Fig. 2

MLL3/4 is required for all dynamic H3K4me1 deposition during pluripotent transition. A Differential signal enrichment between naive and formative WT H3K4me1 peaks identifies significant peaks (Black, FDR <0.05, Log2 Foldchange (Log2FC) > 1). B Scatterplot of H3K4me1 peak intensities between naive and formative WT samples (gray, shared peaks, FDR > 0.1 & Log2FC < 0.7, red or blue, FDR < 0.05 & Log2FC > 1). C,D H3K4me1 signal in naive and formative MLL3KO or DKO samples at peaks called from WT. Colors correspond to peak categories derived from WT. E Differential signal enrichment of naive and formative DKO samples. F Same as C,D but with naive and formative dCD cells. G Differential signal enrichment of naive and formative dCD samples. H Feature annotation of WT peaks stratified by peak category including intergenic/intronic (Distal), Promoter, and all else (Others). I Distal H3K4me1 peak categories further stratified by MLL3/4 independent (DKO/WT Log2FC > −0.7) or dependent (DKO/WT Log2FC < −1). J Heatmap of MLL3/4-independent and MLL3/4-dependent H3K4me1 peak categories, rows sorted on “S” columns. All heatmap values and range are in CPM. For metagene analysis the range in CPM is the same as shown in heatmap for each factor. K Nearest neighbor TSS analysis of expression levels in Log2CPM for each RNA-seq dataset near H3K4me1 peak categories. Multi-comparison paired Wilcoxon rank-sum test, Benjamini-Hochberg corrected. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001