biostudies-literatureWang TNational Institute of Diabetes and Digestive and Kidney DiseasesNIDDK NIH HHSNational Cancer InstituteNCI NIH HHS101629https://www.ebi.ac.uk/biostudies/studies/S-EPMC7567049biostudies-literatureUnknown23(10)Madin-Darby canine kidney II (MDCKII) cells are widely used to study epithelial morphogenesis. To better understand this process, we performed time course RNA-seq analysis of MDCKII 3D cystogenesis, along with polarized 2D cells for comparison. Our study reveals a biphasic change in the transcriptome that occurs after the first cell cycle and coincides with lumen establishment. This change appears to be linked to translocation of β-catenin, supported by analyses with <i>AVL9</i>- and <i>DENND5A</i>-knockdown clones, and regulation by HNF1B, supported by ATAC-seq study. These findings indicate a qualitative change model for transcriptome remodeling during epithelial morphogenesis, leading to cell proliferation decrease and cell polarity establishment. Furthermore, our study reveals that actiScienceA Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis.PMC7567049R01 DK120510R01 DK091530R01 CA182093Peng XSchmitz RJUrdy SZhao SWang TLu ZKwon SHMostov KEDalton SfalseA Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis.Madin-Darby canine kidney II (MDCKII) cells are widely used to study epithelial morphogenesis. To better understand this process, we performed time course RNA-seq analysis of MDCKII 3D cystogenesis, along with polarized 2D cells for comparison. Our study reveals a biphasic change in the transcriptome that occurs after the first cell cycle and coincides with lumen establishment. This change appears to be linked to translocation of β-catenin, supported by analyses with <i>AVL9</i>- and <i>DENND5A</i>-knockdown clones, and regulation by HNF1B, supported by ATAC-seq study. These findings indicate a qualitative change model for transcriptome remodeling during epithelial morphogenesis, leading to cell proliferation decrease and cell polarity establishment. Furthermore, our study reveals that act2020-01-01T00:00:00Z2020 Oct2026-05-03T20:37:11.502Z2020-10-29T12:32:26ZS-EPMC75670493308911410.1016/j.isci.2020.101629