Fig. 6

ILF3 binds closely to the differential editing sites in editing-expression-correlated genes. a Histogram of distances between differential editing sites in editing-correlated genes and the closest ILF3 eCLIP peaks in A549 cells (turquoise), up to 10 kb. Gray curves represent distances for 10 sets of randomly picked A’s in the same genes as differential editing sites. Number of differential editing sites is given by n. p value was calculated by comparing the area under the curve (AUC) of the distance distribution for differential editing sites to a normal distribution fit to the AUC values of 10,000 sets of random gene-matched A’s. b Scatterplot of Pearson correlation coefficient and significance (log10-transformed adjusted p value) of correlation between ILF3 mRNA expression and mRNA expression of editing-correlated genes. Genes passing 10% FDR are labeled as significant (sig, turquoise), others as nonsig. c Cumulative distributions of distances between ILF3 eCLIP peaks and differential editing sites within editing-expression-associated genes (sig) or differential editing sites in genes without editing-expression associations (nonsig), up to 1 kb. Only genes associated with immune and viral related GO terms were included. p value calculated by the Kolmogorov-Smirnov test. d For each cell type in the lung cancer scRNA-seq dataset, ILF3 mRNA expression was correlated with mRNA expression of editing-expression-correlated genes (identified in the TCGA data) by Pearson correlation. Genes associated with any immune or viral-related GO term are shown. The size of each point indicates significance of correlation and color corresponds to values of the correlation coefficient. e Normalized mCherry expression (mean ± SD) for nonedited or edited versions of sites in the 3′ UTR of PKR in A549 cells. Five biological replicates were performed. p value calculated by two-sided t-test (same below), *p < 0.05. f Normalized mRNA expression (mean ± SD) of endogenous PKR in siControl, siADAR1, and siADAR2 A549 cells. Three biological replicates were performed. *p < 0.05. n.s., not significant. g Read coverage of ILF3 eCLIP-seq in A549 cells for two biological replicates (ILF3 IP1 and ILF3 IP2, turquoise) and size-matched input (SMInput, gray). The five validated 3′ UTR editing sites affecting PKR mRNA abundance in A549 cells are labeled in magenta (left). Right: Validation of PKR eCLIP signal overlapping two editing sites. PKR expression (mean ± SD) was measured by qRT-PCR in the IP or SMInput samples and normalized against the expression of 18s rRNA, *p < 0.05. (n = 3)