Fig. 4: C9ORF78 regulates alternative splicing. | Nature Communications

Fig. 4: C9ORF78 regulates alternative splicing.

From: A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing

Fig. 4

a Results from RT-qPCR analyses, showing normalized C9ORF78 expression levels relative to GAPDH expression, in cells transfected with control siRNA (si control) or C9ORF78-targeting siRNA (si C9ORF78). Bars represent means ± SD, n = 3 biologically independent experiments. b Alternative splicing changes upon siRNA-mediated C9ORF78 KD, as determined by rMATS. MXE, mutually exclusive exons; SE, skipped exon; RI, retained intron; A5’/3’ss, alternative 5′/3′-splice sites. More inclusion upon C9ORF78 KD is indicated in light gray (up), skipping in black (down). c Volcano plots of significantly changed skipped exons (left; n = 390), and alternative 3′-splice sites (right, n = 105; red, NAGNAG splice sites, n = 59) upon C9ORF78 KD. Targets selected for validation PCR (PTBP2, C9ORF131, SMARCA4) are indicated by large data points and labeled. d Validation PCRs confirm C9ORF78 KD-induced changes in alternative splicing. Top, representative gels. Bottom, quantifications (n = 3 biologically independent experiments). Horizontal lines, medians; whiskers, minimum/maximum values. PSI, percent spliced-in (gel analysis), ratio of the quantified band representing exon inclusion and the sum of the quantified bands representing exon inclusion and exon skipping. Statistical significance was determined by unpaired, two-sided t-tests; **p = 0.0038; ****p < 0.0001. Source data for a–d are provided as a Source Data file.

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