Perturb-seq delineates gene regulatory programs governing the biology of hematopoietic stem and progenitor cells

How genetic perturbations shape these elemental programs in HSPCs, and how such programs relate to stem-cell-associated phenotypes, remains incompletely understood. Here we use Perturb-seq to profile the transcriptional consequences of targeting 520 genes by CRISPRi in primary mouse HSPC cultures.

To resolve perturbation effects in this heterogeneous primary-cell system, we develop an analysis strategy that separates changes in cell-state abundance from local transcriptional effects within cell states, and use these local perturbation signatures to identify 19 gene regulatory programs (GRPs) comprising genes respond coherently to genetic perturbations. Most GRPs map to defined cell biological programs, including protein biosynthesis, cell cycle, inflammatory signaling, and HSC identity.