Fig. 4

RNA-binding protein SFPQ binds and regulates subsets of circRNAs during neuronal differentiation. a SFPQ motif enriched among circRNAs increased at D28 v D5. b TIAL1 motif enriched among circRNAs increased at D28 v NES. c Normalised counts of SFPQ RNA during NES differentiation. d Normalised counts of TIAL1 RNA during NES differentiation. FC, LFC from DEseq2 analysis; **** adjusted p-value < 0.0001. e Detection of SFPQ and TIAL1 mRNA following siRNA treatment (n = 3). f Relative expression of SFPQ targets following SFPQ knockdown (n = 3). In e, f, ****p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05, one-way ANOVA, Tukey post hoc analysis, Bonferroni adjusted. g–j In situ detection of circERC2 and its linear isoform in undifferentiated NES cells (g), and cells at D5 (h) and D28 (i, j) of differentiation. Blue = Hoechst nuclear counter stain, magenta = linear ERC2 probe, green = circERC2 probe. Scale bar in g = 25 μm, applies to g–j. images are representative of staining from biological replicates (n = 3). k SFPQ RIP followed by RT-qPCR analysis to identify SFPQ targets and 5S rRNA control, normalised to IgG RIP samples from D28 differentiated neurons (n = 2). Error bars represent standard error