Fig. 4: The isogenic differentiation and reprogramming system confirms that TNT reprogramming enhances epigenome resetting. | Nature

Fig. 4: The isogenic differentiation and reprogramming system confirms that TNT reprogramming enhances epigenome resetting.

From: Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Fig. 4

a, Experimental design for differentiating hES cells to fibroblast-like cells and then reprogramming them to hiPS cells using the primed, TNT and NTP methods. b, Principal component analysis of CG methylation at GeneHancer elements, mCA/CA of 50-kb genome windows, normalized ATAC–seq read counts in peaks, normalized global gene expression, normalized global transposable element (TE) expression and normalized H3K9me3 ChIP–seq read counts. Data were quantile-normalized counts per million (CPM). c, Differential-testing MA plots for gene expression (determined by RNA-seq), TE expression (RNA-seq), and chromatin accessibility (ATAC–seq) for hiPS cells versus hES cells. Red points indicate FDR <0.05. Numbers on plots enumerate the ‘up’ or ‘down’ significant-features counts for each comparison. d, Differential testing of hES cells versus hiPS cell types for CG-DMRs, gene expression, TE expression and ATAC–seq peaks. ‘hiPS cell higher’ indicates that the value is higher in hiPS cells than in hES cells, and ‘hiPS cell lower’ indicates that the value is lower in hiPS cells than in hES cells. e, Aggregate profile plot of CA methylation levels in hypo-methylated CH-DMRs. f, Permutation testing enrichment (z-scores) of differential elements. z-scores larger than 5 were reduced to 5 for visualization. REs, regulatory elements. g, Relative expression heatmap of HERV-H-int elements that are differentially expressed between hES cells and primed-hiPS cells (n = 167). h, Genome track of a CH-DMR region detected in hES cells versus primed-hiPS cells and associated epigenomic features. Red lines show fibroblast LAD, fibroblast PMD in the primed-hiPS cells and fold enrichment (FE) of H3K9me3 in primary fibroblasts, as indicated. i, Normalized ATAC–seq signal at the LARGE1 promoter. The red arrow highlights the absence of an ATAC–seq peak in primed-hiPS cells. j, Gene expression of LARGE1 in isogenic hES cells, hiPS cells and progenitor fibroblasts. Red arrows indicate repression in primed-hiPS cells and fibroblasts.

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