Fig. 5: hnRNP F controls Cd40 AS.
From: The RNA-binding protein hnRNP F is required for the germinal center B cell response
a Scatter plots of inclusion level difference between WT and Hnrnpf KO FOB cells. Each dot represents a significantly altered splicing event (|inclusion level difference | > 10%, FDR < 0.05). b A list of top ten genes with the highest aberrant AS events. c Relative expression of Hnrnpf and Cd40 mRNA in FOB cells based on the RNA-seq data (n = 2 per group). Data are from one single experiment. FDR was calculated by DESeq2 Bioconductor package based on the negative binomial distribution and and Benjamini–Hochberg method. d Sashimi plot of changes in AS of Cd40 exon 6-8 in WT and Hnrnpf KO FOB cells. The full-length version and different variants of Cd40 were shown. e The comparison of inclusion levels of indicated Cd40 AS events between WT and Hnrnpf KO FOB cells. FDR was calculated by rMATS. Likelihood-ratio test was used to calculate p value of the Inclusion Level between two groups. Benjamini Hochberg algorithm was used to correct p value to get FDR value (n = 2 per group). Data are from one single experiment. f Schematics of various isoforms of Cd40 mRNA generated by AS. The red lines above the exon indicate exon junctions, and the red line in CD40 V3 indicates CD40 intron 7. The red dotted line indicates exon sequences that are missing in CD40 V4 compared to CD40 V1. The arrows indicate the position of PCR primers for measuring Cd40 AS. g RT-PCR analysis of Cd40 variants using primers P1 and P2. The ratios of CD40 V2 to V1 and V6 to V1 were shown below the gel image. h RT-PCR analysis of Cd40 intron 7 retention using primers P3 and P4. The ratio of the variant with I7 retention to that without was shown below the gel image. Data are representative of three independent experiments (g) or two independent experiments (h). Data are presented as mean values ± SD (c and e). Source data are provided as a Source Data file.
