Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.
Bottom Line: Here, we use digital footprinting and chromatin immunoprecipitation sequencing (ChIP-seq) to identify the core RUNX1/ETO-responsive transcriptional network of t(8;21) cells.We show that the transcriptional program underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind to identical DNA sites in a mutually exclusive fashion.Perturbation of this equilibrium in t(8;21) cells by RUNX1/ETO depletion leads to a global redistribution of transcription factor complexes within preexisting open chromatin, resulting in the formation of a transcriptional network that drives myeloid differentiation.
Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.Show MeSH
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Mentions: We next examined how the t(8;21) core transcriptional network changed 2 days after RUNX1/ETO depletion. Depletion had no immediate influence on the expression levels of any of the other factors studied above, with the notable exception of C/EBPα (Figure 3A). Nevertheless, loss of RUNX1/ETO had a profound effect on the binding of these transcription factors (Figure S5A). As exemplified by the CEBPE locus, depletion led to increased RUNX1 occupancy at several thousand sites, confirming that RUNX1/ETO and RUNX1 binding are in equilibrium (Figures 5A, top left, 5B, S5B, and S5C). Furthermore, increased RUNX1 occupancy, including RUNX1 sites that were not previously bound by RUNX1/ETO, was associated with a strong increase in p300 binding (Figure 3D). In contrast, more than 3,000 LMO2 binding sites were lost, mainly outside the regions bound by RUNX1/ ETO and RUNX1 (Figures 5A, bottom-right panel, and S5C). Furthermore, whereas 80% of all PU.1 binding sites remained unchanged, the number of sites bound by C/EBPα increased 4-fold. Interestingly, 65% of all C/EBPα de novo sites colocalized with PU.1 (Figures 5A, top left, S5B, and S5D). In agreement with these results, C/EBPα binding sites clustered more strongly with both RUNX1 and PU.1 sites upon depletion of RUNX1/ETO (Figure S5E).
Affiliation: School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.