Fig. 3: LSD1 activity is necessary for repressing transiently expressed retinoic acid-dependent genes.

a Volcano plot of differentially expressed genes at PP2 after LSD1 inhibition from PP1 to PP2 (TCP, LSD1i^early). Differential expression calculated with DESeq2 and genes with ≥1.5-fold change up or down. Adjusted p-values of <0.05 were considered differentially expressed. 445 genes were downregulated and 955 were upregulated in LSD1i^early PP2 cells. Black dots indicate genes not significantly changed (p-value > 0.05), grey dots genes significantly changed (p-value < 0.05) but less than 1.5-fold compared to control, red and green dots genes significantly up- and downregulated (p-value < 0.05 and ≥1.5-fold change), respectively (n = 2 replicates from independent differentiations). b Enrichment analysis of genes upregulated by LSD1i^early within 100 kb of G1, G2 and G3 or other distal LSD1 peaks. Dashed lines indicate p-value = 0.05 for enrichment (positive value) or depletion (negative value), permutation test. c Percentage of LSD1i^early upregulated genes near G1 (n = 139), G2 (n = 78) and G3 (n = 53) enhancers (within 100 kb). d Box plot of mRNA levels for 139 LSD1i^early upregulated genes near G1 enhancers. Plots are centred on median, with box encompassing 25th–75th percentile and whiskers extending up to 1.5 interquartile range (Tukey style). P = 2.30 e−3, 4.38 e−6, and 2.25 e−7, respectively, Wilcoxon rank-sum test, 2 sided. e Gene ontology analysis for 139 LSD1i^early upregulated genes near G1 enhancers. GT, primitive gut tube; PP1, early pancreatic progenitors; PP2, late pancreatic progenitors.