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Abstract
Madin-Darby canine kidney II (MDCKII) cells, originally derived from canine kidney epithelial tissues, are widely employed in various research areas, including the study of cell polarity, epithelial morphogenesis, kidney disease, EMT, etc. In MDCKII 3D culture, epithelial morphogenesis takes place as a single cell develops into a cyst consisting of a monolayer of cells enclosing a central lumen through tightly regulated cell proliferation and establishment of cell polarity. In contrast, MDCKII cells develop into a monolayer with well-established cell polarity but without lumen formation in 2D culture. During MDCKII epithelial morphogenesis, transcriptome reprogramming may play a critical role in the regulation of differentiation, as observed in other cell differentiation systems. However, the complete transcriptome profile during the process is largely unknown. Moreover, fundamental questions remain unanswered about the transcriptome changes underlying the process. For instance, does the transcriptome gradually change or suddenly switch at a time point? What are the transcriptome similarities and differences between 3D and 2D epithelial morphogenesis? To answer the questions, we performed a full time-course RNA-seq analysis for MDCKII 3D cystogenesis, together with fully polarized 2D cells. Our analysis revealed that a qualitative transcriptome change occurs after the first cell division and in parallel with lumen formation. Further analysis of DENND5A- and AVL9- knockdown cells indicated intracellular trafficking is related to the transcriptome changes. Specifically, β-catenin translocation from nucleus to cell-cell junctions during the first cell division likely leads to the down-regulation of MYC and other cell cycle genes. Integration of RNA-seq and ATAC-seq data uncovered a possible mechanism that HNF1B activation leads to transcriptome changes that contribute to cell polarity establishment. Based on these findings, our study proposed a model that redistribution of transcription factors during cell division may drive transcriptome remodeling. In addition, we identified some differences between 3D and 2D epithelial morphogenesis. First, chromatin accessibility decreases more drastically during 3D epithelial morphogenesis. Second, active mitochondria are retained only during 3D epithelial morphogenesis. Our work deepens the understanding of MDCKII epithelial morphogenesis and provides insight into mechanisms underlying the qualitative transcriptome change during differentiation.