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Genome-wide analysis of DNA methylation dynamics during early human development.

Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T - PLoS Genet. (2014)

Bottom Line: Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation.These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development.Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development.

View Article: PubMed Central - PubMed

Affiliation: Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan; JST, CREST, Saitama, Japan.

ABSTRACT
DNA methylation is globally reprogrammed during mammalian preimplantation development, which is critical for normal development. Recent reduced representation bisulfite sequencing (RRBS) studies suggest that the methylome dynamics are essentially conserved between human and mouse early embryos. RRBS is known to cover 5-10% of all genomic CpGs, favoring those contained within CpG-rich regions. To obtain an unbiased and more complete representation of the methylome during early human development, we performed whole genome bisulfite sequencing of human gametes and blastocysts that covered>70% of all genomic CpGs. We found that the maternal genome was demethylated to a much lesser extent in human blastocysts than in mouse blastocysts, which could contribute to an increased number of imprinted differentially methylated regions in the human genome. Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation. Furthermore, centromeric satellite repeats were hypermethylated in human oocytes but not in mouse oocytes, which might be explained by differential expression of de novo DNA methyltransferases. These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development. Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development.

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Global changes of DNA methylation during early human development.A, Distribution of methylation levels of individual CpGs. The mean methylation levels of CpGs are also indicated. We included human H9 ES cells (GEO accession number: GSM706059) for comparison. B, Detection of dynamic methylation changes using a sliding window (window size  = 20 CpGs, step size  = 10 CpGs). Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were significant (BH-corrected P<0.05). The other windows were classified as stable. Oo: Oocyte; Sp: Sperm; Blasto: Blastocyst. C, Violin plots of mean methylation levels of windows hypermethylated (≥80%) or hypomethylated (≤20%) in one or both gametes. Oo-specific (Sp-specific) methylated windows are defined as windows hypermethylated in oocytes (sperm) and hypomethylated in sperm (oocytes). Thin and thick lines are box plots and white dots indicate the median. D, Heatmaps of Pearson correlation coefficients. Correlation coefficients were calculated based on the mean methylation levels of individual windows, CGIs, promoters and repeat copies. Correlation coefficients are color-coded as shown. E, A density scatterplot of mean methylation levels of the sliding windows. The Pearson correlation coefficient between oocytes and blastocysts was high (r = 0.87). The density is color-coded as indicated. F, Methylation levels across the long arm of chromosome 21 (smoothed using 50 kb non-overlapping windows). Similar methylation patterns were observed for oocytes and blastocysts whereas the methylation levels of blastocysts were low (note that the vertical maximum scale is 60% for blastocysts).
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pgen-1004868-g001: Global changes of DNA methylation during early human development.A, Distribution of methylation levels of individual CpGs. The mean methylation levels of CpGs are also indicated. We included human H9 ES cells (GEO accession number: GSM706059) for comparison. B, Detection of dynamic methylation changes using a sliding window (window size  = 20 CpGs, step size  = 10 CpGs). Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were significant (BH-corrected P<0.05). The other windows were classified as stable. Oo: Oocyte; Sp: Sperm; Blasto: Blastocyst. C, Violin plots of mean methylation levels of windows hypermethylated (≥80%) or hypomethylated (≤20%) in one or both gametes. Oo-specific (Sp-specific) methylated windows are defined as windows hypermethylated in oocytes (sperm) and hypomethylated in sperm (oocytes). Thin and thick lines are box plots and white dots indicate the median. D, Heatmaps of Pearson correlation coefficients. Correlation coefficients were calculated based on the mean methylation levels of individual windows, CGIs, promoters and repeat copies. Correlation coefficients are color-coded as shown. E, A density scatterplot of mean methylation levels of the sliding windows. The Pearson correlation coefficient between oocytes and blastocysts was high (r = 0.87). The density is color-coded as indicated. F, Methylation levels across the long arm of chromosome 21 (smoothed using 50 kb non-overlapping windows). Similar methylation patterns were observed for oocytes and blastocysts whereas the methylation levels of blastocysts were low (note that the vertical maximum scale is 60% for blastocysts).

