Figure S2. Mutant RUNX1 induction leads to specific changes to endogenous RUNX1 binding and chromatin accessibility.

(A) Representative flow cytometry plots of the cKit-sorted progenitors used for ChIP experiments, shown here for R204X, pre-gated on cKit-APC. (B) Endogenous RUNX1 ChIP-seq data in progenitors at both distal sites and promoters was ranked by fold change of the +dox/−dox tag count and represented as density plots. Chromatin accessibility and density of the RUNX1 motif are plotted alongside based upon the RUNX1 ranking. All density plots are centred around ±1 kb of the RUNX1 ChIP peak summits. The red bar indicates +dox-specific sites, grey shared, and blue −dox-specific sites where specific sites are at least twofold different. The numbers of sites are indicated. (C) ChIP-qPCR was performed using an antibody against the HA-tag following induction of R201Q and R204X, and in the absence of induction. The bars show the mean of three ChIP experiments, where enrichment of two RUNX1-positive control regions are compared with a negative control region, and to the input control. The error bars indicate standard error of the mean. (D) UCSC Genome browser screenshot of counts-per-million-normalised ATAC-seq and ChIP-seq tracks for the different experiments at the Klf2 promoter.