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

ABSTRACT: Preimplantation embryos experience profound resetting of epigenetic information. Genome-wide analysis at single-base resolution had shown relevant species differences between human and mouse preimplantation embryos. Thus, we have extended such analysis to two key livestock species, the pig and the cow. We generated data showing the genome-wide DNA methylation landscape and whole-transcriptomes from gametes to blastocysts in both species. Detailed analysis revealed species specific differences and new insights in biological paradigms. An oocyte-like pattern of methylation in the cleavage stages, albeit with some reduction in methylation level, appears to persist even in cow blastocysts. Hypermethylated domains were prevalent over hypomethylated domains in pigs and cows, similar to human, while in the mouse the pattern is reversed. Interestingly, the behaviour of the oocyte hypo-domains in cleavage embryos revealed a complex dynamic of methylation reprogramming. It shows a pronounced increase in methylation at the 8-16 cell stage in pigs, similar to human, concomitant with ZFP57 expression. Even it is widely accepted that imprinted genes are established in the parental germline and robustly maintained through early development, our data show a greater dynamic of methylation in germline differentially methylated regions and few appear to maintain the expected 50% methylation from the 2-4 cell stage to blastocyst stage. It reveals that an active period of imprint stabilization until the blastocyst stage is required

ORGANISM(S): Sus scrofa Bos taurus

PROVIDER: GSE143848 | GEO | 2020/05/20

REPOSITORIES: GEO

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Project description:The transition between morula and blastocyst stage during preimplantation development represents the first differentiation event of embryogenesis. Morula cells undergo the first cellular specialization and produce two well-defined populations of cells, the trophoblast and the inner cell mass (ICM). Embryonic stem cells (ESCs) with unlimited self-renewal capacity are believed to represent the in vitro counterpart of the ICM. Both mouse and rat ESCs can be derived from the ICM cells, but their in vitro stability differs. In this study we performed a microarray analysis in which we compared the transcriptome of mouse and rat morula, blastocyst, and ICM. This cross-species comparison represents a good model for understanding the differences in derivation and cultivation of ESCs observed in the two species. In order to identify alternative regulation of important molecular mechanisms the investigation of differential gene expression between the two species was extended at the level of signaling pathways, gene families, and single selected genes of interest. Some of the genes differentially expressed between the two species are already known to be important factors in the maintenance of pluripotency in ESCs, like for example Sox2 or Stat3, or play a role in reprogramming somatic cells to pluripotency like c-Myc, Klf4 and p53 and therefore represent interesting candidates to further analyze in vitro in the rat ESCs. This is the first study investigating the gene expression changes during the transition from morula to blastocyst in the rat preimplantation development. Our data show that in the pluripotent pool of cells of the rat and mouse preimplantation embryo substantial differential regulation of genes is present, which might explain the difficulties observed for the derivation and culture of rat ESCs using mouse conditions Casanova EA, Okoniewski MJ, Cinelli P. Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos.PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15. We collected morula and blastocysts stage embryos from mouse and rat and, by immunosurgery, we isolated the ICM cells from the blastocysts. All the embryos and ICMs were pooled into two groups for every developmental stage. Pooling of embryos for RNA extraction in this study was chosen mainly because of the low amounts of RNA that can be isolated from preimplantation embryos, and in addition because of the heterogeneity of the cell populations present in the embryos. For the analysis we pooled a large number (n >100) of the independent isolated embryos to achieve a sufficient accuracy of biological pooling . Due to the difficulties to isolate a larger number of embryos from mice and rats, we performed the microarray study by using two replicate samples per developmental stage.

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

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