Both mESC-specific and differentiation genes are up-regulated after KDM1A loss in undifferentiated mESCs. (A) Schematic showing the number of significantly induced and repressed genes after differentiation of mESCs to epiblast stem cells with Activin A and FGF2 (Acampora et al. 2016). (B,C) Scatterplots of mRNA levels (B) and levels of nascent transcription (C), as measured using RNA-seq and GRO-seq, respectively, in WT and Kdm1a-GT mESCs. Number (n) of significantly up-regulated (q < 0.05) and down-regulated genes in each category are shown in blue and orange, respectively. Upon the loss of KDM1A in mESCs, both groups of induced and repressed genes show a significant increase (P < 2.2−16, Wilcoxon signed-rank test) in mRNA levels and nascent transcription. (D) Elevated transcription of Hmga2 and its nearby enhancers in Kdm1a-GT mESCs. Gray bar: Predicted enhancer, blue bar: significantly up-regulated enhancer in Kdm1a-GT mESCs.
