Fig 2: DHX34, NBAS and UPF1 regulate a common set of transcripts. Venn diagrams illustrate the overlap among genes upregulated by each of these three NMD factors in (A) human cells (B) Zebrafish and (C) C. elegans. Areas are proportional to the number of regulated genes. In each species, target coregulation is significant (P < 0.0001 for all individual overlaps).

Fig 3: The NMD negative feedback loop is conserved in Danio rerio. Zebrafish embryos were injected with MO targeting Dhx34 (A), Nbas (B) or Upf1 (C). As a specificity control for each gene, a 5 bp mismatch MO (cont MO) was also injected. The levels of zebrafish NMD factor mRNAs were analyzed by RT-qPCR relative to a control. The values represent an average of three independent injection experiments (mean ± SEM). Because the MOs affect only the protein level of targeted genes, the upregulation of targeted gene transcripts is a further evidence for a feedback loop regulation.

Fig 4: NMD regulates the expression of genes associated with cellular stress response pathways and membrane trafficking. Functional categories that are significantly enriched within DHX34, NBAS and UPF1 upregulated genes (relative to all expressed genes) are indicated. Functional categories analyzed were Sequence Feature (SF), GO Biological Process (BP) and KEGG Pathway (KP).

Fig 5: Scatter plots show a significant positive correlation between the level of regulation of target genes by DHX34 and NBAS compared with the core NMD factor, UPF1 in (A) human cells (B) Zebrafish (C) C. elegans. Each dot corresponds to a regulated gene and black dots represent coregulated genes. Spearman’s rho and P-values are indicated.