Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction.

The emerging notion of hematopoietic stem and progenitor cells (HSPCs) as a low-primed cloud without sharply demarcated gene expression programs raises the question on how cellular-fate options emerge and at which stem-like stage lineage priming is initiated. Here, we investigate single-cell chromatin accessibility of Lineage⁻, cKit⁺, and Sca1⁺ (LSK) HSPCs spanning the early differentiation landscape. Application of a signal-processing algorithm to detect transition points corresponding to massive alterations in accessibility of 571 transcription factor motifs reveals a population of LSK FMS-like tyrosine kinase 3 (Flt3)^intCD9^high cells that concurrently display stem-like and lineage-affiliated chromatin signatures, pointing to a simultaneous gain of both lympho-myeloid and megakaryocyte-erythroid programs. Molecularly and functionally, these cells position between stem cells and committed progenitors and display multi-lineage capacity in vitro and in vivo but lack self-renewal activity. This integrative molecular analysis resolves the heterogeneity of cells along hematopoietic differentiation and permits investigation of chromatin-mediated transition between multipotency and lineage restriction. [Display omitted] • Distinct chromatin landscapes separate hematopoietic stem and progenitor populations • LSKFlt3^intCD9^high cells display concurrent stem- and multi-lineage chromatin • LSKFlt3^intCD9^high cells bridge multipotency and lineage restriction Safi et al. reveal a unique hematopoietic transition state, displaying concurrent stem- and multi-lineage chromatin-accessibility signatures captured by LSKFlt3^intCD9^high immunophenotype. LSKFlt3^intCD9^high cells represent extensively primed progenitors lacking self-renewal but bridging multipotency and lineage restriction. These findings permit analysis of how self-renewal and multipotency are lost in favor of lineage commitment. [ABSTRACT FROM AUTHOR]