Fig. 4: CAF-1 depletion induces myeloid differentiation in vivo and a mixed-lineage transcriptional signature in HSPCs.
From: Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity
a Schematic of polyI:C (polyinosinic:polycytidylic acid) inducible Mx1-Cre/LoxP system in mice. Flow cytometric analysis of BM MNCs is performed 72 hrs post-induction of mice bearing homozygous Chaf1b floxed alleles and Mx1-Cre (Chaf1bfl/fl; Mx1-Cre) and littermate controls (Chaf1b+/+; Mx1-Cre). b Flow cytometric analysis of myeloid differentiation markers (CD11b and Gr1) showing overlaid density plots and histograms of wild-type (Chaf1b +/+) and Chaf1b-deleted (Chaf1b Δ/ Δ) BM MNCs. c Quantification of gated populations in b showing mean and standard deviation of CD11b and Gr1 double-positive and double negative % populations from live BM MNCs isolated from n = 2 wild-type and n = 3 knockout littermates. d Schematic of Chaf1b depletion in primary HSPCs. HSPCs isolated from homozygous floxed mice (Chaf1bfl/fl) are transduced with retroviral vectors, either empty control (MIGR1-CTRL) or overexpressing Cre recombinase (MIGR1-Cre) and analyzed by RNA-seq 48 h following expansion in myeloid media conditions. e RNA-seq analysis showing percentages and numbers of upregulated or downregulated genes in CAF-1 OFF iGMPs, HOXA9 OFF iGMPs, and Chaf1b Δ/ Δ HSPCs. DEGs are filtered based on fold change ≥ 1.5 and FDR < 0.05. f Venn diagrams of unique and common DEGs between CAF-1 OFF iGMPs, HOXA9 OFF iGMPs, and Chaf1b Δ/ Δ HSPCs shown in e. g Volcano plots depicting differential gene expression in CAF-1 OFF iGMPs, Chaf1b Δ/ Δ HSPCs, and HOXA9 OFF iGMPs (Up = dark gray; Down = light gray). Dashed lines demarcate fold change (FC) and FDR cutoffs for DEGs shown in (e-f). −log10(FDR) and log2(FC) values have been capped at 7 and ±-8, respectively. Triangles (Δ) represent data points exceeding the cap. Genes that are commonly upregulated only in CAF-1 OFF iGMPs and Chaf1b Δ/ Δ HSPCs are shown in red (n = 42 genes; see panel f and Supplementary Data 1). Source data are provided as a Source Data file.
