Fig. 3: The CRY1-sensitive transcriptome identifies alterations in DNA repair processes.

a, c, e CRY1 expression was knocked down in C4-2-shCRY1 cells for 72 h. a RNA-Seq analysis was performed on quadruplet samples for C4-2-shCON and C4-2-shCRY1 cells. MA plot depicts gene expression modulation with the number of significant transcripts upregulated (top) and downregulated (bottom) in blue. b GSEA of RNA-Seq (KEGG and HALLMARKS Pathways) identified enriched and deenriched pathways for CRY1-regulated pathways using FDR < 0.25. c Flow analysis was performed. d C4-2 and 22Rv1 cells were treated with 10 µM KL001 at Day 0 and harvested for flow analysis. e After CRY1 was knocked down, cells were treated with 5 Gy IR for 4 or 24 h. f C4-2 and 22Rv1 cells were treated with 10 µM KL001 for 6 and 24 h, respectively. g C4-2-shCRY1 and 22Rv1-shCRY1 cells were treated with 5 Gy IR at Day 0 and harvested at indicated days for Pico Green to assess relative growth. N = 3 independent experiments. Data are presented as mean values ± SEM and analyzed using two-way Anova (*p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001). Statistical significance was evaluated at 0.05 alpha level with GraphPadPrism, version 8.3.1, Mac. Source data are provided in the Source Data file.