Analysis of an RNA consensus sequence associated with human PUM proteins.

<p>(A) PUF consensus motif in 3′-UTR sequences associated with PUM1, PUM2, <i>Drosophila</i> Pum and yeast Puf3, Puf4 and Puf5 proteins <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003164#pone.0003164-Gerber1" target="_blank">[35]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003164#pone.0003164-Gerber2" target="_blank">[36]</a>. 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 <i>p</i>-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 <i>p</i>-value of 0.05, the continuous black line at a <i>p</i>-value of 0.01, and the red line at a <i>p</i>-value of 10<sup>−5</sup>, which is the threshold for significance considering multiple testing.</p>

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