Population snapshots predict early haematopoietic and erythroid hierarchies

The formation of red blood cells begins with the differentiation of multipotent haematopoietic progenitors. Reconstructing the steps of this differentiation represents a general challenge in stem-cell biology. Here we used single-cell transcriptomics, fate assays and a theory that allows the prediction of cell fates from population snapshots, to demonstrate that mouse hematopoietic progenitors differentiate through a continuous, hierarchical structure into seven blood lineages. We uncovered coupling between the erythroid and the basophil or mast cell fates, a global haematopoietic response to erythroid stress and novel growth factor receptors that regulate erythropoiesis. We defined a flow cytometry sorting strategy to purify early stages of erythroid differentiation, completely isolating classically defined burst-forming and colony-forming progenitors. We also found that the cell cycle is progressively remodelled during erythroid development and during a sharp transcriptional switch that ends the colony-forming progenitor stage and activates terminal differentiation. Our work showcases the utility of linking transcriptomic data to predictive fate models, and provides insights into lineage development in vivo. Overall design: Single-cell mRNA sequencing of hematopoietic progenitors from mouse bone marrow and fetal liver. Sample Bone marrow, basal: 5432 single cells. Sample Bone marrow, Epo-stimulated: 2954 single cells. Sample Fetal liver: 9482 single cells. Sample P1: 3104 single cells. Sample P1-CD71hi: 752 single cells. Sample P2: 2435 single cells. Sample P3: 2032 single cells. Sample P4: 1210 single cells. Sample P5: 2460 single cells.