Fig. 2

Genome-wide deficit in DNA methylation in KHDC3L^c.1A>G oocytes. a Global CpG methylation as determined by scBS-seq in KHDC3L^c.1A>G MII oocytes (n = 5) compared with PBAT from a bulk population of control GV/MI oocytes (denoted by Okae et al. [30]) and scBS-seq of MII oocytes (n = 32, denoted by Zhu et al. [31]). Indicated are mean methylation levels for each single oocyte (dots) and the median of each group. b Scatterplot of methylation values of 20-kb windows in grouped KHDC3L^c.1A>G oocytes (n = 5) compared with grouped control oocytes (Zhu et al. [31]; n = 32). c Seqmonk browser screenshot of genomic methylation in grouped KHDC3L^c.1A>G oocytes (n = 5) compared with bulk (Okae et al. [30]) and grouped (Zhu et al. [31]; n = 32) control oocytes. The zoomed-in view shows methylation over the KCNQ1OT1 imprinted domain. Each vertical bar in both zoomed-out and zoomed-in views is a 20-kb window, height and colour-coded for % methylation. d–f Box and whisker plots showing methylation in grouped control (Zhu et al. [31]; n = 32) and KHDC3L^c.1A>G oocytes (n = 5) of oocyte methylated and unmethylated domains (d), methylated and unmethylated CpG islands (CGIs; > 70 and < 20% in control oocytes, respectively) (e) and maternal gDMRs (f). Boxes represent the interquartile range; lines, the medians; whiskers, the 1.5× the interquartile range; dots beyond the whiskers, outliers. The numbers of features per category are given in Additional file 4: Table S3. g Heatmap showing methylation of maternal gDMRs in grouped KHDC3L^c.1A>G oocytes (n = 5) and bulk GV/MI (Okae et al. [30]) or grouped MII (Zhu et al. [31]; n = 32) control oocytes. h Stripcharts reporting percentage of methylated CpG sites (115) in ZFP57 binding motifs overlapping 32 maternal gDMRs in each single oocyte of control (Zhu et al. [31]; n = 32) and KHDC3L^c.1A>G oocytes (n = 5). Dots represent the mean methylation % of all the ZFP57-CpG sites measured in a single oocyte, lines the median of each group. Comparisons in a and d–h are all statistically significant (p < 0.0001). Detailed statistical measures are given in Additional file 4: Table S3