Fig. 4: USP39 knockdown reduces global splicing efficiency and selectively regulates alternative splicing. | Cell Death & Disease

Fig. 4: USP39 knockdown reduces global splicing efficiency and selectively regulates alternative splicing.

From: USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC

Fig. 4: USP39 knockdown reduces global splicing efficiency and selectively regulates alternative splicing.The alternative text for this image may have been generated using AI.

A PLC-8024 USP39-knockdown (sh1, sh2) and control (shCtrl) cells were collected for transcriptome sequencing. Sh1 showed a similar DEG pattern to sh2. B The GO biological process (BP) enrichment analysis of the overlapping DEGs. C Global splicing efficiency analysis at 5′ and 3′ splice sites in PLC-8024 cells with and without USP39 depletion. D DAS events were highly correlated in sh1 vs. shCtrl and sh2 vs. shCtrl datasets. E Venn diagram displayed the DAS events in sh1 vs. shCtrl and sh2 vs. shCtrl datasets after the intersection (left). Pie chart depicting the proportions of different types of overlapping DAS events (right). A5SS alternative 5’ splice site, A3SS alternative 3’ splice site, MXE mutually exclusive exons, RI retained intron, SE skipped exon. F Three events with down-regulated PSI values (left) and two targets with up-regulated PSI values (right) in USP39 depletion PLC-8024 cells were validated with RT-PCR and agarose gel electrophoresis. The percentages of cassette exon inclusion over the total transcripts were presented using PSI.

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