Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo

Abstract

BackgroundDNA methylomes are extensively reprogrammed during mouse pre-implantation and early germ cell development. The main feature of this reprogramming is a genome-wide decrease in 5-methylcytosine (5mC). Standard high-resolution single-stranded bisulfite sequencing techniques do not allow discrimination of the underlying passive (replication-dependent) or active enzymatic mechanisms of 5mC loss. We approached this problem by generating high-resolution deep hairpin bisulfite sequencing (DHBS) maps, allowing us to follow the patterns of symmetric DNA methylation at CpGs dyads on both DNA strands over single replications.ResultsWe compared DHBS maps of repetitive elements in the developing zygote, the early embryo, and primordial germ cells (PGCs) at defined stages of development. In the zygote, we observed distinct effects in paternal and maternal chromosomes. A significant loss of paternal DNA methylation was linked to replication and to an increase in continuous and dispersed hemimethylated CpG dyad patterns. Overall methylation levels at maternal copies remained largely unchanged, but showed an increased level of dispersed hemi-methylated CpG dyads. After the first cell cycle, the combined DHBS patterns of paternal and maternal chromosomes remained unchanged over the next three cell divisions. By contrast, in PGCs the DNA demethylation process was continuous, as seen by a consistent decrease in fully methylated CpG dyads over consecutive cell divisions.ConclusionsThe main driver of DNA demethylation in germ cells and in the zygote is partial impairment of maintenance of symmetric DNA methylation at CpG dyads. In the embryo, this passive demethylation is restricted to the first cell division, whereas it continues over several cell divisions in germ cells. The dispersed patterns of CpG dyads in the early-cleavage embryo suggest a continuous partial (and to a low extent active) loss of methylation apparently compensated for by selective de novo methylation. We conclude that a combination of passive and active demethylation events counteracted by de novo methylation are involved in the distinct reprogramming dynamics of DNA methylomes in the zygote, the early embryo, and PGCs.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-8935-8-1) contains supplementary material, which is available to authorized users.

Mechanism and Reconstitution In Vitro of Germ Cell Development in Mammals

“…These findings indicated that, contrary to what had been proposed , the imprint erasure is initiated in early mPGCs and the demethylation can be explained largely by a replication-coupled passive mechanism. Consistent with this report, independent studies for the methylation states of the repetitive elements in mPGCs by highthroughput hairpin bisulfite sequencing demonstrated the prevalence of hemimethylated DNA in mPGCs, indicating that the replication-coupled passive demethylation is a major mechanism for genome-wide DNA demethylation in mPGCs (Seisenberger et al 2012;Arand et al 2015). Accordingly, mPGCs lacking TET1, an active DNA demethylase and the only TET protein expressed at a high level in mPGCs, undergo genome-wide DNA demethylation in an apparently normal fashion (Dawlaty et al 2011).…”

DNA methylation profiling in human lung tissue identifies genes associated with COPD

“…With respect to the ConsensusPathDB results, EGFR1 signaling has been implicated in chronic bronchitis 22 and WNT signaling is involved in the pathogenesis of lung development, COPD, 23 and asthma. 24 Differential methylation in multiple sites across a defined genomic region may reveal more biological relevance than single CpG associations, and in contrast to previous methods, such as bump hunting, that are agnostic to genomic annotation, 25,26 we defined regions using multi-site associations for annotated genes. Among these multi-site genes, 3 are of particular interest: CHRM1, as it was the top result among 10% b-diff results; ESM1, a gene mainly expressed in the endothelial cells in human lung and kidney tissues 27 ; and PITPNM1, a gene found within a linkage disequilibrium block surrounding the susceptibility gene identified in a previous association study of childhood asthma.…”

Oxytocin pathways in the intergenerational transmission of maternal early life stress

“…Lastly, the unresolved issue of how meaningful peripherally derived methylation patterns are with respect to brain activity and consequently behavior and psychiatric risk remains controversial. Epigenetic changes are highly tissue specific and only a subset of DNA methylation changes show cross-tissue correlation between peripheral tissues and the brain (Davies et al, 2012; Farré et al, 2015; Hannon et al, 2015). Taken together, it would be premature to draw general conclusions from the reported findings.…”