Whole-Genome DNA Methylation Dynamics of Sheep Preimplantation Embryo Investigated by Single-Cell DNA Methylome Sequencing

Abstract

The early stages of mammalian embryonic development involve the participation and cooperation of numerous complex processes, including nutritional, genetic, and epigenetic mechanisms. However, in embryos cultured in vitro, a developmental block occurs that affects embryo development and the efficiency of culture. Although the block period is reported to involve the transcriptional repression of maternal genes and transcriptional activation of zygotic genes, how epigenetic factors regulate developmental block is still unclear. In this study, we systematically analyzed whole-genome methylation levels during five stages of sheep oocyte and preimplantation embryo development using single-cell level whole genome bisulphite sequencing (SC-WGBS) technology. Then, we examined several million CpG sites in individual cells at each evaluated developmental stage to identify the methylation changes that take place during the development of sheep preimplantation embryos. Our results showed that two strong waves of methylation changes occurred, namely, demethylation at the 8-cell to 16-cell stage and methylation at the 16-cell to 32-cell stage. Analysis of DNA methylation patterns in different functional regions revealed a stable hypermethylation status in 3′UTRs and gene bodies; however, significant differences were observed in intergenic and promoter regions at different developmental stages. Changes in methylation at different stages of preimplantation embryo development were also compared to investigate the molecular mechanisms involved in sheep embryo development at the methylation level. In conclusion, we report a detailed analysis of the DNA methylation dynamics during the development of sheep preimplantation embryos. Our results provide an explanation for the complex regulatory mechanisms underlying the embryo developmental block based on changes in DNA methylation levels.

Global DNA methylation, DNA methyltransferase and stress‐related gene expression in ovine oocytes and embryos after exposure to metabolic stressors

“…Both paternal and maternal genomes were highly methylated at the time of fertilization, and earlier studies showed that in bovine preimplantation embryos the paternal genome underwent sharp active demethylation within only a few hours of fertilization, whereas the maternal genome underwent passive demethylation from cleavage division to the 8‐cell stage (Perillo et al, 2008). Yet, Zhang et al (2021) reported that two strong waves of methylation changes occurred, (a) demethylation at the 8‐cell to 16‐cell stage and (b) methylation at the 16‐cell to 32‐cell stage in sheep. It was also reported that the elevated concentration of metabolic stressors was associated with low blastocyst rates and abnormal embryo development (Van Hoeck et al, 2015).…”

Preimplantation embryo gene expression: 56 years of discovery, and counting

“…The maternal genome undergoes largely passive DNA demethylation. The dynamics of methylation changes vary with species (Zhang et al, 2021). Sequestration of DNA methyltransferases to the ooplasm, including within the subcortical maternal complex (SCMC) (see below) and associated with cytoplasmic UHRF1, and preferential association of DPPA3/Stella (which inhibits DNA methylation by inhibiting DNA methyltransferase 1 recruitment by binding UHRF1) with the maternal genome may limit de novo methylation within the maternal genome (Eckersley‐Maslin et al, 2018; Han et al, 2019).…”

“…The maternal genome undergoes largely passive DNA demethylation. The dynamics of methylation changes vary with species (Zhang et al, 2021).…”

Current status of genome‐wide epigenetic profiling of mammalian preimplantation embryos

“…Other species of economic or medical research importance have also been the subjects of DNA methylome studies. [20][21][22][23] In addition, mammalian genomes have kilo-to mega-base scale regions with low average methylation levels called partially methylated regions (PMDs), 24 which are also observed in oocytes in genepoor and transcriptionally inactive regions, as shown in Figure 1B.…”