Fig. 4: Chromatin and transcriptome reconfigurations in cellular intermediates.
a, PCA conducted on ATAC-Seq data. Untreated MEFs (black), BLTL and BHTH cells FACS sorted after 5 d of reprogramming (red) or transformation (blue) are represented. b, Example of ATAC chromatin sites at the Thy1 locus. c, Definition of the clusters described in the main text (n = 2 independent experiments). Central lines represents medians, box edges represent upper and lower quartiles and whiskers show the highest and lowest values, excluding outliers (at most 1.5× the interquartile range above or below the upper and lower quartile). d, Enrichment in TF motifs. Each point represents significant enrichment in the motif (x axis) for the cluster (y axis). The point size represents the proportion of sequences in the cluster featuring the motif and the colour gradient represents the enrichment significance. e, PCA conducted on RNA-Seq data. f, Venn diagram showing the numbers of differentially expressed genes in MEFs versus R-BLTL cells (red), MEFs versus T-BLTL cells (blue) and control MEFs versus Bcl11b KD MEFs (green) (log2[FC] < −0.5 or >0.5; base mean < 40; adjusted P value < 5 × 10−2). g, Visualization of R-BLTL and T-BLTL score activities on single-cell trajectories. h, Venn diagram showing the numbers of differentially expressed genes in T-BLTL versus T-BHTH cells (blue) and R-BLTL versus R-BHTH cells (red) (log2[FC] < −1 or >1; adjusted P value < 5 × 10−2). i, Statistical over-representation assays conducted with PantherDB. Statistical significance was determined by Fisher’s exact two-sided test. j, Top, patterns of the downregulated genes signature plotted on the diffusion map. Bottom, patterns of the upregulated genes signature plotted on the diffusion map. k, Heatmap clustering the 301 commonly deregulated genes. The MEF sample was excluded from the representation. l, Western blot depicting Atoh8, Id4, Twist2 and Gapdh levels in cellular intermediates. m, Western blot depicting Atoh8, Id4, Twist2 and Actin levels in MEFs, iPS and transformed cells.
