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J Am Soc Nephrol. 2019 Apr;30(4):594-609. doi: 10.1681/ASN.2018070687. Epub 2019 Mar 8.

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

Li SY1,2,3,4, Park J1,2, Guan Y1,2, Chung K1,2, Shrestha R1,2, Palmer MB5, Susztak K6,2.

Author information

1
Renal-Electrolyte and Hypertension Division, Department of Medicine.
2
Department of Genetics, and.
3
Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; and.
4
School of Medicine, National Yang-Ming University, Taipei, Taiwan.
5
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
6
Renal-Electrolyte and Hypertension Division, Department of Medicine, ksusztak@pennmedicine.upenn.edu.

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 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.

KEYWORDS:

DNA methylation; DNMT; Transposable element; kidney development; podocyte

PMID:
30850438
PMCID:
PMC6442333
[Available on 2020-04-01]
DOI:
10.1681/ASN.2018070687

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