Figure 2. TDP-43 overexpression induces exon repression in humans.

(A) To investigate whether exon skipping events also occur in humans, we infected human iPS cells with a lentivirus expressing human TDP-43 and analyzed the resulting RNA-Seq dataset. (B) Our analysis revealed several genes with skipping events, including genes involved in several molecular pathways. (C) Network analysis identified genes related to intellectual disability, synaptic activity, and mitochondrial proteins. We identified genes that had exons with particularly high levels of exon skipping, including HYOU1, NUP93, and XPNPEP1 (arrows). (D-F) When we cross-referenced these results with samples from transgenic mice, we found that exons repressed in humans were not repressed in mice. We validated these findings using RT-PCR in i3Neurons. We used double band RT-PCR (G) with primers located in the adjacent exon to the repressed exon or single band RT-PCR (H) with primers spanning the skipped junction. (I) Analysis of UG repeats in 25 targets revealed that these TDP-43 recognition motives are found in both repressed exons and intronic sequences. UG motifs appear slightly more frequently around the downstream 5’ splice site, but with far shorter UG repeat lengths than those found adjacent to cryptic exons (73).