Fig. 1: Distinct trajectories of DNA methylation change during human naive and primed reprogramming.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a, Experimental design for time-course profiling of epigenomic changes that occur as cells are reprogrammed from fibroblasts to naive-hiPS and primed-hiPS cells. iMEFs, irradiated mouse embryonic fibroblasts; FACS, fluorescence-activated cell sorting. D indicates day of experiment and P indicates passage number. b,c, Dynamics of global CG methylation (b) and CA methylation (c) during naive and primed reprogramming compared with primed and naive hES cells. DNA methylation levels were calculated as a coverage-weighted mean (Methods). d, Principal component analysis of CG DNA methylation levels at GeneHancer regulatory elements throughout reprogramming. e, c-Means fuzzy cluster analysis of CG DNA methylation levels in regulatory elements throughout primed and naive reprogramming. Gene-expression plots of genes identified through GeneHancer’s double-elite set of gene–enhancer validated pairs47. The line is the nonparametric bootstrap mean and the ribbon shows the 99% confidence interval. f, Transcription factors (grouped by family) with significantly enriched motifs for DNA binding domains in regulatory elements for each cluster in e. Homer hypergeometric enrichment test; false discovery rate (FDR) < 0.01.
