Fig. 1: TDP-43 depletion in neurons leads to altered splicing in synaptic genes UNC13A and UNC13B.
From: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
a, Differential splicing analysis by MAJIQ33 in control (n = 4) and CRISPRi TDP-43 depleted (KD) (n = 3) iPS cell-derived cortical-like i3Neurons. Each point denotes a splice junction. b, Representative sashimi plots showing cryptic exon (CE) inclusion between exons 20 and 21 of UNC13A upon TDP-43 knockdown. c, f, Schematics showing intron retention (IR) (orange; bottom), TDP-43 binding region22(green), and two ALS- and FTLD-associated SNPs (red) in UNC13A (c) and UNC13B (f). d, LocusZoom plot of the UNC13A locus in the most recent ALS GWAS15; the dashed line indicates the risk threshold used in that study. Lead SNP rs12973192 is plotted as a purple diamond, other SNPs are coloured by linkage disequilibrium (LD) with rs12973192 in European individuals from 1000 Genomes. Ref. var., reference variant. e, Representative sashimi plot of UNC13B showing inclusion of the FSE upon TDP-43 knockdown. g, BaseScope detection of UNC13A CE (white puncta) in control (top) and TDP-43-knockdown (bottom) i3Neurons co-stained for TDP-43 (green), neuronal processes (stained for TUBB3, pink) and nuclei (blue). Scale bar, 5 μm. h, Quantification of RT–PCR products using iPS cell-derived neurons made from an independent iPS cell line, NCRM5, with a non-targeting control short guide RNA (sgRNA) (sgTARDBP−), an intermediate TDP-43 knockdown (sgTARDBP+) or stronger TDP-43 knockdown (sgTARDBP++). Data are mean ± s.e.m. sgControl, n = 6; sgTARDBP+, n = 5; sgTARDBP++, n = 6; one-way ANOVA with multiple comparisons. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. i, Schematic of nanopore long reads quantified in j, Extended Data Figs. 2d, e, 5e, f. j, Percentage of targeted UNC13A long reads with TDP-43-regulated splice events that contain CE, intron retention or both in TDP-43-knockdown SH-SY5Y cells.
