Fig. 3: CAF-1 depletion in iGMPs results in a mixed-lineage state.
From: Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity
a, b Time series UMAP analysis of single-cell transcriptomes in iGMPs upon induction of HOXA9 OFF or CAF-1 OFF in shCTRL or shChaf1b expressing clones, respectively. Single cells are colored based on timepoints in a or unsupervised clustering in b. Clustering was performed with the SLM algorithm using PC1-10 (see methods). c Heatmap ordered left to right by clusters 1–10 shown in b displaying relative expression of the top 10 enriched genes in each cluster. Corresponding time-course samples are highlighted on the top of the heatmap. Select candidate genes discussed in the text are highlighted to the left of the heatmap. d Heatmap of single-cell time series of HOXA9 OFF and CAF-1 OFF inductions displaying relative gene expression levels of a curated set of hematopoietic lineage genes: GMP granulocyte-macrophage progenitor, Gr granulocyte, Mn monocyte/macrophage, MEP megakaryocyte-erythroid progenitor, MegP megakaryocyte progenitor, Meg megakaryocyte, EryP erythroid progenitor, Ery erythrocyte. e Bubble plots reflecting the percentage of cells expressing the lineage markers shown in d and their abundance in CAF-1 OFF versus HOXA9 OFF cells. The color of the dots shows the relative expression level, and the size of the dots represents the percentage of cells that express the corresponding gene. f UMAP feature plots displaying the expression of select markers that characterize different lineages: Ly6c2 and CD11b for neutrophils, Pf4 and CD41 for megakaryocyte progenitors and Car2 and CD105 for erythrocyte progenitors. g Time-course flow cytometric analysis of GFP, CD41, and CD105 activation in CAF-1 OFF and HOXA9 OFF cells. Gated populations are cells co-expressing GFP and CD41 or GFP and CD105. h Sequential HOXA9 inactivation after CAF-1 depletion. Top panel: schematic for sequential CAF-1 OFF and HOXA9 OFF treatments. Bottom panels: flow cytometric analysis of GFP (left) and CD41(right) in uninduced cells, 96 h post CAF-1 OFF or HOXA9 OFF, and sequential treatment. Fine-tuned sequential and combined pulses from n = 3 independent experiments are shown in Supplementary Fig. 5.
