BRAT- and PUM-associated mRNAs are translationally repressed, and BRAT-associated mRNAs are degraded during the MZT. (A) Boxplots depicting the translation indices from wild-type 0 to 2 h embryos  for all expressed transcripts (that is, all transcripts found to be expressed in our 0 to 3 h embryos used for the RIP-Chip experiments), BRAT non-target transcripts, PUM non-target transcripts, all BRAT target transcripts, BRAT-not-PUM target transcripts (that is, all BRAT targets excluding BRAT-PUM co-targets), all PUM target transcripts, PUM-not-BRAT target transcripts (that is, all PUM targets excluding BRAT-PUM co-targets), and BRAT-and-PUM co-target transcripts. A higher translation index indicates more actively translated mRNAs. The dotted line represents the median translation index of all expressed transcripts detected in our 0 to 3 h RIP input embryo lysate. (B) Boxplots depicting the proportion of RNA present in 2 to 4 h embryos compared to 0 to 2 hour embryos, according to modENCODE RNAseq data available on FlyBase, for the same sets of transcripts described in (A). Note that outliers (that is, transcripts for which the value is greater than 1.5 times the interquartile distance higher or lower than the upper or lower quartiles, respectively) are not shown to allow the y-axis to be magnified around the median values. The dotted line represents the median for all expressed transcripts detected in our 0 to 3 h RIP input embryo lysate. For both (A) and (B) Wilcoxon Rank Sum tests were performed to determine the significance of the differences between BRAT and PUM targets compared to ‘All expressed transcripts’: *P <0.01, **P <10−5, ***P <10−27.