Red cell formation begins with the differentiation of multipotent hematopoietic progenitors. Reconstructing the steps of differentiation represents a stereotypical challenge in stem cell biology. Combining single-cell transcriptomics, fate assays, and theory for predicting fate from population snapshots, we inferred a continuous, hierarchical structure of murine hematopoietic progenitors committing to seven blood lineages. We uncovered coupling between erythroid and basophil/mast cell fates, a global hematopoietic response to erythroid stress, and novel growth factor receptor regulators of erythropoiesis. We also defined a new flow-cytometric sorting strategy to purify progressive early stages of erythroid differentiation, completely isolating classically-defined burst-forming (BFU-e) and colony-forming progenitors (CFU-e). Intriguingly, profound remodeling of the cell cycle is intimately entwined with erythroid development and with a sharp transcriptional switch that extinguishes the CFU-e stage and activates terminal differentiation. Our work showcases the utility of theory linking transcriptomic data to predictive fate models, providing insights into lineage development in vivo.

The switch from self-renewal to differentiation coincides with a shorter S phase in which replication forks are faster.