Extended Data Fig. 1: Distinct trajectories of DNA methylation change throughout human naive and primed reprogramming.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a) Phase contrast images of reprogramming intermediates and hiPSCs throughout primed and naive reprogramming, n = 2 independent experiments. Scale bar: 100 µm. b) Gene expression profiling of marker genes for fibroblasts, Primed-hiPSCs, and Naive-hiPSCs throughout the time course of human reprogramming into both pluripotent states. c) Genome-wide proportion of CG dinucleotides in four categories of methylation levels: high, intermediate, low, and zero. d) Proportion of unmethylated, partially methylated, and fully methylated reads from WGBS libraries. e) Genome-wide levels of CH context DNA methylation (mCH/CH) for all dinucleotide contexts. f) Expression levels of genes encoding key enzymes in the cytosine DNA methylation (DNMTs) and demethylation (TETs) pathways. g) Regulatory element cluster gene examples from Fig. 1e where C-means fuzzy clustering of CG DNA methylation levels in GeneHancer regulatory elements was performed throughout primed and naive reprogramming. h) Genome track of CG DNA methylation levels and gene expression of a cluster 1 element (horizontal bar) encompassing the TWIST1 gene. i) Number of enhancers and promoters that change DNA methylation level > 0.2 between day 0 and day 7 of reprogramming, before cells are cultured in primed or naive media. Motif enrichment analysis shows enhancers that undergo CG demethylation before day 7 are enriched for OKSM factors and AP1 motifs. Enhancers with increased CG methylation between day 0 and day 7 are enriched for HAND1/JUNB motifs. j) Cell lines used to test for CG context differentially methylated regions (DMRs) between Primed-hiPSCs and hESCs. Background column indicates genetic background identifier for the cell line. k) Heatmap representation of CG methylation levels in the CG-DMRs. l) Mean CG DNA methylation changes across hypo-methylated memory CG-DMRs and aberrant hyper-methylated CG DMRs relative to the progenitor fibroblast state (day 0). Each datapoint represents mean CG DNA methylation change compared to d0 for individual samples. m) Genome track showing CG methylation levels for examples of each of the six CG-DMR classes indicated in Fig 1b. n) CG methylation at imprint control regions (ICRs) for paternal germline ICRs and secondary ICRs. Boxplots: median and IQR, whiskers = 1.5 × IQR. n = 1 independent experiment per boxplot. ICRs defined in21.
