Extended Data Fig. 4: G4switch-mediated optical control of gene expression in U2OS cells.
From: Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch
a, Cell viability measured by the Cell Titer-Glo luminescent cell viability assay after treatment of U2OS cells with a series of concentrations of 4sU for 60 min. Results represent the mean ± s.d. from four technical replicates (n = 4). b, Cell viability after treatment with 9 in the dark and under all illumination conditions used in this study for 30 min, followed by 60 min of 4sU (250 µM) labelling. Results are shown as mean ± s.d. from four technical replicates (n = 4). c, Volcano plot displaying the most significantly downregulated genes (fold change >2, q < 0.05, p < 10-8), highlighted in red, by trans-9 under pulsed 405 nm illumination compared to the dark-adapted DMSO control. d, Venn diagram displaying the overlap of downregulated genes (q ≤ 0.05) by 9 between dark treatment and 405 nm illumination, and the 405 + 525 nm illumination, compared to the DMSO treatment in the dark. The pie chart illustrates that, among the 75 overlapping downregulated genes under the 405 nm and 405 + 525 nm illumination conditions, 44 genes show partial recovery (reduced downregulation, q ≤ 0.05) under the 405 + 525 nm illumination (Supplementary Fig. 6b and Supplementary Table 7), while 31 genes show no recovery compared to the 405 nm condition. e, The overlap between downregulated genes (fold change >2, q < 0.05) by trans-9 under 405 nm illumination and genes displaying trans-9 Chem-map binding sites in their promoter regions. f, DNA damage marker γH2AX was examined by Western blot after treating cells with compound 9 (125 nM) with or without 405 nm illumination (60 s continuous illumination, followed by 75 ms pulses every 22.5 s) and its parent molecule PDS (10 μM) for 72 h, compared to the dark-adapted DMSO control. Cells treated with Camptothecin, a DNA topoisomerase I inhibitor, for 5 h served as a positive control. A representative image from one of three independent biological replicates with similar results is shown.
