Fig. 3: Reprogramming through the naive state erases somatic cell memory and produces hiPS cells that closely resemble hES cells.
From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically
a, New reprogramming strategies for TNT-hiPS and NTP-hiPS cells. b, The proportion of CG-DMRs for primed-hiPS cells and hES cells corrected by TNT and NTP reprogramming to a difference of less than 0.2 mCG/CG. c, Differences in DNA methylation between hiPS and hES cells at CG-DMRs. Dashed lines indicate the threshold of 0.2 difference in CG-DMR methylation level. d, Methylation levels in corrected (top) and uncorrected (bottom) CG-DMRs. e, Enrichment permutation testing of corrected and uncorrected CG-DMRs in repressive chromatin. f, H3K9me3 enrichment in corrected CG-DMRs. Primed-hiPS: n = 2; TNT-hiPS: n = 2; NTP-hPSC, n = 3 independent experiments. 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. g, Aggregate profile of CA methylation in hypo-methylated CH-DMRs. Lines represent flank-normalized means. h, H3K9me3 enrichment in hypo-methylated CH-DMRs. Lines represent flank-normalized means. i, Genome track of a CH-DMR intersecting a PMD, fibroblast LAD and a CG-DMR cluster. Arrows indicate partial CG methylation, CA methylation depletion and H3K9me3 enrichment in a fibroblast LAD, as indicated. j, CG methylation in ICRs. The horizontal line is the median, the box represents the IQR and whiskers show either 1.5 × IQR or the data range. n = 1 independent experiment per box plot. k, WGBS reads at the MEST ICR. l, Schematic of NSC differentiation and profiling. m, The proportion of NCAM+FAP− cells during differentiation into NSCs. Primed-hiPS: n = 9; TNT-hiPS: n = 9; H9-hES: n = 6 independent differentiation experiments. Data are mean ± s.d. n, Proportions of different cell types detected in early NSC cultures by single-cell RNA-seq (scRNA-seq). o, Methylation levels in CG-DMRs corrected by NTP reprogramming (as in Fig. 3d) in hiPS cells and derived NSC cultures. p, CG methylation (flank-normalized mCG/CG) in hypo-methylated CH-DMRs in NSCs and progenitor fibroblasts.
