Fig. 2: LSD1 inhibition prevents decommissioning of transiently active early pancreatic enhancers.

a Heatmap showing density of ChIP-seq reads for LSD1 and H3K27ac centred on LSD1 peaks, spanning 10 kb. G1, G2 and G3 groups of LSD1-bound enhancers are deactivated (G1; n = 1345), remain active (G2; n = 765), or are activated (G3; n = 511) from PP1 to PP2. b Box plots of H3K4me1 and H3K4me2 ChIP-seq counts at G1, G2 and G3 enhancers at PP1 and PP2 stages. Plots are centred on median, with box encompassing 25th–75th percentile and whiskers extending up to 1.5 interquartile range (Tukey style). P = 5.0 e−12, < 2.2 e−16, <2.2 e−16, 1.73 e−2, <2.2 e−16, and 8.23 e−14, respectively, Wilcoxon rank-sum test, 2 sided. c Tag density plots displaying LSD1 tag distribution at G1, G2 and G3 enhancers at GT, PP1 and PP2 stages, centred on PP1 LSD1 peaks. d Tag density plots (left) for G1 enhancers displaying H3K27ac, H3K4me2 and H3K4me1 tag distribution at GT and PP1 stages, and at PP2 stage with and without early LSD1 inhibition (TCP, LSD1i^early). Plots are centred on PP1 LSD1 peaks. Box plots (right) of H3K27ac, H3K4me2 and H3K4me1 ChIP-seq counts at G1 enhancers at PP2 stage with and without early LSD1 inhibition (LSD1i^early). Plots are centred on median, with box encompassing 25th–75th percentile and whiskers extending up to 1.5 interquartile range (Tukey style). P = 4.59 e−5, <2.2 e−16, and <2.2 e−16, respectively, Wilcoxon rank-sum test, 2 sided. e LSD1, H3K4me2, and H3K27ac ChIP-seq profiles at an enhancer near HOXA1. f Model for LSD1-dependent enhancer decommissioning. Enhancer deactivation by removal of acetylation from H3K27 occurs independent of LSD1 activity. LSD1 subsequently mediates enhancer decommissioning by removal of H3K4me2 marks. KC, KAAD-cyclopamine; KGF, keratinocyte growth factor; RA, retinoic acid; EGF, epidermal growth factor. GT, primitive gut tube; PP1, early pancreatic progenitors; PP2, late pancreatic progenitors. All ChIP-seq experiments, n = 2 replicates from independent differentiations.