FIGURE 3.

NMD substrates are principally degraded by decapping and 5′–3′ exonucleolytic decay. (A) RNA-seq libraries from WT, dcp1Δ, dcp2Δ, and xrn1Δ strains display normal and comparable overall read count distributions. As in Figure 1A, violin and box-plots were used to visualize the average sequence reads distribution of the transcriptomes of the indicated strains from three independent experiments. (B) Transcripts up- or down-regulated in dcp1Δ, dcp2Δ, and xrn1Δ strains show significant overlap. Transcripts up- or down-regulated in dcp1Δ, dcp2Δ, and xrn1Δ strains were identified by comparisons to the WT strain. (C) Transcripts commonly up- or down-regulated from transcriptome 1 in all three UPF deletion strains show significant overlap with transcripts up-regulated in both dcp1Δ and dcp2Δ strains or an xrn1Δ strain. Venn diagrams were used to display the relationships among the up- or down-regulated transcripts from the indicated strains.