Extended Data Fig. 8: Dominant clones possess a distinct chromatin accessibility landscape.

a, Number of clones comprising the 95^th percentile at Baseline (T₀) and Endpoint (T_N) bone marrow and spleen samples in NSG and Ptprc^a mice that received transplants from the same pool of barcoded MLL-AF9 + Kras^G12D cells. b, Proportional bubble plots of clones identified via Barcode-seq at Baseline and Disease timepoints for each mouse in each immune background. For each sample, clones are sorted in descending rank order according to their percentage abundance in the Baseline sample (n = 3 mice per group) c, Permutation analysis of Shannon diversity scores derived from the Louvain cluster occupancy of Ptprc^a only (n = 398 cells) or Ptprc^a and NSG specific (Shared, n = 150 cells) dominant clones from Fig. 2. Center point indicates raw Shannon diversity values with error bars reflecting the standard error of 1000 resampling events with replacement. Two-sided Mann Whitney U test. *, p = 1e⁻¹¹. d, Gene expression heat map showing the top differentially expressed genes in dominant clones from the NSG-only, Ptprc^a-only and shared groups vs all other cells at the Baseline timepoint. A random sample of all other cells is shown on the heat map. Genes of interest are highlighted. e, Biological pathways enriched in the set of genes upregulated in NSG-specific clones (NSG_up) or downregulated in NSG (NSG_down) and Ptprc^a specific clones (BL6_down). Number of genes in each group are indicated above. f, UMAP projections of scRNA-seq dataset from Baseline MLL-AF9 + Kras^G12D cells from Fig. 3 showing expression of Cebpα, Cebpβ and Cebpδ. g, UMAP projection of scATAC-seq dataset from Baseline MLL-AF9 + Kras^G12D cells from Fig. 3 showing results of Louvain clustering and label transfer to the corresponding scRNA-seq dataset as in Fig. 3. h, Results of differential accessibility analysis of cells in scATAC-seq clusters 1 and 7 (Dominant) vs cells in all other clusters (Other) at three exemplar loci B2m (top), Kit (middle) Cebpε (bottom). Boxes indicate regions of significantly altered accessibility in the Dominant group. i, The top six enriched transcription factor motifs in regions significantly differentially accessibile in cells comprising scATAC-seq clusters 1 and 7 (clusters enriched for dominant clones) vs cells in all other clusters. j, Results of Cebpε, Cebpα and isotype control (IgG/Neg) Chromatin Immuno-precipitation coupled qPCR using primers against the promoter of Slpi and a negative-control region (Gene desert) in MLL-AF9 + Kras^G12D cells. Mean ± s.d. of n = 3 independent experiments are shown. k, Western blot analysis of Baseline Slpi protein levels in MLL-AF9 + Kras^G12D cells transduced with guides targeting Slpi or non-targeting guide control immediately prior to the in vitro and in vivo competition assays in Fig. 2. (representative of n = 2 independent experiments). For uncropped blot, see Supplementary Information Figure 2. l, Flow cytometry analysis of bone marrow cells collected from 50:50 group mice. Representative results from n = 4 mice.