Epithelial cells are polarized with defined apical tight junctions (TJs), lateral adherens junctions (AJs), and basal integrinâmatrix interactions. However, it is increasingly recognized that resident cell junction proteins can be found in varying locations and with previously unrecognized functions. Our study here presents the nanoarchitecture and nanocolocalization of cell junction proteins in culture and tissue by stochastic optical reconstruction microscopy (STORM). The Zâaxial view of noncancerous MDCKâII and PZâHPVâ7 cellâcell junctions resolved βâcatenin and p120ctn localizations to TJs and AJs, with p120ctn apical to βâcatenin and colocalizing with TJ protein claudinâ7. More basally, p120ctn and βâcatenin become colocalized. This topography was lost in isogenic Rasâtransformed MDCK cells and cancerous PC3 cells, where p120ctn becomes basally localized in relation to βâcatenin. Claudinâ7 gene conditional knockout (cKO) in mice also have altered polarity of p120ctn relative to βâcatenin, like that seen in normalâtoâcancer cell phenotypic transformation. Additionally, claudinâ7 cKO resulted in redistribution and relocalization of other cell junction proteins, including claudinâ1, zonula occludensâ1, integrin Îą2, epithelial cell adhesion molecule, and focal adhesion kinase (FAK); specifically, integrin Îą2 and FAK were observed at the apicalâlateral compartment. Our data show that STORM reveals regional cellular junction nanoarchitecture previously uncharacterized, providing new insight into potential transâcompartmental modulation of protein functions.