Extended Data Fig. 8: Loss of MLL3/4 enzymatic activities results in redistribution of MLL4 genomic binding.

a, D4 EBs were collected for ChIP-seq of MLL4. 34,772 MLL4⁺ regions were identified in f/f or KI ESCs. MLL4⁺ distal regions or promoters were split based on the MLL4 binding intensities in KI EBs compared to f/f EBs. Average profiles (left) and heat maps (right) of 34,772 MLL4⁺ regions in f/f and KI EBs are shown. b, MLL4⁺ AEs in ESCs and D4 EBs are depicted by the Venn diagram. 10,767 de novo MLL4⁺ AEs were divided into three groups based on the changes of MLL4 binding intensities from f/f to KI EBs: increased (Group I), unchanged (Group II) and decreased (Group III). c, Motif analysis of the three groups of de novo MLL4⁺ AEs. GATA family transcription factors were highlighted in bold. Statistical significance was determined using the SeqPos motif tool with default parameters. d, Heat maps of GATA6 and MLL4 genomic bindings as well as H3K4me1 and H3K27ac enrichments on de novo GATA6⁺ MLL4⁺ AEs in f/f and KI D4 EBs. e, Expression fold changes (log₂) of genes associated predominantly with each group of de novo MLL4⁺ AEs. Sample size and RNA-seq data are presented in box plots. Center lines represent median values; the bottom and top of the boxes represent lower and upper quartiles; whiskers were calculated using the Tukey method. Statistical significance was determined by the two-sided Wilcoxon signed-rank test.