Fig. 2: Perturb-seq highlights disparate lineage dependencies for chromatin complexes during hematopoiesis.
From: In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis
a, Schematic drawing of the in vivo Perturb-seq: LSK progenitors were sorted from Cas9-GFP mice infected with the chromatin factor knockout library and transplanted into irradiated recipient mice; bone marrow was collected 14 days after transplant, sorted for an immature phenotype (lineage− and Lin+c-Kit+) and the Perturb-seq and downstream analyses were performed. b, Uniform manifold approximation and projection (UMAP) of the single-cell transcriptomes. Clusters are annotated using external reference maps56. The analysis integrates seven different biological replicates. CLP, common lymphoid progenitor; Eo/Ba, esosinophil-basophil progenitor; Ery, erythroblast; G1, G1 phase; Gran, granulocyte; IMP, immature myeloid progenitor; MEP, mega-erythroid progenitor; MKP, megakaryocyte progenitor; Mono, monocyte; S, S phase. c, UMAP showing the distribution of unperturbed cells (NTC sgRNAs) and specific perturbations. d, Scatterplot showing comparisons between experimental batches. Each dot represents the abundance of two NTC sgRNAs in a given population. Pearson correlation between NTC and sgRNAs per experimental batch = 0.962 with P = 1.20 × 10−67. e, Enrichment and depletion of chromatin factor knockouts across hematopoietic populations (Supplementary Table 4). Dot color and size relate to the log2 odds ratio (OR) and the percentage of significant enrichments. f, Effect of specific chromatin factor knockouts on myeloid versus erythroid priming. Positive values (red) show enhanced myeloid priming. Negative values (blue) indicate reduced myeloid priming. g, Trajectory analysis of specific chromatin factor knockouts along myeloid differentiation. Cells are ordered from HSCs to mature granulocytes using pseudotime. DC1, diffusion component 1; DC2, diffusion component 2. h–j, Graphic representation of the roles of key chromatin regulatory complexes.
