Analysis of an RNA consensus sequence associated with human PUM proteins.
(A) PUF consensus motif in 3′-UTR sequences associated with PUM1, PUM2, Drosophila Pum and yeast Puf3, Puf4 and Puf5 proteins [35], [36]. Height of the letters indicates the probability of appearing at the position in the motif. Nucleotides with less than 10% appearance were omitted. (B) Distribution of PUF consensus motifs. (C) Number of PUF motifs in the 3′-UTRs of PUM bound messages. (D) Distances between double PUF motifs present in 3′-UTR. Represented bins are 50 nts (0–4000 nts distance) and 10 nts (0–200 nts distance). (E) Analysis of PUF motif conservation among PUM1 and PUM2 targets. The x-axis shows the position (relative to the middle of the PUF motif), and the y-axis shows the logarithm (base 10) of the p-value from the Wilcoxon test determining whether conservation scores come from the same distribution for PUM targets and non-targets. The vertical blue line is drawn at position 0 corresponding to the PUF motif. The dashed black line is drawn at a p-value of 0.05, the continuous black line at a p-value of 0.01, and the red line at a p-value of 10−5, which is the threshold for significance considering multiple testing.
