A Qualitative Change in the Transcriptome During MDCKII 3D Epithelial Morphogenesis is Linked to the First Cell Cycle and Intracellular Trafficking

Madin-Darby canine kidney II (MDCKII) cells are used widely 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 after the 1st cell cycle. This change appears to be linked to translocation of β-catenin, supported by analyses with AVL9- or DENND5A-knockdown clones, and HNF1B mitotic bookmarking, supported by ATAC-seq study. Specifically, β-catenin is depleted from the nucleus and enriched at the cell-cell junctions following the 1st cell cycle, downregulating the MYC network and decreasing cell proliferation. Meanwhile, HNF1B is retained in the nucleus, upregulating its targets and contributing to the cell polarity establishment. Our study supports a qualitative change model for transcriptome remodeling during epithelial morphogenesis and that this qualitative change results from transcription factor redistribution during the first cell cycle.