Fig. 5
SRSF7 levels decrease and 3′UTRs are globally extended during neuronal differentiation. a Morphological changes of P19 cells during neuronal differentiation monitored by bright field microscopy at days 4 and 8 after initiation. b Western blot to monitor P19 differentiation using antibodies specific for the pluripotency factor OCT4 and the neuronal markers Synapsin 1 and Nestin. Protein levels of SRSF3, SRSF7, FIP1, and CPSF6 were analyzed using specific antibodies. β-catenin (CTNNB) was used as loading control. c Volcano plot of differential gene expression upon P19 differentiation analyzed by DESeq2. Significant genes (adjusted P value ≤ 0.1, log2-transformed fold change ≥ 0.5) are highlighted in purple. Genes of CPA factors, Srsf3 and Srsf7, are indicated with significant changes highlighted in bold. d Scatterplot of PDUIs in undifferentiated and differentiated P19 cells. Genes with significant changes in 3′UTR-APA (adjusted P value ≤ 0.1, |ΔPDUI| ≥ 0.05) are highlighted in purple. e Venn diagram showing overlap of genes with changes in 3′UTR length upon differentiation or Srsf7 KD. f Scatter plot comparing dPAS usage upon differentiation and Srsf7 KD for all genes with significant changes in 3′UTR-APA upon differentiation as in d, irrespective of their regulation upon Srsf7 knockdown. Number of genes given in each quadrant, excluding data points on axes. g Metaprofiles of normalized iCLIP crosslink events of SRSF3 and SRSF7 around pPASs and dPASs of transcripts with extended 3′UTRs upon differentiation compared to randomly sampled PASs that are not affected. Raw signal and loess smoothing are shown. Significant differences in SRSF3 and SRSF7 binding are computed by a z-score approach. Positions with FDR ≤ 0.01 are indicated below