Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b

TLDR

Dnmt3a and Dnmt3b mediate de novo methylation of the mouse genome during early post‑implantation development and imprinting in oocytes. The study aimed to determine whether Dnmt3a and Dnmt3b are essential for the stable inheritance of DNA methylation patterns. Loss of Dnmt3a and Dnmt3b in embryonic stem cells leads to progressive demethylation of repeats and single‑copy genes, but reintroducing specific Dnmt3a/b isoforms restores most methylation patterns (except maternal imprints); Dnmt1 or Dnmt3b3 cannot, and hyper‑methylation by Dnmt3a/b is required for teratoma formation, indicating that isoform expression partly determines genomic methylation patterns.

Abstract

We have previously shown that the DNA methyltransferases Dnmt3a and Dnmt3b carry out de novo methylation of the mouse genome during early postimplantation development and of maternally imprinted genes in the oocyte. In the present study, we demonstrate that Dnmt3a and Dnmt3b are also essential for the stable inheritance, or "maintenance," of DNA methylation patterns. Inactivation of both Dnmt3a and Dnmt3b in embryonic stem (ES) cells results in progressive loss of methylation in various repeats and single-copy genes. Interestingly, introduction of the Dnmt3a, Dnmt3a2, and Dnmt3b1 isoforms back into highly demethylated mutant ES cells restores genomic methylation patterns; these isoforms appear to have both common and distinct DNA targets, but they all fail to restore the maternal methylation imprints. In contrast, overexpression of Dnmt1 and Dnmt3b3 failed to restore DNA methylation patterns due to their inability to catalyze de novo methylation in vivo. We also show that hypermethylation of genomic DNA by Dnmt3a and Dnmt3b is necessary for ES cells to form teratomas in nude mice. These results indicate that genomic methylation patterns are determined partly through differential expression of different Dnmt3a and Dnmt3b isoforms.