Fig. 1.

Chemical genomics of core regulatory TF-driven transcription. a Genetic regulatory element activated by CR TFs at the ALK SE in FP-RMS. CR TF-binding region highlighted in gray was cloned upstream of luciferase into a lentiviral expression vector for high-throughput chemical screening. b Chemical benchmarking of CMV-promoter driven transcription vs. super enhancer-driven transcription, by dose-dependent inhibition of luciferase expression in FP-RMS cells (RH4). Compounds shown are illustrative of key steps in RNA-Pol2 transcription: initiation (CDK7, XBP dependent), elongation (CDK9 dependent), and enhancer-mediated (BRD4 dependent). Measurements are mean and standard deviation of four technical replicates. c Scatter plots of chemical probe selectivity among target classes. Color representative of four transcriptional response categories as shown: non-specific inhibition (high activity against both constructs), inactive, SE-down regulating which also increase CMV-promoter-driven transcription, and SE selective inhibition. d Maximum SE selectivity per compound, rank ordered. Mechanistic classes of compounds are distinguished by bar color as shown. e Overlay of SE-dependent transcriptional response with cell viability at 24 and 48 h of drug exposure for a SE-selective inhibitor (HDAC inhibitor Vorinostat) and a transcriptionally unselective compound (LSD1 inhibitor LSD690). Heatmap above dose–response curves is calculated as the difference between SE-transcription and cell viability. Points represent mean and standard deviation of three technical replicates