Figure 8

Transcriptome analysis of Mysm1^−/−Puma^−/− MPPs reveals widespread p53 stress-response activation and rescue of lymphoid-priming genes. Data shown represent RNA-Seq analysis of FACS-sorted MPPs from wild-type, Puma^−/−, Mysm1^−/−Puma^+/− (phenocopy Mysm1^−/−), and Mysm1^−/−Puma^−/− mice. (a) Hierarchical clustering of differentially regulated genes (defined as statistically significant based on adjusted P-values <0.05, and with ≥2-fold change in expression over wild type in at least one group). Four major clusters are labeled and color-coded. Heatmap scale represents Log2 of fold change. All representative RNA-Seq tracks and bar charts in other panels show genes included in heat map. (b) Mysm1 KO and DKO upregulated gene cluster 1: genes upregulated in Mysm1^−/−Puma^−/− and Mysm1^−/− as compared with wild type. Gene ontology enrichment analysis and RNA-seq tracks representative of expression trends in this cluster. (c) p53 target genes from heatmap cluster 1 that were significantly upregulated (more than twofold change) in both Mysm1^−/−Puma^−/− (purple bars) and Mysm1^−/− (orange bars) as compared with wild-type (blue bars) MPPs. All expression values shown as normalized counts per million reads (CPM). (d) DKO downregulated cluster 4: genes downregulated in Mysm1^−/−Puma^−/− and unchanged in Mysm1^−/− as compared with wild type. Gene ontology enrichment analysis and RNA-seq tracks representative of expression trends in this cluster. (e) Mysm1 KO downregulated cluster 3: genes downregulated in Mysm1^−/− and unchanged in Mysm1^−/−Puma^−/− as compared with wild type. Gene ontology enrichment analysis and RNA-seq tracks representative of expression trends in this cluster. Note: Flt3 was significantly differentially expressed between Mysm1^−/− and wild-type groups but had less than twofold change, so did not pass the heatmap threshold. Data from three mice per group; RNA-Seq tracks represent composite files of all three data sets within each genotype