Fig. 2: SPF45 is generally required for splicing of pre-mRNAs including short introns.
From: SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns
a RNA-Seq data exhibit deferential splicing patterns between control siRNA- and SPF45 siRNA-treated HEK293 cells. The numbers of significant splicing changes and total splicing events are indicated and the ratios are shown on the right. b Boxplots are comparing the intron-length distributions of all introns in human RefGene with those of the retained introns in SPF45-knockdown HEK293 cells. The retained introns in U2AF65- and SF3b155-knockdown HeLa cells obtained from the RNA-Seq data in GEO database are shown for comparison (significant for all pairs, P < 0.05). The numbers of introns are indicated in parentheses. Boxplots show the summary of the dataset; median (middle line), 25–75th percentile (box), and <5th and >95th percentile (whiskers), together with outliers (single points). c SPF45-knockdown selectively repressed splicing of pre-mRNAs with short introns. After the siRNA transfection in HEK293 cells, endogenous splicing of the indicated two control introns and three short introns were analyzed by RT-PCR. Arrowheads indicate nonspecific PCR products. Means ± SEM are given for three independent experiments and two-tailed Student t-test values were calculated (DUSP1 intron: p = 0.0951 for Control vs SPF45 siRNA; NFKBIA intron: p = 0.0236 for Control vs SPF45 siRNA; MUS81 intron: p = 0.00004 for Control vs SPF45 siRNA; RECQL4 intron: p = 0.0019 for Control vs SPF45 siRNA; MTA intron: p = 0.0067 for Control vs SPF45 siRNA). *P < 0.05, **P < 0.01, ****P < 0.0001, n.s.(not statistically significant) P > 0.05. Source data of all the above panels are provided as a Source Data file.