Mentions: Similar to findings for the mouse, human oocytes showed an intermediate methylation level of CpGs and blastocysts were globally hypomethylated (Fig. 1A). To further characterize global DNA methylation changes, we used a system of sliding windows of 20 CpGs with a step size change of 10 CpGs. Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were statistically significant (Benjamini-Hochberg (BH) corrected P<0.05). We found that 57% and 83% of windows showed decreased methylation levels in blastocysts compared with oocytes and sperm, respectively (Fig. 1B). In contrast,>90% of windows showed increased methylation in ES or blood cells compared with blastocysts (Fig. 1B). To explore the differences in demethylation dynamics between parental genomes, we focused on windows hypermethylated in one gamete and hypomethylated in the other. In this study, we defined regions that were ≥80% methylated as hypermethylated and those that were ≤20% methylated as hypomethylated. Windows hypermethylated in sperm and hypomethylated in oocytes (sperm-specific methylated windows) were abundant in intergenic regions. In contrast, oocyte-specific ones showed a relatively uniform distribution (S2A Figure). In blastocysts, oocyte-specific methylated windows showed intermediate methylation levels (median  = 35.1%), in contrast to the nearly complete demethylation of sperm-specific ones (Fig. 1C). Almost all windows hypomethylated in both gametes remained hypomethylated and very few windows (0.04%) were hypermethylated in blastocysts, suggesting that genome-wide de novo methylation occurred after implantation (Fig. 1C and S2B Figure). Consistently, the methylation patterns of oocytes and blastocysts were very similar to each other (Figs. 1E, F), suggesting that the global methylation pattern of the maternal genome, but not the paternal genome, was inherited by blastocysts.


Genome-wide analysis of DNA methylation dynamics during early human development.

Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T - PLoS Genet. (2014)

Global changes of DNA methylation during early human development.A, Distribution of methylation levels of individual CpGs. The mean methylation levels of CpGs are also indicated. We included human H9 ES cells (GEO accession number: GSM706059) for comparison. B, Detection of dynamic methylation changes using a sliding window (window size  = 20 CpGs, step size  = 10 CpGs). Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were significant (BH-corrected P<0.05). The other windows were classified as stable. Oo: Oocyte; Sp: Sperm; Blasto: Blastocyst. C, Violin plots of mean methylation levels of windows hypermethylated (≥80%) or hypomethylated (≤20%) in one or both gametes. Oo-specific (Sp-specific) methylated windows are defined as windows hypermethylated in oocytes (sperm) and hypomethylated in sperm (oocytes). Thin and thick lines are box plots and white dots indicate the median. D, Heatmaps of Pearson correlation coefficients. Correlation coefficients were calculated based on the mean methylation levels of individual windows, CGIs, promoters and repeat copies. Correlation coefficients are color-coded as shown. E, A density scatterplot of mean methylation levels of the sliding windows. The Pearson correlation coefficient between oocytes and blastocysts was high (r = 0.87). The density is color-coded as indicated. F, Methylation levels across the long arm of chromosome 21 (smoothed using 50 kb non-overlapping windows). Similar methylation patterns were observed for oocytes and blastocysts whereas the methylation levels of blastocysts were low (note that the vertical maximum scale is 60% for blastocysts).
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Related In: Results  -  Collection

