Fig. 5: CRISPR screen for UHRF1-dependent tumor suppressor genes.

a Screen setup in A549 Cas9-expressing cells. b Screen results in control (sgNeg, left) cells and UHRF knock-out cells (sgUHRF1, right). Genes ranked by increasing z-score. Genes labeled in green – positive control, blue – UHRF1 and DNMT1, red – statistically significant hits (p-value < 0.05). In red frames – genes with positive effect on growth in UHRF1 knock-out cells but with negative or no effect in control (sgNeg) cells. c Scatterplot of z-scores in control (sgNeg) samples versus z-scores in UHRF1 knock-out (sgUHRF1) samples. Green – positive control genes, blue – UHRF1 and DNMT1, red – genes with p-value < 0.05 in UHRF1 knock-out cells. d Venn diagram of positive hits identified in sgUHRF1 and in sgNeg conditions (excluding control genes). Only hits with p-value < 0.05 were included. Hits in UHRF1-depleted cells are listed. e RNA expression of four UHRF1-specific tumor suppressor genes identified in the minipool CRISPR screen in two KRAS mutant cell lines (red bars – H358, A549) and two KRAS wild-type cell lines (gray bars – H1437, NL20) treated with control (siNeg) or UHRF1 siRNA (siUHRF1). Expression of UHRF1 is shown as control of knock-down efficiency. Bars represent mean fold expression of the indicated gene in siUHRF1-treated cells relative to cells treated with a negative control siRNA (siNeg); error bars represent standard deviation; points represent technical replicates (n = 3) from two biological replicates. f Plots show probes in the EPIC methylation array with statistically significant hypomethylation (adjusted p-value < 0.05) in regions related to the promoter (annotated as promoter-associated, 5′ UTR, 3′ UTR, TSS, and/or related to the 1st exon of the gene). The y-axis represents beta values color-coded by siRNA treatment (blue – siUHRF1, gray – siNeg). Shape of the data points represents cell line. Source data are provided as a Source data file.