Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation

Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the chromatin accessibility and transcriptome dynamics of zinc-containing HDACs during cell differentiation in vitro coupled with chemical perturbation to identify the role of HDACs in mesendoderm cell fate specification. Single-cell RNA sequencing analyses of HDAC expression during human pluripotent stem cell (hPSC) differentiation in vitro and mouse gastrulation in vivo reveal a unique association of HDAC1 and -3 with mesendoderm gene programs during exit from pluripotency. Functional perturbation with small molecules reveals that inhibition of HDAC1 and -3, but not HDAC2, induces mesoderm while impeding endoderm and early cardiac progenitor specification. These data identify unique biological functions of the structurally homologous enzymes HDAC1–3 in influencing hPSC differentiation from pluripotency toward mesendodermal and cardiac progenitor populations. [Display omitted] •Single-cell transcriptomics find HDAC1–3 to be regulators of cardiac differentiation•Inhibition of HDAC1–3 activity results in dynamic chromatin accessibility changes•Loss of HDAC1 and -3, but not HDAC2, impairs cardiac progenitor specification•HDAC1 and -3 are required during early stages of mesendoderm specification Sinniah et al. identify HDAC1 and -3 as required for early mesendoderm and cardiac progenitor specification during human pluripotent stem cell differentiation. Changes to chromatin accessibility and transcriptome dynamics upon perturbation of HDAC activity reveal distinct roles of HDAC1–3 in germ-layer and cardiac-lineage commitment following exit from pluripotency.