Fig. 4

LSD1 knockout led to increased H3K4me1 at promoter CGIs. A Average plot showing the distribution pattern and level of H3K4me1 (left) and H3K4me3 (right) at promoter CGIs and flanked regions of bivalent and non-bivalent genes in HCT116 and LSD1 KO cells. B Box plots showing levels of H3K4me1 (left) and H3K4me3 (right) at promoter CGIs of bivalent and non-bivalent genes in WT and LSD1 KO HCT116 cells. Data were presented as mean ± SD. Statistical analysis was performed by Wilcoxon Rank Sum. C Average plot showing the distribution pattern and level of DNA methylation at promoter CGIs and flanked regions of 4 groups of genes in WT and LSD1 KO HCT116 cells. common: group of genes with H3K4me1 peaks in both WT and LSD1 KO cells (n = 1,669); LSD1 KO-specific-H3K4me1: group of genes with H3K4me1 peaks only in LSD1 KO cells (n = 3,040); WT-specific-H3K4me1: group of genes with H3K4me1 peaks only in WT cells (n = 364); other: other genes (n = 9,897). D Volcano plot showing DEGs between WT and LSD1 KO HCT116 cells. Up: genes that are upregulated in LSD1 KO cells compared with WT cells (n = 96); Down: genes that are downregulated in LSD1 KO cells compared with WT cells (n = 61). q value < 0.1 was set as a cutoff for DEGs. E The stacked bar plot showing the percentage of bivalent and non-bivalent genes in different groups of DEGs. F GO analysis of genes that were up- and down-regulated in LSD1 KO cells compared with WT cells. G, H Box plots showing levels of DNA methylation (DNAm), H3K4me1 and H3K4me3 level at promoters of Up genes and Down genes in WT and LSD1 KO cells. Up genes, genes that are upregulated in LSD1 KO cells compared with WT cells. Down genes, genes that are downregulated in LSD1 KO cells compared with WT cells. Data were presented as mean ± SD. Statistical analysis was performed by Wilcoxon Rank Sum