The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation Lei Zhao, Ming-an Sun, Zejuan Li, et al. Genome Res. published online May 16, 2014 Access the most recent version at doi:10.1101/gr.163147.113
Supplemental Material P
=5 reads on both strands) for both E14-d0 and
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E14-d6. Among these cytosines, 7,583,856 are located in CpG context, 35,228,969 in CHG
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context, and 115,745,872 in CHH context. They represent 17.3%, 16.0% and 13.8% of the total
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number of CpG, CHG and CHH sites in the mouse genome, respectively.
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We first analyzed the methylation levels (ML) of CpG and non-CpG sites in E14-d0 and
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E14-d6. Similar to previous reports (Ramsahoye et al. 2000; Lister et al. 2009; Xie et al. 2012), 5 / 30
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we detected abundant DNA methylation calls (8.0%) in non-CpG context in E14-d0 and the
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number decreased to 4.3% in E14-d6 (Figure S3A&B). Most cytosines in CpG context are
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highly methylated in both E14-d0 and E14-d6, and their methylation levels are characterized by
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a bimodal distribution (Figure S3C&D). The average methylation level of CpG dyads is 86.3%
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in E14-d0, and increases to 91.5% in E14-d6 (Figure S3C&D). In contrast, most cytosines in
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non-CpG context are either unmethylated or lowly methylated (Figure S3E-H).
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We further determined the methylation fidelity (MF), as defined in the method section,
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which represents the percentage of symmetrically methylated or unmethylated CpG dyads for a
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given position. A symmetrical methylation status of CpG dyad (either methylated or
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unmethylated) indicates successful methylation inheritance, while an asymmetrical methylation
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status (hemi-methylated CpG dyad) indicates gain or loss of the methylation pattern. Most CpG
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dyads have high methylation fidelity and the average methylation fidelity is as high as 88.5% and
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91.9% for E14-d0 and E14-d6, respectively (Figure S4). While most CpG dyads maintain
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similar methylation levels and fidelities during mES cell differentiation, our results indicate that
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both the methylation level and fidelity increase for a considerable fraction of CpG dyads in E14-
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d6 (Figure S5). More specifically, 24.7% of CpG dyads (17.0% increased, and 7.7% decreased)
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have methylation level changes over 20% (Figure S5C), and 27.5% of CpG dyads (17.3%
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increased, and 8.3% decreased) have methylation fidelity changes over 20% (Figure S5D).
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Methylation level and fidelity vary at distinct genomic regions
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Numerous studies indicate that DNA methylation levels tend to vary across distinct
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genomic regions (Doi et al. 2009; Lister et al. 2009; Laurent et al. 2010). Consistently, we
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observed low methylation levels in promoter regions, and the methylation levels are highly
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correlated with the distance to transcription starting sites (Figure 2). Low methylation levels
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were also observed for CGIs and CGI shores (p
