Figure 3.

miRNA complementarity signatures are enriched in Ago2-binding sites that strengthened upon arsenite stress and, conversely, are depleted in Ago2 sites that weaken upon stress. (A) Occurrences of 7mer seed complements (nucleotides 2–8) for the 50 most abundant miRNA families in 293S cells were counted within Ago2-binding sites. The sites were ordered from weakening to strengthening, and a rolling average of the seed density (with a window of 1/20th of the number of sites) was plotted (black line). As a control, seed densities in dinucleotide-shuffled sites ± 1 SD are plotted in gray. (B) 7mer sequences starting from each position in the top 20 abundant miRNAs were used to look for complementary sites in Ago2 binding peaks. For each starting position (arranged along the X-axis), the peaks were binned into 10 equal-sized groups ordered from weakening to strengthening upon arsenite treatment, and the density of 7mer complements in Ago2 sites were plotted. See Supplemental Figure 7A for the corresponding control analysis with sequence-shuffled peaks. (C) Similar to B, except searching for complementarity involving a 1-nt bulge in the target mRNA after position 2 in the 7mer. See Supplemental Figure 7B for the corresponding control analysis with sequence-shuffled peaks.