Fig. 2: MLL-AF4 binding is required for the maintenance of enhancer signatures.

a Mean distribution of MLL (left) and AF4 (right) at MLL-AF4-bound and non-MLL-AF4-bound intergenic (solid line) or intragenic (dashed line) enhancers in SEM cells. Plots are centered on ATAC-seq peaks found within enhancers. b Upper: Mean log-fold change in gene expression in SEM cells following 96 h MLL-AF4 knockdown for genes associated with an MLL-AF4-bound enhancer or genes associated with an enhancer not bound by MLL-AF4, n = 3 independent experiments. Statistical significance calculated using a two-sided Mann–Whitney U test, p = 2.96 × 10⁻²¹. Midline shows median, with upper and lower hinges showing the 25th and 75th percentile, respectively. Upper and lower hinges extend to the largest and smallest datapoints within 1.5 times the interquartile range of either hinge. Lower: Proportion of enhancers associated with genes displaying each transcriptional response to MLL-AF4 knockdown. c Mean distribution of H3K27ac (left) and strand-specific nascent RNA-seq (enhancer RNA; right) levels at MLL-AF4-bound and non-MLL-AF4-bound enhancers, in SEM cells under control (NT) and 96 h MLL-AF4 knockdown conditions. Lines represent mean, shading represents ± SEM, n = 3 independent experiments for eRNA. d Reference-normalized ChIP-seq for H3K27ac and H3K79me3 at CDK6 and FLT3 in SEM cells under control (NT) and 96 h MLL-AF4 knockdown conditions. ChIP-seq for MLL, AF4, H3K4me1 and H3K4me3 is shown for context. e ChIP-qPCR for H3K27ac at the indicated enhancer regions in SEM and RS4;11 cells, under control (NT) and 96 h MLL-AF4 knockdown conditions. Data are represented as mean ± SEM, n = 3 independent experiments. Source data are provided as a Source Data file. f Mean distribution of H3K79me3 at MLL-AF4-bound and non-MLL-AF4-bound inter- and intragenic enhancers in SEM cells under control (NT) and MLL-AF4 knockdown conditions.