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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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A bimodal gene body methylation pattern associated with transcription in human oocytes.A, A density scatterplot of gene body methylation levels and transcription levels [43] in human oocytes. The data of mouse oocytes [5], [11] are also shown for comparison. Only genes longer than 5 kb were analyzed. For genes with RPKM less than 0.01, RPKM was set as 0.01. The density is color-coded as indicated. B, Mean methylation levels within 5 kb of transcription start sites (TSS) in human oocytes. Genes (>5 kb) were classified into two groups (log2(RPKM)>−5 and ≤−5). Methylation levels were smoothed using 5 bp non-overlapping sliding windows. C, Conservation of gene body methylation levels between human and mouse oocytes. 783 and 188 genes showed human-specific and mouse-specific gene body hypermethylation, respectively. 5076 and 1151 genes were hypermethylated and hypomethylated in both types of oocytes, respectively. The raw data are shown in S2 Table. D, GO analysis of 783 genes with human-specific gene body hypermethylation. The top three GO terms (biological process and molecular function) are indicated with gene counts, the proportion (%) and BH-corrected P-values. No GO term was enriched in genes with mouse-specific gene body hypermethylation. E, Gene body methylation levels and transcription levels of DNA methylation regulators in human and mouse oocytes. DNMT3L and ZFP57 showed gene body hypomethylation and were not expressed (RPKM<0.01) in human oocytes. DNMT3B (RPKM = 76.0) showed 10-fold higher expression than DNMT3A (RPKM = 7.6) in human oocytes. In contrast, Dnmt3b (RPKM = 4.9) showed ∼6-fold lower expression than Dnmt3a (RPKM = 30.6) in mouse oocytes. F, Methylation patterns at human DNMT3L and ZFP57 loci and mouse Dnmt3l and Zfp57 loci. The vertical line indicates the methylation level (%) and the baseline is set at 50% to highlight unmethylated CpGs. CpGs with>50% and <50% methylation are shown in red and grey, respectively.
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pgen-1004868-g003: A bimodal gene body methylation pattern associated with transcription in human oocytes.A, A density scatterplot of gene body methylation levels and transcription levels [43] in human oocytes. The data of mouse oocytes [5], [11] are also shown for comparison. Only genes longer than 5 kb were analyzed. For genes with RPKM less than 0.01, RPKM was set as 0.01. The density is color-coded as indicated. B, Mean methylation levels within 5 kb of transcription start sites (TSS) in human oocytes. Genes (>5 kb) were classified into two groups (log2(RPKM)>−5 and ≤−5). Methylation levels were smoothed using 5 bp non-overlapping sliding windows. C, Conservation of gene body methylation levels between human and mouse oocytes. 783 and 188 genes showed human-specific and mouse-specific gene body hypermethylation, respectively. 5076 and 1151 genes were hypermethylated and hypomethylated in both types of oocytes, respectively. The raw data are shown in S2 Table. D, GO analysis of 783 genes with human-specific gene body hypermethylation. The top three GO terms (biological process and molecular function) are indicated with gene counts, the proportion (%) and BH-corrected P-values. No GO term was enriched in genes with mouse-specific gene body hypermethylation. E, Gene body methylation levels and transcription levels of DNA methylation regulators in human and mouse oocytes. DNMT3L and ZFP57 showed gene body hypomethylation and were not expressed (RPKM<0.01) in human oocytes. DNMT3B (RPKM = 76.0) showed 10-fold higher expression than DNMT3A (RPKM = 7.6) in human oocytes. In contrast, Dnmt3b (RPKM = 4.9) showed ∼6-fold lower expression than Dnmt3a (RPKM = 30.6) in mouse oocytes. F, Methylation patterns at human DNMT3L and ZFP57 loci and mouse Dnmt3l and Zfp57 loci. The vertical line indicates the methylation level (%) and the baseline is set at 50% to highlight unmethylated CpGs. CpGs with>50% and <50% methylation are shown in red and grey, respectively.

Mentions: In mouse oocytes, gene-body methylation levels are reported to positively correlate with the transcription levels [5]. In human oocytes, a positive correlation between gene-body methylation and transcription levels was also observed. Interestingly, there was an expression-level boundary at around log2(RPKM)  = −5 (RPKM: reads per kilobase per million) (Fig. 3A). Genes with log2(RPKM)>−5 and <−5 may be transcriptionally active and inactive genes, respectively (Fig. 3B). We analyzed previously reported mouse methylome and transcriptome data and found that a bimodal distribution of gene body methylation was also observed while there was a boundary at around log2(RPKM)  = 0 (Fig. 3A). It is unclear whether the difference between the human and mouse expression-level boundaries reflects experimental or functional differences. We found that 971 genes showed differential gene body methylation between human and mouse oocytes (Fig. 3C and S2 Table). Gene ontology (GO) analysis revealed an abundance of genes encoding cell adhesion molecules with human-specific gene body hypermethylation (Fig. 3D), which could have important roles during human oogenesis. In mouse oocytes, Dnmt3l and Zfp57 are highly expressed and essential for DNA methylation regulation [18], [19] whereas human DNMT3L is undetectable in oocytes [20]. Here we found that the gene body regions of DNMT3L and ZFP57 were hypomethylated in human oocytes and neither gene was expressed (Figs. 3E, F), implying that DNMT3L and ZFP57 might not be essential for regulation of DNA methylation in human oocytes.


