Fig. 2

Differential splicing in proliferating and quiescent fibroblasts. a rMATS was applied to RNA-Seq data from three biological replicates of proliferating fibroblasts and three biological replicates of contact-inhibited fibroblasts. Splicing events with an FDR < 0.05 are shown. The total numbers of splicing events are reported. In parentheses, the number of events with higher inclusion in proliferating fibroblasts is provided, followed by the number of events with higher inclusion in quiescent fibroblasts. Skipped exons were significantly more likely to be included in quiescent fibroblasts (Fisher’s exact test, two-tailed p value = 0.013). Introns were significantly more likely to be retained in quiescent fibroblasts (Fisher’s exact test, two-tailed p value < 0.0001). b Immunoblotting of splicing factors in proliferating and quiescent fibroblasts. Levels of core splicing factor U2AF65 were similar in proliferating and quiescent fibroblasts. U1-70 K and auxiliary factors TRA2β and FUS were expressed at lower levels in 7dCI and 7dSS compared with proliferating fibroblasts. α-Tubulin was analyzed as a loading control. The ratio of splicing factor to tubulin, normalized to proliferating cells, is shown below. c Sequence logos [120] are provided for 5′ and 3′ sequences for exons that are constitutively spliced, and introns that are preferentially retained in proliferating or quiescent cells. The y-axis indicates bits of information [121]. 3′ splice site sequences were different between proliferating versus constitutive conditions (p value < 0.01 for constitutive versus retained in proliferating conditions, ANOVA with Tukey’s multiple comparison test) and quiescent versus constitutive conditions (p value < 0.01 for constitutive versus retained in quiescent conditions)