chronic regulation of the NHE isoforms, although recent investigations are beginning to provide some insight. Prolonged exposure of cultured renal epithelial cells to acidic medium, which serves as a paradigm for studying physiological adaptations to chronic metabolic and respiratory acidosis, elevates the activities and/or mRNA abundances of NHE1 (21, 22) and NHE3 (22, 23), but inhibits those of NHE2 (24). Interestingly, acid-mediated stimulation of NHE1 in renal MCT cells is associated with activation of protein kinase C and the transcription factor AP-1 (25), whereas acid induction of NHE3 in renal OKP cells is linked to the c-src family of nonreceptor protein-tyrosine kinases (26). Aside from acidosis, chronic incubation of renal IMCD cells in hyperosmotic media also stimulates Na ϩ /H ϩ exchanger activity, which is associated with increased NHE2 and reduced NHE1 mRNA abundances (24). Last, long-term administration of glucocorticoids to rabbits or sheep sel...