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De novo DNA methylation during monkey pre-implantation embryogenesis

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ABSTRACT

Critical epigenetic regulation of primate embryogenesis entails DNA methylome changes. Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. Promoters of genes associated with oxidative phosphorylation are preferentially remethylated at the 8-cell stage, suggesting that this mode of energy metabolism may not be favored. Unlike in rodents, X chromosome inactivation is not observed during monkey pre-implantation development. Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis.

No MeSH data available.


Monkey paternal and maternal DNA is actively demethylated. (A) Dynamics of CpG methylation reprogramming in paternal and maternal genomes during early embryogenesis. (B) Tracing of representative paternal-specific and maternal-specific CpG sites in oocytes, sperm, and other developmental stages. (C) Genomic distribution of paternal-specific and maternal-specific active demethylation CpG sites (relative demethylation level (RDL) value ≥ 0.6).
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fig2: Monkey paternal and maternal DNA is actively demethylated. (A) Dynamics of CpG methylation reprogramming in paternal and maternal genomes during early embryogenesis. (B) Tracing of representative paternal-specific and maternal-specific CpG sites in oocytes, sperm, and other developmental stages. (C) Genomic distribution of paternal-specific and maternal-specific active demethylation CpG sites (relative demethylation level (RDL) value ≥ 0.6).

Mentions: To address whether both paternal and maternal genomes similarly undergo active DNA demethylation or whether only one parental genome goes through this process, we applied Bis-SNP algorithm22 (see Materials and Methods) to call single-nucleotide polymorphisms (SNPs) to track paternal and maternal genomes. We obtained 5 070 SNPs whose parental origin could be clearly identified (Supplementary information, Table S2). Consistent with the global patterns, both the paternal and maternal DNA undergoes robust demethylation following fertilization, suggesting that active demethylation occurs on both paternal- and maternal-contributed DNA in the zygotes. From the 2-cell stage and onward, the paternal and maternal genomes display identical patterns of DNA methylation dynamics (Figure 2A). When we tracked methylation changes of 2 058 paternal and 1 173 maternal CpG sites during the transition from gametes to zygotes, we observed both demethylation and remethylation occurring in a significant portion of paternal and maternal CpG sites. There are also large portions of CpG sites that maintain their methylation levels (Figure 2B). These data clearly indicate only a portion of paternal and maternal DNA undergoes active demethylation right after fertilization as no cell division takes place during this period. When the distribution of active demethylation CpG sites with the relative demethylation level value ≥ 0.65 is plotted, both paternal and maternal actively demethylated CpG sites in zygotes are located mainly in intronic and intergenic genomic regions (Figure 2C).


De novo DNA methylation during monkey pre-implantation embryogenesis
Monkey paternal and maternal DNA is actively demethylated. (A) Dynamics of CpG methylation reprogramming in paternal and maternal genomes during early embryogenesis. (B) Tracing of representative paternal-specific and maternal-specific CpG sites in oocytes, sperm, and other developmental stages. (C) Genomic distribution of paternal-specific and maternal-specific active demethylation CpG sites (relative demethylation level (RDL) value ≥ 0.6).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5385613&req=5

fig2: Monkey paternal and maternal DNA is actively demethylated. (A) Dynamics of CpG methylation reprogramming in paternal and maternal genomes during early embryogenesis. (B) Tracing of representative paternal-specific and maternal-specific CpG sites in oocytes, sperm, and other developmental stages. (C) Genomic distribution of paternal-specific and maternal-specific active demethylation CpG sites (relative demethylation level (RDL) value ≥ 0.6).
Mentions: To address whether both paternal and maternal genomes similarly undergo active DNA demethylation or whether only one parental genome goes through this process, we applied Bis-SNP algorithm22 (see Materials and Methods) to call single-nucleotide polymorphisms (SNPs) to track paternal and maternal genomes. We obtained 5 070 SNPs whose parental origin could be clearly identified (Supplementary information, Table S2). Consistent with the global patterns, both the paternal and maternal DNA undergoes robust demethylation following fertilization, suggesting that active demethylation occurs on both paternal- and maternal-contributed DNA in the zygotes. From the 2-cell stage and onward, the paternal and maternal genomes display identical patterns of DNA methylation dynamics (Figure 2A). When we tracked methylation changes of 2 058 paternal and 1 173 maternal CpG sites during the transition from gametes to zygotes, we observed both demethylation and remethylation occurring in a significant portion of paternal and maternal CpG sites. There are also large portions of CpG sites that maintain their methylation levels (Figure 2B). These data clearly indicate only a portion of paternal and maternal DNA undergoes active demethylation right after fertilization as no cell division takes place during this period. When the distribution of active demethylation CpG sites with the relative demethylation level value ≥ 0.65 is plotted, both paternal and maternal actively demethylated CpG sites in zygotes are located mainly in intronic and intergenic genomic regions (Figure 2C).

View Article: PubMed Central - PubMed

ABSTRACT

Critical epigenetic regulation of primate embryogenesis entails DNA methylome changes. Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. Promoters of genes associated with oxidative phosphorylation are preferentially remethylated at the 8-cell stage, suggesting that this mode of energy metabolism may not be favored. Unlike in rodents, X chromosome inactivation is not observed during monkey pre-implantation development. Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis.

No MeSH data available.