UX1-deficient cells upregulate expression of genes involved in proliferation and DNA repair. (A) Ren and Cux1^low mice were treated with Dox for 5 days, and HSCs (lineage-negative/cKit⁺/Sca1⁺/CD135⁻) were sorted for RNA-seq, for a total of 3 biological replicates. Cux1 transcript levels (excluding Casp isoforms) by RNA-seq are shown. (B) Volcano plot showing gene-expression changes in HSCs by RNA-seq after CUX1 knockdown. Blue color indicates differentially expressed genes with an FDR <5%. (C) A heatmap clustering the samples by the 3323 differentially expressed genes. The z score is indicated by the box color (scale on right). (D-E) Gene-set enrichment analysis (GSEA) using the “Hallmarks” gene set from the MSig Database⁵⁶  of murine HSCs (D) and shRen and shCUX1 K562 cells (E)(previously published RNA-seq).³⁵  Hallmark gene sets involved in proliferation and DNA damage repair with an FDR ≤0.1 are shown. Nominal enrichment score (NES) is plotted. (F) Twenty-four hours after irradiation (6 Gy) or mock irradiation, proliferation was assessed in gHPRT and gCUX1 K562 cells via BrdU incorporation 1 hour before analysis. Mean ± SD is shown for 3 biological replicates. Significance was determined with a Student t test between indicated samples.