Suz12 and Jarid2 regulate common genes in HSPCs enriched for genes important in fetal and long-term HSCs. (A-B) Expression of (A) PRC2 core components and (B) accessory factors as measured by RNA-seq performed on transduced HSPCs sorted from FL primary recipients at 16 weeks posttransplant. There were 5 shRNA-NS, 4 shRNA-Suz12, 4 shRNA-Jarid2.1, and 3 shRNA-Jarid2.2 transduced HSPC samples used for the analysis. Expression is shown in reads per kilobase per million reads (RPKM). (C) Box plots showing that genes upregulated in Suz12 knockdown HSPCs compared with NS are significantly upregulated in Jarid2 knockdown (shRNA-Jarid2.1 and shRNA-Jarid2.2 samples combined) HSPCs (log2 fold-change [LFC], Mann-Whitney test). Genes differentially expressed in Suz12 and Jarid2 knockdown HSPCs (P < .01, Fisher’s method of combining P values) were split into those with positive LFC (Suz12 up) or negative LFC (Suz12 down) in Suz12 knockdown compared with half of the control samples. The LFC for Jarid2 knockdown compared with the other half of the controls was plotted for the same genes (y-axis), and a significantly higher mean LFC in the Jarid2 knockdown HSPCs was observed for genes upregulated in Suz12 knockdown HSPCs (P = 9.9 × 10⁻⁶), suggesting that Jarid2 and Suz12 share common targets. (D-E) Gene set enrichment analysis performed on Suz12-depleted (top panel) and Jarid2-depleted (bottom panel) HSPCs demonstrates significant enrichment of a fetal HSC signature (D, P < .0001 Suz12 shRNA, P = .02 Jarid2 shRNA) and LT-HSC genes (E, FDR <0.0001 Suz12 shRNA, FDR = 0.061 Jarid2 shRNA). NES, normalized enrichment score.