Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals

Abstract

Vertebrate genomes are marked by notably high levels of 5-cytosine DNA methylation (5meC). The clearest function of DNA methylation among members of the subphylum is repression of potentially deleterious transposable elements (TEs). However, enrichment in the bodies of protein coding genes and pericentromeric heterochromatin indicate an important role for 5meC in those genomic compartments as well. Moreover, DNA methylation plays an important role in silencing of germline-specific genes. Impaired function of major components of DNA methylation machinery results in lethality in fish, amphibians and mammals. Despite such apparent importance, mammals exhibit a dramatic loss and regain of DNA methylation in early embryogenesis prior to implantation, and then again in the cells specified for the germline. In this minireview we will highlight recent studies that shine light on two major aspects of embryonic DNA methylation reprogramming: (1) The mechanism of DNA methylation loss after fertilization and (2) the protection of discrete loci from ectopic DNA methylation deposition during reestablishment. Finally, we will conclude with some extrapolations for the evolutionary underpinnings of such extraordinary events that seemingly put the genome under unnecessary risk during a particularly vulnerable window of development.

Keywords: DNA methylation; embryonic stem cells (ESC); epigenetics; mammalian development; reprogramming.

Figure 1

Mechanism of DPPA3-mediated DNA demethylation. (A) After DNA replication, the SRA domain of UHRF1 binds to hemimethylated CpG, flipping out the methylated cytosine. Recruitment of DNMT1 directs methylation of the symmetrical unmethylated cytosine on the daughter strand. Crucially, UHRF1 must bind to histone H3 through its PHD domain. DPPA3 binds to the PHD domain, disrupting UHRF1's interaction with chromatin leading to impaired DNA maintenance methylation. (B) Top panel: In mouse ESCs, PRDM14 recruits TET1 and TET2 roughly 2 kb upstream of the Dppa3 promoter, leading to its demethylation and activation. Bottom panel: in Tet1/2 double mutants, increased DNA methylation at the Dppa3 gene corresponds with repression. Thus, active demethylation of this one gene is required for global passive demethylation. This mechanism likely does not occur during embryonic DNA methylation reprogramming, but may help explain the wave of DNA demethylation that occurs in the male and female germlines.

Figure 2

DPPA2/4-mediated regulation of developmental genes. (A) DPPA2/4 bind a subset of developmental genes, and recruit the COMPASS and PRC2 complexes, which deposit H3K4me3 and H3K27me3, respectively. These genes are then poised to activate in the proper developmental context. The H3K4me3 protects this class of promoter from de novo DNA methylation. (B) In Dppa2/4 mutant ESCs, genes that are normally targeted by DPPA2/4 are susceptible to aberrant de novo DNA methyltransferase activity, preventing the ability of this class of genes to activate during differentiation.