Fig. 1: AutoCUT&RUN profiling of KMT2A fusion protein binding.

a, A general strategy for mapping KMT2A fusion proteins. The wild-type KMT2A protein (black) is cleaved (white lines) into KMT2A-N and KMT2A-C proteins. Common oncogenic lesions (black arrowhead) produce in-frame translation of oncogenic KMT2A with numerous fusion partners (gray). Antibodies to C-terminal KMT2A (blue) recognize wild-type KMT2A-C. Antibodies to N-terminal KMT2A (red) recognize wild-type KMT2A-N and oncogenic KMT2A fusion proteins. b, Example of a wild-type KMT2A-binding site (EIF4E) and an oncoprotein-binding site (HOXA locus). Black scale bars, 10 kb. c, Scatterplot comparing KMT2A peak width and relative enrichment of the KMT2A N versus C terminus in control (CD34⁺ and K562) samples and KMT2Ar (SEM and ML-2) samples. d, Heatmap comparison of KMT2A signal over 10-kb windows centered on wide KMT2A-binding sites (top) and narrow KMT2A-binding sites (bottom) in CD34⁺ HSPCs and KMT2A fusion protein-binding sites (top) and wild-type KMT2A-binding sites (bottom) in SEM cells. e, Pie charts showing the fraction of wide KMT2A peaks (CD34⁺ and H1 cells) and KMT2A fusion-bound sites (KMT2Ar samples) overlapping transcriptional start sites (TSSs), gene bodies and intergenic regions. P values were computed using Fisher’s exact test. f, Box plots of KMT2A-N and KMT2A-C signal showing that the antibody to N-terminal KMT2A is enriched relative to the antibody to the C-terminal portion of KMT2A at fusion-binding sites. The center line indicates the median, box limits represent the first and third quartiles, and whiskers show all data within 1.5 times the interquartile range (IQR) of the lower and upper quartiles; outliers are not shown. P values were computed using a two-sample t test (two sided). CD34⁺, n = 131; K562, n = 65; ML-2, n = 144; SEM, n = 91; RS4;11, n = 92; KOPN-8, n = 192; 1° ALL-1, n = 156; 1° AML-1, n = 349; 1° AML-2, n = 423; 1° AML-3, n = 103; 1° AML-4, n = 270; 1° AML-5, n = 186; 1° MPAL-1, n = 248; 1° MPAL-2, n = 189. g, Principal-component analysis (PCA) of fusion oncoprotein-binding sites in KMT2Ar samples. The first two components are shown.