Fig. 3: The effect of SRSF1 KD.

a Outline of the experimental procedure; cells were transfected first with a pool of siRNAs. After 48 they were transfected with NucLibA libraries, and were fractionated after an additional 24 h into nuclear and cytoplasmic fractions. Libraries for sequencing were generated from total, nuclear, and cytoplasmic RNA. b Nuc/Cyto ratios of tiles with the indicated number of SRSF1 motifs in each context; spliced (red), unspliced (blue), and circular (yellow). n = 3 biologically independent samples. Box plots show median, first to third quartile, whiskers are 1.5× interquartile range. P-values were computed using two-sided Wilcoxon rank-sum test. c Nuc/Cyto ratio of tiles with the indicated number of SRSF1 motifs following transfection of NT control (white) and siSRSF1 (colored as in b). n = 3 biologically independent samples. Box plots are as in (b). P-values were computed using two-sided Wilcoxon rank-sum test. d The effect of factors depletion on subcellular localization; Nuc/Cyto ratio of tiles in SRSF1 KD samples vs. NT control samples of all tiles (black), and tiles that have >1 motif (colored). Red line indicates X = Y. e qPCR analysis of nuclear and cytoplasmic fractions following transfection of siNT and siSRSF1 n = 6 biologically independent samples. Data are presented as mean values +/− SEM. The average number of SRSF1 eCLIP clusters across replicates in HepG2 cells is shown below each circRNA. f Change in Nuc/Cyto ratio for circRNAs with the indicated number of SRSF1 binding motifs. P-values are for comparing the indicated group with circRNAs with no SRSF1 motifs and were computed using a two-sided Wilcoxon rank-sum test. Number of circRNAs in each group is indicated in parentheses. Source data are provided as a Source data file.