Global changes of DNA methylation during early human development.

<p><b>A,</b> 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>B,</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 <i>P</i><0.05). The other windows were classified as stable. Oo: Oocyte; Sp: Sperm; Blasto: Blastocyst. <b>C,</b> 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. <b>D,</b> 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. <b>E,</b> A density scatterplot of mean methylation levels of the sliding windows. The Pearson correlation coefficient between oocytes and blastocysts was high (<i>r</i> = 0.87). The density is color-coded as indicated. <b>F,</b> 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).