DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development.

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 methyltransferases ( Dnmt1 , Dnmt3a , and Dnmt3b ) and Ten-eleven translocation methylcytosine hydroxylases ( Tet2 ) in nephron progenitor cells ( Six2 Cre ) in mice.

RESULTS: Genome-wide methylome analysis indicated dynamic changes on promoters and enhancers during development. Six2 Cre Dnmt3a f/f , Six2 Cre Dnmt3b f/f , and Six2 Cre Tet2 f/f mice showed no significant structural or functional renal abnormalities. In contrast, Six2 Cre Dnmt1 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 Dnmt1 , Dnmt3a , Dnmt3b , or Tet2 did not lead to functional or structural differences at baseline or after toxic injury.

CONCLUSIONS: 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.