DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes

Abstract

Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed. An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8-16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8-16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

“…Preimplantation DNA demethylation has been documented in every boreoeutherian species tested to date (e.g. mice, humans, monkeys, pigs, cows, sheep, rabbits) 19,[36][37][38][39][40][41][42][43] , however early embryonic DNA methylation dynamics have not been investigated in Eutherian lineages other than Boreoeutheria, i.e Afrotheria and Xenarthra, not to mention the more distant marsupial and monotreme groups. Likewise, the functional importance of ERV activity in early developmental and placental gene expression programs has also only been demonstrated in boreoutherian species.…”

“…Both active and passive demethylation pathways have been implicated in the genome-wide erasure of 5mC accompanying mammalian preimplantation development [28][29][30][31][32][33][34] . Despite the extensive conservation of the TET enzymes and DNA methylation machinery throughout metazoa 35 , developmental DNA demethylation appears to be unique to placental mammals 19,[36][37][38][39][40][41][42][43] . In contrast, 5mC patterns have been found to remain constant throughout early development in all non-mammalian vertebrates examined to date 15,[44][45][46][47][48] .…”

Effect of Embryo Vitrification on the Steroid Biosynthesis of Liver Tissue in Rabbit Offspring

“…Among reproductive technologies, cryopreservation produces the most hostile conditions for embryos, and consequently, an increased number of studies have demonstrated both a direct effect on embryos and long-term effects on gene expression, proteome and metabolome on adult animals, providing a modified foetal and postnatal phenotype [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 ]. The early stage of mammalian development from fertilisation to implantation is a period in which global changes in the epigenetic scenery take place [ 1 , 12 , 13 , 14 , 15 ]. In ART, all of those global changes take place under in vitro conditions when the embryos develop in culture conditions that attempt to mimic the uterine environment.…”

Impact of Embryo Transfer on the phenotype of the offspring in pigs

“…The research and development of different ART protocols in the porcine species, with the nal objective of improving their e ciency in a holistic sense, represents an area of increasing interest for two main reasons: rst, for the porcine species, the potential existence of an embryo market, allows farmers the exchange of genetic material without risk of disease transmission and reducing transportation costs (reviewed by [19]); second, for the human species, there is compelling evidence that the pig is an useful model to decipher the long term impact of each aspect of the ART without confounding factors such as those related to the fertility of the parents, a fact that has been recently reinforced with the discovery of the similarities between the pig and the human regarding the DNA methylation reprogramming events during the rst week of development [20].…”