Prediction of phosphorylated UPF1-binding sites on 3′ UTRs of UPF1 target RNAs. (A) Cumulative distribution of all mRNAs (black) and UPF1 targets (red) in association with phospho-UPF1. P-values were calculated using the Wilcoxon rank-sum test. (B) The distribution of mapped reads derived from mRNAs associated with p-UPF1 in the indicated RNA regions. (C) Examples of p-UPF1 association with bona fide UPF1 target mRNAs. The y-axis indicates numbers of sequencing reads derived from mRNAs associated with p-UPF1. mRNAs transcribed from these genes are UPF1 targets. (D) Relative ratio of nucleotides in p-UPF1-binding sites in 3′ UTRs of mRNAs. (E) p-UPF1-binding motifs in 3′ UTRs of UPF1 target mRNAs were predicted using MEME software. The motif length was restricted to 5–8 bp. The motif with the lowest P-value (P = 4.0 × 10−107) is shown.
