DHX34 is an NMD factor and regulates pre-mRNA splicing in K562 cells. (A) Outline of experimental design for RNA sequencing and analysis. RNA-seq was performed for DHX34 knockdown (siDHX34), UPF1 knockdown (siUPF1) and compared to a nontargeting siRNA (ctrl). Sequencing reads were mapped using Salmon, and differential gene expression (DGE) was performed with Sleuth. Splicing changes were detected with SUPPA2. (B) Volcano plot of DGE changes upon DHX34 depletion are indicated by altered b-value and −log10 adjusted P-value. (C) Splicing changes upon DHX34 depletion. Significant splice changes detected with SUPPA2 algorithm are depicted in red (dPSI > 0.05, P ≤ 0.05). Bar plot indicates pre-mRNAs that show AS changes as well as changes in gene expression: up-regulated expression (DGE UP, dark red), down-regulated (DGE DOWN, blue), not changed (gray). (D) Scatter plot of the correlation between expression changes in DHX34 and UPF1 depletion. Each dot represents a common differentially expressed gene. Genes significantly up-regulated in both DHX34 and UPF1 are labeled in red; genes which are down-regulated in blue. (E) Venn diagram showing the number of common transcripts up-regulated (UP) in DHX34 and UPF1 knockdown cells. (F) Pie chart showing different splicing events upon DHX34 knockdown detected with SUPPA2. (G) Table listing AS events in genes linked to AML.
