Tight junctions (TJ) regulate the passage of solutes across epithelial sheets, contribute to the establishment and maintenance of epithelial apico-basal polarity and are involved in the regulation of gene expression and cell proliferation. Cingulin, a Mr 140 kDa protein localized in the cytoplasmic region of TJ, is not directly required for TJ formation and epithelial polarity but regulates RhoA signaling, through its interaction with the RhoA activator GEF-H1, and gene expression. Here we describe in more detail the effect of cingulin mutation in embryoid bodies (EB) on gene expression, by identifying the genes that show the highest degree of up- or downregulation, and the putative canonical pathways that might be affected by cingulin. Furthermore, we show that full-length canine GEF-H1, produced in baculovirus-infected insect cells, interacts with regions both in the cingulin globular head, and in the coiled-coil rod domain. These results extend our previous studies and provide new perspectives for the mechanistic analysis of cingulin function.