@article{56f7c9b4b6e0465183d1f322490a5aab,
title = "A Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis",
abstract = "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 AVL9- and DENND5A-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 active mitochondria are retained and chromatin accessibility decreases in 3D cysts but not in 2D polarized cells. This indicates that 3D culture is a better model than 2D culture for studying epithelial morphogenesis.",
keywords = "Developmental Biology, Embryology, Transcriptomics",
author = "Tianfang Wang and Kwon, {Sang Ho} and Xiao Peng and Severine Urdy and Zefu Lu and Schmitz, {Robert J.} and Stephen Dalton and Mostov, {Keith E.} and Shaying Zhao",
note = "Funding Information: We thank Ms. Yaping Li for her contributions for this study, Mr. Roger Nelson and Mr. Jeff Wagner at Georgia Genomics and Bioinformatics Core and BGI for sequencing, Dr. Muthugapatti K. Kandasamy at UGA Biomedical Microscopy Core and Ms. Jin Qian for their helps with confocal microscopy, Ms. Julie Nelson at UGA Cytometry Shared Resources Laboratory for her help with flow cytometry, Dr. Kevin Dobbin for his help with statistical analysis, and Mr. Josh Watson and Mr. Max Colonna for their help with manuscript proofreading. This work was funded by NCI R01 CA182093 to S.Z. NIDDK R01 DK091530 to K.E.M. and NIDDK R01 DK120510 to S.-H.K. Conceptualization, S.Z. and K.E.M.; Methodology, T.W. Z.L. S.Z. P.X. S.-H.K. and S.U.; Investigation, T.W. and S.Z.; Writing, S.Z. T.W. K.E.M. and R.J.S.; Visualization, T.W.; Resources, R.J.S. and S.D.; Supervision, S.Z. and K.E.M.; Funding Acquisition, S.Z. K.E.M. and S.-H.K. The authors declare no competing interests. Funding Information: We thank Ms. Yaping Li for her contributions for this study, Mr. Roger Nelson and Mr. Jeff Wagner at Georgia Genomics and Bioinformatics Core and BGI for sequencing, Dr. Muthugapatti K. Kandasamy at UGA Biomedical Microscopy Core and Ms. Jin Qian for their helps with confocal microscopy, Ms. Julie Nelson at UGA Cytometry Shared Resources Laboratory for her help with flow cytometry, Dr. Kevin Dobbin for his help with statistical analysis, and Mr. Josh Watson and Mr. Max Colonna for their help with manuscript proofreading. This work was funded by NCI R01 CA182093 to S.Z., NIDDK R01 DK091530 to K.E.M., and NIDDK R01 DK120510 to S.-H.K. Publisher Copyright: {\textcopyright} 2020 The Author(s)",
year = "2020",
month = oct,
day = "23",
doi = "10.1016/j.isci.2020.101629",
language = "English (US)",
volume = "23",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier Inc.",
number = "10",
}