Fig. 2: Aberrant CG DNA methylation is acquired after day 13 of primed reprogramming and is absent in naive-hiPS cells.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a, Number of CG-DMRs detected in primed-hiPS versus hES cells. Hypo-methylated CG-DMRs are those that are less methylated in primed-hiPS cells than in hES cells, and hyper-methylated CG-DMRs are those that are more methylated in primed-hiPS cells than in hES cells. b, Relative CG DNA methylation difference at CG-DMRs in primed-hiPS cells versus hES cells (x axis) and fibroblasts (y axis). Each point on the graph represents an individual CG-DMR; blue points represent hypo-methylated DMRs and orange points represent hyper-methylated DMRs. The plot is divided into segments using a cut-off of 0.2 difference in mCG/CG between cell types for classification purposes. Kernel density estimate plots (top and right of the main graph) show the distribution of CG-DMR methylation differences for hypo- and hyper-methylated DMRs. c,d, Time-course of mean CG methylation change across aberrant hyper-methylated CG-DMRs (c) and hypo-methylated memory CG-DMRs (d) relative to the progenitor fibroblast state (day 0). Each point represents mean CG DNA methylation change compared to day 0 for individual samples. The hiPS cell time point includes all passages. e, Methylation at maternal germline ICRs throughout naive and primed reprogramming. In box plots, the horizontal line is the median, the box represents the interquartile range (IQR) and whiskers show either 1.5 × IQR or the data range. n = 1 independent experiment per box plot. ICRs are defined in ref. 21.
