Figure 3. Examples of neuronally spliced cassette exons that are PTBP1 repressed.
(A-D) Genome Browser tracks show aligned RNA-seq reads from ESCs (red), NPCs (blue), and GFP+ MNs (yellow). The scale indicates the number of mapped reads in the highest peak. PSI values for the cassette exons were calculated with SpliceTrap (Wu et al., 2011). Significant PTBP1 iCLIP sequencing reads from ESCs (magenta) and NPCs (green) are overlaid on the Genome Browser tracks.
DOI: http://dx.doi.org/10.7554/eLife.09268.014
Figure 3—source data 1. PTBP1-regulated cassette exons with PTBP1 binding.
elife-09268-fig3-data1.xlsx (77.6KB, xlsx)
DOI: 10.7554/eLife.09268.015
Figure 3—source data 2. Direct PTBP1 target exons during neuronal differentiation.
elife-09268-fig3-data2.xlsx (71.4KB, xlsx)
DOI: 10.7554/eLife.09268.016
Figure 3—figure supplement 1. The base content and location of PTBP1 iCLIP-sequencing reads are consistent with known PTBP1 binding properties.
(A) Autoradiograph of the nitrocellulose membrane containing protein-RNA complexes isolated from ESCs and NPCs using either Flag or PTBP1 antibodies. Boxes indicate the region of the membrane used for iCLIP library preparation. (B) Scatter plot compares the calculated pentamer Z-scores from ESCs with scores from NPCs. The top 23 pentamer motifs, which had Z scores >200, are listed. (C, D) Pie charts showing the percent of the significant PTBP1 iCLIP reads that were found in 5’ UTR (blue), coding sequence (CDS) (red), intron (green), and 3’ UTR (purple) regions. (E, F) All expressed cassette exons with nearby PTBP1 iCLIP clusters (within 500 nt, blue circles) are overlapped with PTBP1-responsive cassette exons (green circles, ΔPSI ≥ 15%) (Figure 3—source data 1). P-values were calculated using the hypergeometric test.