Pumilio regulates neural mRNA stability. (A) Enrichment or depletion of candidate cis-regulatory elements as follows: AREs, miR-124 target sites, and PREs. Odds ratios were calculated as the frequency of each element within the low-stability (t1/2 ≤ 75 min) ‘neural fate’ mRNAs or high-stability (t1/2 ≥ 80 min) ‘localized’ mRNAs versus the frequency of that element in all low-stability or high-stability neural mRNAs. ** = P value < 1.0 × 10−15 (Fisher’s test). (B) Pumilio expression in a stage 15 embryo detected with an anti-Pumilio antibody (green). Anti-Fas2 antibody stain (magenta) shows a subset of longitudinal axon fiber tracts and axons leaving the ventral nerve cord. (C) Cumulative distribution function plots of mRNA half-life changes in Pumilio RNAi versus control embryos (Pumilio RNAi/control ratio). The distribution for all neural mRNAs is plotted in blue. The distribution for predicted Pumilio targets is plotted in red. The shift to the right for predicted Pumilio targets indicates a trend of stabilization in Pumilio RNAi embryos. The P value is from a Kolmogorov-Smirnoff test comparing the half-life changes (Pumilio RNAi/control) for predicted Pumilio targets and non-targets. (D) Examples of predicted neural fate Pumilio targets with increased mRNA stability in Pumilio RNAi embryos. These transcripts had reproducible changes in half-life with FDRs ≤0.30 (based on SAM analysis).