Fig 2: Cell-signaling requirements for NFATc2 co-occupation with p300 and HDAC1 on RFX6 and MCT1 gene promoters(A–L). Effects of 16.7 mM glucose (G16.7) and IL-1ß in the presence of (A-F) FK506, RAPA, and WM and (G-L) Nif, Dant, and NAC on association of NFATc2 (A, D, G, and J), p300 (B, E, H, and (K), and HDAC1 (C, F, I, and L) on RFX6 and MCT1 gene promoters by ChIP-Re-ChIP assay in MIN6. Data shown are representative of results from at least three independent experiments (n = 3) using replicate assays. Asterisks denote statistical significance (#p < 0.05, ##p < 0.01, ###p < 0.001 as compared to control, *p < 0.05, **p < 0.01, ***p < 0.001 as compared to no drug) in mean values based on the two-tailed Student t test.

Fig 3: P300/CBP contribute to the gene misregulation and defective differentiation caused by LSD1 loss.a Genome browser view of P300 ChIP-Rx signals at Rnf213 locus in WT and LSD1 KO ESCs. b Heatmaps showing P300 ChIP-Rx levels at LSD1 enriched regions in WT and LSD1 KO ESCs. Three clusters were generated by k-means clustering. c Box plots indicating the signals of P300 ChIP-Rx in WT and LSD1 KO cells at LSD1 peaks in the three clusters in (b). n = 2 biologically independent experiments. d Box plots of RNA-seq signals of nearest genes to LSD1 peaks in WT and LSD1 KO cells in the three clusters in (b). P-values in (c) and (d) were calculated using two-sided Wilcoxon signed-rank tests. Center line: median; top and bottom hinges of box: the third and first quantiles; whiskers: quartiles ± 1.5 × interquartile range. e Western blotting of H3K27ac in ESCs treated with DMSO or 10 μM A485 for 24 h. Experiments were repeated three times independently with similar results observed. Source data are provided as a Source data file. f Genome browser view of H3K27ac ChIP-Rx signals at Rnf213 locus in LSD1 KO ESCs treated with DMSO or 10 μM A485 for 24 h. g Correlation analysis of upregulated genes upon LSD1 deletion (1696 red genes in Fig. 1c) in A485 vs. DMSO treated LSD1 null cells. h Genome browser view of RNA-seq signals of Rnf213 gene in LSD1 KO cells treated with DMSO or 10 μM A485 for 24 h. i Phase-contrast images of day 6 EBs generated from LSD1KO ESCs treated with DMSO or 0.4 μM A485. Experiments were repeated three times independently with similar results observed. Scale bar: 100 μm. j Quantification of EB sizes in (i). Data are presented as mean values ± SD. n = 3 biologically independent experiments. P-values were calculated using two-sided student’s t-test. Source data are provided as a Source data file. k Correlation analysis of upregulated genes in LSD1 null EBs (1156 red genes in Fig. 3c) treated with respective 0.4 μM A485 and DMSO. l GO analysis of 250 genes upregulated in LSD1 KO EBs but downregulated by A485 treatment (green genes in k). m Genome browser view of Nefl RNA-seq signals in WT and LSD1 KO day 6 EBs treated with DMSO or A485. n A working model for the regulation of enhancers by LSD1. P300 occupancy increases at LSD1-targeted enhancers upon LSD1 loss, acetylating nucleosomes at enhancers previously decommissioned by LSD1 and activating gene expression.