Extended Data Fig. 2: Validation of UNC13A and UNC13B misplicing after TDP-43 KD across multiple neuronal cell lines.
From: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
Targeted nanopore sequencing reveals UNC13A CE and IR events occur largely independently in-vitro. (a) Sanger sequencing of cryptic bands in both SH-SY5Y and SK-N-BE(2) cells confirm the CE splice junctions. (b, c) Crosslink density across UNC13A (chr19) (b) and UNC13B (chr9) (c) genomic loci from novel iCLIP on endogenous TDP-43 in SH-SHY5Y cells. Crosslink densities for both genes show peaks at the CE/fsE (red) and retained introns (blue). Coordinates shown in hg38. (d) Percentage of all targeted UNC13A long reads in SH-SY5Y cells containing either neither CE nor IR, both, or either CE or IR. Most reads in both control and TDP-43 KD contain neither event, and while IR event is present in controls, CE is only detected in TDP-43 KD. (e) Representative trace in TDP-43 KD of UNC13A targeted long reads showing transcript containing either the CE or IR, and transcripts with neither.
