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In fishes, variation in paracellular permeability is important for regulating salt and water balance. Paracellular permeability is maintained by TJs in vertebrate epithelia. This study examined the spatial distribution and effects of salinity on claudin-3 isoform mRNA expression and abundance along the gastrointestinal (GI) tract of the euryhaline puffer fish (Tetraodon nigroviridis) and related these to morphological heterogeneity of the TJ complex. The puffer fish GI tract was divided into three regions (anterior, middle and posterior) and four isoforms of claudin-3 (Tncldn3a, Tncldn3b, Tncldn3c and Tncldn3d) were found to be expressed in each section. The effect of freshwater (FW) or seawater (SW) acclimation on regional 1) Tncldn3 isoform mRNA abundance, 2) TJ complex morphology and 3) Na(+)-K(+)-ATPase (NKA) activity was examined. In situ hybridization indicated that all Tncldn3 isoforms localized to the mucosal epithelium in the intestine. The mRNA abundance of Tncldn3 isoforms varied spatially along the GI tract. Furthermore, region as well as isoform specific alterations in mRNA abundance could be observed along the GI tract in response to salinity change. Qualitative TEM observations suggested that the depth of TJ complexes increased from anterior to posterior along the GI tract and that TJ complexes in the GI tract of FW fish were deeper than those in SW. NKA activity increased from anterior to posterior in fish acclimated to FW, whereas activity in fish acclimated to SW was uniformly high along the length of the intestine. Taken together data; (1) suggest a progressive decrease in epithelial permeability from anterior to posterior along the longitudinal axis of the puffer fish GI tract, (2) indicate that claudin-3 protein isoforms may play a role in regulating paracellular movement of solutes across this epithelium, and (3) provide further evidence that claudin-3 proteins are involved in the homeostatic control of salt and water balance in fishes., (2009 Elsevier Inc. All rights reserved.)