Fig. 3

CBFA2T3 and RUNX1 colocalize. a, b, c, e and f Quantitation of protein co-localization per nucleus and visualized by Proximity Ligation Assay (PLA) dots in REH cells (a, e), Nalm6 cells (b, f) and BCP-ALL patient cells (c), presented with the mean values ± S.D. Antibodies used are indicated under each plot. Positive controls (total CBFA2T3, where primary antibodies against two different epitopes of CBFA2T3 were used) and negative controls (only one anti-CBFA2T3) were included. One representative experiment of at least two independent experiments is shown. The data are normalized against total CBFA2T3. The mean value is indicated above each plot. The positive threshold value is represented by the dotted line (set at two S.D over the background signal as described in [25]). NS: non-significant, * p < 0.05, **** p < 0.0001 in Fisher’s exact test compared to the negative control condition. d Co-immunoprecipitation (co-IP) using (left panel) IgG or RUNX1 antibody in REH cells, and (in right panel) anti-Flag antibody in HEK293 cells expressing RUNX1-Halotag and/or CBFA2T3-Flag plasmids. Western blots were performed with RUNX1 and CBFA2T3 antibodies. Molecular weights are indicated on the right. g Density plots of CBFA2T3 Chip-Seq signals into RUNX1-bound regions or random regions in REH and Nalm6 cells. h ChIP-Seq profiles across the human CBFA2T3 gene. Genomic tracks display ChIP-Seq profiles for RUNX1 and CBFA2T3 from REH cells. ChIP-Seq reads were aligned to the reference human genome version GRCh37 (hg19). Two enhancers at + 9 kb and − 2 kb have been focused on. i Logo corresponding to the RUNX1 enriched motif for CBFA2T3 regions in REH cells. REH and Nalm6 CBFA2T3 Chip-Seq have been analyzed with the Analysis of Motif Enrichment of the MEME suite [32]. The optimal enrichment p-value of the motif according to the Fisher’s exact test, adjusted for multiple tests using a Bonferroni correction is indicated