Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions

Histone variants (HVs) are a subfamily of epigenetic regulators implicated in embryonic development, but their role in human stem cell fate remains unclear. Here, we reveal that the phosphorylation state of the HV H2A.X (γH2A.X) regulates self-renewal and differentiation of human pluripotent stem cells (hPSCs) and leukemic progenitors. As demonstrated by CRISPR-Cas deletion, H2A.X is essential in maintaining normal hPSC behavior. However, reduced levels of γH2A.X enhances hPSC differentiation toward the hematopoietic lineage with concomitant inhibition of neural development. In contrast, activation and sustained levels of phosphorylated H2A.X enhance hPSC neural fate while suppressing hematopoiesis. This controlled lineage bias correlates to occupancy of γH2A.X at genomic loci associated with ectoderm versus mesoderm specification. Finally, drug modulation of H2A.X phosphorylation overcomes differentiation block of patient-derived leukemic progenitors. Our study demonstrates HVs may serve to regulate pluripotent cell fate and that this biology could be extended to somatic cancer stem cell control. [Display omitted] •H2A.X is critical for self-renewal and normal development of PSCs in humans•Genetic or chemical modulation of H2A.X allows control of hPSC specification•Nucleosomal association of γH2A.X regulates genes involved in hPSC fate decisions•Effects of γH2A.X extend to somatic progenitors to overcome leukemic differentiation Orlando et al. reveal a non-canonical role for the histone variant H2A.X by phosphorylation that is capable of controlling human stem cell self-renewal and lineage-specific differentiation. This observation could be extended to human somatic progenitors to overcome differentiation blockade in human leukemia by using drug modulation of H2A.X phosphorylation.