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BASIC RESEARCH www.jasn.org DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development Szu-Yuan Li,1,2,3,4 Jihwan Park ,1,2 Yuting Guan,1,2 Kiwung Chung,1,2 Rojesh Shrestha,1,2 Matthew B. Palmer,5 and Katalin Susztak 1,2 1Renal-Electrolyte and Hypertension Division, Department of Medicine, 2Department of Genetics, and 5Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; 3Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; and 4School of Medicine, National Yang-Ming University, Taipei, Taiwan ABSTRACT Background Cytosine methylation of regulatory regions, such as promoters and enhancers, plays a key role in regulating gene expression, however, its role in kidney development has not been analyzed. Methods To identify functionally important epigenome-modifying enzymes and genome regions where methylation modifications are functionally important for kidney development, we performed genome- wide methylation analysis, expression profiling, and systematic genetic targeting of DNA methyltrans- ferases (Dnmt1, Dnmt3a,andDnmt3b) and Ten-eleven translocation methylcytosine hydroxylases (Tet2) in nephron progenitor cells (Six2Cre)inmice. Results Genome-wide methylome analysis indicated dynamic changes on promoters and enhancers dur- ing development. Six2CreDnmt3af/f, Six2CreDnmt3bf/f, and Six2CreTet2f/f mice showed no significant struc- tural or functional renal abnormalities. In contrast, Six2CreDnmt1f/f mice died within 24 hours of birth, from a severe kidney developmental defect. Genome-wide methylation analysis indicated a marked loss of methylation of transposable elements. RNA sequencing detected endogenous retroviral transcripts. Expression of intracellular viral sensing pathways (RIG-I), early embryonic, nonrenal lineage genes and increased cell death contributed to the phenotype development.
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