Fig. 1. Chromatin regulators affecting AZA sensitivity are identified by an optimized loss-of-function shRNA screen.

a Composition of the hEPI9 library. b Illustration of the human HNRPA2B1-CBX3 locus including the ubiquitous chromatin opening element (UCOE) and schematic of the cSGEP backbone vector containing the UCOE, spleen focus-forming virus (SFFV) promoter, green fluorescent protein (GFP) marker gene, shRNA integration site, phosphoglycerate kinase (PGK) promoter and puromycin (Puro) resistance gene. c Schematic workflow of the shRNA screen-targeting genes encoding chromatin regulators. d Percentage of live SKK-1 cells determined at different time points throughout the shRNA screen after initiation of AZA treatment (0.25 µM every 2 days for 2 weeks) in three biological replicates. e Volcano plot of genes corresponding to enriched (“Genes inhibit survival in presence of AZA”) or depleted (“Genes required for survival in presence of AZA”) shRNAs. Selected genes are named. FC, fold change. CREBBP, P = 0.0001; NAA15, P = 0.0001; HMGA2, P = 0.0032; CBX3, P = 0.0061; EP300, P = 0.7405. f Percentage of live SKK-1 cells stably expressing cSGEP, shNAA15-1 or shNAA15-2 determined after 4 days of treatment with indicated concentrations of AZA. g, h SKK-1 cells stably expressing cSGEP, shCBP-1 or shCBP-2 were treated for 4 days with indicated concentrations of AZA and the percentage of live cells (g) or the percentage of GFP-positive cells was assessed (h). f–h Data represent the mean ± SEM of four independent experiments. Statistical analysis was performed using two-way ANOVA. ***p-value < 0.0001. Source data are provided as a Source Data file and in Supplementary Data 1 and 3.