The DNA methylation landscape of human early embryos

Abstract

DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic development. However, its dynamic patterns have not been analysed at the genome scale in human pre-implantation embryos due to technical difficulties and the scarcity of required materials. Here we systematically profile the methylome of human early embryos from the zygotic stage through to post-implantation by reduced representation bisulphite sequencing and whole-genome bisulphite sequencing. We show that the major wave of genome-wide demethylation is complete at the 2-cell stage, contrary to previous observations in mice. Moreover, the demethylation of the paternal genome is much faster than that of the maternal genome, and by the end of the zygotic stage the genome-wide methylation level in male pronuclei is already lower than that in female pronuclei. The inverse correlation between promoter methylation and gene expression gradually strengthens during early embryonic development, reaching its peak at the post-implantation stage. Furthermore, we show that active genes, with the trimethylation of histone H3 at lysine 4 (H3K4me3) mark at the promoter regions in pluripotent human embryonic stem cells, are essentially devoid of DNA methylation in both mature gametes and throughout pre-implantation development. Finally, we also show that long interspersed nuclear elements or short interspersed nuclear elements that are evolutionarily young are demethylated to a milder extent compared to older elements in the same family and have higher abundance of transcripts, indicating that early embryos tend to retain higher residual methylation at the evolutionarily younger and more active transposable elements. Our work provides insights into the critical features of the methylome of human early embryos, as well as its functional relation to the regulation of gene expression and the repression of transposable elements.

Diagnosis of abnormal human fertilization status based on pronuclear origin and/or centrosome number

“…On the other hand, maternal PN is protected from this demethylation by PGC7 [33]. Recently, it has been reported that the DNA methylation patterns were different between male-and female-derived nuclei in human pronuclear stage embryos [34]. We utilized this phenomenon to identify the origin of the PN in order to reveal the fertilization pattern of abnormal zygotes.…”

DOHaD et programmation pré- et péri-conceptionnelle

“…Elle présente, elle aussi, une asymétrie parentale lors de la fécondation. Chez la souris comme chez l'homme, le génome du spermatozoïde est plus méthylé que celui de l'ovocyte [10][11][12]. La distribution de la méthylation n'est pas strictement identique dans les deux types de gamètes.…”

“…La distribution de la méthylation n'est pas strictement identique dans les deux types de gamètes. Ainsi les ovocytes humains et murins présentent des méthylations en dehors des îlots CpG [10,11]. Ces génomes gamétiques sont globalement déméthylés durant la période s'étendant entre la fécondation et les premiers stades de clivage selon des cinétiques qui peuvent varier selon l'espèce [12].…”

“…Toutefois, le génome embryonnaire reste globalement hypométhylé jusqu'au stade blastocyste inclus. À ce stade, une méthylation différentielle, entre la masse cellulaire interne et le trophectoderme, est rapportée par certaines études chez l'homme [10] et chez la souris, comme dans plusieurs modèles de mammifères domestiques, où la différence entre lignages s'installe progressivement au cours du stade blastocyste. Chez la souris, la reméthylation du génome embryonnaire a lieu après l'implantation de l'embryon.…”

Repeats as global DNA methylation marker in bovine preimplantation embryos

“…By comparing the sequences the methylation pattern can be determined. More recently, new methods based on bisulfite conversion and whole genome sequencing have been developed (Guo et al 2014;Salilew-Wondim et al 2015). These platforms can determine the methylation status of thousands of genes at CpG site-level, but are still very expensive and require intensive bioinformatics (data analysis) expertise, which makes it impractical when a large number of treatments or samples are studied.…”