Identification of CCR4–NOT-regulated transcripts in response to knockdown of Not1 or Pop2 in Drosophila cells. Volcano plots of RNA level changes measured by RNA-seq in Not1 (A) and Pop2 (C) RNAi conditions relative to NTC RNAi. The LFC (RNAi/NTC) is shown on the x-axis. Vertical dashed lines indicate a LFC value of ±log2(1.3). A statistical significance threshold (q-value ≤ 0.05) is shown with a horizontal dashed line. Red or blue markers (×) indicate genes passing both statistical significance and fold change thresholds in positive (Up) or negative (Down) directions, respectively. Scatterplots of RNA levels measured in the Not1 (B) and Pop2 (D) RNAi conditions (y-axis) versus the NTC control (x-axis). (E) RNAi knockdown of Not1 and Pop2 mRNA was confirmed by RT-qPCR and RNA-seq. Mean LFC values ± standard error of the mean (SEM) are plotted relative to the NTC RNAi condition. n = 3. (F) Venn overlaps of genes from all three KD data sets that were significantly up. Significance was based on the same thresholds as in A–D. All two-set and three-set overlaps were significantly enriched ((**) P ≤ 0.01, (***) P < 0.001, permutation test n = 1000), compared to chance (null hypothesis = no correlation between the KDs).