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pgen-1004868-g001: Global changes of DNA methylation during early human development.A, Distribution of methylation levels of individual CpGs. The mean methylation levels of CpGs are also indicated. We included human H9 ES cells (GEO accession number: GSM706059) for comparison. B, Detection of dynamic methylation changes using a sliding window (window size  = 20 CpGs, step size  = 10 CpGs). Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were significant (BH-corrected P<0.05). The other windows were classified as stable. Oo: Oocyte; Sp: Sperm; Blasto: Blastocyst. C, Violin plots of mean methylation levels of windows hypermethylated (≥80%) or hypomethylated (≤20%) in one or both gametes. Oo-specific (Sp-specific) methylated windows are defined as windows hypermethylated in oocytes (sperm) and hypomethylated in sperm (oocytes). Thin and thick lines are box plots and white dots indicate the median. D, Heatmaps of Pearson correlation coefficients. Correlation coefficients were calculated based on the mean methylation levels of individual windows, CGIs, promoters and repeat copies. Correlation coefficients are color-coded as shown. E, A density scatterplot of mean methylation levels of the sliding windows. The Pearson correlation coefficient between oocytes and blastocysts was high (r = 0.87). The density is color-coded as indicated. F, Methylation levels across the long arm of chromosome 21 (smoothed using 50 kb non-overlapping windows). Similar methylation patterns were observed for oocytes and blastocysts whereas the methylation levels of blastocysts were low (note that the vertical maximum scale is 60% for blastocysts).
Mentions: Similar to findings for the mouse, human oocytes showed an intermediate methylation level of CpGs and blastocysts were globally hypomethylated (Fig. 1A). To further characterize global DNA methylation changes, we used a system of sliding windows of 20 CpGs with a step size change of 10 CpGs. Windows were classified as increasing (or decreasing) if the methylation levels increased (or decreased) by>20% and the changes were statistically significant (Benjamini-Hochberg (BH) corrected P<0.05). We found that 57% and 83% of windows showed decreased methylation levels in blastocysts compared with oocytes and sperm, respectively (Fig. 1B). In contrast,>90% of windows showed increased methylation in ES or blood cells compared with blastocysts (Fig. 1B). To explore the differences in demethylation dynamics between parental genomes, we focused on windows hypermethylated in one gamete and hypomethylated in the other. In this study, we defined regions that were ≥80% methylated as hypermethylated and those that were ≤20% methylated as hypomethylated. Windows hypermethylated in sperm and hypomethylated in oocytes (sperm-specific methylated windows) were abundant in intergenic regions. In contrast, oocyte-specific ones showed a relatively uniform distribution (S2A Figure). In blastocysts, oocyte-specific methylated windows showed intermediate methylation levels (median  = 35.1%), in contrast to the nearly complete demethylation of sperm-specific ones (Fig. 1C). Almost all windows hypomethylated in both gametes remained hypomethylated and very few windows (0.04%) were hypermethylated in blastocysts, suggesting that genome-wide de novo methylation occurred after implantation (Fig. 1C and S2B Figure). Consistently, the methylation patterns of oocytes and blastocysts were very similar to each other (Figs. 1E, F), suggesting that the global methylation pattern of the maternal genome, but not the paternal genome, was inherited by blastocysts.

Bottom Line: Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation.These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development.Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development.

View Article: PubMed Central - PubMed

Affiliation: Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan; JST, CREST, Saitama, Japan.

ABSTRACT
DNA methylation is globally reprogrammed during mammalian preimplantation development, which is critical for normal development. Recent reduced representation bisulfite sequencing (RRBS) studies suggest that the methylome dynamics are essentially conserved between human and mouse early embryos. RRBS is known to cover 5-10% of all genomic CpGs, favoring those contained within CpG-rich regions. To obtain an unbiased and more complete representation of the methylome during early human development, we performed whole genome bisulfite sequencing of human gametes and blastocysts that covered>70% of all genomic CpGs. We found that the maternal genome was demethylated to a much lesser extent in human blastocysts than in mouse blastocysts, which could contribute to an increased number of imprinted differentially methylated regions in the human genome. Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation. Furthermore, centromeric satellite repeats were hypermethylated in human oocytes but not in mouse oocytes, which might be explained by differential expression of de novo DNA methyltransferases. These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development. Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development.

Show MeSH