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)

A bimodal gene body methylation pattern associated with transcription in human oocytes.A, A density scatterplot of gene body methylation levels and transcription levels [43] in human oocytes. The data of mouse oocytes [5], [11] are also shown for comparison. Only genes longer than 5 kb were analyzed. For genes with RPKM less than 0.01, RPKM was set as 0.01. The density is color-coded as indicated. B, Mean methylation levels within 5 kb of transcription start sites (TSS) in human oocytes. Genes (>5 kb) were classified into two groups (log2(RPKM)>−5 and ≤−5). Methylation levels were smoothed using 5 bp non-overlapping sliding windows. C, Conservation of gene body methylation levels between human and mouse oocytes. 783 and 188 genes showed human-specific and mouse-specific gene body hypermethylation, respectively. 5076 and 1151 genes were hypermethylated and hypomethylated in both types of oocytes, respectively. The raw data are shown in S2 Table. D, GO analysis of 783 genes with human-specific gene body hypermethylation. The top three GO terms (biological process and molecular function) are indicated with gene counts, the proportion (%) and BH-corrected P-values. No GO term was enriched in genes with mouse-specific gene body hypermethylation. E, Gene body methylation levels and transcription levels of DNA methylation regulators in human and mouse oocytes. DNMT3L and ZFP57 showed gene body hypomethylation and were not expressed (RPKM<0.01) in human oocytes. DNMT3B (RPKM = 76.0) showed 10-fold higher expression than DNMT3A (RPKM = 7.6) in human oocytes. In contrast, Dnmt3b (RPKM = 4.9) showed ∼6-fold lower expression than Dnmt3a (RPKM = 30.6) in mouse oocytes. F, Methylation patterns at human DNMT3L and ZFP57 loci and mouse Dnmt3l and Zfp57 loci. The vertical line indicates the methylation level (%) and the baseline is set at 50% to highlight unmethylated CpGs. CpGs with>50% and <50% methylation are shown in red and grey, respectively.
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Related In: Results  -  Collection

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Show All Figures
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pgen-1004868-g003: A bimodal gene body methylation pattern associated with transcription in human oocytes.A, A density scatterplot of gene body methylation levels and transcription levels [43] in human oocytes. The data of mouse oocytes [5], [11] are also shown for comparison. Only genes longer than 5 kb were analyzed. For genes with RPKM less than 0.01, RPKM was set as 0.01. The density is color-coded as indicated. B, Mean methylation levels within 5 kb of transcription start sites (TSS) in human oocytes. Genes (>5 kb) were classified into two groups (log2(RPKM)>−5 and ≤−5). Methylation levels were smoothed using 5 bp non-overlapping sliding windows. C, Conservation of gene body methylation levels between human and mouse oocytes. 783 and 188 genes showed human-specific and mouse-specific gene body hypermethylation, respectively. 5076 and 1151 genes were hypermethylated and hypomethylated in both types of oocytes, respectively. The raw data are shown in S2 Table. D, GO analysis of 783 genes with human-specific gene body hypermethylation. The top three GO terms (biological process and molecular function) are indicated with gene counts, the proportion (%) and BH-corrected P-values. No GO term was enriched in genes with mouse-specific gene body hypermethylation. E, Gene body methylation levels and transcription levels of DNA methylation regulators in human and mouse oocytes. DNMT3L and ZFP57 showed gene body hypomethylation and were not expressed (RPKM<0.01) in human oocytes. DNMT3B (RPKM = 76.0) showed 10-fold higher expression than DNMT3A (RPKM = 7.6) in human oocytes. In contrast, Dnmt3b (RPKM = 4.9) showed ∼6-fold lower expression than Dnmt3a (RPKM = 30.6) in mouse oocytes. F, Methylation patterns at human DNMT3L and ZFP57 loci and mouse Dnmt3l and Zfp57 loci. The vertical line indicates the methylation level (%) and the baseline is set at 50% to highlight unmethylated CpGs. CpGs with>50% and <50% methylation are shown in red and grey, respectively.
Mentions: In mouse oocytes, gene-body methylation levels are reported to positively correlate with the transcription levels [5]. In human oocytes, a positive correlation between gene-body methylation and transcription levels was also observed. Interestingly, there was an expression-level boundary at around log2(RPKM)  = −5 (RPKM: reads per kilobase per million) (Fig. 3A). Genes with log2(RPKM)>−5 and <−5 may be transcriptionally active and inactive genes, respectively (Fig. 3B). We analyzed previously reported mouse methylome and transcriptome data and found that a bimodal distribution of gene body methylation was also observed while there was a boundary at around log2(RPKM)  = 0 (Fig. 3A). It is unclear whether the difference between the human and mouse expression-level boundaries reflects experimental or functional differences. We found that 971 genes showed differential gene body methylation between human and mouse oocytes (Fig. 3C and S2 Table). Gene ontology (GO) analysis revealed an abundance of genes encoding cell adhesion molecules with human-specific gene body hypermethylation (Fig. 3D), which could have important roles during human oogenesis. In mouse oocytes, Dnmt3l and Zfp57 are highly expressed and essential for DNA methylation regulation [18], [19] whereas human DNMT3L is undetectable in oocytes [20]. Here we found that the gene body regions of DNMT3L and ZFP57 were hypomethylated in human oocytes and neither gene was expressed (Figs. 3E, F), implying that DNMT3L and ZFP57 might not be essential for regulation of DNA methylation in human oocytes.

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