Fig 2: The effect of IMPDH2 compartmentalization on gene expression.A Representative immunofluorescence images showing IMPDH2 (FIRE_Lut and Green) and DAPI (Gray) staining in IMPDH2 KO MDA-MB-231 cells reconstituted with IMPDH2-WT (WT), NLS and NES. Scale bar, 10 µm. Experiment was conducted in three biological replicates. B, C Volcano plots of differential gene expression in MDA-MB-231 IMPDH2-KO cells reconstituted with IMPDH2-NES (NES) (B) or IMPDH2-NLS (NLS) (C) compared with IMPDH2-WT (WT). Statistical significant was assessed by a moderated two-sided t-test, and with Benjamini–Hochberg multiple testing correction. Significantly up- and downregulated genes were defined by adjusted P < 0.01 and |log₂ fold-change|>1. Selected genes of interest (IL13RA2, CCL2, OLFML1, IMPDH2, DCAF8L1) are labeled. D, E Quantification of BRCA1 foci per nucleus (D) and nuclear BRCA1 integrated intensity (E) in IMPDH2 KO MDA-MB-231 cells reconstituted with IMPDH2-WT or IMPDH2-NLS cells across cell-cycle phases (G1, S, G2). Outliers (±5 s.d.) were removed; 1172 cells in D and 1173 cells in E were analyzed per phase and condition. Statistical significance was assessed by unpaired two-tailed Wilcoxon test. Boxplots were generated using ggplot2 with default Tukey definitions: the horizontal line is the median, the box spans the interquartile range (IQR), and whiskers extend to the farthest points within 1.5×IQR. F Representative immunofluorescence images of BRCA1, γH2AX, and DAPI staining in IMPDH2 KO MDA-MB-231 cells reconstituted with IMPDH2-WT (WT) or IMPDH2-NLS. Scale bar, 10 µm. G Quantification of γH2AX foci per nucleus in MDA-MB-231 WT and NLS cells across cell-cycle phases (G1, S, G2). Outliers (±5 s.d.) were removed; 1184 cells per phase and condition were analyzed. P values were determined by unpaired two-tailed Wilcoxon test. Boxplots were generated using ggplot2 with default Tukey definitions: the horizontal line is the median, the box spans the interquartile range (IQR), and whiskers extend to the farthest points within 1.5×IQR. H Heatmaps of GO DNA repair signatures showing activity scores in IMPDH2 KO MDA-MB-231 cells, and reconstituted with IMPDH2-WT, IMPDH2-NES, IMPDH2-NLS, or treated with guanosine [400 µM; KO( + G)]. I Heatmaps of curated GO and Reactome ERK signaling signatures showing activity scores in IMPDH2 KO MDA-MB-231 cells, and reconstituted with IMPDH2-WT, IMPDH2-NES, IMPDH2-NLS, or treated with guanosine [400 µM; KO(+G)]. J Heatmap of genes within the REACTOME pathways “REACTOME_MAPK1_ERK2_ACTIVATION” and “REACTOME_MAPK3_ERK1_ACTIVATION” showing differential activity in IMPDH2 KO MDA-MB-231 cells, and reconstituted with IMPDH2-WT, IMPDH2-NES, IMPDH2-NLS, or treated with guanosine [400 µM; KO(+G)]. Source data are provided as a Source Data file.