Phosphorylated UPF1-binding motifs are related to RNA decay in a UPF1-dependent manner. (A,B) Cumulative distribution of relative half-lives (UPF1 knockdown/control) of mRNAs harboring the indicated number of any four UPF1-binding motifs (CCUGGGG, CCUGGGA, CCUGGAA, CCUGAGA; these are compressed as CCUG[GA][GA][GA] in the caption) (A), or PUM1-binding motif (UGUANAUA) (B) in their 3′ UTRs. Data were constructed from BRIC-seq data. The numbers shown to the right indicate the number of mRNAs included in the group. P-values were calculated using the Wilcoxon rank-sum test. (C,D) Cumulative distribution of the relative enrichment (IP of UPF1/normal IgG control) of mRNAs harboring the indicated number of any four UPF1-binding motifs (C), or PUM1-binding motif (D) in their 3′ UTRs in a RIP-seq experiment. (E,F) Cumulative distribution of the relative enrichment (IP of p-UPF1/normal IgG control) of mRNAs harboring the indicated number of any four UPF1-binding motifs (E), or PUM1-binding motif (F) in their 3′ UTRs in a genome-wide RNA footprinting experiment. (G) The RNA half-life distribution for all mRNAs (leftmost box); mRNAs with any predicted UPF1-binding motifs (top 1–4) (CCUGGGG, CCUGGGA, CCUGGAA, or CCUGAGA) (second box from the left); mRNAs with predicted UPF1-binding motifs (top 1) (CCUGGGG) (third box from the left); and mRNAs with PUM1-binding motifs (UGUANAUA) (rightmost box) in the control (left panel) and UPF1 siRNA transfected cells (right panel). Red horizontal lines indicate the median value of the half-life distribution for all mRNAs.