Fig. 2: QKI-6 binds conserved UTR regions in a cooperative manner.

A UTRs bound by QKI-6 are significantly longer than average UTRs. N = 574 Qk targets, n = 39,337 all controls, and n = 574 matched-length controls. Rightmost plot: matched-length controls selected for B–G. The significant levels represent Mann–Whitney test by comparing to UTRs bound by QKI-6. The p values of comparing all controls UTRs to QKI-6 bounded UTRs, matched-length controls UTRs to QKI-6 bounded UTRs, and matched-length controls UTRs to all controls UTRs are <2.2e−16, 0.68, and <2.2e−16, respectively. B Conservation levels (PhyloP) of 200 bp flanking QKI-6 bound sites reveal QKI-6 bound sites are more conserved than random sites in matched-length controls. C A violin plot illustration of the same data showing the distribution of conservation across all targets (p value < 2.2e−16). N = 200 bp flanking QKI-6 bound sites and n = 200 bp flanking random sites in matched-length controls. D A violin plot for number of PolyA sites near QKI-6 peaks reveals they are not enriched for PolyA sites (p value = 0.97). N = 141 unique 3’ UTR for Qk targets and n = 547 unique 3’ UTR for matched-length controls. E Examining the QKI peak location relative to the length of the UTRs (scaled to 100% of distance between PAS and stop codon) shows QKI-6 binding tends to be closer to stop codons (p value = 0.031). N = 426 3’ UTR for Qk targets in which QKI-6 bound sites are between their nearest PAS and stop codon and n = 307 3’ UTR for matched-length controls in which random sites are between their nearest PAS and stop codon. F Metagene of QKI-6 shows binding is elevated at stop codon, with flanking peaks, and extends substantially, especially 3’. G Metagene of QKI-6 shows binding is elevated at PAS, with flanking peaks, and extends substantially, especially 5’. QKI-6 binding at any (H) QBM or (I) peak extends to flanking sequence. Here, and for all box-and-whiskers plots in the manuscript, the center line represents the median, the body of the box goes from the first quartile to the third quartile (IQR), the whiskers represent 1.5x IQR from the upper or lower quartile, and points represent values that go beyond 1.5 IQR. The p values represent two-sided Student’s t test. In B–E, p values represent two-sided Student’s t tests. In F–I, ribbons represent the 95% confidence interval of the mean calculated using 1000 bootstraps. Purple = QKI-6 CLIP, light gray = Input, dark gray = IgG.