Comparative binding patterns of Chromatin Regulators in normal versus leukemic hematopoiesis [ATAC-Seq]

Cellular differentiation-trajectories require extensive alterations in chromatin structure and function, elicited by a diverse array of chromatin-factors (CFs). Using haematopoiesis as a model-system, we combined bulk ex vivo and single-cell in vivo CRISPR screens to comprehensively characterise the role of CF families in cell-fate decisions. We uncover marked lineage specificities for many CFs, dissecting specific CF-dependencies in vivo at single-cell resolution. This highlights functional diversity among related CFs (i.e. BAF-subcomplexes, MLL-methyltransferases), but also reveals functional redundancy among unrelated Repressive-complexes that restrain excessive myeloid differentiation. Epigenetic-profiling, molecularly explains CF lineage-dependencies, identifying differentiation stage-specific interactions between individual CFs and lineage-determining Transcription Factors (TFs). Intriguingly, non-canonical BAF remodeler disruption abrogates myeloid-TF function generating a pre-leukaemia phenotype. Screening CF functions in leukemia, we show that leukaemia cells abrogate normal CF function, restraining differentiation trajectories by engaging in novel CF-TF interactions that suggest potential therapeutic avenues. Together, our work greatly elucidates the role of CFs and their TF-partners across normal and malignant haematopoiesis. Here we have used ATAC-seq to analyse the chromatin accessibility patterns of multipotent blood progenitors (LSK cells) knocked-out for specific Chromatin Factors exvivo differentiated under conditions permiting multilineage (Lin. priming) or myeloid (Mye) differentiation.