Fig. 3: Menin and SUZ12 maintain bivalency balance on developmental genes.
From: Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing
a, Pie charts of Menin and SUZ12 peaks in the H9 control hESCs mapped to 3′UTR, 5′UTR, distal intergenic, exon, introns and promoter regions. b,c, Differential analysis for binding of H3K4me3 (b) and H3K27me3 (c) counts. Each dot represents one H3K4me3 or H3K27me3 peak. Peaks that are significantly enriched (red, Padj < 0.05, log2FC > 0) and peaks that are significantly depleted (blue, Padj < 0.05, log2FC < 0) in the KO hESCs, compared to H9 control, are indicated. d, Heatmaps show genomic regions with increased (top panel, each row corresponds to a red dot in b left panel) and decreased (bottom panel, each row corresponds to a blue dot in b left panel) H3K4me3 level in MEN1 KO hESCs compared with control hESCs. NT hESCs were used as control for ATAC-seq, and unmodified H9 hESCs were used as control for CUT&RUN. The genomic regions are ordered according to the H3K4me3 level in the control sample. e, GO analysis on the genes annotated to the peaks with increased H3K4me3 level in MEN1 KO hESCs. Top five GO terms are shown in the dot plot. f, Normalized counts for H3K4me3, H3K27me3 and ATAC peaks for the 265 regions with increased H3K4me3 level in MEN1 KO hESCs. g, Heatmaps show genomic regions with increased (top panel, each row corresponds to a red dot in b right panel) and decreased (bottom panel, each row corresponds to a blue dot in b right panel) H3K4me3 level in SUZ12 KO ESCs compared with control hESCs. The genomic regions are ordered according to the H3K4me3 level in the control sample. h, GO analysis on the genes annotated to the peaks with increased H3K4me3 level in SUZ12 KO hESCs. Top five GO terms are shown in the dot plot. i, Normalized counts for H3K4me3, H3K27me3 and ATAC peaks for the 575 regions with increased H3K4me3 level in SUZ12 KO hESCs. f,i, Box-and-whisker plots: the whiskers represent the minima and maxima, the boxes represent the interquartile range and the centre line represents the median. P values were calculated using two-tailed unpaired t-test comparing KO to control.
