Fig. 3

Causes of aberrant transcripts in cancer cells. a The number of PTC-containing splicing isoforms in each cell line are shown in gray. Arrows represent somatic mutations of NMD factors in each cell line. b The relative UPF1 and SF3B1 mRNA levels normalized to GAPDH levels in A549 cells at 72 h post-transfection (analyzed by RT-PCR). Error bars represent the standard error of the mean (SEM). c The proportion of PTC-containing isoforms after knockdown experiments in A549. The UPF1-depleted sample showed a significant increase in the proportion of PTC-containing isoforms. ***P < 0.001 (Fisher’s exact test). d The full-length structure of splicing isoforms of SURF2 in UPF1-depleted A549. Some MinION reads showed an alternative 5′ splice site in exon 2 containing a PTC. e The relative SURF2 mRNA levels of the RefSeq type and isoform in UPF1-depleted A549 cells. Each expression level was detected with primers flanking exon 2 and was normalized with a common region level shown in Additional file 12: Fig. S10C. Error bars represent the SEM. f The proportion of exon-skipping isoforms after knockdown experiments in A549. SF3B1- and UPF1-depleted samples showed significant increases in the proportion of exon-skipping isoforms. ***P < 0.001, *P < 0.05 (Fisher’s exact test). g The full-length structure of splicing isoforms of PSMD7 in SF3B1-depleted A549. Some MinION reads showed a combination of skipping events at exons 3 and 6. h The relative PSMD7 mRNA levels of the RefSeq type and isoform in SF3B1-depleted A549 cells. Each expression level was detected with primers flanking exons 3 and 6, then was normalized with a common region level (shown in Additional file 12: Fig. S10E). Error bars represent the SEM