Fig. 4

RBP association at retrotransposable and other repetitive elements. a (left) Heatmap indicates fold-enrichment in eCLIP versus paired input, averaged across two biological replicates. Shown are 30 RepBase elements which had average RPM > 100 in input experiments and at least one RBP with greater than 5-fold enrichment and 65 eCLIP experiments with greater than 5-fold enrichment for at least one element. (right) Color indicates correlation in fold-enrichment between elements across the 65 experiments. b, c Points indicate fold-enrichment for b Alu elements and c L1 LINE elements in individual biological replicates. Shown are all RBPs with average enrichment of at least 2 (for Alu elements) or 5 (for L1 elements). d Bars indicate L1 retrotransposition casTLE effect score (positive score indicates increased retrotransposition upon RBP knockout), with error bars indicating 95% minimum and maximum credible interval estimates (data from Liu et al. [38]). e (left) Each point indicates significance (from two-sided Kolmogorov-Smirnov test) between fold changes observed in RNA-seq of RBP knockdown for the set of genes with one or more RBP-bound L1 (or antisense L1) elements versus the set of genes containing one or more L1 (or antisense L1) elements but lacking RBP binding (defined as overlap with an IDR peak). RBPs were separated based on requiring 5-fold enrichment for L1 elements as in c. (right) Cumulative distribution plots for (top) MATR3 in HepG2 and (bottom) SUGP2 in HepG2. Significance shown is versus the set of genes containing one or more L1 (or antisense L1) elements but lacking RBP binding (red line). f Points indicate the fraction of antisense L1-assigned reads that map to canonical (RepBase) elements for six expression-altering antisense L1-enriched eCLIP datasets (from e), five other antisense-L1 enriched eCLIP datasets, and 11 paired input samples. Significance is from the two-sided non-parametric Kolmogorov-Smirnov test. See Additional file 3: Fig. S4g for the full distribution of read assignments