Figure 7

Cis -regulators of mRNA decay in early Drosophila embryos. (a-c) Motif discovery in 3' UTRs using SYLAMER [70]. Genes were ranked by mRNA net decay values (Figure 2) and enrichment analyses for words of lengths 6 and 8 were performed; -log10 of enrichment P-values (y-axis) are plotted for words enriched in 3' UTRs of unstable mRNAs (x-axis). P-value profiles for the top five enriched motifs are highlighted and shown for each enrichment analysis; a total of 27 unique motifs is shown (asterisk indicates motifs recovered in more than one enrichment). For a peak occurring on the positive y-axis, the corresponding word is overrepresented in the 3' UTRs for the genes to the left of that peak (colored brackets) while the word is underrepresented in the genes to the right. Note that all motifs (1 to 27) are complementary to seed sequences of characterized miRNAs (Supplementary Table 6 in Additional file 1). Enrichment analyses are shown for: (a) all transcripts preloaded onto the oocyte (Figure 3); (b) stable and maternally degraded mRNAs; and (c) stable and zygotically degraded mRNAs (compare Figure 3). (d) mRNAs with AU-rich elements (ARE) were recovered from a genome-wide screen [71]. An enrichment analysis (Fisher's exact test) was performed to address the correlation between AREs and RNA stability. We found that RNA decay (classes II, IV and V) is positively correlated with the presence of AREs in transcript 3' UTRs. Odds ratios (enrichments and depletions) within transcript classes (Figure 3) are shown on a log2 scale (y-axis); color code as in Figure 5; significance of enrichments is indicated by multiple testing corrected P-values (q-values).