DNMT1 in <i>Six2</i> Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development.

Abstract

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. 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 methyltransferases (<i>Dnmt1</i>, <i>Dnmt3a</i>, and <i>Dnmt3b</i>) and Ten-eleven translocation methylcytosine hydroxylases (<i>Tet2</i>) in nephron progenitor cells (<i>Six2</i>^Cre) in mice. Genome-wide methylome analysis indicated dynamic changes on promoters and enhancers during development. <i>Six2</i>^Cre<i>Dnmt3a</i>^f/f, <i>Six2</i>^Cre<i>Dnmt3b</i>^f/f, and <i>Six2</i>^Cre<i>Tet2</i>^f/f mice showed no significant structural or functional renal abnormalities. In contrast, <i>Six2</i>^Cre<i>Dnmt1</i>^f/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. In podocytes, loss of <i>Dnmt1</i>, <i>Dnmt3a</i>, <i>Dnmt3b</i>, or <i>Tet2</i> did not lead to functional or structural differences at baseline or after toxic injury. Genome-wide cytosine methylation and gene expression profiling showed that by silencing embryonic, nonrenal lineage genes and transposable elements, DNMT1-mediated cytosine methylation is essential for kidney development.