Fig. 1: Nuclear depletion of TDP-43 causes CE inclusion in UNC13A RNA and reduced expression of UNC13A protein.
From: TDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A
a, Splicing analyses were performed on RNA-sequencing results from TDP-43-positive and TDP-43-negative neuronal nuclei isolated from frontal cortices of seven patients with FTD or FTD–ALS. Some illustrations were created with BioRender.com. b, Sixty-six alternatively spliced genes identified by both MAJIQ (P(ΔΨ > 0.1) > 0.95) and LeafCutter (P < 0.05). Genes in blue are previously validated TDP-43 splicing targets3,4,11,15. c, f, RT–qPCR confirmed inclusion of CE in UNC13A mRNA upon TDP-43 depletion in SH-SY5Y cells (n = 5 cell culture experiments for each condition; two sided-Welch two-sample t-test; mean ± s.e.m.) (c) and in 3 independent lines of iPSC-MNs (n = 2 independent cell culture experiments, each with 2 technical replicates for each iPSC-MN) (f). RPLP0 was used to normalize RT–qPCR. Three-way ANOVA; mean ± s.e.m. TDP-43 is also known as TARDBP. d, e, g, h, Immunoblotting for UNC13A and TDP-43 protein levels in SH-SY5Y cells (d; quantified in e) and iPSC-MNs (g; quantified in h) treated with scramble (shScramble) or TDP-43 shRNA (n = 3 independent cell culture experiments for each condition). GAPDH served as a loading control. Two-sided Welch two-sample t-test, mean ± s.e.m. Gel source data are shown in Supplementary Fig. 1a, b.
