Fig. 3: Rescue of the meso-endoderm phenotype in Dnmt3b^−/− cells.

a Western blot analysis of DNMT3B expression in 3BKO (two independent clones) EpiLC derived from ESCs transfected with Empty vector (control) or Avitag-Dnmt3b (Rescued). WT cells and β-actin serve as control. Representative of two independent experiments. Uncropped gels are provided in Supplementary Fig. 11. b Trends of gene expression dynamics for all the DEGs (activated at the top, repressed at the bottom) between 3BKO + empty (3BKO) (orange) and 3BKO + 3B (rescued) (purple) during differentiation from EpiLC to ME24 and ME48h. Genes are grouped as early, medium and late according to when the biggest difference in transcription between 3BKO + 3B (rescued) and 3BKO + empty (3BKO) occurs. Dark lines represent the median, the shaded areas represent the interquartile range of each gene set. c Heatmap showing selected GO terms for enriched biological processes in activated and repressed genes, grouped as in b. d Pie chart showing the proportion of rescued genes by DNMT3B ectopic expression in 3BKO cells (***p-value < 0.0001, Odds ratio > 1, one-sided Fisher’s exact test). e Heatmaps showing the expression patterns of rescued genes from panel d.