In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis

Abstract

Cellular differentiation requires extensive alterations in chromatin structure and function, elicited by a diverse array of chromatin-factors (CFs). Using hematopoiesis as a model-system, we combined bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of CF families in blood differentiation. We uncover marked lineage specificities for 142 CFs and followed up 60 CFs with single-cell resolution in vivo. This reveals functional diversity among related CFs (i.e. BAF-subcomplexes and H3K4-methyltransferases) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Epigenetic-profiling molecularly explains CF lineage dependencies, identifying interactions between specific CFs and lineage-determining Transcription Factors (TFs). Furthermore, in vivo disruption of the non-canonical BAF subunit, Brd9, abrogates myeloid-TF function, generating a preleukemia-like phenotype. Studying CF functions in leukemia, we show that leukemia cells corrupt homeostatic CF roles to facilitate differentiation, instead blocking differentiation trajectories by engaging in leukemia specific CF-TF interactions that suggest novel therapeutic avenues. Together, our work elucidates the lineage-determining properties of CFs across normal and malignant hematopoiesis.