Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease

Abstract

Significance Statement Cytosine methylation plays a key role in determining cell fate and response to stimuli. Using mice with kidney-specific deletion of genes encoding de novo DNA methyltransferases Dnmt3a and Dnmt3b, the authors showed that these genes are responsible for methylation of gene regulatory regions that act as enhancers during kidney development but are then decommissioned in adult mice. Although the knock-out mice displayed no obvious kidney abnormalities at baseline, they showed resistance to induced AKI. The authors also discovered that human kidney disease risk loci were enriched on fetal regulatory regions (enhancers) that were decommissioned by Dnmt3a / 3b and no longer active in the adult kidney. These findings suggest that adult kidney diseases could have a developmental origin and that genetic and epigenetic (such as Dnmt3a / 3b ) factors could converge on the same genetic regions resulting in kidney disease development. Background Cytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation. Methods We generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells ( Six2 Cre Dnmt3a/3b ) and kidney tubule cells ( Ksp Cre Dnmt3a/3b ). We characterized Ksp Cre Dnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing and RNA sequencing were performed on whole-kidney samples and isolated renal tubule cells. Results Ksp Cre Dnmt3a/3b mice showed no obvious morphologic and functional alterations at baseline. Knockout animals exhibited increased resistance to cisplatin-induced kidney injury, but not to folic acid–induced fibrosis. Whole-genome bisulfite sequencing indicated that Dnmt3a and Dnmt3b play an important role in methylation of gene regulatory regions that act as fetal-specific enhancers in the developing kidney but are decommissioned in the mature kidney. Loss of Dnmt3a and Dnmt3b resulted in failure to silence developmental genes. We also found that fetal-enhancer regions methylated by Dnmt3a and Dnmt3b were enriched for kidney disease genetic risk loci. Methylation patterns of kidneys from patients with CKD showed defects similar to those in mice with Dnmt3a and Dnmt3b deletion. Conclusions Our results indicate a potential locus-specific convergence of genetic, epigenetic, and developmental elements in kidney disease development.

Topics & Concepts