Motif analysis and genomic location of Ago HITS-CLIP cross-linking regions. (A) Motif analysis of identified candidate cross-linking regions. Flanking regions (−10 to +10 nucleotides) around identified reliable mutation sites within the cross-linking regions were used as input for the motif search tool MEME. All five motifs are complementary to microRNA seed regions. (B) Example of an miR-124 binding site within the transcript of Zcchc14. Top panel: reads enriched in the 3’ UTR region of Zcchc14. Bottom panel: a zoomed-in view of the candidate cross-linking region. The highlighted nucleotides correspond to the seed-binding region of miR-124.